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@article{DBLP:journals/bib/SebastianRK23,
author = {Softya Sebastian and
Swarup Roy and
Jugal Kalita},
title = {A generic parallel framework for inferring large-scale gene regulatory
networks from expression profiles: application to Alzheimer's disease
network},
journal = {Briefings Bioinform.},
volume = {24},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bib/bbac482},
doi = {10.1093/BIB/BBAC482},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SebastianRK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/HeDHZZZLL23,
author = {Hao He and
Hongrui Duo and
Youjin Hao and
Xiaoxi Zhang and
Xinyi Zhou and
Yujie Zeng and
Yinghong Li and
Bo Li},
title = {Computational drug repurposing by exploiting large-scale gene expression
data: Strategy, methods and applications},
journal = {Comput. Biol. Medicine},
volume = {155},
pages = {106671},
year = {2023},
url = {https://doi.org/10.1016/j.compbiomed.2023.106671},
doi = {10.1016/J.COMPBIOMED.2023.106671},
timestamp = {Tue, 28 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/HeDHZZZLL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-10383,
author = {Sergio Pelaez and
Gaurav Verma and
Barbara Ribeiro and
Philip Shapira},
title = {Large-Scale Text Analysis Using Generative Language Models: {A} Case
Study in Discovering Public Value Expressions in {AI} Patents},
journal = {CoRR},
volume = {abs/2305.10383},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.10383},
doi = {10.48550/ARXIV.2305.10383},
eprinttype = {arXiv},
eprint = {2305.10383},
timestamp = {Wed, 24 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-10383.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FigueiredoSRHKM22,
author = {Rebeca Queiroz Figueiredo and
Sara D{\'{\i}}az del Ser and
Tamara Raschka and
Martin Hofmann{-}Apitius and
Alpha Tom Kodamullil and
Sarah Mubeen and
Daniel Domingo{-}Fern{\'{a}}ndez},
title = {Elucidating gene expression patterns across multiple biological contexts
through a large-scale investigation of transcriptomic datasets},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {231},
year = {2022},
url = {https://doi.org/10.1186/s12859-022-04765-0},
doi = {10.1186/S12859-022-04765-0},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FigueiredoSRHKM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GaoHLLXSZZ21,
author = {Shengqiao Gao and
Lu Han and
Dan Luo and
Gang Liu and
Zhiyong Xiao and
Guangcun Shan and
Yongxiang Zhang and
Wenxia Zhou},
title = {Modeling drug mechanism of action with large scale gene-expression
profiles using GPAR, an artificial intelligence platform},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {17},
year = {2021},
url = {https://doi.org/10.1186/s12859-020-03915-6},
doi = {10.1186/S12859-020-03915-6},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GaoHLLXSZZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DizajiCH21,
author = {Kamran Ghasedi Dizaji and
Wei Chen and
Heng Huang},
title = {Deep Large-Scale Multitask Learning Network for Gene Expression Inference},
journal = {J. Comput. Biol.},
volume = {28},
number = {5},
pages = {485--500},
year = {2021},
url = {https://doi.org/10.1089/cmb.2020.0438},
doi = {10.1089/CMB.2020.0438},
timestamp = {Thu, 09 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/DizajiCH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SolorzanoPW20,
author = {Leslie Solorzano and
Gabriele Partel and
Carolina W{\"{a}}hlby},
title = {TissUUmaps: interactive visualization of large-scale spatial gene
expression and tissue morphology data},
journal = {Bioinform.},
volume = {36},
number = {15},
pages = {4363--4365},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa541},
doi = {10.1093/BIOINFORMATICS/BTAA541},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SolorzanoPW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/DizajiCH20,
author = {Kamran Ghasedi Dizaji and
Wei Chen and
Heng Huang},
editor = {Russell Schwartz},
title = {Deep Large-Scale Multi-task Learning Network for Gene Expression Inference},
booktitle = {Research in Computational Molecular Biology - 24th Annual International
Conference, {RECOMB} 2020, Padua, Italy, May 10-13, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12074},
pages = {19--36},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-45257-5\_2},
doi = {10.1007/978-3-030-45257-5\_2},
timestamp = {Thu, 09 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/DizajiCH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2005-07567,
author = {Lu Han and
Guangcun Shan and
H. Y. Wang and
Shengqiao Gao and
Wenxia Zhou},
title = {Accelerating drug repurposing for {COVID-19} via modeling drug mechanism
of action with large scale gene-expression profiles},
journal = {CoRR},
volume = {abs/2005.07567},
year = {2020},
url = {https://arxiv.org/abs/2005.07567},
eprinttype = {arXiv},
eprint = {2005.07567},
timestamp = {Wed, 13 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2005-07567.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SimonovskySL19,
author = {Eyal Simonovsky and
Ronen Schuster and
Esti Yeger Lotem},
title = {Large-scale analysis of human gene expression variability associates
highly variable drug targets with lower drug effectiveness and safety},
journal = {Bioinform.},
volume = {35},
number = {17},
pages = {3028--3037},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz023},
doi = {10.1093/BIOINFORMATICS/BTZ023},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SimonovskySL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DhifliPDE19,
author = {Wajdi Dhifli and
J{\'{u}}lia Puig and
Aur{\'{e}}lien Dispot and
Mohamed Elati},
title = {Latent network-based representations for large-scale gene expression
data analysis},
journal = {{BMC} Bioinform.},
volume = {19-S},
number = {13},
pages = {81--90},
year = {2019},
url = {https://doi.org/10.1186/s12859-018-2481-y},
doi = {10.1186/S12859-018-2481-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DhifliPDE19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Taguchi19,
author = {Yoshihiro Taguchi},
title = {Drug candidate identification based on gene expression of treated
cells using tensor decomposition-based unsupervised feature extraction
for large-scale data},
journal = {{BMC} Bioinform.},
volume = {19-S},
number = {13},
pages = {27--42},
year = {2019},
url = {https://doi.org/10.1186/s12859-018-2395-8},
doi = {10.1186/S12859-018-2395-8},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Taguchi19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bdca/ZenboutM18,
author = {Imene Zenbout and
Souham Meshoul},
editor = {Youness Tabii and
Mohamed Lazaar and
Mohammed Al Achhab and
Nourddine Enneya},
title = {Advanced Machine Learning Models for Large Scale Gene Expression Analysis
in Cancer Classification: Deep Learning Versus Classical Models},
booktitle = {Big Data, Cloud and Applications - Third International Conference,
{BDCA} 2018, Kenitra, Morocco, April 4-5, 2018, Revised Selected Papers},
series = {Communications in Computer and Information Science},
volume = {872},
pages = {210--221},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-319-96292-4\_17},
doi = {10.1007/978-3-319-96292-4\_17},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bdca/ZenboutM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TangLZYH17,
author = {Zefang Tang and
Chenwei Li and
Karena Zhang and
Mingyu Yang and
Xueda Hu},
title = {GE-mini: a mobile {APP} for large-scale gene expression visualization},
journal = {Bioinform.},
volume = {33},
number = {6},
pages = {941--943},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw775},
doi = {10.1093/BIOINFORMATICS/BTW775},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TangLZYH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LiuAW17,
author = {Ruifeng Liu and
Mohamed Diwan M. AbdulHameed and
Anders Wallqvist},
title = {Molecular Structure-Based Large-Scale Prediction of Chemical-Induced
Gene Expression Changes},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {9},
pages = {2194--2202},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00281},
doi = {10.1021/ACS.JCIM.7B00281},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/LiuAW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sp/XuHSL17,
author = {Lixiong Xu and
Yuan Huang and
Xiaodong Shen and
Yang Liu},
title = {Parallelizing Gene Expression Programming Algorithm in Enabling Large-Scale
Classification},
journal = {Sci. Program.},
volume = {2017},
pages = {5081526:1--5081526:10},
year = {2017},
url = {https://doi.org/10.1155/2017/5081526},
doi = {10.1155/2017/5081526},
timestamp = {Thu, 30 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/sp/XuHSL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/SasicBLAF17,
author = {Isidora Sasic and
Sanja Brdar and
Tatjana Loncar{-}Turukalo and
Helena Aidos and
Ana L. N. Fred},
editor = {Hesham H. Ali and
Ana L. N. Fred and
Hugo Gamboa and
M{\'{a}}rio Vaz},
title = {Consensus Clustering for Cancer Gene Expression Data - Large-Scale
Analysis using Evidence Accumulation Approach},
booktitle = {Proceedings of the 10th International Joint Conference on Biomedical
Engineering Systems and Technologies {(BIOSTEC} 2017) - Volume 3:
BIOINFORMATICS, Porto, Portugal, February 21-23, 2017},
pages = {176--183},
publisher = {SciTePress},
year = {2017},
url = {https://doi.org/10.5220/0006174501760183},
doi = {10.5220/0006174501760183},
timestamp = {Fri, 04 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/biostec/SasicBLAF17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/basesearch/Mpindi16,
author = {John Mpindi},
title = {Bioinformatic tools for analysis, mining and modelling large-scale
gene expression and drug testing datasets: Bioinformatic tools for
analyzing large-scale biomedical datasets},
school = {University of Helsinki, Finland},
year = {2016},
url = {http://hdl.handle.net/10138/160326},
timestamp = {Mon, 02 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/phd/basesearch/Mpindi16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/HallCS16,
author = {Michelle Lynn Hall and
David Calkins and
Woody Sherman},
title = {Automated Protocol for Large-Scale Modeling of Gene Expression Data},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {11},
pages = {2216--2224},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.6b00260},
doi = {10.1021/ACS.JCIM.6B00260},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/HallCS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iv/RiveiroLASS16,
author = {Maria Riveiro and
Mikael Lebram and
Christian X. Andersson and
Peter Sartipy and
Jane Synnergren},
editor = {Ebad Banissi and
Mark W. McK. Bannatyne and
Fatma Bouali and
Remo Burkhard and
John Counsell and
Urska Cvek and
Martin J. Eppler and
Georges G. Grinstein and
Weidong Huang and
Sebastian Kernbach and
Chun{-}Cheng Lin and
Feng Lin and
Francis T. Marchese and
Chi Man Pun and
Muhammad Sarfraz and
Marjan Trutschl and
Anna Ursyn and
Gilles Venturini and
Theodor G. Wyeld and
Jian J. Zhang},
title = {Interactive Visualization of Large-Scale Gene Expression Data},
booktitle = {20th International Conference Information Visualisation, {IV} 2016,
Lisbon, Portugal, July 19-22, 2016},
pages = {348--354},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/IV.2016.58},
doi = {10.1109/IV.2016.58},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iv/RiveiroLASS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pacbb/SoutoGAGP16,
author = {Laura Do Souto and
Alfonso Gonz{\'{a}}lez{-}Briones and
Andreia J. Amaral and
Margarida Gama{-}Carvalho and
Juan Francisco de Paz},
editor = {Mohd Saberi Mohamad and
Miguel P. Rocha and
Florentino Fdez{-}Riverola and
Francisco Jos{\'{e}} Dom{\'{\i}}nguez Mayo and
Juan F. De Paz},
title = {Large-Scale Transcriptomic Approaches for Characterization of Post-Transcriptional
Control of Gene Expression},
booktitle = {10th International Conference on Practical Applications of Computational
Biology {\&} Bioinformatics, {PACBB} 2016, Sevilla, Spain, 1-3
June 2016},
series = {Advances in Intelligent Systems and Computing},
volume = {477},
pages = {109--119},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-40126-3\_12},
doi = {10.1007/978-3-319-40126-3\_12},
timestamp = {Wed, 12 Oct 2022 08:58:54 +0200},
biburl = {https://dblp.org/rec/conf/pacbb/SoutoGAGP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/SimoesDWE15,
author = {Ricardo de Matos Simoes and
Sabine Dalleau and
Kate E. Williamson and
Frank Emmert{-}Streib},
title = {Urothelial cancer gene regulatory networks inferred from large-scale
RNAseq, Bead and Oligo gene expression data},
journal = {{BMC} Syst. Biol.},
volume = {9},
pages = {21},
year = {2015},
url = {https://doi.org/10.1186/s12918-015-0165-z},
doi = {10.1186/S12918-015-0165-Z},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/SimoesDWE15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KimZT15,
author = {Minseung Kim and
Violeta Zorraquino and
Ilias Tagkopoulos},
title = {Microbial Forensics: Predicting Phenotypic Characteristics and Environmental
Conditions from Large-Scale Gene Expression Profiles},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {3},
year = {2015},
url = {https://doi.org/10.1371/journal.pcbi.1004127},
doi = {10.1371/JOURNAL.PCBI.1004127},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KimZT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RamsdenSMN15,
author = {Helen L. Ramsden and
G{\"{u}}lsen S{\"{u}}rmeli and
Steven G. McDonagh and
Matthew F. Nolan},
title = {Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal
Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {1},
year = {2015},
url = {https://doi.org/10.1371/journal.pcbi.1004032},
doi = {10.1371/JOURNAL.PCBI.1004032},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RamsdenSMN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcgenomics/LaiZNMLM14,
author = {Yinglei Lai and
Fanni Zhang and
Tapan K. Nayak and
Reza Modarres and
Norman H. Lee and
Timothy A. McCaffrey},
title = {Concordant integrative gene set enrichment analysis of multiple large-scale
two-sample expression data sets},
journal = {{BMC} Genom.},
volume = {15},
number = {{S-1}},
pages = {S6},
year = {2014},
url = {https://doi.org/10.1186/1471-2164-15-S1-S6},
doi = {10.1186/1471-2164-15-S1-S6},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcgenomics/LaiZNMLM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/naacl/PachecoDD12,
author = {Fabi{\'{a}}n Pacheco and
Pablo Ariel Duboue and
Mart{\'{\i}}n Ariel Dom{\'{\i}}nguez},
title = {On The Feasibility of Open Domain Referring Expression Generation
Using Large Scale Folksonomies},
booktitle = {Human Language Technologies: Conference of the North American Chapter
of the Association of Computational Linguistics, Proceedings, June
3-8, 2012, Montr{\'{e}}al, Canada},
pages = {641--645},
publisher = {The Association for Computational Linguistics},
year = {2012},
url = {https://aclanthology.org/N12-1082/},
timestamp = {Sat, 21 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/naacl/PachecoDD12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1211-2073,
author = {Yang Lu and
Mengying Wang and
Kenny Q. Zhu and
Bo Yuan},
title = {{LAGE:} {A} Java Framework to reconstruct Gene Regulatory Networks
from Large-Scale Continues Expression Data},
journal = {CoRR},
volume = {abs/1211.2073},
year = {2012},
url = {http://arxiv.org/abs/1211.2073},
eprinttype = {arXiv},
eprint = {1211.2073},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1211-2073.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/ndltd/Palmer11,
author = {Nathan Palmer},
title = {Data mining techniques for large-scale gene expression analysis},
school = {Massachusetts Institute of Technology, Cambridge, MA, {USA}},
year = {2011},
url = {https://hdl.handle.net/1721.1/68493},
timestamp = {Wed, 04 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/ndltd/Palmer11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AsifS11,
author = {Hafiz Muhammad Shahzad Asif and
Guido Sanguinetti},
title = {Large-scale learning of combinatorial transcriptional dynamics from
gene expression},
journal = {Bioinform.},
volume = {27},
number = {9},
pages = {1277--1283},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr113},
doi = {10.1093/BIOINFORMATICS/BTR113},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/AsifS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DottoriniSMMC11,
author = {Tania Dottorini and
Nicola Senin and
Giorgio Mazzoleni and
Kalle Magnusson and
Andrea Crisanti},
title = {Gepoclu: a software tool for identifying and analyzing gene positional
clusters in large-scale gene expression analysis},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {34},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-34},
doi = {10.1186/1471-2105-12-34},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DottoriniSMMC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fini/FrenchTP11,
author = {Leon French and
Powell Patrick Cheng Tan and
Paul Pavlidis},
title = {Large-Scale Analysis of Gene Expression and Connectivity in the Rodent
Brain: Insights through Data Integration},
journal = {Frontiers Neuroinformatics},
volume = {5},
pages = {12},
year = {2011},
url = {https://doi.org/10.3389/fninf.2011.00012},
doi = {10.3389/FNINF.2011.00012},
timestamp = {Thu, 28 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fini/FrenchTP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodatamining/DuanPSZN10,
author = {Fenghai Duan and
Mark A. Pauley and
Eliot R. Spindel and
Li Zhang and
Robert B. Norgren},
title = {Large scale analysis of positional effects of single-base mismatches
on microarray gene expression data},
journal = {BioData Min.},
volume = {3},
pages = {2},
year = {2010},
url = {https://doi.org/10.1186/1756-0381-3-2},
doi = {10.1186/1756-0381-3-2},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodatamining/DuanPSZN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BrigandRMB10,
author = {Kevin Le Brigand and
Karine Robbe{-}Sermesant and
Bernard Mari and
Pascal Barbry},
title = {MiRonTop: mining microRNAs targets across large scale gene expression
studies},
journal = {Bioinform.},
volume = {26},
number = {24},
pages = {3131--3132},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq589},
doi = {10.1093/BIOINFORMATICS/BTQ589},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BrigandRMB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangZLYTTYKAF10,
author = {Ming Zhang and
Yudong Zhang and
Li Liu and
Lijuan Yu and
Shirley Tsang and
Jing Tan and
Wenhua Yao and
Manjit S. Kang and
Yongqiang An and
Xingming Fan},
title = {Gene Expression Browser: large-scale and cross-experiment microarray
data integration, management, search {\&} visualization},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {433},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-433},
doi = {10.1186/1471-2105-11-433},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangZLYTTYKAF10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijdmb/CarkaciogluAKAC10,
author = {Levent {\c{C}}arkacioglu and
Reng{\"{u}}l {\c{C}}etin{-}Atalay and
{\"{O}}zlen Konu and
Volkan Atalay and
Tolga Can},
title = {Bi-k-bi clustering: mining large scale gene expression data using
two-level biclustering},
journal = {Int. J. Data Min. Bioinform.},
volume = {4},
number = {6},
pages = {701--721},
year = {2010},
url = {https://doi.org/10.1504/IJDMB.2010.037548},
doi = {10.1504/IJDMB.2010.037548},
timestamp = {Fri, 01 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijdmb/CarkaciogluAKAC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HaoZPTGWZL09,
author = {Pei Hao and
Siyuan Zheng and
Jie Ping and
Kang Tu and
Christian Gieger and
Rui Wang{-}Sattler and
Yang Zhong and
Yixue Li},
title = {Human gene expression sensitivity according to large scale meta-analysis},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-1}},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-S1-S56},
doi = {10.1186/1471-2105-10-S1-S56},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HaoZPTGWZL09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PitzerLHKGO09,
author = {Erik Pitzer and
Ronilda Lacson and
Christian Hinske and
Jihoon Kim and
Pedro A. F. Galante and
Lucila Ohno{-}Machado},
title = {Towards large-scale sample annotation in gene expression repositories},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-9}},
pages = {9},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-S9-S9},
doi = {10.1186/1471-2105-10-S9-S9},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PitzerLHKGO09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ChuWCR09,
author = {Jen{-}hwa Chu and
Scott T. Weiss and
Vincent J. Carey and
Benjamin A. Raby},
title = {A graphical model approach for inferring large-scale networks integrating
gene expression and genetic polymorphism},
journal = {{BMC} Syst. Biol.},
volume = {3},
pages = {55},
year = {2009},
url = {https://doi.org/10.1186/1752-0509-3-55},
doi = {10.1186/1752-0509-3-55},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/ChuWCR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/YuanL09,
author = {Yinyin Yuan and
Chang{-}Tsun Li},
editor = {Jeffrey J. P. Tsai and
Phillip C.{-}Y. Sheu and
Han C. W. Hsiao},
title = {Inferring Causal Relations from Multivariate Time Series: {A} Fast
Method for Large-Scale Gene Expression Data},
booktitle = {Ninth {IEEE} International Conference on Bioinformatics and Bioengineering,
{BIBE} 2009, June 22-24, 2009, Taichung, Taiwan},
pages = {92--99},
publisher = {{IEEE} Computer Society},
year = {2009},
url = {https://doi.org/10.1109/BIBE.2009.8},
doi = {10.1109/BIBE.2009.8},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibe/YuanL09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iscis/StasioEKLC09,
author = {Alessandro De Stasio and
Marcus Ertelt and
Wolfgang Kemmner and
Ulf Leser and
Michele Ceccarelli},
title = {Exploiting scientific workflows for large-scale gene expression data
analysis},
booktitle = {The 24th International Symposium on Computer and Information Sciences,
{ISCIS} 2009, 14-16 September 2009, North Cyprus},
pages = {448--453},
publisher = {{IEEE}},
year = {2009},
url = {https://doi.org/10.1109/ISCIS.2009.5291850},
doi = {10.1109/ISCIS.2009.5291850},
timestamp = {Sun, 04 Jun 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iscis/StasioEKLC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Wu08,
author = {Fang{-}Xiang Wu},
title = {Genetic weighted k-means algorithm for clustering large-scale gene
expression data},
journal = {{BMC} Bioinform.},
volume = {9},
number = {{S-6}},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-S6-S12},
doi = {10.1186/1471-2105-9-S6-S12},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Wu08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FujitaSFS07,
author = {Andr{\'{e}} Fujita and
Jo{\~{a}}o Ricardo Sato and
Carlos Eduardo Ferreira and
Mari Cleide Sogayar},
title = {{GEDI:} a user-friendly toolbox for analysis of large-scale gene expression
data},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-457},
doi = {10.1186/1471-2105-8-457},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FujitaSFS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LanCPB07,
author = {Hui Lan and
Rachel Carson and
Nicholas J. Provart and
Anthony J. Bonner},
title = {Combining classifiers to predict gene function in Arabidopsis thaliana
using large-scale gene expression measurements},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-358},
doi = {10.1186/1471-2105-8-358},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LanCPB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YoonYCS06,
author = {Sukjoon Yoon and
Young Yang and
Jiwon Choi and
Jeeweon Seong},
title = {Large scale data mining approach for gene-specific standardization
of microarray gene expression data},
journal = {Bioinform.},
volume = {22},
number = {23},
pages = {2898--2904},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl500},
doi = {10.1093/BIOINFORMATICS/BTL500},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YoonYCS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cbms/WangZA06,
author = {Haiying Wang and
Huiru Zheng and
Francisco Azuaje},
title = {Computational Approaches to Supporting Large-Scale Analysis of Photoreceptor-Enriched
Gene Expression},
booktitle = {19th {IEEE} International Symposium on Computer-Based Medical Systems
{(CBMS} 2006), 22-23 June 2006, Salt Lake City, Utah, {USA}},
pages = {533--538},
publisher = {{IEEE} Computer Society},
year = {2006},
url = {https://doi.org/10.1109/CBMS.2006.70},
doi = {10.1109/CBMS.2006.70},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cbms/WangZA06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hpcc/Ernst06,
author = {Jens Ernst},
editor = {Michael Gerndt and
Dieter Kranzlm{\"{u}}ller},
title = {A Distributed, Parallel System for Large-Scale Structure Recognition
in Gene Expression Data},
booktitle = {High Performance Computing and Communications, Second International
Conference, {HPCC} 2006, Munich, Germany, September 13-15, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4208},
pages = {21--30},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11847366\_3},
doi = {10.1007/11847366\_3},
timestamp = {Tue, 14 May 2019 10:00:45 +0200},
biburl = {https://dblp.org/rec/conf/hpcc/Ernst06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KlosterTW05,
author = {M. Kloster and
Chao Tang and
Ned S. Wingreen},
title = {Finding regulatory modules through large-scale gene-expression data
analysis},
journal = {Bioinform.},
volume = {21},
number = {7},
pages = {1172--1179},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti096},
doi = {10.1093/BIOINFORMATICS/BTI096},
timestamp = {Tue, 27 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KlosterTW05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/IhmelsB04,
author = {Jan Ihmels and
Sven Bergmann},
title = {Challenges and prospects in the analysis of large-scale gene expression
data},
journal = {Briefings Bioinform.},
volume = {5},
number = {4},
pages = {313--327},
year = {2004},
url = {https://doi.org/10.1093/bib/5.4.313},
doi = {10.1093/BIB/5.4.313},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/IhmelsB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IhmelsBB04,
author = {Jan Ihmels and
Sven Bergmann and
Naama Barkai},
title = {Defining transcription modules using large-scale gene expression data},
journal = {Bioinform.},
volume = {20},
number = {13},
pages = {1993--2003},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth166},
doi = {10.1093/BIOINFORMATICS/BTH166},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/IhmelsBB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KyodaBOK04,
author = {Koji Kyoda and
Kotaro Baba and
Shuichi Onami and
Hiroaki Kitano},
title = {{DBRF-MEGN} method: an algorithm for deducing minimum equivalent gene
networks from large-scale gene expression profiles of gene deletion
mutants},
journal = {Bioinform.},
volume = {20},
number = {16},
pages = {2662--2675},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth306},
doi = {10.1093/BIOINFORMATICS/BTH306},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KyodaBOK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TheilhaberUMCXNHBB04,
author = {Joachim Theilhaber and
Anatoly Ulyanov and
Anish Malanthara and
Jack Cole and
Dapeng Xu and
Robert Nahf and
Michael Heuer and
Christoph Brockel and
Steven Bushnell},
title = {{GECKO:} a complete large-scale gene expression analysis platform},
journal = {{BMC} Bioinform.},
volume = {5},
pages = {195},
year = {2004},
url = {https://doi.org/10.1186/1471-2105-5-195},
doi = {10.1186/1471-2105-5-195},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/TheilhaberUMCXNHBB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:series/cb/OoiT04,
author = {Chia Huey Ooi and
Patrick Tan},
editor = {Werner Dubitzky and
Francisco Azuaje},
title = {Analysis of Large-Scale mRNA Expression Data Sets by Genetic Algorithms},
booktitle = {Artificial Intelligence Methods And Tools For Systems Biology},
series = {Computational Biology},
volume = {5},
pages = {51--66},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-1-4020-5811-0\_4},
doi = {10.1007/978-1-4020-5811-0\_4},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/series/cb/OoiT04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Wu02,
author = {Thomas D. Wu},
title = {Large-scale analysis of gene expression profiles},
journal = {Briefings Bioinform.},
volume = {3},
number = {1},
pages = {7--17},
year = {2002},
url = {https://doi.org/10.1093/bib/3.1.7},
doi = {10.1093/BIB/3.1.7},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Wu02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/CheungWHGRNMSLLZLASMW02,
author = {Kei{-}Hoi Cheung and
Kevin P. White and
Janet Hager and
Mark Gerstein and
Valerie Reinke and
Kenneth Nelson and
Peter Masiar and
Ranjana Srivastava and
Yuli Li and
Ju Li and
Hongyu Zhao and
Jinming Li and
David B. Allison and
Michael Snyder and
Perry L. Miller and
Kenneth R. Williams},
title = {{YMD:} a microarray database for large-scale gene expression analysis},
booktitle = {{AMIA} 2002, American Medical Informatics Association Annual Symposium,
San Antonio, TX, USA, November 9-13, 2002},
publisher = {{AMIA}},
year = {2002},
url = {https://knowledge.amia.org/amia-55142-a2002a-1.610020/t-001-1.612667/f-001-1.612668/a-028-1.613169/a-029-1.613164},
timestamp = {Wed, 17 Apr 2024 11:48:33 +0200},
biburl = {https://dblp.org/rec/conf/amia/CheungWHGRNMSLLZLASMW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Sherlock01,
author = {Gavin Sherlock},
title = {Analysis of Large-scale Gene Expression Data},
journal = {Briefings Bioinform.},
volume = {2},
number = {4},
pages = {350--362},
year = {2001},
url = {https://doi.org/10.1093/bib/2.4.350},
doi = {10.1093/BIB/2.4.350},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Sherlock01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/HennigHCAMOBRPPL00,
author = {Steffen Hennig and
Ralf Herwig and
Matthew Clark and
Pia Aanstad and
A. Musa and
John O'Brien and
C. Bull and
Uwe Radelof and
Georgia Panopoulou and
Albert J. Poustka and
Hans Lehrach},
editor = {Ron Shamir and
Satoru Miyano and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {A data-analysis pipeline for large-scale gene expression analysis},
booktitle = {Proceedings of the Fourth Annual International Conference on Computational
Molecular Biology, {RECOMB} 2000, Tokyo, Japan, April 8-11, 2000},
pages = {165--173},
publisher = {{ACM}},
year = {2000},
url = {https://doi.org/10.1145/332306.332362},
doi = {10.1145/332306.332362},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/HennigHCAMOBRPPL00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/MjolsnessMCW99,
author = {Eric Mjolsness and
Tobias Mann and
Rebecca Casta{\~{n}}o and
Barbara J. Wold},
editor = {Sara A. Solla and
Todd K. Leen and
Klaus{-}Robert M{\"{u}}ller},
title = {From Coexpression to Coregulation: An Approach to Inferring Transcriptional
Regulation among Gene Classes from Large-Scale Expression Data},
booktitle = {Advances in Neural Information Processing Systems 12, {[NIPS} Conference,
Denver, Colorado, USA, November 29 - December 4, 1999]},
pages = {928--934},
publisher = {The {MIT} Press},
year = {1999},
url = {http://papers.nips.cc/paper/1706-from-coexpression-to-coregulation-an-approach-to-inferring-transcriptional-regulation-among-gene-classes-from-large-scale-expression-data},
timestamp = {Mon, 16 May 2022 15:41:51 +0200},
biburl = {https://dblp.org/rec/conf/nips/MjolsnessMCW99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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