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@article{DBLP:journals/bmcbi/AbdollahiJSDB23,
author = {Nika Abdollahi and
Lucile Jeusset and
Anne Langlois De Septenville and
Fr{\'{e}}d{\'{e}}ric Davi and
Juliana S. Bernardes},
title = {Reconstructing {B} cell lineage trees with minimum spanning tree and
genotype abundances},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {70},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05112-z},
doi = {10.1186/S12859-022-05112-Z},
timestamp = {Thu, 02 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AbdollahiJSDB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AbnoosianFB23,
author = {Karlo Abnoosian and
Rahman Farnoosh and
Mohammad Hassan Behzadi},
title = {Prediction of diabetes disease using an ensemble of machine learning
multi-classifier models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {337},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05465-z},
doi = {10.1186/S12859-023-05465-Z},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AbnoosianFB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AdamsSWBBH23,
author = {Thomas M. Adams and
Moray Smith and
Yuhan Wang and
Lynn H. Brown and
Micha Bayer and
Ingo Hein},
title = {{HISS:} Snakemake-based workflows for performing SMRT-RenSeq assembly,
AgRenSeq and dRenSeq for the discovery of novel plant disease resistance
genes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {204},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05335-8},
doi = {10.1186/S12859-023-05335-8},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AdamsSWBBH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AdhisantosoVRTOO23,
author = {Yeremia Gunawan Adhisantoso and
Jan Voges and
Christian Rohlfing and
Viktor Tunev and
Jens{-}Rainer Ohm and
J{\"{o}}rn Ostermann},
title = {{GVC:} efficient random access compression for gene sequence variations},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {121},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05240-0},
doi = {10.1186/S12859-023-05240-0},
timestamp = {Fri, 31 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AdhisantosoVRTOO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AfricaPFDQ23,
author = {Pasquale Claudio Africa and
Roberto Piersanti and
Marco Fedele and
Luca Dede' and
Alfio Quarteroni},
title = {lifex-fiber: an open tool for myofibers generation in cardiac computational
models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {143},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05260-w},
doi = {10.1186/S12859-023-05260-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AfricaPFDQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AfricaPRBSFPDQ23,
author = {Pasquale Claudio Africa and
Roberto Piersanti and
Francesco Regazzoni and
Michele Bucelli and
Matteo Salvador and
Marco Fedele and
Stefano Pagani and
Luca Dede' and
Alfio Quarteroni},
title = {lifex-ep: a robust and efficient software for cardiac electrophysiology
simulations},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {389},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05513-8},
doi = {10.1186/S12859-023-05513-8},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AfricaPRBSFPDQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AfsharBHL23,
author = {Shiva Afshar and
Patricia R. Braun and
Shizhong Han and
Ying Lin},
title = {A multimodal deep learning model to infer cell-type-specific functional
gene networks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {47},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05146-x},
doi = {10.1186/S12859-023-05146-X},
timestamp = {Fri, 17 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AfsharBHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AhmadKTM23,
author = {Fareed Ahmad and
Muhammad Usman Ghani Khan and
Ahsen Tahir and
Farhan Masud},
title = {Deep ensemble approach for pathogen classification in large-scale
images using patch-based training and hyper-parameter optimization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {273},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05398-7},
doi = {10.1186/S12859-023-05398-7},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AhmadKTM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AhmadSSTLBAK23,
author = {Nouman Ahmad and
Robin Strand and
Bj{\"{o}}rn Sparres{\"{a}}ter and
Sambit Tarai and
Elin Lundstr{\"{o}}m and
G{\"{o}}ran Bergstr{\"{o}}m and
H{\aa}kan Ahlstr{\"{o}}m and
Joel Kullberg},
title = {Automatic segmentation of large-scale {CT} image datasets for detailed
body composition analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {346},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05462-2},
doi = {10.1186/S12859-023-05462-2},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AhmadSSTLBAK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AhnGD23,
author = {Seungjun Ahn and
Tyler Grimes and
Somnath Datta},
title = {A pseudo-value regression approach for differential network analysis
of co-expression data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {8},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05123-w},
doi = {10.1186/S12859-022-05123-W},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AhnGD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AisoposP23,
author = {Fotis Aisopos and
Georgios Paliouras},
title = {Comparing methods for drug-gene interaction prediction on the biomedical
literature knowledge graph: performance versus explainability},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {272},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05373-2},
doi = {10.1186/S12859-023-05373-2},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AisoposP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AkhterM23,
author = {Suraiya Akhter and
John H. Miller},
title = {BaPreS: a software tool for predicting bacteriocins using an optimal
set of features},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {313},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05330-z},
doi = {10.1186/S12859-023-05330-Z},
timestamp = {Thu, 31 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AkhterM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlAamriADAH23,
author = {Amira Al{-}Aamri and
Syafiq Kamarul Azman and
Gihan Dawelbait and
Habiba AlSafar and
Andreas Henschel},
title = {Critical assessment of on-premise approaches to scalable genome analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {354},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05470-2},
doi = {10.1186/S12859-023-05470-2},
timestamp = {Mon, 25 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AlAamriADAH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlFatlawiRSMOPS23,
author = {Ali Al{-}Fatlawi and
Eka Rusadze and
Alexander Shmelkin and
Negin Malekian and
Cigdem Ozen and
Christian Pilarsky and
Michael Schroeder},
title = {Netrank: network-based approach for biomarker discovery},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {304},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05418-6},
doi = {10.1186/S12859-023-05418-6},
timestamp = {Fri, 18 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AlFatlawiRSMOPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlKurabiAS23,
author = {Nahla AlKurabi and
Ahad AlGahtani and
Turki M. Sobahy},
title = {{CACSV:} a computational web-sever that provides classification for
cancer somatic genetic variants from different tissues},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {95},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05207-1},
doi = {10.1186/S12859-023-05207-1},
timestamp = {Tue, 28 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AlKurabiAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlakusLL23,
author = {Cansu Alakus and
Denis Larocque and
Aur{\'{e}}lie Labbe},
title = {Covariance regression with random forests},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {258},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05377-y},
doi = {10.1186/S12859-023-05377-Y},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AlakusLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlvareRF23,
author = {Graham Alvare and
Abiel Roche{-}Lima and
Brian Fristensky},
title = {BioLegato: a programmable, object-oriented graphic user interface},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {316},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05436-4},
doi = {10.1186/S12859-023-05436-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AlvareRF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AmeenBAHS23,
author = {Yusra A. Ameen and
Dalia M. Badary and
Ahmad Elbadry I. Abonnoor and
Khaled F. Hussain and
Adel A. Sewisy},
title = {Which data subset should be augmented for deep learning? a simulation
study using urothelial cell carcinoma histopathology images},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {75},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05199-y},
doi = {10.1186/S12859-023-05199-Y},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AmeenBAHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AmiriRPI23,
author = {Ramin Amiri and
Jafar Razmara and
Sepideh Parvizpour and
Habib Izadkhah},
title = {A novel efficient drug repurposing framework through drug-disease
association data integration using convolutional neural networks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {442},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05572-x},
doi = {10.1186/S12859-023-05572-X},
timestamp = {Sun, 10 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AmiriRPI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AndradeTRZE23,
author = {Dhiego Souto Andrade and
Patrick Terrematte and
C{\'{e}}sar Renn{\'{o}}{-}Costa and
Alona Zilberberg and
Sol Efroni},
title = {{GENTLE:} a novel bioinformatics tool for generating features and
building classifiers from {T} cell repertoire cancer data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {32},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05155-w},
doi = {10.1186/S12859-023-05155-W},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AndradeTRZE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AnwardeenDMAE23,
author = {Najeha R. Anwardeen and
Ilhame Diboun and
Younes Mokrab and
Asma A. Althani and
Mohamed A. Elrayess},
title = {Statistical methods and resources for biomarker discovery using metabolomics},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {250},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05383-0},
doi = {10.1186/S12859-023-05383-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AnwardeenDMAE23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ArgyrisLTTV23,
author = {Georgios Argyris and
Alberto Lluch{-}Lafuente and
Mirco Tribastone and
Max Tschaikowski and
Andrea Vandin},
title = {Reducing Boolean networks with backward equivalence},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {212},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05326-9},
doi = {10.1186/S12859-023-05326-9},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ArgyrisLTTV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AroraPGSK23,
author = {Pooja Arora and
Neha Periwal and
Yash Goyal and
Vikas Sood and
Baljeet Kaur},
title = {iIL13Pred: improved prediction of {IL-13} inducing peptides using
popular machine learning classifiers},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {141},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05248-6},
doi = {10.1186/S12859-023-05248-6},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AroraPGSK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AscolaniAMCBPDRAG23,
author = {Gianluca Ascolani and
Fabrizio Angaroni and
Davide Maspero and
Francesco Craighero and
Narra Lakshmi Sai Bhavesh and
Rocco Piazza and
Chiara Damiani and
Daniele Ramazzotti and
Marco Antoniotti and
Alex Graudenzi},
title = {{LACE} 2.0: an interactive {R} tool for the inference and visualization
of longitudinal cancer evolution},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {99},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05221-3},
doi = {10.1186/S12859-023-05221-3},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AscolaniAMCBPDRAG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AsifMLKC23,
author = {Muhammad Asif and
Hugo F. M. C. Martiniano and
Andre Lamurias and
Samina Kausar and
Francisco M. Couto},
title = {{DGH-GO:} dissecting the genetic heterogeneity of complex diseases
using gene ontology},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {171},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05290-4},
doi = {10.1186/S12859-023-05290-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AsifMLKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Atas23,
author = {Pinar Karadayi Atas},
title = {A novel hybrid model to predict concomitant diseases for Hashimoto's
thyroiditis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {319},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05443-5},
doi = {10.1186/S12859-023-05443-5},
timestamp = {Wed, 30 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Atas23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AvrahamTBTS23,
author = {Orly Avraham and
Tomer Tsaban and
Ziv Ben{-}Aharon and
Linoy Tsaban and
Ora Schueler{-}Furman},
title = {Protein language models can capture protein quaternary state},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {433},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05549-w},
doi = {10.1186/S12859-023-05549-W},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AvrahamTBTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BaikHP23,
author = {Seung Min Baik and
Kyung Sook Hong and
Dong Jin Park},
title = {Deep learning approach for early prediction of {COVID-19} mortality
using chest X-ray and electronic health records},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {190},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05321-0},
doi = {10.1186/S12859-023-05321-0},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BaikHP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BaoZZZLX23,
author = {Han Bao and
Jinhui Zhao and
Xinjie Zhao and
Chunxia Zhao and
Xin Lu and
Guowang Xu},
title = {Prediction of plant secondary metabolic pathways using deep transfer
learning},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {348},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05485-9},
doi = {10.1186/S12859-023-05485-9},
timestamp = {Mon, 25 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BaoZZZLX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BarsBBG23,
author = {Sophie Le Bars and
Mathieu Bolteau and
J{\'{e}}r{\'{e}}mie Bourdon and
Carito Guziolowski},
title = {Predicting weighted unobserved nodes in a regulatory network using
answer set programming},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {321},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05429-3},
doi = {10.1186/S12859-023-05429-3},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BarsBBG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BeaulacWGMCRBN23,
author = {C{\'{e}}dric Beaulac and
Sidi Wu and
Erin Gibson and
Michelle F. Miranda and
Jiguo Cao and
Leno Rocha and
Mirza Faisal Beg and
Farouk S. Nathoo},
title = {Neuroimaging feature extraction using a neural network classifier
for imaging genetics},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {271},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05394-x},
doi = {10.1186/S12859-023-05394-X},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BeaulacWGMCRBN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BehdennaCHGAAN23,
author = {Abdelkader Behdenna and
Maximilien Colange and
Julien Haziza and
Aryo Gema and
Guillaume App{\'{e}} and
Chlo{\'{e}}{-}Agathe Azencott and
Akp{\'{e}}li Nordor},
title = {pyComBat, a Python tool for batch effects correction in high-throughput
molecular data using empirical Bayes methods},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {459},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05578-5},
doi = {10.1186/S12859-023-05578-5},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BehdennaCHGAAN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Beikzadeh23,
author = {Babak Beikzadeh},
title = {Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD
and enterotoxin against non-typhoidal salmonellosis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {63},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05183-6},
doi = {10.1186/S12859-023-05183-6},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/Beikzadeh23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BelhechmiTBRM23,
author = {Shaima Belhechmi and
Gw{\'{e}}na{\"{e}}l Le Teuff and
Riccardo De Bin and
Federico Rotolo and
Stefan Michiels},
title = {Favoring the hierarchical constraint in penalized survival models
for randomized trials in precision medicine},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {96},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05162-x},
doi = {10.1186/S12859-023-05162-X},
timestamp = {Sun, 19 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BelhechmiTBRM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BeltGBCMA23,
author = {Matthias van den Belt and
Cameron L. M. Gilchrist and
Thomas J. Booth and
Yit{-}Heng Chooi and
Marnix H. Medema and
Mohammad Alanjary},
title = {{CAGECAT:} The CompArative GEne Cluster Analysis Toolbox for rapid
search and visualisation of homologous gene clusters},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {181},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05311-2},
doi = {10.1186/S12859-023-05311-2},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BeltGBCMA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BenitezHidalgoMDG23,
author = {Antonio Ben{\'{\i}}tez{-}Hidalgo and
Jos{\'{e}} Francisco Aldana Montes and
Ismael Navas{-}Delgado and
Mar{\'{\i}}a del Mar Rold{\'{a}}n Garc{\'{\i}}a},
title = {{SALON} ontology for the formal description of sequence alignments},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {69},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05190-7},
doi = {10.1186/S12859-023-05190-7},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BenitezHidalgoMDG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BerresGWSL23,
author = {Sven Berres and
J{\"{o}}rg Gromoll and
Marius W{\"{o}}ste and
Sarah Sandmann and
Sandra Laurentino},
title = {{OGRE:} calculate, visualize, and analyze overlap between genomic
input regions and public annotations},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {300},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05422-w},
doi = {10.1186/S12859-023-05422-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BerresGWSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BiasiMCSBT23,
author = {Luigi Di Biasi and
Fabiola De Marco and
Alessia Auriemma Citarella and
Modesto Castrill{\'{o}}n Santana and
Paola Barra and
Genoveffa Tortora},
title = {Refactoring and performance analysis of the main {CNN} architectures:
using false negative rate minimization to solve the clinical images
melanoma detection problem},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {386},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05516-5},
doi = {10.1186/S12859-023-05516-5},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BiasiMCSBT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BinatliG23,
author = {Oguz C. Binatli and
Mehmet G{\"{o}}nen},
title = {{MOKPE:} drug-target interaction prediction via manifold optimization
based kernel preserving embedding},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {276},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05401-1},
doi = {10.1186/S12859-023-05401-1},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BinatliG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BinetPOAM23,
author = {Thomas Binet and
S{\'{e}}verine Padiolleau{-}Lef{\`{e}}vre and
St{\'{e}}phane Octave and
B{\'{e}}rang{\`{e}}re Avalle and
Irene Maffucci},
title = {Comparative Study of Single-stranded Oligonucleotides Secondary Structure
Prediction Tools},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {422},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05532-5},
doi = {10.1186/S12859-023-05532-5},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BinetPOAM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BoeykensBPB23,
author = {Fr{\'{e}}derique Boeykens and
Sofie F. M. Bhatti and
Luc Peelman and
Bart J. G. Broeckx},
title = {VariantscanR: an R-package as a clinical tool for variant filtering
of known phenotype-associated variants in domestic animals},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {305},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05426-6},
doi = {10.1186/S12859-023-05426-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BoeykensBPB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BokharaeianDD23,
author = {Behrouz Bokharaeian and
Mohammad Dehghani and
Alberto D{\'{\i}}az},
title = {Automatic extraction of ranked SNP-phenotype associations from text
using a BERT-LSTM-based method},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {144},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05236-w},
doi = {10.1186/S12859-023-05236-W},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BokharaeianDD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BorderM23,
author = {Richard Border and
Osman Asif Malik},
title = {rBahadur: efficient simulation of structured high-dimensional genotype
data with applications to assortative mating},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {314},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05442-6},
doi = {10.1186/S12859-023-05442-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BorderM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BoseBCPD23,
author = {Aritra Bose and
Myson C. Burch and
Agniva Chowdhury and
Peristera Paschou and
Petros Drineas},
title = {Structure-informed clustering for population stratification in association
studies},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {411},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05511-w},
doi = {10.1186/S12859-023-05511-W},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BoseBCPD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BoydST23,
author = {Samuel Boyd and
Chad Slawson and
Jeffrey A. Thompson},
title = {{AMEND:} active module identification using experimental data and
network diffusion},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {277},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05376-z},
doi = {10.1186/S12859-023-05376-Z},
timestamp = {Wed, 19 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BoydST23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BreslinP23,
author = {William Breslin and
Doan Pham},
title = {Machine learning and drug discovery for neglected tropical diseases},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {165},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05076-0},
doi = {10.1186/S12859-022-05076-0},
timestamp = {Fri, 28 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BreslinP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BriscikDD23,
author = {Mitja Briscik and
Marie{-}Agn{\`{e}}s Dillies and
S{\'{e}}bastien D{\'{e}}jean},
title = {Improvement of variables interpretability in kernel {PCA}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {282},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05404-y},
doi = {10.1186/S12859-023-05404-Y},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BriscikDD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BrownDWBH23,
author = {Scott D. Brown and
Lisa Dreolini and
Jessica F. Wilson and
Miruna Balasundaram and
Robert A. Holt},
title = {Complete sequence verification of plasmid {DNA} using the Oxford Nanopore
Technologies' MinION device},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {116},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05226-y},
doi = {10.1186/S12859-023-05226-Y},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BrownDWBH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BrunaLGHHSNEGH23,
author = {Tom{\'{a}}s Bruna and
Heng Li and
Joseph Guhlin and
Daniel Honsel and
Steffen Herbold and
Mario Stanke and
Natalia Nenasheva and
Matthis Ebel and
Lars Gabriel and
Katharina Jasmin Hoff},
title = {Galba: genome annotation with miniprot and {AUGUSTUS}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {327},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05449-z},
doi = {10.1186/S12859-023-05449-Z},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BrunaLGHHSNEGH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BurgyWHMJRG23,
author = {L{\'{e}}o B{\"{u}}rgy and
Martin Weigert and
Georgios Hatzopoulos and
Matthias Minder and
Adrien Journ{\'{e}} and
Sahand Jamal Rahi and
Pierre Gonczy},
title = {CenFind: a deep-learning pipeline for efficient centriole detection
in microscopy datasets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {120},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05214-2},
doi = {10.1186/S12859-023-05214-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BurgyWHMJRG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BurkesPattonCS23,
author = {Shelvasha Burkes{-}Patton and
Elizabeth A. Cooper and
Jessica Schlueter},
title = {RepBox: a toolbox for the identification of repetitive elements},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {317},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05419-5},
doi = {10.1186/S12859-023-05419-5},
timestamp = {Thu, 31 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BurkesPattonCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CaballeMestresBA23,
author = {Adri{\`{a}} Caball{\'{e}}{-}Mestres and
Antoni Berenguer{-}Llergo and
Camille Stephan{-}Otto Attolini},
title = {Roastgsa: a comparison of rotation-based scores for gene set enrichment
analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {408},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05510-x},
doi = {10.1186/S12859-023-05510-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CaballeMestresBA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CaiLZXHLGH23,
author = {Pengli Cai and
Sheng Liu and
Dachuan Zhang and
Huadong Xing and
Mengying Han and
Dongliang Liu and
Linlin Gong and
Qian{-}Nan Hu},
title = {SynBioTools: a one-stop facility for searching and selecting synthetic
biology tools},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {152},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05281-5},
doi = {10.1186/S12859-023-05281-5},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CaiLZXHLGH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CaiZAB23,
author = {Jitong Cai and
Jianan Zhan and
Dan E. Arking and
Joel S. Bader},
title = {Priors, population sizes, and power in genome-wide hypothesis tests},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {170},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05261-9},
doi = {10.1186/S12859-023-05261-9},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CaiZAB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CallePS23,
author = {Malu Luz Calle and
Meritxell Pujolassos and
Antonio Sus{\'{\i}}n},
title = {coda4microbiome: compositional data analysis for microbiome cross-sectional
and longitudinal studies},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {82},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05205-3},
doi = {10.1186/S12859-023-05205-3},
timestamp = {Tue, 28 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CallePS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CamachoBJAM23,
author = {Christiam Camacho and
Grzegorz M. Boratyn and
Victor Joukov and
Roberto Vera Alvarez and
Thomas L. Madden},
title = {ElasticBLAST: accelerating sequence search via cloud computing},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {117},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05245-9},
doi = {10.1186/S12859-023-05245-9},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CamachoBJAM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CanoTZXHMSW23,
author = {Marco Alvarado Cano and
Ginger Tsueng and
Xinghua Zhou and
Jiwen Xin and
Laura D. Hughes and
Julia Mullen and
Andrew I. Su and
Chunlei Wu},
title = {Schema Playground: a tool for authoring, extending, and using metadata
schemas to improve FAIRness of biomedical data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {159},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05258-4},
doi = {10.1186/S12859-023-05258-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CanoTZXHMSW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CaoLL23,
author = {Shenghao Cao and
Mengtian Li and
Lei M. Li},
title = {RegCloser: a robust regression approach to closing genome gaps},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {249},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05367-0},
doi = {10.1186/S12859-023-05367-0},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CaoLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CaoYLL23,
author = {Chao Cao and
Shuhong Yang and
Mengli Li and
Chungui Li},
title = {CircSSNN: circRNA-binding site prediction via sequence self-attention
neural networks with pre-normalization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {220},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05352-7},
doi = {10.1186/S12859-023-05352-7},
timestamp = {Mon, 05 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CaoYLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CardnerMGYTB23,
author = {Mathias Cardner and
Francesco Marass and
Erika Gedvilaite and
Julie L. Yang and
Dana W. Y. Tsui and
Niko Beerenwinkel},
title = {Predicting tumour content of liquid biopsies from cell-free {DNA}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {368},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05478-8},
doi = {10.1186/S12859-023-05478-8},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CardnerMGYTB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CarpenterGBKG23,
author = {Charlie M. Carpenter and
Lucas A. Gillenwater and
Russell Bowler and
Katerina J. Kechris and
Debashis Ghosh},
title = {TreeKernel: interpretable kernel machine tests for interactions between
-omics and clinical predictors with applications to metabolomics and
{COPD} phenotypes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {398},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05459-x},
doi = {10.1186/S12859-023-05459-X},
timestamp = {Mon, 30 Oct 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CarpenterGBKG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CarrascoFUTC23,
author = {Alexis Germ{\'{a}}n Murillo Carrasco and
Tatiane Katsue Furuya and
Miyuki Uno and
Tharcisio Citrangulo Tortelli and
Roger Chammas},
title = {deltaXpress ({\(\Delta\)}Xpress): a tool for mapping differentially
correlated genes using single-cell qPCR data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {402},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05541-4},
doi = {10.1186/S12859-023-05541-4},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CarrascoFUTC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CarryVVKDBLYNK23,
author = {Patrick M. Carry and
Tim Vigers and
Lauren A. Vanderlinden and
Carson Keeter and
Fran Dong and
Teresa Buckner and
Elizabeth Litkowski and
Ivana Yang and
Jill M. Norris and
Katherina J. Kechris},
title = {Propensity scores as a novel method to guide sample allocation and
minimize batch effects during the design of high throughput experiments},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {86},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05202-6},
doi = {10.1186/S12859-023-05202-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CarryVVKDBLYNK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CascianelliCMM23,
author = {Silvia Cascianelli and
Gaia Ceddia and
Alberto Marchesi and
Marco Masseroli},
title = {Identification of transcription factor high accumulation {DNA} zones},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {395},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05528-1},
doi = {10.1186/S12859-023-05528-1},
timestamp = {Mon, 30 Oct 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CascianelliCMM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CaseyFSM23,
author = {Michael J. Casey and
J{\"{o}}rg Fliege and
Rub{\'{e}}n J. S{\'{a}}nchez{-}Garc{\'{\i}}a and
Ben D. MacArthur},
title = {An information-theoretic approach to single cell sequencing analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {311},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05424-8},
doi = {10.1186/S12859-023-05424-8},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CaseyFSM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CastanhoLHM23,
author = {Eduardo N. Castanho and
Jo{\~{a}}o Lobo and
Rui Henriques and
Sara C. Madeira},
title = {G-bic: generating synthetic benchmarks for biclustering},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {457},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05587-4},
doi = {10.1186/S12859-023-05587-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CastanhoLHM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CastellanosRodriguezET23,
author = {{\'{O}}scar Castellanos{-}Rodr{\'{\i}}guez and
Roberto R. Exp{\'{o}}sito and
Juan Touri{\~{n}}o},
title = {SeQual-Stream: approaching stream processing to quality control of
{NGS} datasets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {403},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05530-7},
doi = {10.1186/S12859-023-05530-7},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CastellanosRodriguezET23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChangZWTlC23,
author = {Fan Chang and
Jiang{-}Hui Zhang and
Wen{-}Song Wu and
Shuai Tang and
Zheng lv and
Fang{-}Min Chen},
title = {{FDC-SP} as a diagnostic and prognostic biomarker and modulates immune
infiltrates in renal cell carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {91},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05215-1},
doi = {10.1186/S12859-023-05215-1},
timestamp = {Sun, 19 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChangZWTlC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CharoenkwanKSCS23,
author = {Phasit Charoenkwan and
Sasikarn Kongsompong and
Nalini Schaduangrat and
Pramote Chumnanpuen and
Watshara Shoombuatong},
title = {TIPred: a novel stacked ensemble approach for the accelerated discovery
of tyrosinase inhibitory peptides},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {356},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05463-1},
doi = {10.1186/S12859-023-05463-1},
timestamp = {Mon, 25 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CharoenkwanKSCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CharoenkwanSS23,
author = {Phasit Charoenkwan and
Nalini Schaduangrat and
Watshara Shoombuatong},
title = {StackTTCA: a stacking ensemble learning-based framework for accurate
and high-throughput identification of tumor {T} cell antigens},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {301},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05421-x},
doi = {10.1186/S12859-023-05421-X},
timestamp = {Sun, 06 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CharoenkwanSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChavezKKK23,
author = {Willow Carretero Chavez and
Marcus Krantz and
Edda Klipp and
Irina Kufareva},
title = {kboolnet: a toolkit for the verification, validation, and visualization
of reaction-contingency (rxncon) models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {246},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05329-6},
doi = {10.1186/S12859-023-05329-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChavezKKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenC23,
author = {Chun{-}Chi Chen and
Yi{-}Ming Chan},
title = {REDfold: accurate {RNA} secondary structure prediction using residual
encoder-decoder network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {122},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05238-8},
doi = {10.1186/S12859-023-05238-8},
timestamp = {Fri, 31 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenDLYH23,
author = {Min Chen and
Yingwei Deng and
Zejun Li and
Yifan Ye and
Ziyi He},
title = {{KATZNCP:} a miRNA-disease association prediction model integrating
{KATZ} algorithm and network consistency projection},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {229},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05365-2},
doi = {10.1186/S12859-023-05365-2},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenDLYH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenGZ23,
author = {Yu Chen and
Lixin Gao and
Tianjiao Zhang},
title = {Stack-VTP: prediction of vesicle transport proteins based on stacked
ensemble classifier and evolutionary information},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {137},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05257-5},
doi = {10.1186/S12859-023-05257-5},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenGZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenJHLZH23,
author = {Linjun Chen and
Xiao{-}Yuan Jing and
Yaru Hao and
Wei Liu and
Xiaoke Zhu and
Wei Han},
title = {A novel two-way rebalancing strategy for identifying carbonylation
sites},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {429},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05551-2},
doi = {10.1186/S12859-023-05551-2},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenJHLZH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenKGYCC23,
author = {Nae{-}Chyun Chen and
Alexey Kolesnikov and
Sidharth Goel and
Taedong Yun and
Pi{-}Chuan Chang and
Andrew Carroll},
title = {Improving variant calling using population data and deep learning},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {197},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05294-0},
doi = {10.1186/S12859-023-05294-0},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenKGYCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenMXX23,
author = {Xue{-}Qin Chen and
Jie Ma and
Di Xu and
Zuo{-}Lin Xiang},
title = {Comprehensive analysis of {KLF2} as a prognostic biomarker associated
with fibrosis and immune infiltration in advanced hepatocellular carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {270},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05391-0},
doi = {10.1186/S12859-023-05391-0},
timestamp = {Mon, 03 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenMXX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenNLZL23,
author = {Jiaxing Chen and
Yen Kaow Ng and
Lu Lin and
Xianglilan Zhang and
Shuaicheng Li},
title = {On triangle inequalities of correlation-based distances for gene expression
profiles},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {40},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05161-y},
doi = {10.1186/S12859-023-05161-Y},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenNLZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenPCDLSLSY23,
author = {Xu Chen and
Chuang Peng and
Yu Chen and
Bai Ding and
Sulai Liu and
Yinghui Song and
Yuhang Li and
Bo Sun and
Ranzhiqiang Yang},
title = {A T-cell-related signature for prognostic stratification and immunotherapy
response in hepatocellular carcinoma based on transcriptomics and
single-cell sequencing},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {216},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05344-7},
doi = {10.1186/S12859-023-05344-7},
timestamp = {Mon, 05 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenPCDLSLSY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenPF23,
author = {Haoyu Chen and
Marta Pelizzola and
Andreas Futschik},
title = {Haplotype based testing for a better understanding of the selective
architecture},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {322},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05437-3},
doi = {10.1186/S12859-023-05437-3},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenPF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenSL23,
author = {Lin Chen and
Qing Shen and
Jungang Lou},
title = {Magicmol: a light-weighted pipeline for drug-like molecule evolution
and quick chemical space exploration},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {173},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05286-0},
doi = {10.1186/S12859-023-05286-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenTEKRS23,
author = {Chaoran Chen and
Alexander Taepper and
Fabian Engelniederhammer and
Jonas Kellerer and
Cornelius Roemer and
Tanja Stadler},
title = {{LAPIS} is a fast web {API} for massive open virus sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {232},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05364-3},
doi = {10.1186/S12859-023-05364-3},
timestamp = {Thu, 15 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenTEKRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenW23,
author = {Rui Chen and
Jun{-}Min Wei},
title = {Integrated analysis identifies oxidative stress-related lncRNAs associated
with progression and prognosis in colorectal cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {76},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05203-5},
doi = {10.1186/S12859-023-05203-5},
timestamp = {Tue, 07 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenWCLPS23,
author = {Liang Chen and
Yiming Weng and
Xue Cui and
Qian Li and
Min Peng and
Qibin Song},
title = {Comprehensive analyses of a CD8\({}^{\mbox{+}}\) {T} cell infiltration
related gene signature with regard to the prediction of prognosis
and immunotherapy response in lung squamous cell carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {238},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05302-3},
doi = {10.1186/S12859-023-05302-3},
timestamp = {Tue, 05 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenWCLPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenWLXHB23,
author = {Jing Chen and
Lianlian Wu and
Kunhong Liu and
Yong Xu and
Song He and
Xiaochen Bo},
title = {{EDST:} a decision stump based ensemble algorithm for synergistic
drug combination prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {325},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05453-3},
doi = {10.1186/S12859-023-05453-3},
timestamp = {Tue, 05 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenWLXHB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenWZJLLL23,
author = {Danyi Chen and
Xiaowen Wang and
Hongming Zhu and
Yizhi Jiang and
Yulong Li and
Qi Liu and
Qin Liu},
title = {Predicting anticancer synergistic drug combinations based on multi-task
learning},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {448},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05524-5},
doi = {10.1186/S12859-023-05524-5},
timestamp = {Mon, 04 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenWZJLLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenZ23,
author = {Peng Chen and
Haoran Zheng},
title = {Drug-target interaction prediction based on spatial consistency constraint
and graph convolutional autoencoder},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {151},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05275-3},
doi = {10.1186/S12859-023-05275-3},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenZWHLL23,
author = {Kai Chen and
Xiaodong Zhu and
Jiahao Wang and
Lei Hao and
Zhen Liu and
Yuanning Liu},
title = {ncDENSE: a novel computational method based on a deep learning framework
for non-coding RNAs family prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {68},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05191-6},
doi = {10.1186/S12859-023-05191-6},
timestamp = {Wed, 12 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenZWHLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChenZYGZF23,
author = {Zhong{-}Hua Chen and
Wen{-}Yuan Zhang and
Hui Ye and
Yu{-}Qian Guo and
Kai Zhang and
Xiang{-}Ming Fang},
title = {A signature of immune-related genes correlating with clinical prognosis
and immune microenvironment in sepsis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {20},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05134-1},
doi = {10.1186/S12859-023-05134-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChenZYGZF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChengMYSW23,
author = {Yi Cheng and
Xiuli Ma and
Lang Yuan and
Zhaoguo Sun and
Pingzhang Wang},
title = {Evaluating imputation methods for single-cell RNA-seq data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {302},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05417-7},
doi = {10.1186/S12859-023-05417-7},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChengMYSW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChoiC23,
author = {Joungmin Choi and
Heejoon Chae},
title = {moBRCA-net: a breast cancer subtype classification framework based
on multi-omics attention neural networks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {169},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05273-5},
doi = {10.1186/S12859-023-05273-5},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChoiC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChoiPC23,
author = {Joungmin Choi and
Chaelin Park and
Heejoon Chae},
title = {meth-SemiCancer: a cancer subtype classification framework via semi-supervised
learning utilizing {DNA} methylation profiles},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {168},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05272-6},
doi = {10.1186/S12859-023-05272-6},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChoiPC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChongXLP23,
author = {Yanwen Chong and
Ningdi Xie and
Xin Liu and
Shaoming Pan},
title = {P-TransUNet: an improved parallel network for medical image segmentation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {285},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05409-7},
doi = {10.1186/S12859-023-05409-7},
timestamp = {Fri, 21 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChongXLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChuW23,
author = {Sz{-}Wei Chu and
Feng{-}Sheng Wang},
title = {Fuzzy optimization for identifying antiviral targets for treating
SARS-CoV-2 infection in the heart},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {364},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05487-7},
doi = {10.1186/S12859-023-05487-7},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChuW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CinagliaMC23,
author = {Pietro Cinaglia and
Marianna Milano and
Mario Cannataro},
title = {Multilayer network alignment based on topological assessment via embeddings},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {416},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05508-5},
doi = {10.1186/S12859-023-05508-5},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CinagliaMC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CongLCLC23,
author = {Hanhan Cong and
Hong Liu and
Yi Cao and
Cheng Liang and
Yuehui Chen},
title = {Protein-protein interaction site prediction by model ensembling with
hybrid feature and self-attention},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {456},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05592-7},
doi = {10.1186/S12859-023-05592-7},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CongLCLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CorePWG23,
author = {Luca Del Core and
Danilo Pellin and
Ernst C. Wit and
Marco Grzegorczyk},
title = {A mixed-effects stochastic model reveals clonal dominance in gene
therapy safety studies},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {228},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05269-1},
doi = {10.1186/S12859-023-05269-1},
timestamp = {Thu, 15 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CorePWG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CostaMSBV23,
author = {S{\'{a}}vio S. Costa and
Gislenne da Silva Moia and
Artur Silva and
Rafael A. Bara{\'{u}}na and
Adonney Allan de Oliveira Veras},
title = {{BADASS:} BActeriocin-Diversity ASsessment Software},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {24},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05106-x},
doi = {10.1186/S12859-022-05106-X},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CostaMSBV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DaneshvarMO23,
author = {Negar Hossein{-}Nezhad Daneshvar and
Yosef Masoudi{-}Sobhanzadeh and
Yadollah Omidi},
title = {A voting-based machine learning approach for classifying biological
and clinical datasets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {140},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05274-4},
doi = {10.1186/S12859-023-05274-4},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DaneshvarMO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DelomasW23,
author = {Thomas A. Delomas and
Stuart C. Willis},
title = {Estimating microhaplotype allele frequencies from low-coverage or
pooled sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {415},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05554-z},
doi = {10.1186/S12859-023-05554-Z},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DelomasW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DepuydtRAF23,
author = {Lore Depuydt and
Luca Renders and
Thomas Abeel and
Jan Fostier},
title = {Pan-genome de Bruijn graph using the bidirectional FM-index},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {400},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05531-6},
doi = {10.1186/S12859-023-05531-6},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DepuydtRAF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DhingraSNAA23,
author = {Ashna Dhingra and
Zayla Schaeffer and
Natalia I. Majewska Nepomuceno and
Jennifer Au and
Joomi Ahn},
title = {A MATLAB-based app to improve {LC-MS/MS} data analysis for N-linked
glycan peak identification},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {259},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05346-5},
doi = {10.1186/S12859-023-05346-5},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DhingraSNAA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DjeddiHYD23,
author = {Warith Eddine Djeddi and
Khalil Hermi and
Sadok Ben Yahia and
Gayo Diallo},
title = {Advancing drug-target interaction prediction: a comprehensive graph-based
approach integrating knowledge graph embedding and ProtBert pretraining},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {488},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05593-6},
doi = {10.1186/S12859-023-05593-6},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DjeddiHYD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DohertyDHMPCSWCMDM23,
author = {Trevor Doherty and
Emma Dempster and
Eilis J. Hannon and
Jonathan Mill and
Richie Poulton and
David Corcoran and
Karen Sugden and
Ben Williams and
Avshalom Caspi and
Terrie E. Moffitt and
Sarah Jane Delany and
Therese M. Murphy},
title = {A comparison of feature selection methodologies and learning algorithms
in the development of a {DNA} methylation-based telomere length estimator},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {178},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05282-4},
doi = {10.1186/S12859-023-05282-4},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DohertyDHMPCSWCMDM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DomingoLD23,
author = {Juan Domingo and
Teresa Le{\'{o}}n and
Esther Dur{\'{a}}},
title = {Scellpam: an {R} package/C++ library to perform parallel partitioning
around medoids on scRNAseq data sets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {342},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05471-1},
doi = {10.1186/S12859-023-05471-1},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DomingoLD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DoreyRobinsonMH23,
author = {Daniel Dorey{-}Robinson and
Giuseppe Maccari and
John A. Hammond},
title = {IgMAT: immunoglobulin sequence multi-species annotation tool for any
species including those with incomplete antibody annotation or unusual
characteristics},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {491},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05624-2},
doi = {10.1186/S12859-023-05624-2},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DoreyRobinsonMH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DuNLYZHLLDW23,
author = {Peng Du and
Xiaofeng Niu and
Xukun Li and
Chiqing Ying and
Yukun Zhou and
Chang He and
Shuangzhi Lv and
Xiaoli Liu and
Weibo Du and
Wei Wu},
title = {Automatically transferring supervised targets method for segmenting
lung lesion regions with {CT} imaging},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {332},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05435-5},
doi = {10.1186/S12859-023-05435-5},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DuNLYZHLLDW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DuWWMZLF23,
author = {Jin Du and
Chaojie Wang and
Lijun Wang and
Shanjun Mao and
Bencong Zhu and
Zheng Li and
Xiaodan Fan},
title = {Automatic block-wise genotype-phenotype association detection based
on hidden Markov model},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {138},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05265-5},
doi = {10.1186/S12859-023-05265-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DuWWMZLF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DuanWFJCZZ23,
author = {Qiaonan Duan and
Weiyi Wang and
Feiling Feng and
Xiaoqing Jiang and
Hao Chen and
Dadong Zhang and
Tongyi Zhang},
title = {Comut-viz: efficiently creating and browsing comutation plots online},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {226},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05351-8},
doi = {10.1186/S12859-023-05351-8},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DuanWFJCZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DunnBDN23,
author = {Timothy Dunn and
David T. Blaauw and
Reetuparna Das and
Satish Narayanasamy},
title = {nPoRe: n-polymer realigner for improved pileup-based variant calling},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {98},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05193-4},
doi = {10.1186/S12859-023-05193-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DunnBDN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EaglesWJC23,
author = {Nicholas J. Eagles and
Richard Wilton and
Andrew E. Jaffe and
Leonardo Collado{-}Torres},
title = {BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing
data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {340},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05461-3},
doi = {10.1186/S12859-023-05461-3},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/EaglesWJC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EbrahimiWBPAN23,
author = {Ali Ebrahimi and
Uffe Kock Wiil and
Ruben Baskaran and
Abdolrahman Peimankar and
Kjeld Andersen and
Anette S{\o}gaard Nielsen},
title = {{AUD-DSS:} a decision support system for early detection of patients
with alcohol use disorder},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {329},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05450-6},
doi = {10.1186/S12859-023-05450-6},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/EbrahimiWBPAN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ElmarakebyTARSAK23,
author = {Haitham Elmarakeby and
Pavel S. Trukhanov and
Vidal M. Arroyo and
Irbaz Bin Riaz and
Deborah Schrag and
Eliezer M. Van Allen and
Kenneth L. Kehl},
title = {Empirical evaluation of language modeling to ascertain cancer outcomes
from clinical text reports},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {328},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05439-1},
doi = {10.1186/S12859-023-05439-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ElmarakebyTARSAK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EsRTSHARH23,
author = {Bram van Es and
Leon C. Reteig and
Sander C. Tan and
Marijn Schraagen and
Myrthe M. Hemker and
Sebastiaan R. S. Arends and
Miguel A. R. Rios and
Saskia Haitjema},
title = {Negation detection in Dutch clinical texts: an evaluation of rule-based
and machine learning methods},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {10},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05130-x},
doi = {10.1186/S12859-022-05130-X},
timestamp = {Tue, 17 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/EsRTSHARH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/EschrichYT23,
author = {Steven A. Eschrich and
Xiaoqing Yu and
Jamie K. Teer},
title = {Fast all versus all genotype comparison using {DNA/RNA} sequencing
data: method and workflow},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {164},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05288-y},
doi = {10.1186/S12859-023-05288-Y},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/EschrichYT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FallonCMWP23,
author = {Timothy R. Fallon and
Tereza Calounov{\'{a}} and
Martin Mokrejs and
Jing{-}Ke Weng and
Tom{\'{a}}s Pluskal},
title = {transXpress: a Snakemake pipeline for streamlined de novo transcriptome
assembly and annotation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {133},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05254-8},
doi = {10.1186/S12859-023-05254-8},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FallonCMWP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FaltejskovaV23,
author = {Katerina Faltejskov{\'{a}} and
Jir{\'{\i}} Vondr{\'{a}}sek},
title = {PAPerFly: Partial Assembly-based Peak Finder for ab initio binding
site reconstruction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {487},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05613-5},
doi = {10.1186/S12859-023-05613-5},
timestamp = {Sat, 13 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FaltejskovaV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FanLS23,
author = {Yongxian Fan and
Xiqian Lu and
Guicong Sun},
title = {{IHCP:} interpretable hepatitis {C} prediction system based on black-box
machine learning models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {333},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05456-0},
doi = {10.1186/S12859-023-05456-0},
timestamp = {Fri, 15 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FanLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FanXS23,
author = {Yongxian Fan and
Hui Xiong and
Guicong Sun},
title = {DeepASDPred: a CNN-LSTM-based deep learning method for Autism spectrum
disorders risk {RNA} identification},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {261},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05378-x},
doi = {10.1186/S12859-023-05378-X},
timestamp = {Mon, 03 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FanXS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FanZHS23,
author = {Kui Fan and
Bo{-}hui Zhang and
Deng Han and
Yun{-}chuan Sun},
title = {{EZH2} as a prognostic-related biomarker in lung adenocarcinoma correlating
with cell cycle and immune infiltrates},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {149},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05271-7},
doi = {10.1186/S12859-023-05271-7},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FanZHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FarrelLVPML23,
author = {Alvin Farrel and
Peng Li and
Sharon Veenbergen and
Khushbu Patel and
John M. Maris and
Warren J. Leonard},
title = {{ROGUE:} an {R} Shiny app for {RNA} sequencing analysis and biomarker
discovery},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {303},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05420-y},
doi = {10.1186/S12859-023-05420-Y},
timestamp = {Fri, 18 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FarrelLVPML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FengCX23,
author = {Xin Feng and
Yihuai Cai and
Ruihao Xin},
title = {Optimizing diabetes classification with a machine learning-based framework},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {428},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05467-x},
doi = {10.1186/S12859-023-05467-X},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FengCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FengZYL23,
author = {Hai{-}Ming Feng and
Ye Zhao and
Wei{-}Jian Yan and
Bin Li},
title = {Genomic and immunogenomic analysis of three prognostic signature genes
in {LUAD}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {19},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05137-y},
doi = {10.1186/S12859-023-05137-Y},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FengZYL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FerreL23,
author = {Arnaud Ferr{\'{e}} and
Philippe Langlais},
title = {An analysis of entity normalization evaluation biases in specialized
domains},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {227},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05350-9},
doi = {10.1186/S12859-023-05350-9},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FerreL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FiedlerBMS23,
author = {Lisa Fiedler and
Matthias Bernt and
Martin Middendorf and
Peter F. Stadler},
title = {Detecting gene breakpoints in noisy genome sequences using position-annotated
colored de-Bruijn graphs},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {235},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05371-4},
doi = {10.1186/S12859-023-05371-4},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FiedlerBMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FigaschewskiSTK23,
author = {Mirjam Figaschewski and
Bilge S{\"{u}}r{\"{u}}n and
Thorsten Tiede and
Oliver Kohlbacher},
title = {The personalized cancer network explorer (PeCaX) as a visual analytics
tool to support molecular tumor boards},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {88},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05194-3},
doi = {10.1186/S12859-023-05194-3},
timestamp = {Tue, 28 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FigaschewskiSTK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FlemingS23,
author = {James F. Fleming and
Torsten H. Struck},
title = {nRCFV: a new, dataset-size-independent metric to quantify compositional
heterogeneity in nucleotide and amino acid datasets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {145},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05270-8},
doi = {10.1186/S12859-023-05270-8},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FlemingS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FuHWC23,
author = {Li Fu and
Qun Huang and
Yongfeng Wu and
Diang Chen},
title = {Prognostic analysis of uveal melanoma based on the characteristic
genes of M2-type macrophages in the tumor microenvironment},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {280},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05396-9},
doi = {10.1186/S12859-023-05396-9},
timestamp = {Tue, 25 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FuHWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FuSKYLY23,
author = {Huancheng Fu and
Ce Shan and
Fanchen Kang and
Ling Yu and
Zhonghan Li and
Yike Yin},
title = {{CRISPR-GRANT:} a cross-platform graphical analysis tool for high-throughput
CRISPR-based genome editing evaluation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {219},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05333-w},
doi = {10.1186/S12859-023-05333-W},
timestamp = {Thu, 13 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FuSKYLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GaoHCWz23,
author = {Xiu{-}e Gao and
Jian{-}Gang Hu and
Bo Chen and
Yun{-}Ming Wang and
Shengbin Zhou},
title = {Causal discovery approach with reinforcement learning for risk factors
of type {II} diabetes mellitus},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {296},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05405-x},
doi = {10.1186/S12859-023-05405-X},
timestamp = {Tue, 26 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GaoHCWz23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GaoLDZ23,
author = {Runtian Gao and
Junwei Luo and
Hongyu Ding and
Haixia Zhai},
title = {INSnet: a method for detecting insertions based on deep learning network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {80},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05216-0},
doi = {10.1186/S12859-023-05216-0},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GaoLDZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GaranaJDHG23,
author = {Belinda B. Garana and
James H. Joly and
Alireza Delfarah and
Hyunjun Hong and
Nicholas A. Graham},
title = {Drug mechanism enrichment analysis improves prioritization of therapeutics
for repurposing},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {215},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05343-8},
doi = {10.1186/S12859-023-05343-8},
timestamp = {Sat, 27 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GaranaJDHG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GaticaNLRPLHRBCC23,
author = {Marilyn Gatica and
Carlos F. Navarro and
Alejandro Lavado and
German Reig and
Eduardo Pulgar and
Paula Llanos and
Steffen H{\"{a}}rtel and
Andrea Ravasio and
Cristina Bertocchi and
Miguel L. Concha and
Mauricio Cerda},
title = {VolumePeeler: a novel {FIJI} plugin for geometric tissue peeling to
improve visualization and quantification of 3D image stacks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {283},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05403-z},
doi = {10.1186/S12859-023-05403-Z},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GaticaNLRPLHRBCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GholipourKAGA23,
author = {Maryam Gholipour and
Reza Khajouei and
Parastoo Amiri and
Sadrieh Hajesmaeel Gohari and
Leila Ahmadian},
title = {Extracting cancer concepts from clinical notes using natural language
processing: a systematic review},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {405},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05480-0},
doi = {10.1186/S12859-023-05480-0},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GholipourKAGA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GhorbanaliZSAM23,
author = {Zahra Ghorbanali and
Fatemeh Zare{-}Mirakabad and
Najmeh Salehi and
Mohammad Akbari and
Ali Masoudi{-}Nejad},
title = {DrugRep-HeSiaGraph: when heterogenous siamese neural network meets
knowledge graphs for drug repurposing},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {374},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05479-7},
doi = {10.1186/S12859-023-05479-7},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GhorbanaliZSAM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GoenagaAGA23,
author = {Iakes Goenaga and
Edgar Andr{\'{e}}s and
Koldo Gojenola and
Aitziber Atutxa},
title = {Advances in monolingual and crosslingual automatic disability annotation
in Spanish},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {265},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05372-3},
doi = {10.1186/S12859-023-05372-3},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GoenagaAGA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GoyalSVH23,
author = {Vishakha Goyal and
Nicholas J. Schaub and
Ty C. Voss and
Nathan Hotaling},
title = {Unbiased image segmentation assessment toolkit for quantitative differentiation
of state-of-the-art algorithms and pipelines},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {388},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05486-8},
doi = {10.1186/S12859-023-05486-8},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GoyalSVH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuL23,
author = {Changlong Gu and
Xiaoying Li},
title = {Prediction of disease-related miRNAs by voting with multiple classifiers},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {177},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05308-x},
doi = {10.1186/S12859-023-05308-X},
timestamp = {Wed, 03 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GuL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuanZ23,
author = {Zhengyi Guan and
Xiaobing Zhou},
title = {A prefix and attention map discrimination fusion guided attention
for biomedical named entity recognition},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {42},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05172-9},
doi = {10.1186/S12859-023-05172-9},
timestamp = {Wed, 15 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GuanZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GudkovTKBWDG23,
author = {Mikhail Gudkov and
Lo{\"{\i}}c Thibaut and
Matloob Khushi and
Gillian M. Blue and
David S. Winlaw and
Sally L. Dunwoodie and
Eleni Giannoulatou},
title = {ConanVarvar: a versatile tool for the detection of large syndromic
copy number variation from whole-genome sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {49},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05154-x},
doi = {10.1186/S12859-023-05154-X},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GudkovTKBWDG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuerlerBBGBCSZSN23,
author = {Aysam Guerler and
Dannon Baker and
Marius van den Beek and
Bj{\"{o}}rn A. Gr{\"{u}}ning and
Dave Bouvier and
Nate Coraor and
Stephen D. Shank and
Jordan D. Zehr and
Michael C. Schatz and
Anton Nekrutenko},
title = {Fast and accurate genome-wide predictions and structural modeling
of protein-protein interactions using Galaxy},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {263},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05389-8},
doi = {10.1186/S12859-023-05389-8},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GuerlerBBGBCSZSN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuichardLTL23,
author = {Anne Guichard and
Fabrice Legeai and
Denis Tagu and
Claire Lemaitre},
title = {MTG-Link: leveraging barcode information from linked-reads to assemble
specific loci},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {284},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05395-w},
doi = {10.1186/S12859-023-05395-W},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GuichardLTL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuoWWZSWC23,
author = {Zhen{-}Hao Guo and
Yan Wu and
Siguo Wang and
Qinhu Zhang and
Jin{-}Ming Shi and
Yan{-}Bin Wang and
Zhan{-}Heng Chen},
title = {scInterpreter: a knowledge-regularized generative model for interpretably
integrating scRNA-seq data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {481},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05579-4},
doi = {10.1186/S12859-023-05579-4},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GuoWWZSWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GuoXDYXTYWL23,
author = {Li Guo and
Yangyang Xiang and
Yuyang Dou and
Zibo Yin and
Xinru Xu and
Lihua Tang and
Jiafeng Yu and
Jun Wang and
Tingming Liang},
title = {GBCdb: {RNA} expression landscapes and ncRNA-mRNA interactions in
gallbladder carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {12},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05133-2},
doi = {10.1186/S12859-023-05133-2},
timestamp = {Mon, 15 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GuoXDYXTYWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HachemSS23,
author = {Elie{-}Julien El Hachem and
Nataliya Sokolovska and
H{\'{e}}di Soula},
title = {Latent dirichlet allocation for double clustering {(LDA-DC):} discovering
patients phenotypes and cell populations within a single Bayesian
framework},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {61},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05177-4},
doi = {10.1186/S12859-023-05177-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HachemSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HafstadHP23,
author = {V{\"{o}}lundur Hafsta{\dh} and
Jari H{\"{a}}kkinen and
Helena Persson},
title = {Fast and sensitive validation of fusion transcripts in whole-genome
sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {359},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05489-5},
doi = {10.1186/S12859-023-05489-5},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HafstadHP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HanHYKK23,
author = {Seokjin Han and
Jinhee Hong and
So Jeong Yun and
Hee Jung Koo and
Tae Yong Kim},
title = {{PWN:} enhanced random walk on a warped network for disease target
prioritization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {105},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05227-x},
doi = {10.1186/S12859-023-05227-X},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HanHYKK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HaoJS23,
author = {Yaru Hao and
Xiao{-}Yuan Jing and
Qixing Sun},
title = {Cancer survival prediction by learning comprehensive deep feature
representation for multiple types of genetic data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {267},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05392-z},
doi = {10.1186/S12859-023-05392-Z},
timestamp = {Mon, 03 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HaoJS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HartEHD23,
author = {Chloe Engler Hart and
Daniel Ence and
David Healey and
Daniel Domingo{-}Fern{\'{a}}ndez},
title = {On the correspondence between the transcriptomic response of a compound
and its effects on its targets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {207},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05337-6},
doi = {10.1186/S12859-023-05337-6},
timestamp = {Sat, 27 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HartEHD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HashemiZHG23,
author = {S. Morteza Hashemi and
Arash Zabihian and
Mohsen Hooshmand and
Sajjad Gharaghani},
title = {DRaW: prediction of {COVID-19} antivirals by deep learning - an objection
on using matrix factorization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {52},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05181-8},
doi = {10.1186/S12859-023-05181-8},
timestamp = {Fri, 24 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HashemiZHG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HatanoIO23,
author = {Yuya Hatano and
Tomohiko Ishihara and
Osamu Onodera},
title = {Accuracy of a machine learning method based on structural and locational
information from AlphaFold2 for predicting the pathogenicity of {TARDBP}
and {FUS} gene variants in {ALS}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {206},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05338-5},
doi = {10.1186/S12859-023-05338-5},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HatanoIO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HatanoKKO23,
author = {Narumi Hatano and
Mayumi Kamada and
Ryosuke Kojima and
Yasushi Okuno},
title = {Network-based prediction approach for cancer-specific driver missense
mutations using a graph neural network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {383},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05507-6},
doi = {10.1186/S12859-023-05507-6},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HatanoKKO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HauptmannK23,
author = {Tony Hauptmann and
Stefan Kramer},
title = {A fair experimental comparison of neural network architectures for
latent representations of multi-omics for drug response prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {45},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05166-7},
doi = {10.1186/S12859-023-05166-7},
timestamp = {Fri, 17 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HauptmannK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HayesLG23,
author = {Molly G. Hayes and
Morgan G. I. Langille and
Hong Gu},
title = {Cross-study analyses of microbial abundance using generalized common
factor methods},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {380},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05509-4},
doi = {10.1186/S12859-023-05509-4},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HayesLG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HeinsbergW23,
author = {Lacey W. Heinsberg and
Daniel E. Weeks},
title = {dbGaPCheckup: pre-submission checks of dbGaP-formatted subject phenotype
files},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {77},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05200-8},
doi = {10.1186/S12859-023-05200-8},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HeinsbergW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HerrickW23,
author = {Noah Herrick and
Susan Walsh},
title = {{ILIAD:} a suite of automated Snakemake workflows for processing genomic
data for downstream applications},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {424},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05548-x},
doi = {10.1186/S12859-023-05548-X},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HerrickW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HosseiniGeramiHCLEBB23,
author = {Layla Hosseini{-}Gerami and
Ixavier Alonzo Higgins and
David A. Collier and
Emma Laing and
David Evans and
Howard Broughton and
Andreas Bender},
title = {Benchmarking causal reasoning algorithms for gene expression-based
compound mechanism of action analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {154},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05277-1},
doi = {10.1186/S12859-023-05277-1},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HosseiniGeramiHCLEBB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HosseiniGeramiHLBCB23,
author = {Layla Hosseini{-}Gerami and
Rosa D. Hernansaiz{-}Ballesteros and
Anika Liu and
Howard Broughton and
David A. Collier and
Andreas Bender},
title = {{MAVEN:} compound mechanism of action analysis and visualisation using
transcriptomics and compound structure data in R/Shiny},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {344},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05416-8},
doi = {10.1186/S12859-023-05416-8},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HosseiniGeramiHLBCB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HouLYXW23,
author = {Zhichao Hou and
Jiacheng Leng and
Jiating Yu and
Zheng Xia and
Ling{-}Yun Wu},
title = {PathExpSurv: pathway expansion for explainable survival analysis and
disease gene discovery},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {434},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05535-2},
doi = {10.1186/S12859-023-05535-2},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HouLYXW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuFRCYXXT23,
author = {Lingzhi Hu and
Chengzhou Fu and
Zhonglu Ren and
Yongming Cai and
Jin Yang and
Siwen Xu and
Wenhua Xu and
Deyu Tang},
title = {SSELM-neg: spherical search-based extreme learning machine for drug-target
interaction prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {38},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05153-y},
doi = {10.1186/S12859-023-05153-Y},
timestamp = {Tue, 07 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HuFRCYXXT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuJLWLGT23,
author = {Shuwen Hu and
Yi Jing and
Tao Li and
You{-}Gan Wang and
Zhenyu Liu and
Jing Gao and
Yu{-}Chu Tian},
title = {Inferring circadian gene regulatory relationships from gene expression
data with a hybrid framework},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {362},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05458-y},
doi = {10.1186/S12859-023-05458-Y},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HuJLWLGT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuangZZW23,
author = {Jing Huang and
Yuting Zhou and
Haoran Zhang and
Yiming Wu},
title = {A neural network model to screen feature genes for pancreatic cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {193},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05322-z},
doi = {10.1186/S12859-023-05322-Z},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HuangZZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuckvaleM23,
author = {Erik Huckvale and
Hunter N. B. Moseley},
title = {kegg{\_}pull: a software package for the RESTful access and pulling
from the Kyoto Encyclopedia of Gene and Genomes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {78},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05208-0},
doi = {10.1186/S12859-023-05208-0},
timestamp = {Tue, 07 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HuckvaleM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HussainLANAT23,
author = {Sadam Hussain and
Yareth Lafarga{-}Osuna and
Mansoor Ali and
Usman Naseem and
Masroor Ahmed and
Jos{\'{e}} Gerardo Tamez{-}Pe{\~{n}}a},
title = {Deep learning, radiomics and radiogenomics applications in the digital
breast tomosynthesis: a systematic review},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {401},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05515-6},
doi = {10.1186/S12859-023-05515-6},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HussainLANAT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/IsmailGH23,
author = {Eman Ismail and
Walaa K. Gad and
Mohamed Hashem},
title = {A hybrid Stacking-SMOTE model for optimizing the prediction of autistic
genes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {379},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05501-y},
doi = {10.1186/S12859-023-05501-Y},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/IsmailGH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JacobPPLCBBMK23,
author = {Evgueni Jacob and
Ang{\'{e}}lique Perrillat{-}Mercerot and
Jean{-}Louis Palgen and
Ad{\`{e}}le L'Hostis and
Nicoletta Ceres and
Jean{-}Pierre Boissel and
Jim Bosley and
Cl{\'{a}}udio Monteiro and
Riad Kahoul},
title = {Empirical methods for the validation of time-to-event mathematical
models taking into account uncertainty and variability: application
to {EGFR} + lung adenocarcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {331},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05430-w},
doi = {10.1186/S12859-023-05430-W},
timestamp = {Fri, 15 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JacobPPLCBBMK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JainJMLD23,
author = {Rishab Jain and
Aditya Jain and
Elizabeth Mauro and
Kevin LeShane and
Douglas Densmore},
title = {{ICOR:} improving codon optimization with recurrent neural networks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {132},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05246-8},
doi = {10.1186/S12859-023-05246-8},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JainJMLD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JainX23,
author = {Rahi Jain and
Wei Xu},
title = {Artificial Intelligence based wrapper for high dimensional feature
selection},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {392},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05502-x},
doi = {10.1186/S12859-023-05502-X},
timestamp = {Mon, 30 Oct 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/JainX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JanssenDBGBRS23,
author = {Kobe Janssen and
Ramon Duran{-}Roma{\~{n}}a and
Guy Bottu and
Mainak Guharoy and
Alexander Botzki and
Frederic Rousseau and
Joost Schymkowitz},
title = {SNPeffect 5.0: large-scale structural phenotyping of protein coding
variants extracted from next-generation sequencing data using AlphaFold
models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {287},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05407-9},
doi = {10.1186/S12859-023-05407-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JanssenDBGBRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JiCLSL23,
author = {Xiangjun Ji and
Junwei Cai and
Lixin Liang and
Tieliu Shi and
Jinghua Liu},
title = {Gene expression variability across cells and species shapes the relationship
between renal resident macrophages and infiltrated macrophages},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {72},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05198-z},
doi = {10.1186/S12859-023-05198-Z},
timestamp = {Tue, 07 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/JiCLSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JiS23,
author = {Cong Ji and
Junbin Shao},
title = {Shine: {A} novel strategy to extract specific, sensitive and well-conserved
biomarkers from massive microbial genomic datasets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {128},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05195-2},
doi = {10.1186/S12859-023-05195-2},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JiS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JiaWS23,
author = {Jianhua Jia and
Zhangying Wei and
Mingwei Sun},
title = {EMDL{\_}m6Am: identifying N6,2{\({'}\)}-O-dimethyladenosine sites
based on stacking ensemble deep learning},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {397},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05543-2},
doi = {10.1186/S12859-023-05543-2},
timestamp = {Mon, 30 Oct 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/JiaWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JiangGBSM23,
author = {Jiaxiang Jiang and
Michael Goebel and
Cezar Borba and
William Smith and
B. S. Manjunath},
title = {A robust approach to 3D neuron shape representation for quantification
and classification},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {366},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05482-y},
doi = {10.1186/S12859-023-05482-Y},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JiangGBSM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JiangHLF23,
author = {Hanjing Jiang and
Yabing Huang and
Qianpeng Li and
Boyuan Feng},
title = {ScLSTM: single-cell type detection by siamese recurrent network and
hierarchical clustering},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {417},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05494-8},
doi = {10.1186/S12859-023-05494-8},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/JiangHLF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JiangLG23,
author = {Tao Jiang and
Shiqi Liu and
Hongzhe Guo},
title = {Reply: Correspondence on NanoVar's performance outlined by Jiang T.
et al. in 'Long-read sequencing settings for efficient structural
variation detection based on comprehensive evaluation'},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {352},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05483-x},
doi = {10.1186/S12859-023-05483-X},
timestamp = {Mon, 25 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JiangLG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JohLKP23,
author = {Yoonsung Joh and
Kangbae Lee and
Hyunwoo Kim and
Heejin Park},
title = {Progressive search in tandem mass spectrometry},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {94},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05222-2},
doi = {10.1186/S12859-023-05222-2},
timestamp = {Sat, 30 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/JohLKP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JonesMWLRC23,
author = {Jeff Jones and
Elliot J. MacKrell and
Ting{-}Yu Wang and
Brett Lomenick and
Michael L. Roukes and
Tsui{-}Fen Chou},
title = {Tidyproteomics: an open-source {R} package and data object for quantitative
proteomics post analysis and visualization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {239},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05360-7},
doi = {10.1186/S12859-023-05360-7},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JonesMWLRC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Juliusdottir23,
author = {Thorhildur Juliusdottir},
title = {topr: an {R} package for viewing and annotating genetic association
results},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {268},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05301-4},
doi = {10.1186/S12859-023-05301-4},
timestamp = {Mon, 03 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Juliusdottir23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KafkasAUAAH23,
author = {Senay Kafkas and
Marwa Abdelhakim and
Mahmut Uludag and
Azza Althagafi and
Malak Alghamdi and
Robert Hoehndorf},
title = {Starvar: symptom-based tool for automatic ranking of variants using
evidence from literature and genomes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {294},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05406-w},
doi = {10.1186/S12859-023-05406-W},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KafkasAUAAH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KaneKELGG23,
author = {Michael J. Kane and
Casey King and
Denise Esserman and
Nancy K. Latham and
Erich J. Greene and
David A. Ganz},
title = {A compressed large language model embedding dataset of {ICD} 10 {CM}
descriptions},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {482},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05597-2},
doi = {10.1186/S12859-023-05597-2},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KaneKELGG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KaraaslanliSMA23,
author = {Abdullah Karaaslanli and
Satabdi Saha and
Tapabrata Maiti and
Selin Aviyente},
title = {Kernelized multiview signed graph learning for single-cell {RNA} sequencing
data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {127},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05250-y},
doi = {10.1186/S12859-023-05250-Y},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KaraaslanliSMA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KarkeraAP23,
author = {Nikitha Karkera and
Sathwik Acharya and
Sucheendra K. Palaniappan},
title = {Leveraging pre-trained language models for mining microbiome-disease
relationships},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {290},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05411-z},
doi = {10.1186/S12859-023-05411-Z},
timestamp = {Fri, 21 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KarkeraAP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KavithaAJMMAAS23,
author = {P. Kavitha and
G. Ayyappan and
Prabhu Jayagopal and
Sandeep Kumar Mathivanan and
Saurav Mallik and
Amal Al{-}Rasheed and
Mohammed S. Alqahtani and
Ben Othman Soufiene},
title = {Detection for melanoma skin cancer through ACCF, BPPF, and {CLF} techniques
with machine learning approach},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {458},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05584-7},
doi = {10.1186/S12859-023-05584-7},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KavithaAJMMAAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KeshriKRAPKMTP23,
author = {Anand K. Keshri and
Rimanpreet Kaur and
Suraj S. Rawat and
Naina Arora and
Rajan K. Pandey and
Bajarang V. Kumbhar and
Amit Mishra and
Shweta Tripathi and
Amit Prasad},
title = {Designing and development of multi-epitope chimeric vaccine against
Helicobacter pylori by exploring its entire immunogenic epitopes:
an immunoinformatic approach},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {358},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05454-2},
doi = {10.1186/S12859-023-05454-2},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KeshriKRAPKMTP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KhandelwalR23,
author = {Monika Khandelwal and
Ranjeet Kumar Rout},
title = {PRMxAI: protein arginine methylation sites prediction based on amino
acid spatial distribution using explainable artificial intelligence},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {376},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05491-x},
doi = {10.1186/S12859-023-05491-X},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KhandelwalR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KimC23,
author = {Gwangwoo Kim and
Hyonho Chun},
title = {Similarity-assisted variational autoencoder for nonlinear dimension
reduction with application to single-cell {RNA} sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {432},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05552-1},
doi = {10.1186/S12859-023-05552-1},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KimC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KimJHWS23,
author = {Kipoong Kim and
Tae{-}Hwan Jun and
Bo{-}Keun Ha and
Shuang Wang and
Hokeun Sun},
title = {New statistical selection method for pleiotropic variants associated
with both quantitative and qualitative traits},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {381},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05505-8},
doi = {10.1186/S12859-023-05505-8},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KimJHWS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KimK23,
author = {Youjin Kim and
Junseok Kwon},
title = {AttSec: protein secondary structure prediction by capturing local
patterns from attention map},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {183},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05310-3},
doi = {10.1186/S12859-023-05310-3},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KimK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KlailaVS23,
author = {Gideon Klaila and
Vladimir Vutov and
Anastasios Stefanou},
title = {Supervised topological data analysis for {MALDI} mass spectrometry
imaging applications},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {279},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05402-0},
doi = {10.1186/S12859-023-05402-0},
timestamp = {Sat, 05 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KlailaVS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KofmanYMY23,
author = {Eric Kofman and
Brian Yee and
Hugo C. Medina{-}Munoz and
Gene W. Yeo},
title = {{FLARE:} a fast and flexible workflow for identifying {RNA} editing
foci},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {370},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05452-4},
doi = {10.1186/S12859-023-05452-4},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KofmanYMY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KotovZM23,
author = {Aleksandr Kotov and
Andrei Zinovyev and
Anne{-}Helene Monsoro{-}Burq},
title = {scEvoNet: a gradient boosting-based method for prediction of cell
state evolution},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {83},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05213-3},
doi = {10.1186/S12859-023-05213-3},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KotovZM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KrinosCFA23,
author = {Arianna I. Krinos and
Natalie R. Cohen and
Michael J. Follows and
Harriet Alexander},
title = {Reverse engineering environmental metatranscriptomes clarifies best
practices for eukaryotic assembly},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {74},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05121-y},
doi = {10.1186/S12859-022-05121-Y},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KrinosCFA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KrinosCFA23a,
author = {Arianna I. Krinos and
Natalie R. Cohen and
Michael J. Follows and
Harriet Alexander},
title = {Correction: Reverse engineering environmental metatranscriptomes clarifies
best practices for eukaryotic assembly},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {185},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05313-0},
doi = {10.1186/S12859-023-05313-0},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KrinosCFA23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KuangMS23,
author = {Junyao Kuang and
Kristin Michel and
Caterina M. Scoglio},
title = {GeCoNet-Tool: a software package for gene co-expression network construction
and analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {281},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05382-1},
doi = {10.1186/S12859-023-05382-1},
timestamp = {Wed, 19 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KuangMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KumarGB23,
author = {Anup Kumar and
Bj{\"{o}}rn A. Gr{\"{u}}ning and
Rolf Backofen},
title = {Transformer-based tool recommendation system in Galaxy},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {446},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05573-w},
doi = {10.1186/S12859-023-05573-W},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KumarGB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KumarMLP23,
author = {Rajnish Kumar and
Rajkrishna Mondal and
Tapobrata Lahiri and
Manoj Kumar Pal},
title = {Application of sequence semantic and integrated cellular geography
approach to study alternative biogenesis of exonic circular {RNA}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {148},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05279-z},
doi = {10.1186/S12859-023-05279-Z},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KumarMLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KumlerHI23,
author = {William Kumler and
Bryna J. Hazelton and
Anitra E. Ingalls},
title = {Picky with peakpicking: assessing chromatographic peak quality with
simple metrics in metabolomics},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {404},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05533-4},
doi = {10.1186/S12859-023-05533-4},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KumlerHI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KunzmannMGKABIH23,
author = {Patrick Kunzmann and
Tom David M{\"{u}}ller and
Maximilian Greil and
Jan Hendrik Krumbach and
Jacob Marcel Anter and
Daniel Bauer and
Faisal Islam and
Kay Hamacher},
title = {Biotite: new tools for a versatile Python bioinformatics library},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {236},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05345-6},
doi = {10.1186/S12859-023-05345-6},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KunzmannMGKABIH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KwanFMFHHMNPRRSYZSN23,
author = {Brian Kwan and
Tobias Fuhrer and
Daniel Montemayor and
Jeffery C. Fink and
Jiang He and
Chi{-}yuan Hsu and
Karen Messer and
Robert G. Nelson and
Minya Pu and
Ana C. Ricardo and
Hernan Rincon{-}Choles and
Vallabh O. Shah and
Hongping Ye and
Jing Zhang and
Kumar Sharma and
Loki Natarajan},
title = {A generalized covariate-adjusted top-scoring pair algorithm with applications
to diabetic kidney disease stage classification in the Chronic Renal
Insufficiency Cohort {(CRIC)} Study},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {57},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05171-w},
doi = {10.1186/S12859-023-05171-W},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KwanFMFHHMNPRRSYZSN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LaPoliceH23,
author = {Troy M. LaPolice and
Yi{-}Fei Huang},
title = {An unsupervised deep learning framework for predicting human essential
genes from population and functional genomic data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {347},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05481-z},
doi = {10.1186/S12859-023-05481-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LaPoliceH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LabordeSCCB23,
author = {Jose Laborde and
Paul A. Stewart and
Zhihua Chen and
Yian A. Chen and
Naomi C. Brownstein},
title = {Sparse clusterability: testing for cluster structure in high dimensions},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {125},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05210-6},
doi = {10.1186/S12859-023-05210-6},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LabordeSCCB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LateganSP23,
author = {F. Adriaan Lategan and
Caroline Schreiber and
Hugh{-}George Patterton},
title = {SeqPredNN: a neural network that generates protein sequences that
fold into specified tertiary structures},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {373},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05498-4},
doi = {10.1186/S12859-023-05498-4},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LateganSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LeeSJKYKNCKSBY23,
author = {Sungyoung Lee and
Choong{-}Hyun Sun and
Heejun Jang and
Daeyoon Kim and
Sung{-}Soo Yoon and
Youngil Koh and
Seung Chan Na and
Sung Im Cho and
Man Jin Kim and
Moon{-}Woo Seong and
Ja Min Byun and
Hongseok Yun},
title = {ITDetect: a method to detect internal tandem duplication of FMS-like
tyrosine kinase {(FLT3)} from next-generation sequencing data with
high sensitivity and clinical application},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {62},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05173-8},
doi = {10.1186/S12859-023-05173-8},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LeeSJKYKNCKSBY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiCLQZWYH23,
author = {Ran Li and
Haiyan Chen and
Chaoxi Li and
Yiwei Qi and
Kai Zhao and
Junwen Wang and
Chao You and
Haohao Huang},
title = {The prognostic value and immune landscaps of m6A/m5C-related lncRNAs
signature in the low grade glioma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {274},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05386-x},
doi = {10.1186/S12859-023-05386-X},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiCLQZWYH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiCYX23,
author = {Wei Li and
Yuhuan Chi and
Kun Yu and
Weidong Xie},
title = {A two-stage hybrid biomarker selection method based on ensemble filter
and binary differential evolution incorporating binary African vultures
optimization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {130},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05247-7},
doi = {10.1186/S12859-023-05247-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiCYX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiKTSGGAMZC23,
author = {Zhijian Li and
Chao{-}Chung Kuo and
Fabio Ticconi and
Mina Shaigan and
Julia Gehrmann and
Eduardo G. Gusm{\~{a}}o and
Manuel Allhoff and
Martin Manolov and
Martin Zenke and
Ivan G. Costa},
title = {{RGT:} a toolbox for the integrative analysis of high throughput regulatory
genomics data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {79},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05184-5},
doi = {10.1186/S12859-023-05184-5},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiKTSGGAMZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiQLTZHJMYJGCD23,
author = {Ruowen Li and
Wenjie Qu and
Qingqing Liu and
Yilin Tan and
Wenjing Zhang and
Yiping Hao and
Nan Jiang and
Zhonghao Mao and
Jinwen Ye and
Jun Jiao and
Qun Gao and
Baoxia Cui and
Taotao Dong},
title = {Development and validation of a deep learning survival model for cervical
adenocarcinoma patients},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {146},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05239-7},
doi = {10.1186/S12859-023-05239-7},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiQLTZHJMYJGCD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiWLLXZ23,
author = {Rongyuan Li and
Jingli Wu and
Gaoshi Li and
Jiafei Liu and
Junbo Xuan and
Qi Zhu},
title = {Mdwgan-gp: data augmentation for gene expression data based on multiple
discriminator {WGAN-GP}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {427},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05558-9},
doi = {10.1186/S12859-023-05558-9},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiWLLXZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiX23,
author = {Canxuan Li and
Weibin Xie},
title = {Identification and validation of tumor-infiltrating lymphocyte-related
prognosis signature for predicting prognosis and immunotherapeutic
response in bladder cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {118},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05241-z},
doi = {10.1186/S12859-023-05241-Z},
timestamp = {Fri, 31 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiYWWCZW23,
author = {He Li and
Lei Yang and
Yuanyuan Wang and
Lingchan Wang and
Gang Chen and
Li Zhang and
Dongchang Wang},
title = {Integrative analysis of {TP53} mutations in lung adenocarcinoma for
immunotherapies and prognosis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {155},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05268-2},
doi = {10.1186/S12859-023-05268-2},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiYWWCZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiYXT23,
author = {Yan Li and
Yinying Yao and
Yu Xia and
Mingjing Tang},
title = {Searching for protein variants with desired properties using deep
generative models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {297},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05415-9},
doi = {10.1186/S12859-023-05415-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiYXT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiZZSLZHH23,
author = {Dong{-}Xu Li and
Peng Zhou and
Bo{-}Wei Zhao and
Xiao{-}Rui Su and
Guo{-}Dong Li and
Jun Zhang and
Peng{-}Wei Hu and
Lun Hu},
title = {Biocaiv: an integrative webserver for motif-based clustering analysis
and interactive visualization of biological networks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {451},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05574-9},
doi = {10.1186/S12859-023-05574-9},
timestamp = {Mon, 04 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiZZSLZHH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiangLSLZLLLW23,
author = {Shiyang Liang and
Siwei Liu and
Junliang Song and
Qiang Lin and
Shihong Zhao and
Shuaixin Li and
Jiahui Li and
Shangsong Liang and
Jingjie Wang},
title = {{HMCDA:} a novel method based on the heterogeneous graph neural network
and metapath for circRNA-disease associations prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {335},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05441-7},
doi = {10.1186/S12859-023-05441-7},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiangLSLZLLLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiaoW23,
author = {Chenqi Liao and
Xiong Wang},
title = {TCGAplot: an {R} package for integrative pan-cancer analysis and visualization
of {TCGA} multi-omics data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {483},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05615-3},
doi = {10.1186/S12859-023-05615-3},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiaoW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiebhoffMLFSB23,
author = {Anna{-}Maria Liebhoff and
Kevin Menden and
Alena Laschtowitz and
Andre Franke and
Christoph Schramm and
Stefan Bonn},
title = {Pathogen detection in RNA-seq data with Pathonoia},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {53},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05144-z},
doi = {10.1186/S12859-023-05144-Z},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiebhoffMLFSB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LietzSW23,
author = {Kristina Lietz and
Babak Saremi and
Lena Wiese},
title = {Genealyzer: web application for the analysis and comparison of gene
expression data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {150},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05266-4},
doi = {10.1186/S12859-023-05266-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LietzSW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LinW23,
author = {Chun{-}Ling Lin and
Kun{-}Chi Wu},
title = {Development of revised ResNet-50 for diabetic retinopathy detection},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {157},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05293-1},
doi = {10.1186/S12859-023-05293-1},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LinW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LinYZLLYS23,
author = {Qun{-}ting Lin and
Wei Yang and
Xin Zhang and
Qi{-}gang Li and
Yong{-}feng Liu and
Qin Yan and
Lei Sun},
title = {Systematic and benchmarking studies of pipelines for mammal {WGBS}
data in the novel {NGS} platform},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {33},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05163-w},
doi = {10.1186/S12859-023-05163-W},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LinYZLLYS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuGFHJMMSSWLB23,
author = {Nuo Liu and
Tonatiuh A. Gonzalez and
Jacob Fischer and
Chan Hong and
Michelle Johnson and
Ross Mawhorter and
Fabrizia Mugnatto and
Rachael Soh and
Shifa Somji and
Joseph S. Wirth and
Ran Libeskind{-}Hadas and
Eliot C. Bush},
title = {xenoGI 3: using the {DTLOR} model to reconstruct the evolution of
gene families in clades of microbes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {295},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05410-0},
doi = {10.1186/S12859-023-05410-0},
timestamp = {Sat, 05 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuGFHJMMSSWLB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuHAH23,
author = {Xuehan Liu and
Md. Rakibul Hasan and
Khandaker Asif Ahmed and
Md. Zakir Hossain},
title = {Machine learning to analyse omic-data for {COVID-19} diagnosis and
prognosis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {7},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05127-6},
doi = {10.1186/S12859-022-05127-6},
timestamp = {Tue, 17 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuHAH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuJAB23,
author = {Yining Liu and
Yinuo Jin and
Elham Azizi and
Andrew J. Blumberg},
title = {Cellstitch: 3D cellular anisotropic image segmentation via optimal
transport},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {480},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05608-2},
doi = {10.1186/S12859-023-05608-2},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuJAB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuL23,
author = {Yunze Liu and
Gang Li},
title = {Empowering biologists to decode omics data: the Genekitr {R} package
and web server},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {214},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05342-9},
doi = {10.1186/S12859-023-05342-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuLCLLHWWD23,
author = {YaLing Liu and
Dan Li and
Yong Chen and
YiJuan Liu and
YiJuan Lin and
XunRu Huang and
Ting Wu and
ChengDang Wang and
Jian Ding},
title = {Integrated bioinformatics analysis for conducting a prognostic model
and identifying immunotherapeutic targets in gastric cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {191},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05312-1},
doi = {10.1186/S12859-023-05312-1},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuLCLLHWWD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuLMGLCZ23,
author = {Peiqiang Liu and
Chang Liu and
Yanyan Mao and
Junhong Guo and
Fanshu Liu and
Wangmin Cai and
Feng Zhao},
title = {Identification of essential proteins based on edge features and the
fusion of multiple-source biological information},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {203},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05315-y},
doi = {10.1186/S12859-023-05315-Y},
timestamp = {Sat, 27 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuLMGLCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuLTLXY23,
author = {Puyu Liu and
Jihang Luo and
Na Tan and
Chengfang Li and
Jieyu Xu and
Xiaorong Yang},
title = {Establishing a prognostic model of chromatin modulators and identifying
potential drug candidates in renal clear cell patients},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {104},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05229-9},
doi = {10.1186/S12859-023-05229-9},
timestamp = {Sat, 25 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuLTLXY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuQZWZZ23,
author = {Chunxun Liu and
Zhaowei Qu and
Haoran Zhao and
Peng Wang and
Chao Zhan and
Yubao Zhang},
title = {Pan-cancer analysis of {SYNGR2} with a focus on clinical implications
and immune landscape in liver hepatocellular carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {192},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05323-y},
doi = {10.1186/S12859-023-05323-Y},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuQZWZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuTZZXS23,
author = {Xiao Liu and
Li Teng and
Wenqi Zuo and
Shixun Zhong and
Yuqiao Xu and
Jing Sun},
title = {Deafness gene screening based on a multilevel cascaded {BPNN} model},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {56},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05182-7},
doi = {10.1186/S12859-023-05182-7},
timestamp = {Thu, 28 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuTZZXS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuWL23,
author = {Chaozhong Liu and
Linhua Wang and
Zhandong Liu},
title = {Single-cell multi-omics integration for unpaired data by a siamese
network with graph-based contrastive loss},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {5},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05126-7},
doi = {10.1186/S12859-022-05126-7},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuWL23a,
author = {Chaozhong Liu and
Linhua Wang and
Zhandong Liu},
title = {Correction: Single-cell multi-omics integration for unpaired data
by a siamese network with graph-based contrastive loss},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {123},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05249-5},
doi = {10.1186/S12859-023-05249-5},
timestamp = {Sun, 16 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuWL23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuWLLGYC23,
author = {Chunhua Liu and
Simin Wu and
Liying Lai and
Jinyu Liu and
Zhaofu Guo and
Zegen Ye and
Xiang Chen},
title = {Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration
and prognosis in hepatocellular carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {4},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05091-1},
doi = {10.1186/S12859-022-05091-1},
timestamp = {Tue, 17 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuWLLGYC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuZAWSWMCKWY23,
author = {Yunqing Liu and
Jiayi Zhao and
Taylor Sterling Adams and
Ningya Wang and
Jonas Schupp and
Weimiao Wu and
John E. McDonough and
Geoffrey Lowell Chupp and
Naftali Kaminski and
Zuoheng Wang and
Xiting Yan},
title = {iDESC: identifying differential expression in single-cell {RNA} sequencing
data with multiple subjects},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {318},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05432-8},
doi = {10.1186/S12859-023-05432-8},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuZAWSWMCKWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiuZAWSWMCKWY23a,
author = {Yunqing Liu and
Jiayi Zhao and
Taylor Sterling Adams and
Ningya Wang and
Jonas Schupp and
Weimiao Wu and
John E. McDonough and
Geoffrey Lowell Chupp and
Naftali Kaminski and
Zuoheng Wang and
Xiting Yan},
title = {Correction: iDESC: identifying differential expression in single-cell
{RNA} sequencing data with multiple subjects},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {394},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05523-6},
doi = {10.1186/S12859-023-05523-6},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiuZAWSWMCKWY23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LozanoDAL23,
author = {Aur{\'{e}}lie C. Lozano and
Hantian Ding and
Naoki Abe and
Alexander E. Lipka},
title = {Regularized multi-trait multi-locus linear mixed models for genome-wide
association studies and genomic selection in crops},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {399},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05519-2},
doi = {10.1186/S12859-023-05519-2},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LozanoDAL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LuGCW23,
author = {Zhiwen Lu and
Lu Guo and
Jianhua Chen and
Rongshu Wang},
title = {Reference-based genome compression using the longest matched substrings
with parallelization consideration},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {369},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05500-z},
doi = {10.1186/S12859-023-05500-Z},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LuGCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LuJWAWY23,
author = {Miaoshan Lu and
Hengxuan Jiang and
Ruimin Wang and
Shaowei An and
Jiawei Wang and
Changbin Yu},
title = {Injectiondesign: web service of plate design with optimized stratified
block randomization for modern GC/LC-MS-based sample preparation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {489},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05598-1},
doi = {10.1186/S12859-023-05598-1},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LuJWAWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LuoFWLSCW23,
author = {Junwei Luo and
Yading Feng and
Xuyang Wu and
Ruimin Li and
Jiawei Shi and
Wenjing Chang and
Junfeng Wang},
title = {ForestSubtype: a cancer subtype identifying approach based on high-dimensional
genomic data and a parallel random forest},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {289},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05412-y},
doi = {10.1186/S12859-023-05412-Y},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LuoFWLSCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LuoLTLZZZX23,
author = {Ximei Luo and
Qun Li and
Yifan Tang and
Yan Liu and
Quan Zou and
Jie Zheng and
Ying Zhang and
Lei Xu},
title = {Predicting active enhancers with {DNA} methylation and histone modification},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {414},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05547-y},
doi = {10.1186/S12859-023-05547-Y},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LuoLTLZZZX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LvXQZTCYWG23,
author = {Guohao Lv and
Yingchun Xia and
Zhao Qi and
Zihao Zhao and
Lianggui Tang and
Cheng Chen and
Shuai Yang and
Qingyong Wang and
Lichuan Gu},
title = {LncRNA-protein interaction prediction with reweighted feature selection},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {410},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05536-1},
doi = {10.1186/S12859-023-05536-1},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LvXQZTCYWG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaSHD23,
author = {Chenyu Ma and
Yuanbo Shi and
Yueyang Huang and
Gongwei Dai},
title = {Raman spectroscopy-based prediction of ofloxacin concentration in
solution using a novel loss function and an improved {GA-CNN} model},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {409},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05542-3},
doi = {10.1186/S12859-023-05542-3},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MaSHD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaSMZLLZ23,
author = {Yang Ma and
Wan{-}liang Sun and
Shuo Shuo Ma and
Guanru Zhao and
Zhong Liu and
Zheng Lu and
Dengyong Zhang},
title = {LincRNA {ZNF529-AS1} inhibits hepatocellular carcinoma via {FBXO31}
and predicts the prognosis of hepatocellular carcinoma patients},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {54},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05189-0},
doi = {10.1186/S12859-023-05189-0},
timestamp = {Fri, 24 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MaSMZLLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaTW23,
author = {Qing Ma and
Yaqin Tan and
Lei Wang},
title = {{GACNNMDA:} a computational model for predicting potential human microbe-drug
associations based on graph attention network and CNN-based classifier},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {35},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05158-7},
doi = {10.1186/S12859-023-05158-7},
timestamp = {Tue, 07 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MaTW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaZCHY23,
author = {Huidong Ma and
Cheng Zhong and
Danyang Chen and
Haofa He and
Feng Yang},
title = {cnnLSV: detecting structural variants by encoding long-read alignment
information and convolutional neural network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {119},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05243-x},
doi = {10.1186/S12859-023-05243-X},
timestamp = {Fri, 31 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MaZCHY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaZLHWPXZTTQ23,
author = {Lina Ma and
Sitao Zhang and
Qi Liang and
Wenting Huang and
Hui Wang and
Emily Pan and
Ping Xu and
Shuguang Zhang and
Fei Tao and
Jin Tang and
Rui Qing},
title = {CrMP-Sol database: classification, bioinformatic analyses and comparison
of cancer-related membrane proteins and their water-soluble variant
designs},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {360},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05477-9},
doi = {10.1186/S12859-023-05477-9},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MaZLHWPXZTTQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaanssonAUMS23,
author = {Christoffer Trier Maansson and
Emma Roger Andersen and
Maiken Parm Ulhoi and
Peter Meldgaard and
Boe Sandahl Sorensen},
title = {DNAfusion: an R/Bioconductor package for increased sensitivity of
detecting gene fusions in liquid biopsies},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {131},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05259-3},
doi = {10.1186/S12859-023-05259-3},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MaanssonAUMS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MagillS23,
author = {Damian J. Magill and
Timofey A. Skvortsov},
title = {DePolymerase Predictor (DePP): a machine learning tool for the targeted
identification of phage depolymerases},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {208},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05341-w},
doi = {10.1186/S12859-023-05341-W},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MagillS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaharSSG23,
author = {Nirmal Singh Mahar and
Rohit Satyam and
Durai Sundar and
Ishaan Gupta},
title = {A systematic comparison of human mitochondrial genome assembly tools},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {341},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05445-3},
doi = {10.1186/S12859-023-05445-3},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MaharSSG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MahdiEsferiziHMGNESGT23,
author = {Roohallah Mahdi{-}Esferizi and
Behnaz Haji Molla Hoseyni and
Amir Mehrpanah and
Yazdan Golzade and
Ali Najafi and
Fatemeh Elahian and
Amin Zadeh Shirazi and
Guillermo A. Gomez and
Shahram Tahmasebian},
title = {DeeP4med: deep learning for {P4} medicine to predict normal and cancer
transcriptome in multiple human tissues},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {275},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05400-2},
doi = {10.1186/S12859-023-05400-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MahdiEsferiziHMGNESGT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MahtoARARMLS23,
author = {Rajul Mahto and
Saboor Uddin Ahmed and
Rizwan ur Rahman and
Rabia Musheer Aziz and
Priyanka Roy and
Saurav Mallik and
Aimin Li and
Mohd Asif Shah},
title = {A novel and innovative cancer classification framework through a consecutive
utilization of hybrid feature selection},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {479},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05605-5},
doi = {10.1186/S12859-023-05605-5},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MahtoARARMLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaigneNHKBDGKMSTCGLV23,
author = {{\'{E}}lise Maign{\'{e}} and
C{\'{e}}line Noirot and
Julien Henry and
Yaa Adu Kesewaah and
Ludovic Badin and
S{\'{e}}bastien D{\'{e}}jean and
Camille Guilmineau and
Arielle Krebs and
Fanny Mathevet and
Audrey Segalini and
Laurent Thomassin and
David Colongo and
Christine Gaspin and
Laurence Liaubet and
Nathalie Vialaneix},
title = {Asterics: a simple tool for the ExploRation and Integration of omiCS
data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {391},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05504-9},
doi = {10.1186/S12859-023-05504-9},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MaigneNHKBDGKMSTCGLV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MalonzoL23,
author = {Maia H. Malonzo and
Harri L{\"{a}}hdesm{\"{a}}ki},
title = {LuxHMM: {DNA} methylation analysis with genome segmentation via hidden
Markov model},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {58},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05174-7},
doi = {10.1186/S12859-023-05174-7},
timestamp = {Fri, 24 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MalonzoL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MarramaCWVKSNGP23,
author = {Daniel Marrama and
William D. Chronister and
Luise Westernberg and
Randi Vita and
Zeynep Kosaloglu{-}Yal{\c{c}}in and
Alessandro Sette and
Morten Nielsen and
Jason A. Greenbaum and
Bjoern Peters},
title = {PEPMatch: a tool to identify short peptide sequence matches in large
sets of proteins},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {485},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05606-4},
doi = {10.1186/S12859-023-05606-4},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MarramaCWVKSNGP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MavaieHS23,
author = {Pegah Mavaie and
Lawrence Holder and
Michael K. Skinner},
title = {Hybrid deep learning approach to improve classification of low-volume
high-dimensional data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {419},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05557-w},
doi = {10.1186/S12859-023-05557-W},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MavaieHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MehtaPRW23,
author = {Rohan S. Mehta and
Robert Petit and
Timothy D. Read and
Daniel B. Weissman},
title = {Detecting patterns of accessory genome coevolution in Staphylococcus
aureus using data from thousands of genomes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {243},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05363-4},
doi = {10.1186/S12859-023-05363-4},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MehtaPRW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MenesesRSM23,
author = {Maria V. Meneses and
Alberto Riva and
Marco Salemi and
Carla Mavian},
title = {{ARCA:} the interactive database for arbovirus reported cases in the
Americas},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {312},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05433-7},
doi = {10.1186/S12859-023-05433-7},
timestamp = {Wed, 23 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MenesesRSM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MillikinRSLTRTKNLBTS23,
author = {Robert J. Millikin and
Kalpana Raja and
John W. Steill and
Cannon Lock and
Xuancheng Tu and
Ian Ross and
Lam C. Tsoi and
Finn Kuusisto and
Zijian Ni and
Miron Livny and
Brian Bockelman and
James A. Thomson and
Ron M. Stewart},
title = {Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge
using co-occurrence and transformer models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {412},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05539-y},
doi = {10.1186/S12859-023-05539-Y},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MillikinRSLTRTKNLBTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MingCWLYWX23,
author = {Zhaoyan Ming and
Xiangjun Chen and
Shunlong Wang and
Hong Liu and
Zhiming Yuan and
Minghui Wu and
Han Xia},
title = {HostNet: improved sequence representation in deep neural networks
for virus-host prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {455},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05582-9},
doi = {10.1186/S12859-023-05582-9},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MingCWLYWX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MohammadSAI23,
author = {Awwab Mohammad and
Farheen Siddiqui and
M. Afshar Alam and
Sheikh Mohammad Idrees},
title = {Tri-model classifiers for {EEG} based mental task classification:
hybrid optimization assisted framework},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {406},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05544-1},
doi = {10.1186/S12859-023-05544-1},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MohammadSAI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MokoatleMMBH23,
author = {Mpho Mokoatle and
Vukosi Marivate and
Darlington S. Mapiye and
Riana Bornman and
Vanessa M. Hayes},
title = {A review and comparative study of cancer detection using machine learning:
{SBERT} and SimCSE application},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {112},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05235-x},
doi = {10.1186/S12859-023-05235-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MokoatleMMBH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MorettiAG23,
author = {Bruno Moretti and
Santiago N. Rodriguez Alvarez and
Hern{\'{a}}n E. Grecco},
title = {Nfinder: automatic inference of cell neighborhood in 2D and 3D using
nuclear markers},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {230},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05284-2},
doi = {10.1186/S12859-023-05284-2},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MorettiAG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MoriTLYAKOYAKF23,
author = {Tomoya Mori and
Toshiro Takase and
Kuan{-}Chun Lan and
Junko Yamane and
Cantas Alev and
Azuma Kimura and
Kenji Osafune and
Jun K. Yamashita and
Tatsuya Akutsu and
Hiroaki Kitano and
Wataru Fujibuchi},
title = {eSPRESSO: topological clustering of single-cell transcriptomics data
to reveal informative genes for spatio-temporal architectures of cells},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {252},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05355-4},
doi = {10.1186/S12859-023-05355-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MoriTLYAKOYAKF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MortuzaGLTDHZA23,
author = {Golam Md Mortuza and
Jorge Guerrero and
Shoshanna Llewellyn and
Michael D. Tobiason and
George D. Dickinson and
William L. Hughes and
Reza Zadegan and
Tim Andersen},
title = {In-vitro validated methods for encoding digital data in deoxyribonucleic
acid {(DNA)}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {160},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05264-6},
doi = {10.1186/S12859-023-05264-6},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MortuzaGLTDHZA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MostadTK23,
author = {Petter Mostad and
Andreas Tillmar and
Daniel Kling},
title = {Improved computations for relationship inference using low-coverage
sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {90},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05217-z},
doi = {10.1186/S12859-023-05217-Z},
timestamp = {Sun, 19 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MostadTK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MotamediASMFAA23,
author = {Hamid Motamedi and
Marzie Mahdizade Ari and
Mohsen Shahlaei and
Sajad Moradi and
Parisa Farhadikia and
Amirhoushang Alvandi and
Ramin Abiri},
title = {Designing multi-epitope vaccine against important colorectal cancer
{(CRC)} associated pathogens based on immunoinformatics approach},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {65},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05197-0},
doi = {10.1186/S12859-023-05197-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MotamediASMFAA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Mourad23,
author = {Rapha{\"{e}}l Mourad},
title = {Semi-supervised learning improves regulatory sequence prediction with
unlabeled sequences},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {186},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05303-2},
doi = {10.1186/S12859-023-05303-2},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Mourad23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MuslehIQAA23,
author = {Saleh Musleh and
Mohammad Tariqul Islam and
Rizwan Qureshi and
Nihad Alajez and
Tanvir Alam},
title = {{MSLP:} mRNA subcellular localization predictor based on machine learning
techniques},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {109},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05232-0},
doi = {10.1186/S12859-023-05232-0},
timestamp = {Sat, 25 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MuslehIQAA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MuslehIQAA23a,
author = {Saleh Musleh and
Mohammad Tariqul Islam and
Rizwan Qureshi and
Nihad Alajez and
Tanvir Alam},
title = {Correction: {MSLP:} mRNA subcellular localization predictor based
on machine learning techniques},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {156},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05276-2},
doi = {10.1186/S12859-023-05276-2},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MuslehIQAA23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MwangaSMMGSWBOB23,
author = {Emmanuel P. Mwanga and
Doreen J. Siria and
Joshua Mitton and
Issa H. Mshani and
Mario Gonz{\'{a}}lez{-}Jim{\'{e}}nez and
Prashanth Selvaraj and
Klaas Wynne and
Francesco Baldini and
Fredros O. Okumu and
Simon A. Babayan},
title = {Using transfer learning and dimensionality reduction techniques to
improve generalisability of machine-learning predictions of mosquito
ages from mid-infrared spectra},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {11},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05128-5},
doi = {10.1186/S12859-022-05128-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MwangaSMMGSWBOB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NakataMT23,
author = {Shuya Nakata and
Yoshiharu Mori and
Shigenori Tanaka},
title = {End-to-end protein-ligand complex structure generation with diffusion-based
generative models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {233},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05354-5},
doi = {10.1186/S12859-023-05354-5},
timestamp = {Thu, 15 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NakataMT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NaleCNCMCGPSZRMMPM23,
author = {Valentina Nale and
Alice Chiodi and
Noemi Di Nanni and
Ingrid Cifola and
Marco Moscatelli and
Cinzia Cocola and
Matteo Gnocchi and
Eleonora Piscitelli and
Ada Sula and
Ileana Zucchi and
Rolland A. Reinbold and
Luciano Milanesi and
Alessandra Mezzelani and
Paride Pelucchi and
Ettore Mosca},
title = {scMuffin: an {R} package to disentangle solid tumor heterogeneity
by single-cell gene expression analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {445},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05563-y},
doi = {10.1186/S12859-023-05563-Y},
timestamp = {Sun, 10 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/NaleCNCMCGPSZRMMPM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NeeWW23,
author = {Mirrelijn M. van Nee and
Lodewyk F. A. Wessels and
Mark A. van de Wiel},
title = {ecpc: an R-package for generic co-data models for high-dimensional
prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {172},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05289-x},
doi = {10.1186/S12859-023-05289-X},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NeeWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NewtonCKM23,
author = {Adam J. H. Newton and
David Chartash and
Steven H. Kleinstein and
Robert A. McDougal},
title = {A pipeline for the retrieval and extraction of domain-specific information
with application to {COVID-19} immune signatures},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {292},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05397-8},
doi = {10.1186/S12859-023-05397-8},
timestamp = {Tue, 25 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NewtonCKM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NulsenHAYUYA23,
author = {Joel Nulsen and
Nosheen Hussain and
Aws Al{-}Deka and
Jason Yap and
Khalil Uddin and
Christopher Yau and
Ahmed Ashour Ahmed},
title = {Completing a genomic characterisation of microscopic tumour samples
with copy number},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {453},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05576-7},
doi = {10.1186/S12859-023-05576-7},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/NulsenHAYUYA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NunnKG23,
author = {Christopher J. Nunn and
Eugene Klyshko and
Sidhartha Goyal},
title = {petiteFinder: an automated computer vision tool to compute Petite
colony frequencies in baker's yeast},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {50},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05168-5},
doi = {10.1186/S12859-023-05168-5},
timestamp = {Fri, 24 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/NunnKG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NurmainiSTRRDFMNB23,
author = {Siti Nurmaini and
Ade Iriani Sapitri and
Bambang Tutuko and
Muhammad Naufal Rachmatullah and
Dian Palupi Rini and
Annisa Darmawahyuni and
Firdaus and
Satria Mandala and
Ria Nova and
Nuswil Bernolian},
title = {Automatic echocardiographic anomalies interpretation using a stacked
residual-dense network model},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {365},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05493-9},
doi = {10.1186/S12859-023-05493-9},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NurmainiSTRRDFMNB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OConnellYCLEGCCMBK23,
author = {Kyle A. O'Connell and
Zelaikha B. Yosufzai and
Ross Campbell and
Collin J. Lobb and
Haley T. Engelken and
Laura M. Gorrell and
Thad B. Carlson and
Josh J. Catana and
Dina Mikdadi and
Vivien R. Bonazzi and
Juergen A. Klenk},
title = {Accelerating genomic workflows using {NVIDIA} Parabricks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {221},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05292-2},
doi = {10.1186/S12859-023-05292-2},
timestamp = {Mon, 05 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OConnellYCLEGCCMBK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ONeillSHRCYZF23,
author = {Nicholas K. O'Neill and
Thor D. Stein and
Junming Hu and
Habbiburr Rehman and
Joshua D. Campbell and
Masanao Yajima and
Xiaoling Zhang and
Lindsay A. Farrer},
title = {Bulk brain tissue cell-type deconvolution with bias correction for
single-nuclei {RNA} sequencing data using DeTREM},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {349},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05476-w},
doi = {10.1186/S12859-023-05476-W},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ONeillSHRCYZF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ObermayerCNTTWCERGMTCS23,
author = {Alyssa N. Obermayer and
Darwin Chang and
Gabrielle Nobles and
Mingxiang Teng and
Aik Choon Tan and
Xuefeng Wang and
Y. Ann Chen and
Steven Eschrich and
Paulo C. Rodriguez and
G. Daniel Grass and
Soheil Meshinchi and
Ahmad Tarhini and
Dung{-}tsa Chen and
Timothy I. Shaw},
title = {{PATH-SURVEYOR:} pathway level survival enquiry for immuno-oncology
and drug repurposing},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {266},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05393-y},
doi = {10.1186/S12859-023-05393-Y},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ObermayerCNTTWCERGMTCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OhKOK23,
author = {Seungwon Oh and
Sae{-}Ryung Kang and
In{-}Jae Oh and
Min{-}Soo Kim},
title = {Deep learning model integrating positron emission tomography and clinical
data for prognosis prediction in non-small cell lung cancer patients},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {39},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05160-z},
doi = {10.1186/S12859-023-05160-Z},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OhKOK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OlbrichKB23,
author = {Michael Olbrich and
Axel K{\"{u}}nstner and
Hauke Busch},
title = {{MBECS:} Microbiome Batch Effects Correction Suite},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {182},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05252-w},
doi = {10.1186/S12859-023-05252-W},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OlbrichKB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OliveiraPD23,
author = {Gabriel Bianchin de Oliveira and
H{\'{e}}lio Pedrini and
Zanoni Dias},
title = {{TEMPROT:} protein function annotation using transformers embeddings
and homology search},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {242},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05375-0},
doi = {10.1186/S12859-023-05375-0},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OliveiraPD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OlshenS23,
author = {Adam B. Olshen and
Mark R. Segal},
title = {Does multi-way, long-range chromatin contact data advance 3D genome
reconstruction?},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {64},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05170-x},
doi = {10.1186/S12859-023-05170-X},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/OlshenS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OrtegaSanzBCRM23,
author = {Irene Ortega{-}Sanz and
Jos{\'{e}} Antonio Barbero{-}Aparicio and
Antonio Canepa{-}Oneto and
Jordi Rovira and
Beatriz Melero},
title = {CamPype: an open-source workflow for automated bacterial whole-genome
sequencing analysis focused on Campylobacter},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {291},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05414-w},
doi = {10.1186/S12859-023-05414-W},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OrtegaSanzBCRM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OuelletFLL23,
author = {S{\'{e}}bastien Ouellet and
Larissa Ferguson and
Angus Z. Lau and
Tony K. Y. Lim},
title = {CysPresso: a classification model utilizing deep learning protein
representations to predict recombinant expression of cysteine-dense
peptides},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {200},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05327-8},
doi = {10.1186/S12859-023-05327-8},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/OuelletFLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/OvreboOKBRHS23,
author = {{\O}ystein {\O}vreb{\o} and
Miina Ojansivu and
Kimmo Kartasalo and
Hanna M. G. Barriga and
Petter Ranefall and
Margaret N. Holme and
Molly M. Stevens},
title = {RegiSTORM: channel registration for multi-color stochastic optical
reconstruction microscopy},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {237},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05320-1},
doi = {10.1186/S12859-023-05320-1},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/OvreboOKBRHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PaklaoSP23,
author = {Thummarat Paklao and
Apichat Suratanee and
Kitiporn Plaimas},
title = {ICON-GEMs: integration of co-expression network in genome-scale metabolic
models, shedding light through systems biology},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {492},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05599-0},
doi = {10.1186/S12859-023-05599-0},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PaklaoSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PalukuriPM23,
author = {Meghana V. Palukuri and
Ridhi S. Patil and
Edward M. Marcotte},
title = {Molecular complex detection in protein interaction networks through
reinforcement learning},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {306},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05425-7},
doi = {10.1186/S12859-023-05425-7},
timestamp = {Fri, 18 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PalukuriPM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PanJMWMD23,
author = {Yue Pan and
T. Landis Justin and
Razia Moorad and
Di Wu and
J. S. Marron and
Dirk P. Dittmer},
title = {The Poisson distribution model fits UMI-based single-cell RNA-sequencing
data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {256},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05349-2},
doi = {10.1186/S12859-023-05349-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PanJMWMD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PanLXC23,
author = {Shaoming Pan and
Xin Liu and
Ningdi Xie and
Yanwen Chong},
title = {EG-TransUNet: a transformer-based U-Net with enhanced and guided models
for biomedical image segmentation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {85},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05196-1},
doi = {10.1186/S12859-023-05196-1},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PanLXC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PanXXL23,
author = {Shourun Pan and
Leiming Xia and
Lei Xu and
Zhen Li},
title = {SubMDTA: drug target affinity prediction based on substructure extraction
and multi-scale features},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {334},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05460-4},
doi = {10.1186/S12859-023-05460-4},
timestamp = {Fri, 15 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PanXXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PangHLSXKC23,
author = {Mingwei Pang and
Wangqiu He and
Xufeng Lu and
Yuting She and
Liangxu Xie and
Ren Kong and
Shan Chang},
title = {CoDock-Ligand: combined template-based docking and CNN-based scoring
in ligand binding prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {444},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05571-y},
doi = {10.1186/S12859-023-05571-Y},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PangHLSXKC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ParkWPAVMNS23,
author = {Ho{-}min Park and
Jongbum Won and
Yunseol Park and
Esla Timothy Anzaku and
Joris Vankerschaver and
Arnout Van Messem and
Wesley De Neve and
Hyunjin Shim},
title = {CRISPR-Cas-Docker: web-based in silico docking and machine learning-based
classification of crRNAs with Cas proteins},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {167},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05296-y},
doi = {10.1186/S12859-023-05296-Y},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ParkWPAVMNS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PatroPSMSAP23,
author = {Kiran Kumar Patro and
Allam Jaya Prakash and
Umamaheswararao Sanapala and
Chaitanya Kumar Marpu and
Nagwan M. Abdel Samee and
Maali Alabdulhafith and
Pawel Plawiak},
title = {An effective correlation-based data modeling framework for automatic
diabetes prediction using machine and deep learning techniques},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {372},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05488-6},
doi = {10.1186/S12859-023-05488-6},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PatroPSMSAP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PaulinRHRHS23,
author = {Luis F. Paulin and
Muthuswamy Raveendran and
R. Alan Harris and
Jeffrey Rogers and
Arndt von Haeseler and
Fritz J. Sedlazeck},
title = {SVhound: detection of regions that harbor yet undetected structural
variation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {23},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05046-6},
doi = {10.1186/S12859-022-05046-6},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PaulinRHRHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PeixotoLMCSGAMCPAMFCFBFMQKGSKVZPG23,
author = {Carolina Peixoto and
Marta B. Lopes and
Marta Martins and
Sandra Casimiro and
Daniel Sobral and
Ana Rita Grosso and
Catarina Abreu and
Daniela Macedo and
Ana L{\'{u}}cia Costa and
Helena Pais and
Cec{\'{\i}}lia Alvim and
Andr{\'{e}} Mansinho and
Pedro Filipe and
Pedro Marques da Costa and
Afonso Fernandes and
Paula Borralho and
Cristina Ferreira and
Jo{\~{a}}o Malaquias and
Ant{\'{o}}nio Quintela and
Shannon Kaplan and
Mahdi Golkaram and
Michael Salmans and
Nafeesa Khan and
Raakhee Vijayaraghavan and
Shile Zhang and
Traci Pawlowski and
Jim Godsey and
Alex So and
Li Liu and
Lu{\'{\i}}s Costa and
Susana Vinga},
title = {Identification of biomarkers predictive of metastasis development
in early-stage colorectal cancer using network-based regularization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {17},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05104-z},
doi = {10.1186/S12859-022-05104-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PeixotoLMCSGAMCPAMFCFBFMQKGSKVZPG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PelizzolaLH23,
author = {Marta Pelizzola and
Ragnhild Laursen and
Asger Hobolth},
title = {Model selection and robust inference of mutational signatures using
Negative Binomial non-negative matrix factorization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {187},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05304-1},
doi = {10.1186/S12859-023-05304-1},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PelizzolaLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PengWDY23,
author = {Wei Peng and
Rong Wu and
Wei Dai and
Ning Yu},
title = {Identifying cancer driver genes based on multi-view heterogeneous
graph convolutional network and self-attention mechanism},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {16},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05140-3},
doi = {10.1186/S12859-023-05140-3},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PengWDY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PermanaBF23,
author = {Budi Permana and
Scott A. Beatson and
Brian M. Forde},
title = {GraphSNP: an interactive distance viewer for investigating outbreaks
and transmission networks using a graph approach},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {209},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05332-x},
doi = {10.1186/S12859-023-05332-X},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PermanaBF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PettersenCJA23,
author = {Jakob P. Pettersen and
Sandra Castillo and
Paula Jouhten and
Eivind Almaas},
title = {Genome-scale metabolic models reveal determinants of phenotypic differences
in non-Saccharomyces yeasts},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {438},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05506-7},
doi = {10.1186/S12859-023-05506-7},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PettersenCJA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PianfettiLFM23,
author = {Elena Pianfetti and
Marta Lovino and
Elisa Ficarra and
Loredana Martignetti},
title = {MiREx: mRNA levels prediction from gene sequence and miRNA target
knowledge},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {443},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05560-1},
doi = {10.1186/S12859-023-05560-1},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PianfettiLFM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PourmirzaeiRESA23,
author = {Mahdi Pourmirzaei and
Shahin Ramazi and
Farzaneh Esmaili and
Seyedehsamaneh Shojaeilangari and
Abdollah Allahvardi},
title = {Machine learning-based approaches for ubiquitination site prediction
in human proteins},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {449},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05581-w},
doi = {10.1186/S12859-023-05581-W},
timestamp = {Mon, 04 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PourmirzaeiRESA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PowellM23,
author = {Christian D. Powell and
Hunter N. B. Moseley},
title = {The metabolomics workbench file status website: a metadata repository
promoting {FAIR} principles of metabolomics data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {299},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05423-9},
doi = {10.1186/S12859-023-05423-9},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PowellM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PragerLRA23,
author = {Maria Prager and
Daniel Lundin and
Fredrik Ronquist and
Anders F. Andersson},
title = {{ASV} portal: an interface to DNA-based biodiversity data in the Living
Atlas},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {6},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05120-z},
doi = {10.1186/S12859-022-05120-Z},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PragerLRA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PratyushPSK23,
author = {Pawel Pratyush and
Suresh Pokharel and
Hiroto Saigo and
Dukka B. KC},
title = {pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation
sites by integrating supervised word embedding and embedding from
pre-trained protein language model},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {41},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05164-9},
doi = {10.1186/S12859-023-05164-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PratyushPSK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PrunierCLLBLBJFRT23,
author = {Gr{\'{e}}goire Prunier and
Mehdi Cherkaoui and
Albane Lysiak and
Olivier Langella and
M{\'{e}}lisande Blein{-}Nicolas and
Virginie Lollier and
Emile Benoist and
G{\'{e}}raldine Jean and
Guillaume Fertin and
H{\'{e}}l{\`{e}}ne Rogniaux and
Dominique Tessier},
title = {Fast alignment of mass spectra in large proteomics datasets, capturing
dissimilarities arising from multiple complex modifications of peptides},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {421},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05555-y},
doi = {10.1186/S12859-023-05555-Y},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PrunierCLLBLBJFRT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/QianLWZ23,
author = {Ying Qian and
Xinyi Li and
Jian Wu and
Qian Zhang},
title = {{MCL-DTI:} using drug multimodal information and bi-directional cross-attention
learning method for predicting drug-target interaction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {323},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05447-1},
doi = {10.1186/S12859-023-05447-1},
timestamp = {Wed, 15 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/QianLWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/QianZS23,
author = {Weiwei Qian and
Jian Zhou and
Songtao Shou},
title = {Exploration of m\({}^{\mbox{6}}\)A methylation regulators as epigenetic
targets for immunotherapy in advanced sepsis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {257},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05379-w},
doi = {10.1186/S12859-023-05379-W},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/QianZS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RajputWC23,
author = {Daniyal Rajput and
Wei{-}Jen Wang and
Chun{-}Chuan Chen},
title = {Evaluation of a decided sample size in machine learning applications},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {48},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05156-9},
doi = {10.1186/S12859-023-05156-9},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RajputWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RaoAPO23,
author = {Yiyun Rao and
Nabeel Ahmed and
Justin Pritchard and
Edward P. O'Brien},
title = {Incorporating mutational heterogeneity to identify genes that are
enriched for synonymous mutations in cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {462},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05521-8},
doi = {10.1186/S12859-023-05521-8},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RaoAPO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RaoPL23,
author = {Li Rao and
Bo Peng and
Tao Li},
title = {Nonnegative matrix factorization analysis and multiple machine learning
methods identified {IL17C} and {ACOXL} as novel diagnostic biomarkers
for atherosclerosis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {196},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05244-w},
doi = {10.1186/S12859-023-05244-W},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RaoPL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RenLCLZW23,
author = {Zilin Ren and
Quan Li and
Kajia Cao and
Marilyn M. Li and
Yunyun Zhou and
Kai Wang},
title = {Model performance and interpretability of semi-supervised generative
adversarial networks to predict oncogenic variants with unlabeled
data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {43},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05141-2},
doi = {10.1186/S12859-023-05141-2},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RenLCLZW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RenauxTCTNL23,
author = {Alexandre Renaux and
Chlo{\'{e}} Terwagne and
Michael Cochez and
Ilaria Tiddi and
Ann Now{\'{e}} and
Tom Lenaerts},
title = {A knowledge graph approach to predict and interpret disease-causing
gene interactions},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {324},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05451-5},
doi = {10.1186/S12859-023-05451-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RenauxTCTNL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RiveraRiveraG23,
author = {Carlos J. Rivera{-}Rivera and
Djordje Grbic},
title = {CastNet: a systems-level sequence evolution simulator},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {247},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05366-1},
doi = {10.1186/S12859-023-05366-1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RiveraRiveraG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RohiniPMMMAAS23,
author = {A. Rohini and
Carol Praveen and
Sandeep Kumar Mathivanan and
V. Muthukumaran and
Saurav Mallik and
Mohammed S. Alqahtani and
Amal Al{-}Rasheed and
Ben Othman Soufiene},
title = {Multimodal hybrid convolutional neural network based brain tumor grade
classification},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {382},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05518-3},
doi = {10.1186/S12859-023-05518-3},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RohiniPMMMAAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RonnebergKZ23,
author = {Leiv R{\o}nneberg and
Paul D. W. Kirk and
Manuela Zucknick},
title = {Dose-response prediction for in-vitro drug combination datasets: a
probabilistic approach},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {161},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05256-6},
doi = {10.1186/S12859-023-05256-6},
timestamp = {Fri, 28 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RonnebergKZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RotermanSK23,
author = {Irena Roterman and
Katarzyna Stapor and
Leszek Konieczny},
title = {Ab initio protein structure prediction: the necessary presence of
external force field as it is delivered by Hsp40 chaperone},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {418},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05545-0},
doi = {10.1186/S12859-023-05545-0},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RotermanSK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RotermanSK23a,
author = {Irena Roterman and
Katarzyna Stapor and
Leszek Konieczny},
title = {Role of environmental specificity in {CASP} results},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {425},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05559-8},
doi = {10.1186/S12859-023-05559-8},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RotermanSK23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RumbaviciusRR23,
author = {Ignas Rumbavicius and
Trine Rounge and
Torbj{\o}rn Rognes},
title = {HoCoRT: host contamination removal tool},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {371},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05492-w},
doi = {10.1186/S12859-023-05492-W},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RumbaviciusRR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RussoCMSSP23,
author = {Giulia Russo and
Elena Crispino and
Avisa Maleki and
Valentina Di Salvatore and
Filippo Stanco and
Francesco Pappalardo},
title = {Beyond the state of the art of reverse vaccinology: predicting vaccine
efficacy with the universal immune system simulator for influenza},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {231},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05374-1},
doi = {10.1186/S12859-023-05374-1},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RussoCMSSP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RyuJJO23,
author = {Jae Yong Ryu and
Woo Dae Jang and
Jidon Jang and
Kwang{-}Seok Oh},
title = {PredAOT: a computational framework for prediction of acute oral toxicity
based on multiple random forest models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {66},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05176-5},
doi = {10.1186/S12859-023-05176-5},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RyuJJO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SapozhnikovPYM23,
author = {Yesol Sapozhnikov and
Jagdish Suresh Patel and
F. Marty Ytreberg and
Craig R. Miller},
title = {Statistical modeling to quantify the uncertainty of FoldX-predicted
protein folding and binding stability},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {426},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05537-0},
doi = {10.1186/S12859-023-05537-0},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SapozhnikovPYM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Schelkunov23,
author = {Mikhail I. Schelkunov},
title = {Mabs, a suite of tools for gene-informed genome assembly},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {377},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05499-3},
doi = {10.1186/S12859-023-05499-3},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Schelkunov23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SchumannNN23,
author = {Yannis Schumann and
Julia E. Neumann and
Philipp Neumann},
title = {Robust classification using average correlations as features {(ACF)}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {101},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05224-0},
doi = {10.1186/S12859-023-05224-0},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SchumannNN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SchurmeyerSR23,
author = {Leonie Sch{\"{u}}rmeyer and
Kirsten Schorning and
J{\"{o}}rg Rahnenf{\"{u}}hrer},
title = {Designs for the simultaneous inference of concentration-response curves},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {393},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05526-3},
doi = {10.1186/S12859-023-05526-3},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SchurmeyerSR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ScireHGALLMBS23,
author = {J{\'{e}}r{\'{e}}mie Scire and
Jana S. Huisman and
Ana Grosu and
Daniel C. Angst and
Adrian Lison and
Jinzhou Li and
Marloes H. Maathuis and
Sebastian Bonhoeffer and
Tanja Stadler},
title = {estimateR: an {R} package to estimate and monitor the effective reproductive
number},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {310},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05428-4},
doi = {10.1186/S12859-023-05428-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ScireHGALLMBS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ScottBLFPITKGCL23,
author = {Darren A. V. Scott and
Ernest D. Benavente and
Julian Libiseller{-}Egger and
Dmitry V. Fedorov and
Jody Phelan and
Elena Ilina and
Polina O. Tikhonova and
Alexander Kudryavstev and
Julia Galeeva and
Taane G. Clark and
Alex Lewin},
title = {Bayesian compositional regression with microbiome features via variational
inference},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {210},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05219-x},
doi = {10.1186/S12859-023-05219-X},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ScottBLFPITKGCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SenanayakeGHR23,
author = {Anjana Senanayake and
Hasindu Gamaarachchi and
Damayanthi Herath and
Roshan G. Ragel},
title = {DeepSelectNet: deep neural network based selective sequencing for
oxford nanopore sequencing},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {31},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05151-0},
doi = {10.1186/S12859-023-05151-0},
timestamp = {Tue, 07 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SenanayakeGHR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShachafRCX23,
author = {Lior I. Shachaf and
Elijah Roberts and
Patrick Cahan and
Jie Xiao},
title = {Gene regulation network inference using k-nearest neighbor-based mutual
information estimation: revisiting an old {DREAM}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {84},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05047-5},
doi = {10.1186/S12859-022-05047-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShachafRCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShafaghiBMRSM23,
author = {Mona Shafaghi and
Zohreh Bahadori and
Hamid Madanchi and
Mohammad Mehdi Ranjbar and
Ali Akbar Shabani and
Seyed Fazlollah Mousavi},
title = {Immunoinformatics-aided design of a new multi-epitope vaccine adjuvanted
with domain 4 of pneumolysin against Streptococcus pneumoniae strains},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {67},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05175-6},
doi = {10.1186/S12859-023-05175-6},
timestamp = {Tue, 28 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShafaghiBMRSM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShangZSLKL23,
author = {Junliang Shang and
Xuhui Zhu and
Yan Sun and
Feng Li and
Xiangzhen Kong and
Jin{-}Xing Liu},
title = {{DM-MOGA:} a multi-objective optimization genetic algorithm for identifying
disease modules of non-small cell lung cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {13},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05136-z},
doi = {10.1186/S12859-023-05136-Z},
timestamp = {Tue, 17 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShangZSLKL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShaoFC23,
author = {Lizhen Shao and
Cong Fu and
Xunying Chen},
title = {A heterogeneous graph convolutional attention network method for classification
of autism spectrum disorder},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {363},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05495-7},
doi = {10.1186/S12859-023-05495-7},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShaoFC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShaoRHWZLCZZ23,
author = {Nan Shao and
Chenshuo Ren and
Tianyuan Hu and
Dianbing Wang and
Xiaofan Zhu and
Min Li and
Tao Cheng and
Yingchi Zhang and
Xian{-}En Zhang},
title = {Detection of continuous hierarchical heterogeneity by single-cell
surface antigen analysis in the prognosis evaluation of acute myeloid
leukaemia},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {450},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05561-0},
doi = {10.1186/S12859-023-05561-0},
timestamp = {Mon, 04 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShaoRHWZLCZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SharkoRSRGNF23,
author = {Fedor Sharko and
Golam Rbbani and
Prabhugouda Siriyappagouder and
Joost A. M. Raeymaekers and
Jorge Galindo{-}Villegas and
Artem Nedoluzhko and
Jorge M. O. Fernandes},
title = {CircPrime: a web-based platform for design of specific circular {RNA}
primers},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {205},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05331-y},
doi = {10.1186/S12859-023-05331-Y},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SharkoRSRGNF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SharmaM23,
author = {Nand Sharma and
Joshua Millstein},
title = {CausNet: generational orderings based search for optimal Bayesian
networks via dynamic programming with parent set constraints},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {46},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05159-6},
doi = {10.1186/S12859-023-05159-6},
timestamp = {Fri, 17 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SharmaM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShebekSBT23,
author = {Kevin M. Shebek and
Jonathan Strutz and
Linda J. Broadbelt and
Keith E. J. Tyo},
title = {Pickaxe: a Python library for the prediction of novel metabolic reactions},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {106},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05149-8},
doi = {10.1186/S12859-023-05149-8},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShebekSBT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShenCS23,
author = {Bingran Shen and
Gloria M. Coruzzi and
Dennis E. Shasha},
title = {EnsInfer: a simple ensemble approach to network inference outperforms
any single method},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {114},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05231-1},
doi = {10.1186/S12859-023-05231-1},
timestamp = {Fri, 31 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShenCS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShenPS23,
author = {Yue Shen and
Jerry M. Parks and
Jeremy C. Smith},
title = {HLA-Clus: {HLA} class {I} clustering based on 3D structure},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {189},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05297-x},
doi = {10.1186/S12859-023-05297-X},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShenPS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShiHHS23,
author = {Yunbin Shi and
Juntao Huang and
Yi Hu and
Yi Shen},
title = {Multiomics data analyses to identify {SLC25A17} as a novel biomarker
to predict the prognosis and immune microenvironment in head and neck
squamous cell carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {269},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05399-6},
doi = {10.1186/S12859-023-05399-6},
timestamp = {Mon, 03 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShiHHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShiZWC23,
author = {Bingye Shi and
Wei Zhang and
Tao Wang and
Zhenyu Cui},
title = {The therapeutic and prognostic role of cuproptosis-related genes in
triple negative breast cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {223},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05348-3},
doi = {10.1186/S12859-023-05348-3},
timestamp = {Mon, 05 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShiZWC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShimKNKCC23,
author = {Changbeom Shim and
Wooil Kim and
Tran Thien Dat Nguyen and
Du Yong Kim and
Yu Suk Choi and
Yon Dohn Chung},
title = {CellTrackVis: interactive browser-based visualization for analyzing
cell trajectories and lineages},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {124},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05218-y},
doi = {10.1186/S12859-023-05218-Y},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShimKNKCC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShinKKSCLKS23,
author = {Incheol Shin and
Keumseok Kang and
Juseong Kim and
Sanghun Sel and
Jeonghoon Choi and
Jae{-}Wook Lee and
Ho{-}Young Kang and
Giltae Song},
title = {AptaTrans: a deep neural network for predicting aptamer-protein interaction
using pretrained encoders},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {447},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05577-6},
doi = {10.1186/S12859-023-05577-6},
timestamp = {Mon, 04 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ShinKKSCLKS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ShinwariWRXBTC23,
author = {Khyber Shinwari and
Yurong Wu and
Hafiz Muzzammel Rehman and
Ningkun Xiao and
Mikhail A. Bolkov and
Irina A. Tuzankina and
Valery Chereshnev},
title = {In-silico assessment of high-risk non-synonymous SNPs in {ADAMTS3}
gene associated with Hennekam syndrome and their impact on protein
stability and function},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {251},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05361-6},
doi = {10.1186/S12859-023-05361-6},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ShinwariWRXBTC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SiddiquiC23,
author = {Mustafa Siddiqui and
Gavin C. Conant},
title = {POInT\({}_{\mbox{browse}}\): orthology prediction and synteny exploration
for paleopolyploid genomes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {174},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05298-w},
doi = {10.1186/S12859-023-05298-W},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SiddiquiC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SierkRWCPWYM23,
author = {Michael L. Sierk and
Shashikala Ratnayake and
Manoj M. Wagle and
Ben Chen and
Brian Park and
Jiyao Wang and
Philippe Youkharibache and
Daoud M. Meerzaman},
title = {3DVizSNP: a tool for rapidly visualizing missense mutations identified
in high throughput experiments in iCn3D},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {244},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05370-5},
doi = {10.1186/S12859-023-05370-5},
timestamp = {Thu, 18 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SierkRWCPWYM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SmithK23,
author = {Chris C. R. Smith and
Andrew D. Kern},
title = {disperseNN2: a neural network for estimating dispersal distance from
georeferenced polymorphism data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {385},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05522-7},
doi = {10.1186/S12859-023-05522-7},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SmithK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SolovievaS23,
author = {Elena Solovieva and
Hiroaki Sakai},
title = {PSReliP: an integrated pipeline for analysis and visualization of
population structure and relatedness based on genome-wide genetic
variant data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {135},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05169-4},
doi = {10.1186/S12859-023-05169-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SolovievaS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SongLZPBKHW23,
author = {Hoseung Song and
Wodan Ling and
Ni Zhao and
Anna M. Plantinga and
Courtney A. Broedlow and
Nichole R. Klatt and
Tiffany Hensley{-}McBain and
Michael C. Wu},
title = {Accommodating multiple potential normalizations in microbiome associations
studies},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {22},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05147-w},
doi = {10.1186/S12859-023-05147-W},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SongLZPBKHW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SongMFTGZL23,
author = {Yuqi Song and
Jianzun Ma and
Linan Fang and
Mingbo Tang and
Xinliang Gao and
Dongshan Zhu and
Wei Liu},
title = {Endoplasmic reticulum stress-related gene model predicts prognosis
and guides therapies in lung adenocarcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {255},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05384-z},
doi = {10.1186/S12859-023-05384-Z},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SongMFTGZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SongW23,
author = {Yabing Song and
Jianbin Wang},
title = {ggcoverage: an {R} package to visualize and annotate genome coverage
for various {NGS} data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {309},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05438-2},
doi = {10.1186/S12859-023-05438-2},
timestamp = {Wed, 23 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SongW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SouriCKT23,
author = {E. Amiri Souri and
A. Chenoweth and
S. N. Karagiannis and
Sophia Tsoka},
title = {Drug repurposing and prediction of multiple interaction types via
graph embedding},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {202},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05317-w},
doi = {10.1186/S12859-023-05317-W},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SouriCKT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SouzaASBF23,
author = {Lu{\'{\i}}sa C. de Souza and
Karolayne S. Azevedo and
Jackson Gomes de Souza and
Raquel de M. Barbosa and
Marcelo A. C. Fernandes},
title = {New proposal of viral genome representation applied in the classification
of SARS-CoV-2 with deep learning},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {92},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05188-1},
doi = {10.1186/S12859-023-05188-1},
timestamp = {Sun, 19 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SouzaASBF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SpanoFPMVPFGS23,
author = {Alvise Span{\`{o}} and
Lorenzo Fanton and
Davide Pizzolato and
Jacopo Moi and
Francesco Vinci and
Alberto Pesce and
Cedrix Jurgal Dongmo Foumthuim and
Achille Giacometti and
Marta Simeoni},
title = {Rinmaker: a fast, versatile and reliable tool to determine residue
interaction networks in proteins},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {336},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05466-y},
doi = {10.1186/S12859-023-05466-Y},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SpanoFPMVPFGS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SpoonerMSBS23,
author = {Annette Spooner and
Gelareh Mohammadi and
Perminder S. Sachdev and
Henry Brodaty and
Arcot Sowmya},
title = {Ensemble feature selection with data-driven thresholding for Alzheimer's
disease biomarker discovery},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {9},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05132-9},
doi = {10.1186/S12859-022-05132-9},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SpoonerMSBS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SreedharanBR23,
author = {Vandana Sreedharan and
Upinder S. Bhalla and
Naren Ramakrishnan},
title = {Using sensitivity analyses to understand bistable system behavior},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {136},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05206-2},
doi = {10.1186/S12859-023-05206-2},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SreedharanBR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SriwastavaHBC23,
author = {Brijesh Kumar Sriwastava and
Anup Kumar Halder and
Subhadip Basu and
Tapabrata Chakraborti},
title = {RUBic: rapid unsupervised biclustering},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {435},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05534-3},
doi = {10.1186/S12859-023-05534-3},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SriwastavaHBC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/StanisciaY23,
author = {Luke Staniscia and
Yun William Yu},
title = {Image-centric compression of protein structures improves space savings},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {437},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05570-z},
doi = {10.1186/S12859-023-05570-Z},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/StanisciaY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/StanzickSGSKKWHW23,
author = {Kira J. Stanzick and
Klaus J. Stark and
Mathias Gorski and
Johannes Sch{\"{o}}del and
Ren{\'{e}} Kr{\"{u}}ger and
Florian Kronenberg and
Richard Warth and
Iris M. Heid and
Thomas W. Winkler},
title = {KidneyGPS: a user-friendly web application to help prioritize kidney
function genes and variants based on evidence from genome-wide association
studies},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {355},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05472-0},
doi = {10.1186/S12859-023-05472-0},
timestamp = {Mon, 25 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/StanzickSGSKKWHW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/StewardRDCLB23,
author = {Katherine F. Steward and
Mohammed Refai and
William E. Dyer and
Val{\'{e}}rie Copi{\'{e}} and
Jennifer Lachowiec and
Brian Bothner},
title = {Acute stress reduces population-level metabolic and proteomic variation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {87},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05185-4},
doi = {10.1186/S12859-023-05185-4},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/StewardRDCLB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SuiCCIS23,
author = {Jianan Sui and
Jiazi Chen and
Yuehui Chen and
Naoki Iwamori and
Jin Sun},
title = {Identification of plant vacuole proteins by using graph neural network
and contact maps},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {357},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05475-x},
doi = {10.1186/S12859-023-05475-X},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SuiCCIS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SunWXYL23,
author = {Yu Sun and
Hongwei Wu and
Zhengrong Xu and
Zhenyu Yue and
Ke Li},
title = {Prediction of hot spots in protein-DNA binding interfaces based on
discrete wavelet transform and wavelet packet transform},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {129},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05263-7},
doi = {10.1186/S12859-023-05263-7},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SunWXYL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SunZXMLW23,
author = {Hui Sun and
Yingfeng Zheng and
Haonan Xie and
Huidong Ma and
Xiaoguang Liu and
Gang Wang},
title = {{PMFFRC:} a large-scale genomic short reads compression optimizer
via memory modeling and redundant clustering},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {454},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05566-9},
doi = {10.1186/S12859-023-05566-9},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SunZXMLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SuoGYYHW23,
author = {Jingwen Suo and
Lize Gu and
Xingyu Yan and
Sijia Yang and
Xiaoya Hu and
Licheng Wang},
title = {{PP-DDP:} a privacy-preserving outsourcing framework for solving the
double digest problem},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {34},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05157-8},
doi = {10.1186/S12859-023-05157-8},
timestamp = {Tue, 07 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SuoGYYHW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SwaertsDSJM23,
author = {Koen Swaerts and
Franceska Dedeurwaerdere and
Dieter De Smet and
Peter De Jaeger and
Geert A. Martens},
title = {DeltaMSI: artificial intelligence-based modeling of microsatellite
instability scoring on next-generation sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {73},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05186-3},
doi = {10.1186/S12859-023-05186-3},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SwaertsDSJM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SyamaJK23,
author = {K. Syama and
J. Angel Arul Jothi and
Namita Khanna},
title = {Automatic disease prediction from human gut metagenomic data using
boosting GraphSAGE},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {126},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05251-x},
doi = {10.1186/S12859-023-05251-X},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SyamaJK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SyamaJK23a,
author = {K. Syama and
J. Angel Arul Jothi and
Namita Khanna},
title = {Correction: Automatic disease prediction from human gut metagenomic
data using boosting GraphSAGE},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {307},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05431-9},
doi = {10.1186/S12859-023-05431-9},
timestamp = {Sun, 06 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/SyamaJK23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TangPHY23,
author = {Guihua Tang and
Jianqiao Peng and
Longwei Huo and
Wen Yin},
title = {An N6-methyladenosine regulation- and mRNAsi-related prognostic index
reveals the distinct immune microenvironment and immunotherapy responses
in lower-grade glioma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {225},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05328-7},
doi = {10.1186/S12859-023-05328-7},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TangPHY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TellecheaLuzardoLLC23,
author = {Jonathan Tellechea{-}Luzardo and
H{\`{e}}ctor Mart{\'{\i}}n L{\'{a}}zaro and
Ra{\'{u}}l Moreno L{\'{o}}pez and
Pablo Carbonell},
title = {Sensbio: an online server for biosensor design},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {71},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05201-7},
doi = {10.1186/S12859-023-05201-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TellecheaLuzardoLLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ThamB23,
author = {Cheng Yong Tham and
Touati Benoukraf},
title = {Correspondence on NanoVar's performance outlined by Jiang T. et al.
in "Long-read sequencing settings for efficient structural variation
detection based on comprehensive evaluation"},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {350},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05484-w},
doi = {10.1186/S12859-023-05484-W},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ThamB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TheorellS23,
author = {Axel Theorell and
J{\"{o}}rg Stelling},
title = {Assumptions on decision making and environment can yield multiple
steady states in microbial community models},
journal = {{BMC} Bioinform.},
volume = {24-S},
number = {1},
pages = {262},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05325-w},
doi = {10.1186/S12859-023-05325-W},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TheorellS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TissierSWLM23,
author = {Renaud L. M. Tissier and
Janne J. M. van Schie and
Rob M. F. Wolthuis and
Job de Lange and
Ren{\'{e}}e X. de Menezes},
title = {ShrinkCRISPR: a flexible method for differential fitness analysis
of CRISPR-Cas9 screen data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {36},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05142-1},
doi = {10.1186/S12859-023-05142-1},
timestamp = {Tue, 07 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/TissierSWLM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TitarenkoT23,
author = {Valeriy Titarenko and
Sofya Titarenko},
title = {PerFSeeB: designing long high-weight single spaced seeds for full
sensitivity alignment with a given number of mismatches},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {396},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05517-4},
doi = {10.1186/S12859-023-05517-4},
timestamp = {Mon, 30 Oct 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/TitarenkoT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TommasiniF23,
author = {Dario Tommasini and
Brent L. Fogel},
title = {multiWGCNA: an {R} package for deep mining gene co-expression networks
in multi-trait expression data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {115},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05233-z},
doi = {10.1186/S12859-023-05233-Z},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TommasiniF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TsuyuzakiIN23,
author = {Koki Tsuyuzaki and
Manabu Ishii and
Itoshi Nikaido},
title = {Sctensor detects many-to-many cell-cell interactions from single cell
RNA-sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {420},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05490-y},
doi = {10.1186/S12859-023-05490-Y},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/TsuyuzakiIN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TsuyuzakiYTSKTIIN23,
author = {Koki Tsuyuzaki and
Kentaro Yamamoto and
Yu Toyoshima and
Hirofumi Sato and
Manami Kanamori and
Takayuki Teramoto and
Takeshi Ishihara and
Yuichi Iino and
Itoshi Nikaido},
title = {WormTensor: a clustering method for time-series whole-brain activity
data from C. elegans},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {254},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05230-2},
doi = {10.1186/S12859-023-05230-2},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TsuyuzakiYTSKTIIN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TuhongjiangWZPQFA23,
author = {Airexiati Tuhongjiang and
Feng Wang and
Chengrong Zhang and
Sisi Pang and
Yujiang Qu and
Bo Feng and
Gulimire Amuti},
title = {Construction of an {RNA} modification-related gene predictive model
associated with prognosis and immunity in gastric cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {147},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05283-3},
doi = {10.1186/S12859-023-05283-3},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TuhongjiangWZPQFA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Turner23,
author = {Tychele Turner},
title = {Acorn: an {R} package for de novo variant analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {330},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05457-z},
doi = {10.1186/S12859-023-05457-Z},
timestamp = {Tue, 05 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Turner23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TurpinBKS23,
author = {Baptiste Turpin and
Eline Y. Bijman and
Hans{-}Michael Kaltenbach and
J{\"{o}}rg Stelling},
title = {Efficient design of synthetic gene circuits under cell-to-cell variability},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {460},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05538-z},
doi = {10.1186/S12859-023-05538-Z},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TurpinBKS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/UlianoSilvaFKBMHHDRKHWTGLLBMHBFAT23,
author = {Marcela Uliano{-}Silva and
Jo{\~{a}}o Gabriel R. N. Ferreira and
Ksenia Krasheninnikova and
Mark L. Blaxter and
Nova Mieszkowska and
Neil Hall and
Peter Holland and
Richard Durbin and
Thomas Richards and
Paul J. Kersey and
Peter Hollingsworth and
Willie Wilson and
Alex Twyford and
Ester Gaya and
Mara Lawniczak and
Owen Lewis and
Gavin Broad and
Fergal Martin and
Michelle Hart and
Ian Barnes and
Giulio Formenti and
Linelle Abueg and
James W. Torrance and
Eugene W. Myers and
Shane A. McCarthy},
title = {MitoHiFi: a python pipeline for mitochondrial genome assembly from
PacBio high fidelity reads},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {288},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05385-y},
doi = {10.1186/S12859-023-05385-Y},
timestamp = {Fri, 18 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/UlianoSilvaFKBMHHDRKHWTGLLBMHBFAT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/UtriainenM23,
author = {Maija Utriainen and
John H. Morris},
title = {clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering
app for Cytoscape},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {134},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05225-z},
doi = {10.1186/S12859-023-05225-Z},
timestamp = {Thu, 20 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/UtriainenM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VaisbandSGGGZH23,
author = {Marc Vaisband and
Maria Schubert and
Franz Josef Gassner and
Roland Geisberger and
Richard Greil and
Nadja Zaborsky and
Jan Hasenauer},
title = {Validation of genetic variants from {NGS} data using deep convolutional
neural networks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {158},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05255-7},
doi = {10.1186/S12859-023-05255-7},
timestamp = {Mon, 24 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/VaisbandSGGGZH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VecchiMLRYHLSH23,
author = {Joseph T. Vecchi and
Sean Mullan and
Josue A. Lopez and
Madeline Rhomberg and
Annamarie Yamamoto and
Annabelle Hallam and
Amy Lee and
Milan Sonka and
Marlan R. Hansen},
title = {Sensitivity of {CNN} image analysis to multifaceted measurements of
neurite growth},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {320},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05444-4},
doi = {10.1186/S12859-023-05444-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/VecchiMLRYHLSH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VersbraegenGNRVNLP23,
author = {Nassim Versbraegen and
Barbara Gravel and
Charlotte Nachtegael and
Alexandre Renaux and
Emma Verkinderen and
Ann Now{\'{e}} and
Tom Lenaerts and
Sofia Papadimitriou},
title = {Faster and more accurate pathogenic combination predictions with VarCoPP2.0},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {179},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05291-3},
doi = {10.1186/S12859-023-05291-3},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/VersbraegenGNRVNLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VieiraBGKCZ23,
author = {Ivo Henrique Provensi Vieira and
Eduardo Buganemi Botelho and
Thales Junior de Souza Gomes and
Roger Kist and
Rafael A. Caceres and
Fernando Berton Zanchi},
title = {Visual dynamics: a {WEB} application for molecular dynamics simulation
using {GROMACS}},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {107},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05234-y},
doi = {10.1186/S12859-023-05234-Y},
timestamp = {Tue, 28 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/VieiraBGKCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangB23,
author = {Peter Y. Wang and
David P. Bartel},
title = {A statistical approach for identifying primary substrates of ZSWIM8-mediated
microRNA degradation in small-RNA sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {195},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05306-z},
doi = {10.1186/S12859-023-05306-Z},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangCYGC23,
author = {Lei Wang and
Han Cao and
Liu Yuan and
Xiaoxu Guo and
Yachao Cui},
title = {Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for
biomedical event extraction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {253},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05336-7},
doi = {10.1186/S12859-023-05336-7},
timestamp = {Tue, 12 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WangCYGC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangGCD23,
author = {Qian Wang and
Maozu Guo and
Jian Chen and
Ran Duan},
title = {A gene regulatory network inference model based on pseudo-siamese
network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {163},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05253-9},
doi = {10.1186/S12859-023-05253-9},
timestamp = {Tue, 02 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangGCD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangGLYWW23,
author = {Binyou Wang and
Jianmin Guo and
Xiaofeng Liu and
Yang Yu and
Jianming Wu and
Yiwei Wang},
title = {Prediction of the effects of small molecules on the gut microbiome
using machine learning method integrating with optimal molecular features},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {338},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05455-1},
doi = {10.1186/S12859-023-05455-1},
timestamp = {Fri, 15 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangGLYWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangJDC23,
author = {Xiaohong Wang and
Xiaoli Jing and
Fangkun Dou and
Haowei Cao},
title = {An approach for proteins and their encoding genes synonyms integration
based on protein ontology},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {339},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05464-0},
doi = {10.1186/S12859-023-05464-0},
timestamp = {Fri, 15 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangJDC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangLAWY23,
author = {Ruimin Wang and
Miaoshan Lu and
Shaowei An and
Jinyin Wang and
Changbin Yu},
title = {G-Aligner: a graph-based feature alignment method for untargeted LC-MS-based
metabolomics},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {431},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05525-4},
doi = {10.1186/S12859-023-05525-4},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangLAWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangWZZ23,
author = {Zile Wang and
Haiyun Wang and
Jianping Zhao and
Chunhou Zheng},
title = {scSemiAAE: a semi-supervised clustering model for single-cell RNA-seq
data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {217},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05339-4},
doi = {10.1186/S12859-023-05339-4},
timestamp = {Mon, 05 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangWZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangZCHL23,
author = {Jiahao Wang and
Xiaodong Zhu and
Kai Chen and
Lei Hao and
Yuanning Liu},
title = {HAHNet: a convolutional neural network for {HER2} status classification
of breast cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {353},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05474-y},
doi = {10.1186/S12859-023-05474-Y},
timestamp = {Mon, 25 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangZCHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangZCMBDGYC23,
author = {Kun Wang and
Xiao Zhang and
Hansen Cheng and
Wenhao Ma and
Guangchao Bao and
Liting Dong and
Yixiong Gou and
Jian Yang and
Haoyang Cai},
title = {SingleScan: a comprehensive resource for single-cell sequencing data
processing and mining},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {463},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05590-9},
doi = {10.1186/S12859-023-05590-9},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WangZCMBDGYC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangZLCYM23,
author = {Jing Wang and
Shuo Zhang and
Runzhi Li and
Gang Chen and
Siyu Yan and
Lihong Ma},
title = {Multi-view feature representation and fusion for drug-drug interactions
prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {93},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05212-4},
doi = {10.1186/S12859-023-05212-4},
timestamp = {Sun, 19 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WangZLCYM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangZTSTS23,
author = {Zixuan Wang and
Yi Zhou and
Tatsuya Takagi and
Jiangning Song and
Yu{-}Shi Tian and
Tetsuo Shibuya},
title = {Genetic algorithm-based feature selection with manifold learning for
cancer classification using microarray data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {139},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05267-3},
doi = {10.1186/S12859-023-05267-3},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WangZTSTS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WilliamsXF23,
author = {Jacob Williams and
Shuangshuang Xu and
Marco A. R. Ferreira},
title = {{BGWAS:} Bayesian variable selection in linear mixed models with nonlocal
priors for genome-wide association studies},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {194},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05316-x},
doi = {10.1186/S12859-023-05316-X},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WilliamsXF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WongJHSMLZ23,
author = {John K. L. Wong and
Lena Jassowicz and
Christel Herold{-}Mende and
Martina Seiffert and
Jan{-}Phillip Mallm and
Peter Lichter and
Marc Zapatka},
title = {scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide
polymorphisms for improved pooled single-cell {RNA} sequencing analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {326},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05440-8},
doi = {10.1186/S12859-023-05440-8},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WongJHSMLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WongWYYHC23,
author = {Leon Wong and
Lei Wang and
Zhu{-}Hong You and
Chang{-}An Yuan and
Yu{-}An Huang and
Mei{-}Yuan Cao},
title = {{GKLOMLI:} a link prediction model for inferring miRNA-lncRNA interactions
by using Gaussian kernel-based method on network profile and linear
optimization algorithm},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {188},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05309-w},
doi = {10.1186/S12859-023-05309-W},
timestamp = {Mon, 25 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WongWYYHC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WuCCX23,
author = {Jianqiu Wu and
Hongyang Chen and
Minhao Cheng and
Haoyi Xiong},
title = {CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting
Protein-Ligand Binding Affinity},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {378},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05503-w},
doi = {10.1186/S12859-023-05503-W},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WuCCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WuLLCMHHL23,
author = {Tong Wu and
Na Li and
Fengyuan Luo and
Zhihong Chen and
Liyuan Ma and
Tao Hu and
Guini Hong and
Hongdong Li},
title = {Screening prognostic markers for hepatocellular carcinoma based on
pyroptosis-related lncRNA pairs},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {176},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05299-9},
doi = {10.1186/S12859-023-05299-9},
timestamp = {Wed, 03 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WuLLCMHHL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WuNLZ23,
author = {Jingli Wu and
Qinghua Nie and
Gaoshi Li and
Kai Zhu},
title = {Identifying driver pathways based on a parameter-free model and a
partheno-genetic algorithm},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {211},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05319-8},
doi = {10.1186/S12859-023-05319-8},
timestamp = {Sat, 27 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WuNLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WuNWF23,
author = {Yue Wu and
Xinran Ni and
Zhihao Wang and
Weike Feng},
title = {Enhancing drug property prediction with dual-channel transfer learning
based on molecular fragment},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {293},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05413-x},
doi = {10.1186/S12859-023-05413-X},
timestamp = {Tue, 25 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WuNWF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WysockaWZLF23,
author = {Magdalena Wysocka and
Oskar Wysocki and
Marie Zufferey and
D{\'{o}}nal Landers and
Andr{\'{e}} Freitas},
title = {A systematic review of biologically-informed deep learning models
for cancer: fundamental trends for encoding and interpreting oncology
data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {198},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05262-8},
doi = {10.1186/S12859-023-05262-8},
timestamp = {Sat, 27 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WysockaWZLF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XiangGASKHAKBZH23,
author = {Guanjue Xiang and
Belinda Giardine and
Lin An and
Chen Sun and
Cheryl A. Keller and
Elisabeth F. Heuston and
Stacie M. Anderson and
Martha Kirby and
David M. Bodine and
Yu Zhang and
Ross C. Hardison},
title = {Snapshot: a package for clustering and visualizing epigenetic history
during cell differentiation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {102},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05223-1},
doi = {10.1186/S12859-023-05223-1},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/XiangGASKHAKBZH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XieSDNH23,
author = {Yangyang Xie and
Xue Song and
Danwei Du and
Zhongkai Ni and
Hai Huang},
title = {Identification of cuproptosis-related lncRNAs to predict prognosis
and immune infiltration characteristics in alimentary tract malignancies},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {184},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05314-z},
doi = {10.1186/S12859-023-05314-Z},
timestamp = {Thu, 18 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/XieSDNH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XieWHS23,
author = {Xuping Xie and
Yan Wang and
Kai He and
Nan Sheng},
title = {Predicting miRNA-disease associations based on {PPMI} and attention
network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {113},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05152-z},
doi = {10.1186/S12859-023-05152-Z},
timestamp = {Fri, 31 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/XieWHS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XieZCSXL23,
author = {Ranze Xie and
Xiangzhen Zan and
Ling Chu and
Yanqing Su and
Peng Xu and
Wenbin Liu},
title = {Study of the error correction capability of multiple sequence alignment
algorithm {(MAFFT)} in {DNA} storage},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {111},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05237-9},
doi = {10.1186/S12859-023-05237-9},
timestamp = {Fri, 31 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/XieZCSXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XiongLLLHZ23,
author = {Zuming Xiong and
Wenxin Li and
Xiangrong Luo and
Yirong Lin and
Wei Huang and
Sen Zhang},
title = {Seven bacterial response-related genes are biomarkers for colon cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {103},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05204-4},
doi = {10.1186/S12859-023-05204-4},
timestamp = {Sat, 25 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/XiongLLLHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Xu23,
author = {Jin Xu},
title = {SBMLKinetics: a tool for annotation-independent classification of
reaction kinetics for {SBML} models},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {248},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05380-3},
doi = {10.1186/S12859-023-05380-3},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Xu23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XuBSJ23,
author = {Xuechun Xu and
Nayanika Bhalla and
Patrik L. St{\aa}hl and
Joakim Jald{\'{e}}n},
title = {Lokatt: a hybrid {DNA} nanopore basecaller with an explicit duration
hidden Markov model and a residual {LSTM} network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {461},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05580-x},
doi = {10.1186/S12859-023-05580-X},
timestamp = {Wed, 22 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/XuBSJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XuWF23,
author = {Shuangshuang Xu and
Jacob Williams and
Marco A. R. Ferreira},
title = {{BG2:} Bayesian variable selection in generalized linear mixed models
with nonlocal priors for non-Gaussian {GWAS} data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {343},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05468-w},
doi = {10.1186/S12859-023-05468-W},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/XuWF23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XuZL23,
author = {Huangchao Xu and
Baohua Zhang and
Qian Liu},
title = {Deep learning-based classification model for {GPR151} activator activity
prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {245},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05369-y},
doi = {10.1186/S12859-023-05369-Y},
timestamp = {Wed, 21 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/XuZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YalimaimaitiLZDLYN23,
author = {Saiyidan Yalimaimaiti and
Xiaoqiao Liang and
Haili Zhao and
Hong Dou and
Wei Liu and
Ying Yang and
Li Ning},
title = {Establishment of a prognostic signature for lung adenocarcinoma using
cuproptosis-related lncRNAs},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {81},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05192-5},
doi = {10.1186/S12859-023-05192-5},
timestamp = {Tue, 14 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YalimaimaitiLZDLYN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YanBNBLB23,
author = {Aimin Yan and
Cristina Baricordi and
Quoc Nguyen and
Luigi Barbarossa and
Mariana Loperfido and
Luca Biasco},
title = {IS-Seq: a bioinformatics pipeline for integration sites analysis with
comprehensive abundance quantification methods},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {286},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05390-1},
doi = {10.1186/S12859-023-05390-1},
timestamp = {Fri, 21 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/YanBNBLB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YangGCZWXLY23,
author = {Wan{-}Xia Yang and
Hong{-}Wei Gao and
Jia{-}Bo Cui and
An{-}An Zhang and
Fang{-}Fang Wang and
Jian{-}Qin Xie and
Ming{-}Hua Lu and
Chong{-}Ge You},
title = {Development and validation of a coagulation-related genes prognostic
model for hepatocellular carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {89},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05220-4},
doi = {10.1186/S12859-023-05220-4},
timestamp = {Sun, 19 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YangGCZWXLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YangL23,
author = {Yingke Yang and
Peiluan Li},
title = {{GPDRP:} a multimodal framework for drug response prediction with
graph transformer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {484},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05618-0},
doi = {10.1186/S12859-023-05618-0},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YangL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YangTJWYJ23,
author = {Zihao Yang and
Kuiyuan Tong and
Shiyu Jin and
Shiyan Wang and
Chao Yang and
Feng Jiang},
title = {CNN-Siam: multimodal siamese CNN-based deep learning approach for
drug{\unicode{8210}}drug interaction prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {110},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05242-y},
doi = {10.1186/S12859-023-05242-Y},
timestamp = {Fri, 31 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/YangTJWYJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YangXYWL23,
author = {Jinghan Yang and
Yuyang Xu and
Minhao Yao and
Gao Wang and
Zhonghua Liu},
title = {ERStruct: a fast Python package for inferring the number of top principal
components from whole genome sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {180},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05305-0},
doi = {10.1186/S12859-023-05305-0},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/YangXYWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YangZCZ23,
author = {Siyu Yang and
Peiliang Zhang and
Chao Che and
Zhaoqian Zhong},
title = {B-LBConA: a medical entity disambiguation model based on Bio-LinkBERT
and context-aware mechanism},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {97},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05209-z},
doi = {10.1186/S12859-023-05209-Z},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/YangZCZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YiZPHKSHSRC23,
author = {Misung Yi and
Tingting Zhan and
Amy R. Peck and
Jeffrey Hooke and
Albert J. Kovatich and
Craig D. Shriver and
Hai Hu and
Yunguang Sun and
Hallgeir Rui and
Inna Chervoneva},
title = {Selection of optimal quantile protein biomarkers based on cell-level
immunohistochemistry data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {298},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05408-8},
doi = {10.1186/S12859-023-05408-8},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YiZPHKSHSRC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YousefOJAB23,
author = {Malik Yousef and
Fatma Ozdemir and
Amhar Jaber and
Jens Allmer and
Burcu Bakir{-}Gungor},
title = {PriPath: identifying dysregulated pathways from differential gene
expression via grouping, scoring, and modeling with an embedded feature
selection approach},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {60},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05187-2},
doi = {10.1186/S12859-023-05187-2},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/YousefOJAB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Yu23,
author = {Xiaoyu Yu},
title = {Genofunc: genome annotation and identification of genome features
for automated pipelining analysis of virus whole genome sequences},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {218},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05356-3},
doi = {10.1186/S12859-023-05356-3},
timestamp = {Mon, 05 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Yu23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YuSLLT23,
author = {Yang Yu and
Yanyan Sun and
Zhaoxian Li and
Jiang Li and
Dazhi Tian},
title = {Systematic analysis identifies {XRCC4} as a potential immunological
and prognostic biomarker associated with pan-cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {44},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05165-8},
doi = {10.1186/S12859-023-05165-8},
timestamp = {Wed, 15 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YuSLLT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YuZSLL23,
author = {Huijing Yu and
Zhenxian Zheng and
Junhao Su and
Tak Wah Lam and
Ruibang Luo},
title = {Boosting variant-calling performance with multi-platform sequencing
data using Clair3-MP},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {308},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05434-6},
doi = {10.1186/S12859-023-05434-6},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YuZSLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YuanCMLP23,
author = {Ye Yuan and
Qushuo Chen and
Jun Mao and
Guipeng Li and
Xiaoyong Pan},
title = {DG-Affinity: predicting antigen-antibody affinity with language models
from sequences},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {430},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05562-z},
doi = {10.1186/S12859-023-05562-Z},
timestamp = {Sun, 26 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YuanCMLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YuenJ23,
author = {Ho Yin Yuen and
Jesper Jansson},
title = {Normalized L3-based link prediction in protein-protein interaction
networks},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {59},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05178-3},
doi = {10.1186/S12859-023-05178-3},
timestamp = {Fri, 24 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YuenJ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZareiSR23,
author = {Diana Zarei and
Amene Saghazadeh and
Nima Rezaei},
title = {Subtyping irritable bowel syndrome using cluster analysis: a systematic
review},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {478},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05567-8},
doi = {10.1186/S12859-023-05567-8},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZareiSR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZenginK23,
author = {Hatice Yagmur Zengin and
Erdem Karabulut},
title = {Biomarker detection using corrected degree of domesticity in hybrid
social network feature selection for improving classifier performance},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {407},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05540-5},
doi = {10.1186/S12859-023-05540-5},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZenginK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhaiHLLWW23,
author = {Haixia Zhai and
Hongli Hou and
Junwei Luo and
Xiaoyan Liu and
Zhengjiang Wu and
Junfeng Wang},
title = {{DGDTA:} dynamic graph attention network for predicting drug-target
binding affinity},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {367},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05497-5},
doi = {10.1186/S12859-023-05497-5},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhaiHLLWW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Zhang23,
author = {Chengxin Zhang},
title = {BeEM: fast and faithful conversion of mmCIF format structure files
to {PDB} format},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {260},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05388-9},
doi = {10.1186/S12859-023-05388-9},
timestamp = {Mon, 03 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Zhang23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangC23,
author = {Hui Zhang and
Weiyang Chen},
title = {Automated recognition and analysis of body bending behavior in C.
elegans},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {175},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05307-y},
doi = {10.1186/S12859-023-05307-Y},
timestamp = {Wed, 03 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangFWDW23,
author = {Yuanyuan Zhang and
Yinfei Feng and
Mengjie Wu and
Zengqian Deng and
Shudong Wang},
title = {{VGAEDTI:} drug-target interaction prediction based on variational
inference and graph autoencoder},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {278},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05387-w},
doi = {10.1186/S12859-023-05387-W},
timestamp = {Wed, 19 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangFWDW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangHSAZLZ23,
author = {Dao{-}Feng Zhang and
Wei He and
Zongze Shao and
Iftikhar Ahmed and
Yuqin Zhang and
Wen{-}Jun Li and
Zhe Zhao},
title = {EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based
on core gene sets},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {390},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05527-2},
doi = {10.1186/S12859-023-05527-2},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangHSAZLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangHZ23,
author = {Jiayao Zhang and
Chunling Hu and
Qianqian Zhang},
title = {Gene regulatory network inference based on a nonhomogeneous dynamic
Bayesian network model with an improved Markov Monte Carlo sampling},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {264},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05381-2},
doi = {10.1186/S12859-023-05381-2},
timestamp = {Wed, 05 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangHZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangJD23,
author = {Renliang Zhang and
Guanqing Jia and
Xianmin Diao},
title = {geneHapR: an {R} package for gene haplotypic statistics and visualization},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {199},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05318-9},
doi = {10.1186/S12859-023-05318-9},
timestamp = {Sat, 27 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangJD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangJGG23,
author = {Junjie Zhang and
Guoli Ji and
Xilin Gao and
Jinting Guan},
title = {Single-nucleus gene and gene set expression-based similarity network
fusion identifies autism molecular subtypes},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {142},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05278-0},
doi = {10.1186/S12859-023-05278-0},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangJGG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLBZYQ23,
author = {Linlin Zhang and
Dianrong Lu and
Xuehua Bi and
Kai Zhao and
Guanglei Yu and
Na Quan},
title = {Predicting disease genes based on multi-head attention fusion},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {162},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05285-1},
doi = {10.1186/S12859-023-05285-1},
timestamp = {Fri, 28 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLBZYQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLGLGW23,
author = {Jianjun Zhang and
Xiaoyu Liang and
Samantha Gonzales and
Jianguo Liu and
Xiaoyi Raymond Gao and
Xuexia Wang},
title = {A gene based combination test using {GWAS} summary data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {2},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05114-x},
doi = {10.1186/S12859-022-05114-X},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLGLGW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLJDWCW23,
author = {Na Zhang and
Juan Liu and
Yu Jin and
Wensi Duan and
Ziling Wu and
Zhaohui Cai and
Meng Wu},
title = {An adaptive multi-modal hybrid model for classifying thyroid nodules
by combining ultrasound and infrared thermal images},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {315},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05446-2},
doi = {10.1186/S12859-023-05446-2},
timestamp = {Wed, 23 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLJDWCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLQ23,
author = {Yixin Zhang and
Wei Liu and
Weiliang Qiu},
title = {A model-based clustering via mixture of hierarchical models with covariate
adjustment for detecting differentially expressed genes from paired
design},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {423},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05556-x},
doi = {10.1186/S12859-023-05556-X},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLW23,
author = {Zicheng Zhang and
Xinyue Lin and
Shanshan Wu},
title = {A hybrid algorithm for clinical decision support in precision medicine
based on machine learning},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {3},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05116-9},
doi = {10.1186/S12859-022-05116-9},
timestamp = {Tue, 17 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLWWL23,
author = {Jidong Zhang and
Bo Liu and
Jiahui Wu and
Zhihan Wang and
Jianqiang Li},
title = {DeepCAC: a deep learning approach on {DNA} transcription factors classification
based on multi-head self-attention and concatenate convolutional neural
network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {345},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05469-9},
doi = {10.1186/S12859-023-05469-9},
timestamp = {Fri, 22 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLWWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangMLCDMC23,
author = {Xusheng Zhang and
Yongxin Ma and
Kejun Liu and
Long Chen and
Lin Ding and
Weihu Ma and
Bendong Chen},
title = {Risk prediction for dermatomyositis-associated hepatocellular carcinoma},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {222},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05353-6},
doi = {10.1186/S12859-023-05353-6},
timestamp = {Mon, 05 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangMLCDMC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangSDXMHSPT23,
author = {Meng Zhang and
Madhuri Sankaranarayanapillai and
Jingcheng Du and
Yang Xiang and
Frank J. Manion and
Marcelline R. Harris and
Cooper Stansbury and
Huy Anh Pham and
Cui Tao},
title = {Machine learning-based donor permission extraction from informed consent
documents},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {477},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05568-7},
doi = {10.1186/S12859-023-05568-7},
timestamp = {Sun, 31 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangSDXMHSPT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangSLSFW23,
author = {Xu Zhang and
Ya Su and
Andrew N. Lane and
Arnold J. Stromberg and
Teresa W.{-}M. Fan and
Chi Wang},
title = {Bayesian kinetic modeling for tracer-based metabolomic data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {108},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05211-5},
doi = {10.1186/S12859-023-05211-5},
timestamp = {Sat, 25 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangSLSFW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangSWLXYZL23,
author = {Ping Zhang and
Weicheng Sun and
Dengguo Wei and
Guodong Li and
Jinsheng Xu and
Zhuhong You and
Bowei Zhao and
Li Li},
title = {{PDA-PRGCN:} identification of Piwi-interacting RNA-disease associations
through subgraph projection and residual scaling-based feature augmentation},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {18},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05073-3},
doi = {10.1186/S12859-022-05073-3},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangSWLXYZL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangTNDH23,
author = {Yifan Zhang and
Duc Tran and
Tin Nguyen and
Sergiu M. Dascalu and
Frederick C. Harris Jr.},
title = {A robust and accurate single-cell data trajectory inference method
using ensemble pseudotime},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {55},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05179-2},
doi = {10.1186/S12859-023-05179-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangTNDH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangWZC23,
author = {Ping Zhang and
Min Wang and
Tao Zhou and
Dao{-}Zhen Chen},
title = {SeqWiz: a modularized toolkit for next-generation protein sequence
database management and analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {201},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05334-9},
doi = {10.1186/S12859-023-05334-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangWZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangX23,
author = {Junjun Zhang and
Minzhu Xie},
title = {Graph regularized non-negative matrix factorization with L\({}_{\mbox{2,1}}\)
norm regularization terms for drug-target interactions prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {375},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05496-6},
doi = {10.1186/S12859-023-05496-6},
timestamp = {Fri, 06 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangZWMLZ23,
author = {Xiaomeng Zhang and
Hongtao Zhang and
Zhihao Wang and
Xiaofei Ma and
Jiancheng Luo and
Yingying Zhu},
title = {{PWSC:} a novel clustering method based on polynomial weight-adjusted
sparse clustering for sparse biomedical data and its application in
cancer subtyping},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {490},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05595-4},
doi = {10.1186/S12859-023-05595-4},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangZWMLZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhaoFLCWMWZJWT23,
author = {Bin Zhao and
Fang Fang and
Yiqun Liao and
Yuji Chen and
Fei Wang and
Yichao Ma and
Chen Wei and
Jiahao Zhao and
Hao Ji and
Daorong Wang and
Dong Tang},
title = {Novel m7G-related lncRNA signature for predicting overall survival
in patients with gastric cancer},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {100},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05228-w},
doi = {10.1186/S12859-023-05228-W},
timestamp = {Sat, 25 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhaoFLCWMWZJWT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhaoLC23,
author = {He Zhao and
Guixia Liu and
Xintian Cao},
title = {A seed expansion-based method to identify essential proteins by integrating
protein-protein interaction sub-networks and multiple biological characteristics},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {452},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05583-8},
doi = {10.1186/S12859-023-05583-8},
timestamp = {Mon, 11 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhaoLC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhaoQZWPWZ23,
author = {Wei Zhao and
Qamar Raza Qadri and
Zhenyang Zhang and
Zhen Wang and
Yuchun Pan and
Qishan Wang and
Zhe Zhang},
title = {PyAGH: a python package to fast construct kinship matrices based on
different levels of omic data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {153},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05280-6},
doi = {10.1186/S12859-023-05280-6},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhaoQZWPWZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhdanovichAWKBD23,
author = {Yauheniya Zhdanovich and
J{\"{o}}rg Ackermann and
Peter J. Wild and
Jens K{\"{o}}llermann and
Katrin Bankov and
Claudia D{\"{o}}ring and
Nadine Flinner and
Henning Reis and
Mike Wenzel and
Benedikt H{\"{o}}h and
Philipp Mandel and
Thomas J. Vogl and
Patrick Harter and
Katharina Filipski and
Ina Koch and
Simon Bernatz},
title = {Evaluation of automatic discrimination between benign and malignant
prostate tissue in the era of high precision digital pathology},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {1},
year = {2023},
url = {https://doi.org/10.1186/s12859-022-05124-9},
doi = {10.1186/S12859-022-05124-9},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhdanovichAWKBD23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhengS23,
author = {Zequn Zheng and
Yongfei Song},
title = {Integrated analysis of the voltage-gated potassium channel-associated
gene {KCNH2} across cancers},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {51},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05180-9},
doi = {10.1186/S12859-023-05180-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhengS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhengS23a,
author = {Yan Zheng and
Xuequn Shang},
title = {SVcnn: an accurate deep learning-based method for detecting structural
variation based on long-read data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {213},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05324-x},
doi = {10.1186/S12859-023-05324-X},
timestamp = {Sat, 27 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhengS23a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhengWLTZ23,
author = {Xiangwen Zheng and
Xuanze Wang and
Xiaowei Luo and
Fan Tong and
Dongsheng Zhao},
title = {BioEGRE: a linguistic topology enhanced method for biomedical relation
extraction based on BioELECTRA and graph pointer neural network},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {486},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05601-9},
doi = {10.1186/S12859-023-05601-9},
timestamp = {Wed, 10 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhengWLTZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhengZLH23,
author = {Peijie Zheng and
Guiyang Zhang and
Yuewu Liu and
Guohua Huang},
title = {MultiScale-CNN-4mCPred: a multi-scale {CNN} and adaptive embedding-based
method for mouse genome {DNA} N4-methylcytosine prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {21},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05135-0},
doi = {10.1186/S12859-023-05135-0},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhengZLH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhongLTLLLML23,
author = {Hua Zhong and
Jing Luo and
Lin Tang and
Shicheng Liao and
Zhonghao Lu and
Guoliang Lin and
Robert W. Murphy and
Lin Liu},
title = {Association filtering and generative adversarial networks for predicting
lncRNA-associated disease},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {234},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05368-z},
doi = {10.1186/S12859-023-05368-Z},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhongLTLLLML23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhouDLLZLY23,
author = {Chen Zhou and
Shuaijian Dai and
Shengzhi Lai and
Yuanqiao Lin and
Xuechen Zhang and
Ning Li and
Weichuan Yu},
title = {{ECL} 3.0: a sensitive peptide identification tool for cross-linking
mass spectrometry data analysis},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {351},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05473-z},
doi = {10.1186/S12859-023-05473-Z},
timestamp = {Fri, 10 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhouDLLZLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhouGZLL23,
author = {Ganghui Zhou and
Jing Gao and
Dongshi Zuo and
Jin Li and
Rui Li},
title = {{MSXFGP:} combining improved sparrow search algorithm with XGBoost
for enhanced genomic prediction},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {384},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05514-7},
doi = {10.1186/S12859-023-05514-7},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhouGZLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhouXL23,
author = {Hongfang Zhou and
Yinbo Xin and
Suli Li},
title = {A diabetes prediction model based on Boruta feature selection and
ensemble learning},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {224},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05300-5},
doi = {10.1186/S12859-023-05300-5},
timestamp = {Sat, 10 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhouXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhuHLY23,
author = {Yidong Zhu and
Jun He and
Zihua Li and
Wenzhong Yang},
title = {Cuproptosis-related lncRNA signature for prognostic prediction in
patients with acute myeloid leukemia},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {37},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05148-9},
doi = {10.1186/S12859-023-05148-9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhuHLY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhuLT23,
author = {Wencan Zhu and
C{\'{e}}line L{\'{e}}vy{-}Leduc and
Nils Tern{\`{e}}s},
title = {Identification of prognostic and predictive biomarkers in high-dimensional
data with PPLasso},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {25},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05143-0},
doi = {10.1186/S12859-023-05143-0},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhuLT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhuZHYWY23,
author = {Xu Zhu and
Lili Zhao and
Lihong Huang and
Wenxian Yang and
Liansheng Wang and
Rongshan Yu},
title = {cgMSI: pathogen detection within species from nanopore metagenomic
sequencing data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {387},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05512-9},
doi = {10.1186/S12859-023-05512-9},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhuZHYWY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZirkleHRSCMCL23,
author = {Joel Zirkle and
Xiaomei Han and
Rebecca Racz and
Mohammadreza Samieegohar and
Anik Chaturbedi and
John Mann and
Shilpa Chakravartula and
Zhihua Li},
title = {Deep learning-enabled natural language processing to identify directional
pharmacokinetic drug-drug interactions},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {413},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05520-9},
doi = {10.1186/S12859-023-05520-9},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZirkleHRSCMCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZlobinaMCG23,
author = {Ksenia Zlobina and
Eric Malekos and
Han Chen and
Marcella Gomez},
title = {Robust classification of wound healing stages in both mice and humans
for acute and burn wounds based on transcriptomic data},
journal = {{BMC} Bioinform.},
volume = {24},
number = {1},
pages = {166},
year = {2023},
url = {https://doi.org/10.1186/s12859-023-05295-z},
doi = {10.1186/S12859-023-05295-Z},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZlobinaMCG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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