Kevin R. Coombes

42 papers Misc 1Journal 39Unranked 2
YearRankTypeTitle / Venue / Authors
2022 J jnl
CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression.
Bioinform.
Yue Zhao, Lianbo Yu, Xue Wu, Haoran Li, Kevin R. Coombes, Kin Fai Au, Lijun Cheng, Lang Li
2021 J jnl
A novel model to label delirium in an intensive care unit from clinician actions.
BMC Medical Informatics Decis. Mak.
Caitlin E. Coombes, Kevin R. Coombes, Naleef Fareed
2021 J jnl
Mercator: a pipeline for multi-method, unsupervised visualization and distance generation.
Bioinform.
Zachary B. Abrams, Caitlin E. Coombes, Suli Li, Kevin R. Coombes
2021 J jnl
Pattern recognition in lymphoid malignancies using CytoGPS and Mercator.
BMC Bioinform.
Zachary B. Abrams, Dwayne G. Tally, Lin Zhang, Caitlin E. Coombes, Philip R. O. Payne, Lynne V. Abruzzo, Kevin R. Coombes
2021 J jnl
RCytoGPS: an R package for reading and visualizing cytogenetics data.
Bioinform.
Zachary B. Abrams, Dwayne G. Tally, Lynne V. Abruzzo, Kevin R. Coombes
2021 J jnl
Simulation-derived best practices for clustering clinical data.
J. Biomed. Informatics
Caitlin E. Coombes, Xin Liu, Zachary B. Abrams, Kevin R. Coombes, Guy N. Brock
2020 Misc conf
CytoGPS: A Web-Enabled Karyotype Analysis Tool for Cytogeneticists and Biomedical Data Scientists.
AMIA
Zachary B. Abrams, Lin Zhang, Ricky Rodriguez, Lynne V. Abruzzo, Kevin R. Coombes, Philip R. P. Payne
2020 J jnl
Explaining Gene Expression Using Twenty-One MicroRNAs.
J. Comput. Biol.
Amir Asiaee T., Zachary B. Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes
2020 J jnl
Generating simulated SNP array and sequencing data to assess genomic segmentation algorithms.
Int. J. Comput. Biol. Drug Des.
Mark R. Zucker, Kevin R. Coombes
2020 J jnl
Umpire 2.0: Simulating realistic, mixed-type, clinical data for machine learning.
F1000Research
Caitlin E. Coombes, Zachary B. Abrams, Samantha Nakayiza, Guy N. Brock, Kevin R. Coombes
2020 J jnl
Unsupervised machine learning and prognostic factors of survival in chronic lymphocytic leukemia.
J. Am. Medical Informatics Assoc.
Caitlin E. Coombes, Zachary B. Abrams, Suli Li, Lynne V. Abruzzo, Kevin R. Coombes
2019 J jnl
A protocol to evaluate RNA sequencing normalization methods.
BMC Bioinform.
Zachary B. Abrams, Travis S. Johnson, Kun Huang, Philip R. O. Payne, Kevin R. Coombes
2019 J jnl
CytoGPS: a web-enabled karyotype analysis tool for cytogenetics.
Bioinform.
Zachary B. Abrams, Lin Zhang, Lynne V. Abruzzo, Nyla A. Heerema, Suli Li, Tom Dillon, Ricky Rodriguez, Kevin R. Coombes, Philip R. O. Payne
2019 J jnl
Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing.
Bioinform.
Mark R. Zucker, Lynne V. Abruzzo, Carmen D. Herling, Lynn L. Barron, Michael J. Keating, Zachary B. Abrams, Nyla A. Heerema, Kevin R. Coombes
2019 J jnl
Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing.
Bioinform.
Mark R. Zucker, Lynne V. Abruzzo, Carmen D. Herling, Lynn L. Barron, Michael J. Keating, Zachary B. Abrams, Nyla A. Heerema, Kevin R. Coombes
2018 J jnl
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient.
CoRR
Amir Asiaee T., Samet Oymak, Kevin R. Coombes, Arindam Banerjee
2018 J jnl
IntLIM: integration using linear models of metabolomics and gene expression data.
BMC Bioinform.
Jalal K. Siddiqui, Elizabeth Baskin, Mingrui Liu, Carmen Z. Cantemir-Stone, Bofei Zhang, Russell Bonneville, Joseph P. McElroy, Kevin R. Coombes, Ewy A. Mathé
2018 J jnl
Thresher: determining the number of clusters while removing outliers.
BMC Bioinform.
Min Wang, Zachary B. Abrams, Steven M. Kornblau, Kevin R. Coombes
2016 — conf
Using Karyotype Data for Automated Disease Classification: A Proof of Concept Demonstration.
CRI
Satyajeet Raje, Zachary B. Abrams, Kevin R. Coombes, Philip R. O. Payne
2015 J jnl
Development of a robust classifier for quality control of reverse-phase protein arrays.
Bioinform.
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
2015 J jnl
drexplorer: A tool to explore dose-response relationships and drug-drug interactions.
Bioinform.
Pan Tong, Kevin R. Coombes, Faye M. Johnson, Lauren A. Byers, Lixia Diao, Diane D. Liu, J. Jack Lee, John V. Heymach, Jing Wang
2014 J jnl
Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Karl B. Gregory, Amin A. Momin, Kevin R. Coombes, Veerabhadran Baladandayuthapani
2013 J jnl
SIBER: systematic identification of bimodally expressed genes using RNAseq data.
Bioinform.
Pan Tong, Yong Chen, Xiao Su, Kevin R. Coombes
2013 J jnl
targetHub: a programmable interface for miRNA-gene interactions.
Bioinform.
Ganiraju Manyam, Cristina Ivan, George A. Calin, Kevin R. Coombes
2012 — conf
Latent feature decompositions for integrative analysis of diverse high-throughput genomic data.
GENSiPS
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
2012 J jnl
Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups.
BMC Bioinform.
Jiexin Zhang, Kevin R. Coombes
2012 J jnl
integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory.
Bioinform.
Pan Tong, Kevin R. Coombes
2009 J jnl
Serial dilution curve: a new method for analysis of reverse phase protein array data.
Bioinform.
Li Zhang, Qingyi Wei, Li Mao, Wenbin Liu, Gordon B. Mills, Kevin R. Coombes
2009 J jnl
Variable slope normalization of reverse phase protein arrays.
Bioinform.
E. Shannon Neeley, Steven M. Kornblau, Kevin R. Coombes, Keith A. Baggerly
2008 J jnl
RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays.
BMC Bioinform.
Romesh Stanislaus, Mark Carey, Helena F. Deus, Kevin R. Coombes, Bryan T. J. Hennessy, Gordon B. Mills, Jonas S. Almeida
2008 J jnl
Real-Time Gene Expression: Statistical Challenges in Design and Inference.
J. Comput. Biol.
David L. Gold, Bani K. Mallick, Kevin R. Coombes
2007 J jnl
Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL.
Briefings Bioinform.
David L. Gold, Kevin R. Coombes, Jing Wang, Bani K. Mallick
2007 J jnl
Non-parametric quantification of protein lysate arrays.
Bioinform.
Jianhua Hu, Xuming He, Keith A. Baggerly, Kevin R. Coombes, Bryan T. J. Hennessy, Gordon B. Mills
2007 J jnl
PrepMS: TOF MS data graphical preprocessing tool.
Bioinform.
Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida
2006 J jnl
Gene sequence signatures revealed by mining the UniGene affiliation network.
Bioinform.
Jiexin Zhang, Li Zhang, Kevin R. Coombes
2005 J jnl
Analysis of dose-response effects on gene expression data with comparison of two microarray platforms.
Bioinform.
Jianhua Hu, Mini Kapoor, Wei Zhang, Stanley R. Hamilton, Kevin R. Coombes
2005 J jnl
Applications of beta-mixture models in bioinformatics.
Bioinform.
Yuan Ji, Chunlei Wu, Ping Liu, Jing Wang, Kevin R. Coombes
2005 J jnl
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.
Bioinform.
Jeffrey S. Morris, Kevin R. Coombes, John M. Koomen, Keith A. Baggerly, Ryuji Kobayashi
2004 J jnl
Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies.
Bioinform.
Jing Wang, Kevin R. Coombes, W. Edward Highsmith, Michael J. Keating, Lynne V. Abruzzo
2004 J jnl
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments.
Bioinform.
Keith A. Baggerly, Jeffrey S. Morris, Kevin R. Coombes
2002 J jnl
Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays.
J. Comput. Biol.
Kevin R. Coombes, W. Edward Highsmith, Tammy A. Krogmann, Keith A. Baggerly, David N. Stivers, Lynne V. Abruzzo
2001 J jnl
Identifying Differentially Expressed Genes in cDNA Microarray Experiments.
J. Comput. Biol.
Keith A. Baggerly, Kevin R. Coombes, Kenneth R. Hess, David N. Stivers, Lynne V. Abruzzo, Wei Zhang