Kevin R. Coombes

Publication Activity (10 Years)

Years Active: 2001-2022
Publications (10 Years): 19

Top Topics

Prognostic Factors

Gene Expression

Top Venues

BMC Medical Informatics Decis. Mak.

Publications

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) (2022)
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) (2021)
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) (2021)
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) (2021)
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) (2021)
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 (2021)
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 (2020)
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) (2020)
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) (2020)
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)
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) (2020)
Zachary B. Abrams, Travis Johnson, Kun Huang, Philip R. O. Payne, Kevin R. Coombes
A protocol to evaluate RNA sequencing normalization methods. BMC Bioinform. (24) (2019)
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) (2019)
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) (2019)
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) (2019)
Min Wang, Zachary B. Abrams, Steven M. Kornblau, Kevin R. Coombes
Thresher: determining the number of clusters while removing outliers. BMC Bioinform. 19 (1) (2018)
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) (2018)
Amir Asiaee T., Samet Oymak, Kevin R. Coombes, Arindam Banerjee
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient. CoRR (2018)
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)
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) (2015)
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) (2015)
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) (2014)
Ganiraju Manyam, Cristina Ivan, George A. Calin, Kevin R. Coombes
targetHub: a programmable interface for miRNA-gene interactions. Bioinform. 29 (20) (2013)
Pan Tong, Yong Chen, Xiao Su, Kevin R. Coombes
SIBER: systematic identification of bimodally expressed genes using RNAseq data. Bioinform. 29 (5) (2013)
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)
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) (2012)
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) (2012)
E. Shannon Neeley, Steven M. Kornblau, Kevin R. Coombes, Keith A. Baggerly
Variable slope normalization of reverse phase protein arrays. Bioinform. 25 (11) (2009)
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) (2009)
David L. Gold, Bani K. Mallick, Kevin R. Coombes
Real-Time Gene Expression: Statistical Challenges in Design and Inference. J. Comput. Biol. 15 (6) (2008)
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)
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) (2007)
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) (2007)
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) (2007)
Jiexin Zhang, Li Zhang, Kevin R. Coombes
Gene sequence signatures revealed by mining the UniGene affiliation network. Bioinform. 22 (4) (2006)
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) (2005)
Yuan Ji, Chunlei Wu, Ping Liu, Jing Wang, Kevin R. Coombes
Applications of beta-mixture models in bioinformatics. Bioinform. 21 (9) (2005)
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) (2005)
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) (2004)
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) (2004)
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) (2002)
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) (2001)