default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBMC Bioinformatics, Volume 22
Volume 22, Number 1, December 2021
- Pedro M. Martins
, Lucianna Helene Santos, Diego C. B. Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de Souza Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina de Azevedo Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira, Raquel Cardoso de Melo Minardi:
Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm. 1 - Panagiotis Moulos:
recoup: flexible and versatile signal visualization from next generation sequencing. 2 - Nick W. Smith, Paul R. Shorten, Eric Altermann, Nicole C. Roy, Warren C. McNabb:
Examination of hydrogen cross-feeders using a colonic microbiota model. 3 - Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes, Baldo Oliva:
SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions. 4 - Yan Zheng, Yuanke Zhong, Jialu Hu, Xuequn Shang:
SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model. 5 - Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron:
MiBiOmics: an interactive web application for multi-omics data exploration and integration. 6 - Yilin Ye, Jian Wang, Yunwan Xu, Yi Wang, Youdong Pan, Qi Song, Xing Liu, Ji Wan:
MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism. 7 - Badri Adhikari, Bikash Shrestha, Matthew Bernardini, Jie Hou, Jamie Lea:
DISTEVAL: a web server for evaluating predicted protein distances. 8 - Edwin A. Solares, Yuan Tao, Anthony D. Long, Brandon S. Gaut:
HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding. 9 - Shuwei Yin, Xiao Tian, Jingjing Zhang, Peisen Sun, Guanglin Li:
PCirc: random forest-based plant circRNA identification software. 10 - Carlos A. Ruiz-Perez, Roth E. Conrad, Konstantinos T. Konstantinidis:
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. 11 - Bing Song, August E. Woerner, John Planz:
mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes. 12 - Jiaxing Lu, Ming Chen, Yufang Qin:
Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm. 13 - Changyong Li, Yongxian Fan, Xiaodong Cai:
PyConvU-Net: a lightweight and multiscale network for biomedical image segmentation. 14 - Joshua D. Mannheimer, Ashok Prasad, Daniel L. Gustafson:
Predicting chemosensitivity using drug perturbed gene dynamics. 15 - João Lobo, Rui Henriques, Sara C. Madeira:
G-Tric: generating three-way synthetic datasets with triclustering solutions. 16 - Shengqiao Gao, Lu Han, Dan Luo, Gang Liu, Zhiyong Xiao, Guangcun Shan, Yongxiang Zhang, Wenxia Zhou:
Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform. 17 - Nan Zhou, Jinku Bao, Yuping Ning:
H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection. 18 - Zhengfeng Wang, Xiujuan Lei:
Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture. 19 - Jose Arturo Molina-Mora, Mariela Solano-Vargas:
Set-theory based benchmarking of three different variant callers for targeted sequencing. 20 - Pascal Holzheu, Ruth Großeholz, Ursula Kummer:
Impact of explicit area scaling on kinetic models involving multiple compartments. 21 - Mike Fang, Brian Richardson, Cheryl M. Cameron, Jean-Eudes J. Dazard, Mark J. Cameron:
Drug perturbation gene set enrichment analysis (dpGSEA): a new transcriptomic drug screening approach. 22 - Xinping Fan, Guanghao Luo, Yu S. Huang:
Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data. 23 - Dipan Shaw, Hao Chen, Minzhu Xie, Tao Jiang:
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms. 24 - Eliza Dhungel, Yassin Mreyoud, Ho-Jin Gwak, Ahmad Rajeh, Mina Rho, Tae-Hyuk Ahn:
MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning. 25 - Mehrdad Kashefi, Mohammad Reza Daliri:
A stack LSTM structure for decoding continuous force from local field potential signal of primary motor cortex (M1). 26 - Lingpeng Kong, Yuanyuan Chen, Fengjiao Xu, Mingmin Xu, Zutan Li, Jingya Fang, Liangyun Zhang, Cong Pian:
Mining influential genes based on deep learning. 27 - Tamer N. Jarada, Jon G. Rokne, Reda Alhajj:
SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks. 28 - Amber N. Habowski, T. J. Habowski, M. L. Waterman:
GECO: gene expression clustering optimization app for non-linear data visualization of patterns. 29 - Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng:
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network. 30 - Lili Jiang, Kaini Qiao, Chunlin Li:
Distance-based functional criticality in the human brain: intelligence and emotional intelligence. 32 - Akram Emdadi, Changiz Eslahchi:
Auto-HMM-LMF: feature selection based method for prediction of drug response via autoencoder and hidden Markov model. 33 - Shawn Gu, Tijana Milenkovic:
Data-driven biological network alignment that uses topological, sequence, and functional information. 34 - Tara Eicher, Jany Chan, Han Luu, Raghu Machiraju, Ewy A Mathé:
Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements. 35 - Takuma Nishimaki, Keiko Sato:
P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps. 36 - Ana M. Vasconcelos, Maria Beatriz Carmo, Beatriz Ferreira, Inês Viegas, Margarida Gama-Carvalho, Antonio Ferreira, Andreia J. Amaral:
IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner. 37 - Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, Jianlin Cheng:
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks. 38 - Ryan B. Patterson-Cross, Ariel J. Levine, Vilas Menon:
Selecting single cell clustering parameter values using subsampling-based robustness metrics. 39 - Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina J. Kechris, Miranda Kroehl:
tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R. 41 - Yulia M. Suvorova, Anastasya M. Kamionskaya, Eugene V. Korotkov:
Search for SINE repeats in the rice genome using correlation-based position weight matrices. 42 - Liangqun Lu, Kevin A. Townsend, Bernie J. Daigle Jr.:
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. 44 - Elisa Pischedda, Cristina Crava, Martina Carlassara, Susanna Zucca, Leila Gasmi, Mariangela Bonizzoni:
ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data. 45 - Marcos José Andrade Viana, Adhemar Zerlotini, Maurício de Alvarenga Mudado:
Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines. 46 - Jiarui Feng, Heming Zhang, Fuhai Li:
Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model. 47 - Paulien Adamse, Emilie Dagand, Karen Bohmert-Tatarev, Daniela Wahler, Manoela Miranda, Esther J. Kok, Joachim Bendiek:
GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms. 48 - Daniella Vo, Shayal Charisma Singh, Sara Safa, Debashis Sahoo:
Boolean implication analysis unveils candidate universal relationships in microbiome data. 49 - Haohan Wang, Fen Pei, Michael M. Vanyukov, Ivet Bahar, Wei Wu, Eric P. Xing:
Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. 50 - Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts:
IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences. 51 - Hailin Chen, Zuping Zhang, Jingpu Zhang:
In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces. 52 - Ermanno Cordelli, Paolo Soda, Giulio Iannello:
Visual4DTracker: a tool to interact with 3D + t image stacks. 53 - Elma Akand, John M. Murray:
NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences. 54 - Nguyen P. Nguyen, Ilker Ersoy, Jacob Gotberg, Filiz Bunyak, Tommi A. White:
DRPnet: automated particle picking in cryo-electron micrographs using deep regression. 55 - Florent Grélard, David Legland, Mathieu Fanuel, Bastien Arnaud, Loïc Foucat, Hélène Rogniaux:
Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images. 56 - Julia Åkesson, Zelmina Lubovac-Pilav, Rasmus Magnusson, Mika Gustafsson:
ComHub: Community predictions of hubs in gene regulatory networks. 58 - Oleksii Bryzghalov, Izabela Makalowska, Michal Wojciech Szczesniak:
lncEvo: automated identification and conservation study of long noncoding RNAs. 59 - Daniele Dall'Olio, Nico Curti, Eugenio Fonzi, Claudia Sala, Daniel Remondini, Gastone C. Castellani, Enrico Giampieri:
Impact of concurrency on the performance of a whole exome sequencing pipeline. 60 - William R. P. Denault, Astanand Jugessur:
Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis. 61 - Cesim Erten, Aissa Houdjedj, Hilal Kazan:
Ranking cancer drivers via betweenness-based outlier detection and random walks. 62 - Pengyu Liu, Jiangning Song, Chun-Yu Lin, Tatsuya Akutsu:
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites. 63 - Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay:
S-conLSH: alignment-free gapped mapping of noisy long reads. 64 - Truong Khanh Linh Dang, Thach Nguyen, Michael Habeck, Mehmet Gültas, Stephan Waack:
A graph-based algorithm for detecting rigid domains in protein structures. 66 - Alina Peluso, Robert C. Glen, Timothy M. D. Ebbels:
Multiple-testing correction in metabolome-wide association studies. 67 - Olga Permiakova, Romain Guibert, Alexandra Kraut, Thomas Fortin, Anne-Marie Hesse, Thomas Burger:
CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis. 68 - Aseel Awdeh, Marcel Turcotte, Theodore J. Perkins:
WACS: improving ChIP-seq peak calling by optimally weighting controls. 69 - Ryan D. Crawford, Evan S. Snitkin:
cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets. 70 - Moustafa Shokrof, C. Titus Brown, Tamer A. Mansour:
MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata. 71 - Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski:
PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. 72 - Momoko Imakubo, Jun Takayama, Hatsumi Okada, Shuichi Onami:
Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes. 73 - Damian Gola, Inke R. König:
Empowering individual trait prediction using interactions for precision medicine. 74 - Xiao Wen, Lin Gao, Tuo Song, Chaoqun Jiang:
CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network. 75 - Matteo Perini, Gherard Batisti Biffignandi, Domenico Di Carlo, Ajay Ratan Pasala, Aurora Piazza, Simona Panelli, Gianvincenzo Zuccotti, Francesco Comandatore:
MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data. 76 - Christopher Paul Wardell, Cody Ashby, Michael Anton Bauer:
FiNGS: high quality somatic mutations using filters for next generation sequencing. 77 - Dörte Wittenburg, Michael Doschoris, Jan Klosa:
Grouping of genomic markers in populations with family structure. 79 - Janet C. Siebert, Martine Saint-Cyr, Sarah J. Borengasser, Brandie D. Wagner, Catherine A. Lozupone, Carsten Görg:
CANTARE: finding and visualizing network-based multi-omic predictive models. 80 - Snorre Sulheim, Fredrik A. Fossheim, Alexander Wentzel, Eivind Almaas:
Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters. 81 - Anna Maria Masci, Scott White, Ben Neely, Maryanne Ardini-Polaske, Carol B. Hill, Ravi S. Misra, Bruce J. Aronow, Nathan Gaddis, Lina Yang, Susan E. Wert, Scott M. Palmer, Cliburn Chan:
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. 82 - Matthew N. Bernstein, Zijian Ni, Michael Collins, Mark E. Burkard, Christina Kendziorski, Ron M. Stewart:
CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets. 83 - Vandhana Krishnan, Sowmithri Utiramerur, Zena Ng, Somalee Datta, Michael Snyder, Euan A. Ashley:
Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. 85 - Camilo Broc, Thérèse Truong, Benoit Liquet:
Penalized partial least squares for pleiotropy. 86 - Raíssa Lorena Silva da Silva, Kleber Padovani de Souza, Fabiana Rodrigues de Góes, Ronnie Alves:
geneRFinder: gene finding in distinct metagenomic data complexities. 87 - Octav Caldararu, Tom L. Blundell, Kasper P. Kepp:
A base measure of precision for protein stability predictors: structural sensitivity. 88 - Amra Omanovic, Hilal Kazan, Polona Oblak, Tomaz Curk:
Sparse data embedding and prediction by tropical matrix factorization. 89 - Titinunt Kitrungrotsakul, Yutaro Iwamoto, Satoko Takemoto, Hideo Yokota, Sari Ipponjima, Tomomi Nemoto, Lanfen Lin, Ruofeng Tong, Jingsong Li, Yen-Wei Chen:
Accurate and fast mitotic detection using an anchor-free method based on full-scale connection with recurrent deep layer aggregation in 4D microscopy images. 91 - Raul Rodriguez-Esteban:
Biomedical articles share annotations with their citation neighbors. 95 - Tongjun Gu, Xiwu Zhao, William Bradley Barbazuk, Ji-Hyun Lee:
miTAR: a hybrid deep learning-based approach for predicting miRNA targets. 96 - Yuqi Wen, Xinyu Song, Bowei Yan, Xiaoxi Yang, Lianlian Wu, Dongjin Leng, Song He, Xiaochen Bo:
Multi-dimensional data integration algorithm based on random walk with restart. 97 - Casey B. Bernhards, Matthew W. Lux, Sarah E. Katoski, Tyler D. P. Goralski, Alvin T. Liem, Henry S. Gibbons:
barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection. 98 - Zachary B. Abrams, Dwayne G. Tally, Lin Zhang, Caitlin E. Coombes, Philip R. O. Payne, Lynne V. Abruzzo, Kevin R. Coombes:
Pattern recognition in lymphoid malignancies using CytoGPS and Mercator. 100 - Sebastian M. Siegner, Mehmet E. Karasu, Markus S. Schröder, Zacharias Kontarakis, Jacob E. Corn:
PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants. 101 - Umesh Kathad, Aditya Kulkarni, Joseph Ryan McDermott, Jordan Wegner, Peter Carr, Neha Biyani, Rama Modali, Jean-Philippe Richard, Panna Sharma, Kishor Bhatia:
A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications. 102 - Dominik Jens Elias Waibel, Sayedali Shetab Boushehri, Carsten Marr:
InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification. 103 - Robert H. Dolin, Shaileshbhai R. Gothi, Aziz A. Boxwala, Bret S. E. Heale, Ammar Husami, James Jones, Himanshu Khangar, Shubham Londhe, Frank Naeymi-Rad, Soujanya Rao, Barbara Rapchak, James Shalaby, Varun Suraj, Ning Xie, Srikar Chamala, Gil Alterovitz:
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. 104 - Jakob Willforss, Valentina Siino, Fredrik Levander:
OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons. 107 - Heeju Noh, Ziyi Hua, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan:
DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. 108 - Marwan A. Hawari, Celine S. Hong, Leslie G. Biesecker:
SomatoSim: precision simulation of somatic single nucleotide variants. 109 - Mateusz Garbulowski, Klev Diamanti, Karolina Smolinska, Nicholas Baltzer, Patricia Stoll, Susanne Bornelöv, Aleksander Øhrn, Lars Feuk, Jan Komorowski:
R.ROSETTA: an interpretable machine learning framework. 110 - Fetulhak Abdurahman, Kinde Anlay Fante, Mohammed Aliy:
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models. 112 - Kevin De Angeli, Shang Gao, Mohammed M. Alawad, Hong-Jun Yoon, Noah Schaefferkoetter, Xiao-Cheng Wu, Eric B. Durbin, Jennifer A. Doherty, Antoinette Stroup, Linda Coyle, Lynne Penberthy, Georgia D. Tourassi:
Deep active learning for classifying cancer pathology reports. 113 - Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu:
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data. 114 - Eleanor F. Miller, Andrea Manica:
mtDNAcombine: tools to combine sequences from multiple studies. 115 - David Toubiana, Helena Maruenda:
Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel. 116 - Xiao Liang, Kyle Akers, Ishi Keenum, Lauren Wind, Suraj Gupta, Chaoqi Chen, Reem Aldaihani, Amy Pruden, Liqing Zhang, Katharine F. Knowlton, Kang Xia, Lenwood S. Heath:
AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata. 117 - Zachary Deng, Eric Delwart:
ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. 119 - Pierre-Julien Viailly, Vincent Sater, Mathieu Viennot, Élodie Bohers, Nicolas Vergne, Caroline Bérard, Hélène Dauchel, Thierry Lecroq, Alison Celebi, Philippe Ruminy, Vinciane Marchand, Marie-Delphine Lanic, Sydney Dubois, Dominique Penther, Hervé Tilly, Sylvain Mareschal, Fabrice Jardin:
Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers. 120 - Elena Tea Russo, Alessandro Laio, Marco Punta:
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. 121 - Richard M. Jiang, Arya A. Pourzanjani, Mitchell J. Cohen, Linda R. Petzold:
Associations of longitudinal D-Dimer and Factor II on early trauma survival risk. 122 - Lisa Amrhein, Christiane Fuchs:
stochprofML: stochastic profiling using maximum likelihood estimation in R. 123 - Samuel Martin, Richard M. Leggett:
Alvis: a tool for contig and read ALignment VISualisation and chimera detection. 124 - Katie L. Ovens, Farhad Maleki, B. Frank Eames, Ian McQuillan:
Juxtapose: a gene-embedding approach for comparing co-expression networks. 125 - Liangliang Zhang, Yushu Shi, Kim-Anh Do, Christine B. Peterson, Robert R. Jenq:
ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries. 126 - Xiaopeng Ma, Ruiqi Huang, Xikun Wu, Pei Zhang:
Dualmarker: a flexible toolset for exploratory analysis of combinatorial dual biomarkers for clinical efficacy. 127