CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression.

Kevin R. Coombes https://zbmath.org/authors/?q=ai:coombes.kevin-r https://orcid.org/0000-0002-7630-2123 https://www.wikidata.org/entity/Q30505720 https://id.loc.gov/authorities/names/n95045272 https://d-nb.info/gnd/123580978

Yue Zhao Lianbo Yu Xue Wu Haoran Li 0015 Kevin R. Coombes Kin Fai Au Lijun Cheng Lang Li 0001 CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression. 5245-5252 2022 November 38 Bioinform. 23 https://doi.org/10.1093/bioinformatics/btac668 db/journals/bioinformatics/bioinformatics38.html#ZhaoYWLCACL22

Zachary B. Abrams Caitlin E. Coombes Suli Li Kevin R. Coombes Mercator: a pipeline for multi-method, unsupervised visualization and distance generation. 2780-2781 2021 37 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btab037 db/journals/bioinformatics/bioinformatics37.html#AbramsCLC21

Zachary B. Abrams Dwayne G. Tally Lynne V. Abruzzo Kevin R. Coombes RCytoGPS: an R package for reading and visualizing cytogenetics data. 4589-4590 2021 37 Bioinform. 23 https://doi.org/10.1093/bioinformatics/btab683 db/journals/bioinformatics/bioinformatics37.html#AbramsTAC21

Zachary B. Abrams Dwayne G. Tally Lin Zhang 0056 Caitlin E. Coombes Philip R. O. Payne Lynne V. Abruzzo Kevin R. Coombes Pattern recognition in lymphoid malignancies using CytoGPS and Mercator. 100 2021 22 BMC Bioinform. 1 https://doi.org/10.1186/s12859-021-03992-1 db/journals/bmcbi/bmcbi22.html#AbramsTZCPAC21

Caitlin E. Coombes Xin Liu Zachary B. Abrams Kevin R. Coombes Guy N. Brock Simulation-derived best practices for clustering clinical data. 103788 2021 118 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2021.103788 db/journals/jbi/jbi118.html#CoombesLACB21

Caitlin E. Coombes Kevin R. Coombes Naleef Fareed A novel model to label delirium in an intensive care unit from clinician actions. 97 2021 21 BMC Medical Informatics Decis. Mak. 1 https://doi.org/10.1186/s12911-021-01461-6 db/journals/midm/midm21.html#CoombesCF21

Mark R. Zucker Kevin R. Coombes Generating simulated SNP array and sequencing data to assess genomic segmentation algorithms. 438-453 2020 13 Int. J. Comput. Biol. Drug Des. 5/6 https://doi.org/10.1504/IJCBDD.2020.113822 db/journals/ijcbdd/ijcbdd13.html#ZuckerC20

Caitlin E. Coombes Zachary B. Abrams Suli Li Lynne V. Abruzzo Kevin R. Coombes Unsupervised machine learning and prognostic factors of survival in chronic lymphocytic leukemia. 1019-1027 2020 27 J. Am. Medical Informatics Assoc. 7 https://doi.org/10.1093/jamia/ocaa060 https://www.wikidata.org/entity/Q96129499 db/journals/jamia/jamia27.html#CoombesALAC20

Amir Asiaee T. Zachary B. Abrams Samantha Nakayiza Deepa Sampath Kevin R. Coombes Explaining Gene Expression Using Twenty-One MicroRNAs. 1157-1170 2020 27 J. Comput. Biol. 7 https://doi.org/10.1089/cmb.2019.0321 https://www.wikidata.org/entity/Q91636259 db/journals/jcb/jcb27.html#TANSC20

Zachary B. Abrams Lin Zhang 0056 Ricky Rodriguez Lynne V. Abruzzo Kevin R. Coombes Philip R. P. Payne CytoGPS: A Web-Enabled Karyotype Analysis Tool for Cytogeneticists and Biomedical Data Scientists. 2020 AMIA https://knowledge.amia.org/72332-amia-1.4602255/t006-1.4604857/t006-1.4604858/3416789-1.4604901 conf/amia/2020 db/conf/amia/amia2020.html#AbramsZRACP20

Caitlin E. Coombes Zachary B. Abrams Samantha Nakayiza Guy N. Brock Kevin R. Coombes Umpire 2.0: Simulating realistic, mixed-type, clinical data for machine learning. 1186 2020 9 F1000Research https://doi.org/10.12688/f1000research.25877.1 db/journals/f1000research/f1000research9.html#CoombesANBC20

Mark R. Zucker Lynne V. Abruzzo Carmen D. Herling Lynn L. Barron Michael J. Keating Zachary B. Abrams Nyla A. Heerema Kevin R. Coombes Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing. 2924-2931 2019 35 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btz057 https://www.wikidata.org/entity/Q91250521 db/journals/bioinformatics/bioinformatics35.html#ZuckerAHBKAHC19

Mark R. Zucker Lynne V. Abruzzo Carmen D. Herling Lynn L. Barron Michael J. Keating Zachary B. Abrams Nyla A. Heerema Kevin R. Coombes Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing. 3216 2019 35 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btz243 https://www.wikidata.org/entity/Q94048940 db/journals/bioinformatics/bioinformatics35.html#ZuckerAHBKAHC19a

Zachary B. Abrams Lin Zhang 0056 Lynne V. Abruzzo Nyla A. Heerema Suli Li Tom Dillon Ricky Rodriguez Kevin R. Coombes Philip R. O. Payne CytoGPS: a web-enabled karyotype analysis tool for cytogenetics. 5365-5366 2019 35 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btz520 https://www.wikidata.org/entity/Q91536358 db/journals/bioinformatics/bioinformatics35.html#AbramsZAHLDRCP19

Zachary B. Abrams Travis S. Johnson Kun Huang 0001 Philip R. O. Payne Kevin R. Coombes A protocol to evaluate RNA sequencing normalization methods. 679 2019 20-S BMC Bioinform. 24 https://doi.org/10.1186/s12859-019-3247-x https://www.wikidata.org/entity/Q92157400 db/journals/bmcbi/bmcbi20S.html#AbramsJHPC19

Min Wang Zachary B. Abrams Steven M. Kornblau Kevin R. Coombes Thresher: determining the number of clusters while removing outliers. 9:1-9:15 2018 19 BMC Bioinform. 1 https://doi.org/10.1186/s12859-017-1998-9 https://www.wikidata.org/entity/Q47196395 db/journals/bmcbi/bmcbi19.html#WangAKC18

Jalal K. Siddiqui Elizabeth Baskin Mingrui Liu Carmen Z. Cantemir-Stone Bofei Zhang Russell Bonneville Joseph P. McElroy Kevin R. Coombes Ewy A. Mathé IntLIM: integration using linear models of metabolomics and gene expression data. 81:1-81:12 2018 19 BMC Bioinform. 1 https://doi.org/10.1186/s12859-018-2085-6 https://www.wikidata.org/entity/Q52366931 db/journals/bmcbi/bmcbi19.html#SiddiquiBLCZBMC18

Amir Asiaee T. Samet Oymak Kevin R. Coombes Arindam Banerjee 0001 High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient. 2018 abs/1806.04047 CoRR http://arxiv.org/abs/1806.04047 db/journals/corr/corr1806.html#abs-1806-04047

Satyajeet Raje Zachary B. Abrams Kevin R. Coombes Philip R. O. Payne Using Karyotype Data for Automated Disease Classification: A Proof of Concept Demonstration. 2016 CRI http://knowledge.amia.org/amia-59309-cri2016-1.3011827/t004-1.3012641/f004-1.3012642/a105-1.3012714/a107-1.3012709 conf/cri/2016 db/conf/cri/cri2016.html#RajeACP16

Zhenlin Ju Wenbin Liu Paul L. Roebuck Doris R. Siwak Nianxiang Zhang Yiling Lu Michael A. Davies Rehan Akbani John N. Weinstein Gordon B. Mills Kevin R. Coombes Development of a robust classifier for quality control of reverse-phase protein arrays. 912-918 2015 31 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btu736 https://www.wikidata.org/entity/Q35221345 db/journals/bioinformatics/bioinformatics31.html#JuLRSZLDAWMC15

Pan Tong Kevin R. Coombes Faye M. Johnson Lauren A. Byers Lixia Diao Diane D. Liu J. Jack Lee John V. Heymach Jing Wang 0006 drexplorer: A tool to explore dose-response relationships and drug-drug interactions. 1692-1694 2015 31 Bioinform. 10 https://doi.org/10.1093/bioinformatics/btv028 https://www.wikidata.org/entity/Q40518281 db/journals/bioinformatics/bioinformatics31.html#TongCJBDLLH015

Karl B. Gregory Amin A. Momin Kevin R. Coombes Veerabhadran Baladandayuthapani Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data. 984-994 2014 11 IEEE ACM Trans. Comput. Biol. Bioinform. 6 https://doi.org/10.1109/TCBB.2014.2325035 https://doi.ieeecomputersociety.org/10.1109/TCBB.2014.2325035 https://dl.acm.org/doi/10.1109/TCBB.2014.2325035 https://www.wikidata.org/entity/Q35683000 db/journals/tcbb/tcbb11.html#GregoryMCB14

Pan Tong Yong Chen 0016 Xiao Su Kevin R. Coombes SIBER: systematic identification of bimodally expressed genes using RNAseq data. 605-613 2013 29 Bioinform. 5 https://doi.org/10.1093/bioinformatics/bts713 https://www.wikidata.org/entity/Q30585364 db/journals/bioinformatics/bioinformatics29.html#TongCSC13

Ganiraju Manyam Cristina Ivan George A. Calin Kevin R. Coombes targetHub: a programmable interface for miRNA-gene interactions. 2657-2658 2013 29 Bioinform. 20 https://doi.org/10.1093/bioinformatics/btt439 https://www.wikidata.org/entity/Q37212920 db/journals/bioinformatics/bioinformatics29.html#ManyamICC13

Pan Tong Kevin R. Coombes integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory. 2861-2869 2012 28 Bioinform. 22 https://doi.org/10.1093/bioinformatics/bts561 https://www.wikidata.org/entity/Q36393797 db/journals/bioinformatics/bioinformatics28.html#TongC12

Jiexin Zhang 0004 Kevin R. Coombes Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups. S1 2012 13 BMC Bioinform. S-13 https://doi.org/10.1186/1471-2105-13-S13-S1 https://www.wikidata.org/entity/Q34548744 db/journals/bmcbi/bmcbi13S.html#ZhangC12

Karl B. Gregory Kevin R. Coombes Amin A. Momin Luc Girard Lauren A. Byers Steven Lin Michael Peyton John V. Heymach John D. Minna Veerabhadran Baladandayuthapani Latent feature decompositions for integrative analysis of diverse high-throughput genomic data. 130-134 2012 GENSiPS https://doi.org/10.1109/GENSIPS.2012.6507746 https://www.wikidata.org/entity/Q57556653 conf/gensips/2012 db/conf/gensips/gensips2012.html#GregoryCMGBLPHMB12

Li Zhang Qingyi Wei Li Mao Wenbin Liu Gordon B. Mills Kevin R. Coombes Serial dilution curve: a new method for analysis of reverse phase protein array data. 650-654 2009 25 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btn663 https://www.wikidata.org/entity/Q33403704 db/journals/bioinformatics/bioinformatics25.html#ZhangWMLMC09

E. Shannon Neeley Steven M. Kornblau Kevin R. Coombes Keith A. Baggerly Variable slope normalization of reverse phase protein arrays. 1384-1389 2009 25 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btp174 https://www.wikidata.org/entity/Q38545364 db/journals/bioinformatics/bioinformatics25.html#NeeleyKCB09

Romesh Stanislaus Mark Carey Helena F. Deus Kevin R. Coombes Bryan T. J. Hennessy Gordon B. Mills Jonas S. Almeida RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays. 2008 9 BMC Bioinform. https://doi.org/10.1186/1471-2105-9-555 https://www.wikidata.org/entity/Q33395131 db/journals/bmcbi/bmcbi9.html#StanislausCDCHMA08

David L. Gold Bani K. Mallick Kevin R. Coombes Real-Time Gene Expression: Statistical Challenges in Design and Inference. 611-623 2008 15 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2007.0220 https://www.wikidata.org/entity/Q50627741 db/journals/jcb/jcb15.html#GoldMC08

David L. Gold Kevin R. Coombes Jing Wang 0006 Bani K. Mallick Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL. 71-77 2007 8 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbl019 https://www.wikidata.org/entity/Q38517482 db/journals/bib/bib8.html#GoldCWM07

Yuliya V. Karpievitch Elizabeth G. Hill Adam J. Smolka Jeffrey S. Morris Kevin R. Coombes Keith A. Baggerly Jonas S. Almeida PrepMS: TOF MS data graphical preprocessing tool. 264-265 2007 23 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btl583 https://www.wikidata.org/entity/Q31079692 db/journals/bioinformatics/bioinformatics23.html#KarpievitchHSMCBA07

Jianhua Hu Xuming He 0002 Keith A. Baggerly Kevin R. Coombes Bryan T. J. Hennessy Gordon B. Mills Non-parametric quantification of protein lysate arrays. 1986-1994 2007 23 Bioinform. 15 https://doi.org/10.1093/bioinformatics/btm283 https://www.wikidata.org/entity/Q48395052 db/journals/bioinformatics/bioinformatics23.html#HuHBCHM07

Jiexin Zhang 0004 Li Zhang Kevin R. Coombes Gene sequence signatures revealed by mining the UniGene affiliation network. 385-391 2006 22 Bioinform. 4 https://doi.org/10.1093/bioinformatics/bti796 https://www.wikidata.org/entity/Q51958593 db/journals/bioinformatics/bioinformatics22.html#ZhangZC06

Jeffrey S. Morris Kevin R. Coombes John M. Koomen Keith A. Baggerly Ryuji Kobayashi Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. 1764-1775 2005 21 Bioinform. 9 https://doi.org/10.1093/bioinformatics/bti254 https://www.wikidata.org/entity/Q31143825 db/journals/bioinformatics/bioinformatics21.html#MorrisCKBK05

Yuan Ji Chunlei Wu Ping Liu Jing Wang 0006 Kevin R. Coombes Applications of beta-mixture models in bioinformatics. 2118-2122 2005 21 Bioinform. 9 https://doi.org/10.1093/bioinformatics/bti318 https://www.wikidata.org/entity/Q57556784 db/journals/bioinformatics/bioinformatics21.html#JiWLWC05

Jianhua Hu Mini Kapoor Wei Zhang 0011 Stanley R. Hamilton Kevin R. Coombes Analysis of dose-response effects on gene expression data with comparison of two microarray platforms. 3524-3529 2005 21 Bioinform. 17 https://doi.org/10.1093/bioinformatics/bti592 https://www.wikidata.org/entity/Q30998413 db/journals/bioinformatics/bioinformatics21.html#HuKZHC05

Keith A. Baggerly Jeffrey S. Morris Kevin R. Coombes Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. 777-785 2004 20 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btg484 https://www.wikidata.org/entity/Q30749426 db/journals/bioinformatics/bioinformatics20.html#BaggerlyMC04

Jing Wang 0006 Kevin R. Coombes W. Edward Highsmith Michael J. Keating Lynne V. Abruzzo Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. 3166-3178 2004 20 Bioinform. 17 https://doi.org/10.1093/bioinformatics/bth381 https://www.wikidata.org/entity/Q47255424 db/journals/bioinformatics/bioinformatics20.html#WangCHKA04

Kevin R. Coombes W. Edward Highsmith Tammy A. Krogmann Keith A. Baggerly David N. Stivers Lynne V. Abruzzo Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays. 655-669 2002 9 J. Comput. Biol. 4 db/journals/jcb/jcb9.html#CoombesHKBSA02 https://doi.org/10.1089/106652702760277372 https://www.wikidata.org/entity/Q30731461

Keith A. Baggerly Kevin R. Coombes Kenneth R. Hess David N. Stivers Lynne V. Abruzzo Wei Zhang 0011 Identifying Differentially Expressed Genes in cDNA Microarray Experiments. 639-659 2001 8 J. Comput. Biol. 6 db/journals/jcb/jcb8.html#BaggerlyCHSAZ01 https://doi.org/10.1089/106652701753307539 https://www.wikidata.org/entity/Q55473888

Zachary B. Abrams Lynne V. Abruzzo Rehan Akbani Jonas S. Almeida Kin Fai Au Keith A. Baggerly Veerabhadran Baladandayuthapani Arindam Banerjee 0001 Lynn L. Barron Elizabeth Baskin Russell Bonneville Guy N. Brock Lauren A. Byers George A. Calin Carmen Z. Cantemir-Stone Mark Carey Yong Chen 0016 Lijun Cheng Caitlin E. Coombes Michael A. Davies Helena F. Deus Lixia Diao Tom Dillon Naleef Fareed Luc Girard David L. Gold Karl B. Gregory Stanley R. Hamilton Xuming He 0002 Nyla A. Heerema Bryan T. J. Hennessy Carmen D. Herling Kenneth R. Hess John V. Heymach William Edward HighsmithW. Edward Highsmith Elizabeth G. Hill Jianhua Hu Kun Huang 0001 Cristina Ivan Yuan Ji Faye M. Johnson Travis S. Johnson Zhenlin Ju Mini Kapoor Yuliya V. Karpievitch Michael J. Keating Ryuji Kobayashi John M. Koomen Steven M. Kornblau Tammy A. Krogmann J. Jack Lee Haoran Li 0015 Lang Li 0001 Suli Li Steven Lin Diane D. Liu Mingrui Liu Ping Liu Wenbin Liu Xin Liu Yiling Lu Bani K. Mallick Ganiraju Manyam Li Mao Ewy A. Mathé Joseph P. McElroy Gordon B. Mills John D. Minna Amin A. Momin Jeffrey S. Morris Samantha Nakayiza E. Shannon Neeley Samet Oymak Philip R. O. Payne Philip R. P. Payne Michael Peyton Satyajeet Raje Ricky Rodriguez Paul L. Roebuck Deepa Sampath Jalal K. Siddiqui Doris R. Siwak Adam J. Smolka Romesh Stanislaus David N. Stivers Xiao Su Amir Asiaee T. Dwayne G. Tally Pan Tong Jing Wang 0006 Min Wang Qingyi Wei John N. Weinstein Chunlei Wu Xue Wu Lianbo Yu Bofei Zhang Jiexin Zhang 0004 Li Zhang Lin Zhang 0056 Nianxiang Zhang Wei Zhang 0011 Yue Zhao Mark R. Zucker