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Kevin R. Coombes
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2020 – today
- 2022
- [j37]Yue Zhao
, Lianbo Yu, Xue Wu, Haoran Li
, Kevin R. Coombes
, Kin Fai Au
, Lijun Cheng, Lang Li
:
CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression. Bioinform. 38(23): 5245-5252 (2022) - 2021
- [j36]Zachary B. Abrams
, Caitlin E. Coombes, Suli Li, Kevin R. Coombes
:
Mercator: a pipeline for multi-method, unsupervised visualization and distance generation. Bioinform. 37(17): 2780-2781 (2021) - [j35]Zachary B. Abrams
, Dwayne G. Tally, Lynne V. Abruzzo, Kevin R. Coombes
:
RCytoGPS: an R package for reading and visualizing cytogenetics data. Bioinform. 37(23): 4589-4590 (2021) - [j34]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. BMC Bioinform. 22(1): 100 (2021) - [j33]Caitlin E. Coombes, Xin Liu
, Zachary B. Abrams, Kevin R. Coombes
, Guy N. Brock
:
Simulation-derived best practices for clustering clinical data. J. Biomed. Informatics 118: 103788 (2021) - [j32]Caitlin E. Coombes, Kevin R. Coombes
, Naleef Fareed
:
A novel model to label delirium in an intensive care unit from clinician actions. BMC Medical Informatics Decis. Mak. 21(1): 97 (2021) - 2020
- [j31]Mark R. Zucker, Kevin R. Coombes
:
Generating simulated SNP array and sequencing data to assess genomic segmentation algorithms. Int. J. Comput. Biol. Drug Des. 13(5/6): 438-453 (2020) - [j30]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. J. Am. Medical Informatics Assoc. 27(7): 1019-1027 (2020) - [j29]Amir Asiaee T., Zachary B. Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes
:
Explaining Gene Expression Using Twenty-One MicroRNAs. J. Comput. Biol. 27(7): 1157-1170 (2020) - [c3]Zachary B. Abrams, Lin Zhang, 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. AMIA 2020 - [i2]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. F1000Research 9: 1186 (2020)
2010 – 2019
- 2019
- [j28]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. Bioinform. 35(17): 2924-2931 (2019) - [j27]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. Bioinform. 35(17): 3216 (2019) - [j26]Zachary B. Abrams, Lin Zhang
, 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. Bioinform. 35(24): 5365-5366 (2019) - [j25]Zachary B. Abrams, Travis S. Johnson, Kun Huang, Philip R. O. Payne
, Kevin R. Coombes
:
A protocol to evaluate RNA sequencing normalization methods. BMC Bioinform. 20-S(24): 679 (2019) - 2018
- [j24]Min Wang, Zachary B. Abrams, Steven M. Kornblau, Kevin R. Coombes
:
Thresher: determining the number of clusters while removing outliers. BMC Bioinform. 19(1): 9:1-9:15 (2018) - [j23]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. BMC Bioinform. 19(1): 81:1-81:12 (2018) - [i1]Amir Asiaee T., Samet Oymak, Kevin R. Coombes, Arindam Banerjee:
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient. CoRR abs/1806.04047 (2018) - 2016
- [c2]Satyajeet Raje, Zachary B. Abrams, Kevin R. Coombes, Philip R. O. Payne:
Using Karyotype Data for Automated Disease Classification: A Proof of Concept Demonstration. CRI 2016 - 2015
- [j22]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. Bioinform. 31(6): 912-918 (2015) - [j21]Pan Tong, Kevin R. Coombes
, Faye M. Johnson, Lauren A. Byers, Lixia Diao, Diane D. Liu, J. Jack Lee
, John V. Heymach
, Jing Wang:
drexplorer: A tool to explore dose-response relationships and drug-drug interactions. Bioinform. 31(10): 1692-1694 (2015) - 2014
- [j20]Karl B. Gregory, Amin A. Momin, Kevin R. Coombes
, Veerabhadran Baladandayuthapani:
Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data. IEEE ACM Trans. Comput. Biol. Bioinform. 11(6): 984-994 (2014) - 2013
- [j19]Pan Tong, Yong Chen, Xiao Su, Kevin R. Coombes
:
SIBER: systematic identification of bimodally expressed genes using RNAseq data. Bioinform. 29(5): 605-613 (2013) - [j18]Ganiraju Manyam
, Cristina Ivan
, George A. Calin
, Kevin R. Coombes
:
targetHub: a programmable interface for miRNA-gene interactions. Bioinform. 29(20): 2657-2658 (2013) - 2012
- [j17]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. Bioinform. 28(22): 2861-2869 (2012) - [j16]Jiexin Zhang, Kevin R. Coombes
:
Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups. BMC Bioinform. 13(S-13): S1 (2012) - [c1]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. GENSiPS 2012: 130-134
2000 – 2009
- 2009
- [j15]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. Bioinform. 25(5): 650-654 (2009) - [j14]E. Shannon Neeley, Steven M. Kornblau, Kevin R. Coombes
, Keith A. Baggerly:
Variable slope normalization of reverse phase protein arrays. Bioinform. 25(11): 1384-1389 (2009) - 2008
- [j13]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. BMC Bioinform. 9 (2008) - [j12]David L. Gold, Bani K. Mallick, Kevin R. Coombes
:
Real-Time Gene Expression: Statistical Challenges in Design and Inference. J. Comput. Biol. 15(6): 611-623 (2008) - 2007
- [j11]David L. Gold, Kevin R. Coombes
, Jing Wang, Bani K. Mallick:
Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL. Briefings Bioinform. 8(2): 71-77 (2007) - [j10]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. Bioinform. 23(2): 264-265 (2007) - [j9]Jianhua Hu, Xuming He, Keith A. Baggerly, Kevin R. Coombes
, Bryan T. J. Hennessy
, Gordon B. Mills:
Non-parametric quantification of protein lysate arrays. Bioinform. 23(15): 1986-1994 (2007) - 2006
- [j8]Jiexin Zhang, Li Zhang, Kevin R. Coombes
:
Gene sequence signatures revealed by mining the UniGene affiliation network. Bioinform. 22(4): 385-391 (2006) - 2005
- [j7]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. Bioinform. 21(9): 1764-1775 (2005) - [j6]Yuan Ji, Chunlei Wu, Ping Liu, Jing Wang, Kevin R. Coombes
:
Applications of beta-mixture models in bioinformatics. Bioinform. 21(9): 2118-2122 (2005) - [j5]Jianhua Hu, Mini Kapoor, Wei Zhang, Stanley R. Hamilton, Kevin R. Coombes
:
Analysis of dose-response effects on gene expression data with comparison of two microarray platforms. Bioinform. 21(17): 3524-3529 (2005) - 2004
- [j4]Keith A. Baggerly, Jeffrey S. Morris, Kevin R. Coombes
:
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinform. 20(5): 777-785 (2004) - [j3]Jing Wang, 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. Bioinform. 20(17): 3166-3178 (2004) - 2002
- [j2]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. J. Comput. Biol. 9(4): 655-669 (2002) - 2001
- [j1]Keith A. Baggerly, Kevin R. Coombes
, Kenneth R. Hess, David N. Stivers, Lynne V. Abruzzo, Wei Zhang:
Identifying Differentially Expressed Genes in cDNA Microarray Experiments. J. Comput. Biol. 8(6): 639-659 (2001)
Coauthor Index
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