K. Coombes

K. Coombes, G. Mills, Jing Wang, 2010, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

Abnormal expression of FLI 1 protein is an adverse prognostic factor in acute myeloid leukemia

K. Coombes, Nianxiang Zhang, A. Qutub, 2011 .

Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1.

J. Weinstein, K. Coombes, G. Mills, 2012, Cancer discovery.

A quantitative analysis of heterogeneities and hallmarks in acute myelogenous leukaemia

Chenyue W. Hu, K. Coombes, A. Qutub, 2019, Nature Biomedical Engineering.

BATTLE-2 program: A biomarker-integrated targeted therapy study in previously treated patients with advanced non-small cell lung cancer (NSCLC).

K. Coombes, J. Lee, W. Hong, 2013 .

A Guide to MATLAB: MATLAB Programming

Kevin R. Coombes, Brian R. Hunt, John E. Osborn, 2001 .

Array CGH analysis of chronic lymphocytic leukemia reveals frequent cryptic monoallelic and biallelic deletions of chromosome 22q11 that include the PRAME gene.

K. Coombes, S. Gunn, L. Abruzzo, 2009, Leukemia research.

Melanoma antigen family A identified by the bimodality index defines a subset of triple negative breast cancers as candidates for immune response augmentation.

Kevin R Coombes, Lajos Pusztai, Eugen Ruckhäberle, 2012, European journal of cancer.

A Two-Gene Signature, SKI and SLAMF1, Predicts Time-to-Treatment in Previously Untreated Patients with Chronic Lymphocytic Leukemia

K. Coombes, L. Medeiros, L. Abruzzo, 2011, PloS one.

Identification and validation of biomarkers of IgV(H) mutation status in chronic lymphocytic leukemia using microfluidics quantitative real-time polymerase chain reaction technology.

K. Coombes, K. Anderson, L. Abruzzo, 2007, The Journal of molecular diagnostics : JMD.

Thirty biologically interpretable clusters of transcription factors distinguish cancer type

Zachary B. Abrams, K. Coombes, L. Abruzzo, 2018, BMC Genomics.

Selecting Reliable mRNA Expression Measurements Across Platforms Improves Downstream Analysis

K. Coombes, Jing Wang, J. Minna, 2016, Cancer informatics.

SITH: An R package for visualizing and analyzing a spatial model of intratumor heterogeneity.

Amir H. Asiaee, Phillip B. Nicol, Dániel L. Barabási, 2022, Computational and systems oncology.

CytoGPS: A large-scale karyotype analysis of CML data.

Zachary B. Abrams, Caitlin E. Coombes, K. Coombes, 2020, Cancer genetics.

Biology of Human Tumors VEGF / VEGFR-2 Upregulates EZH 2 Expression in Lung Adenocarcinoma Cells and EZH 2 Depletion Enhances the Response to Platinum-Based and VEGFR-2 – Targeted Therapy

Milind B. Suraokar, K. Coombes, Jing Wang, 2014 .

VEGF/VEGFR-2 Upregulates EZH2 Expression in Lung Adenocarcinoma Cells and EZH2 Depletion Enhances the Response to Platinum-Based and VEGFR-2–Targeted Therapy

K. Coombes, Jing Wang, J. Minna, 2014, Clinical Cancer Research.

Risk Factors of 131I-Induced Salivary Gland Damage in Thyroid Cancer Patients.

K. Coombes, R. Nagy, R. Kloos, 2016, The Journal of clinical endocrinology and metabolism.

Time-to-progression after frontline chemoimmunotherapy for chronic lymphocytic leukemia: an independently validated retrospective cohort study

K. Coombes, C. Herling, 2020 .

Transcriptomic architecture of the adjacent airway field cancerization in non-small cell lung cancer.

K. Coombes, Jing Wang, W. Hong, 2014, Journal of the National Cancer Institute.

Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome.

John V Heymach, Kevin R Coombes, Lixia Diao, 2012, Journal of the National Cancer Institute.

Transformation of Human Mesenchymal Cells and Skin Fibroblasts into Hematopoietic Cells

K. Coombes, Z. Estrov, D. Harris, 2011, PloS one.

Chapter 1 PRE-PROCESSING MASS SPECTROMETRY DATA

Jeffrey S. Morris, K. Coombes, K. Baggerly, 2006 .

Low expression of ASH2L protein correlates with a favorable outcome in acute myeloid leukemia

K. Coombes, Sharon Y. R. Dent, Nianxiang Zhang, 2017, Leukemia & lymphoma.

Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins.

Kevin R Coombes, John M Koomen, K. Coombes, 2005, Clinical cancer research : an official journal of the American Association for Cancer Research.

Cathepsin G is broadly expressed in acute myeloid leukemia and is an effective immunotherapeutic target

K. Coombes, G. Lizée, E. Mittendorf, 2016, Leukemia.

Functional Proteomic Analysis of Advanced Serous Ovarian Cancer Using Reverse Phase Protein Array: TGF-β Pathway Signaling Indicates Response to Primary Chemotherapy

Fan Zhang, Yiling Lu, Gordon B Mills, 2010, Clinical Cancer Research.

Low Expression Of PP2A Regulatory Subunit B55α Is Associated With T308 Phosphorylation Of AKT And Shorter Complete Remission Duration In Acute Myeloid Leukemia Patients

K. Coombes, Nianxiang Zhang, M. Konopleva, 2011, Leukemia.

Trisomy 12 chronic lymphocytic leukemia expresses a unique set of activated and targetable pathways

K. Coombes, G. Calin, L. Abruzzo, 2018, Haematologica.

Prognostic Role of aMultigene ReverseTranscriptase-PCRAssay in Patients with Node-Negative Breast Cancer Not Receiving Adjuvant

K. Coombes, G. Hortobagyi, M. Cronin, 2005 .

p53 pathway dysfunction is highly prevalent in acute myeloid leukemia independent of TP53 mutational status

Chenyue W. Hu, K. Coombes, Nianxiang Zhang, 2017, Leukemia.

Expression of ARC (apoptosis repressor with caspase recruitment domain), an antiapoptotic protein, is strongly prognostic in AML.

K. Coombes, Nianxiang Zhang, M. Andreeff, 2011, Blood.

Abstract LB-88: Gene expression signatures predictive of clinical outcome and tumor mutations in refractory NSCLC patients (pts) in the BATTLE trial (Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination)

Edward S. Kim, J. Weinstein, K. Coombes, 2011 .

The protein phosphatase 2A regulatory subunit B55α is a modulator of signaling and microRNA expression in acute myeloid leukemia cells.

K. Coombes, G. Calin, Nianxiang Zhang, 2014, Biochimica et biophysica acta.

Synergistic targeting of AML stem/progenitor cells with IAP antagonist birinapant and demethylating agents.

James M. Bogenberger, K. Coombes, M. Andreeff, 2014, Journal of the National Cancer Institute.

Intratumoral heterogeneity and clonal evolution induced by HPV integration

K. Coombes, Sara Goodwin, F. Sedlazeck, 2022, bioRxiv.

Phosphorylation of GSK3α/β correlates with activation of AKT and is prognostic for poor overall survival in acute myeloid leukemia patients

K. Coombes, Nianxiang Zhang, E. Neeley, 2015, BBA clinical.

Cardiomyocyte PDGFR-beta signaling is an essential component of the mouse cardiac response to load-induced stress.

K. Coombes, Lawrence Buja, M. Entman, 2010, The Journal of clinical investigation.

Inversion of abelian integrals on small genus curves

K. Coombes, R. Fisher, 1986 .

Elliptic curves and logarithmic derivatives

K. Coombes, 1999 .

Running title: Functional proteomics of human breast tumors Title: A novel approach to the study of the functional proteome in breast cancer Running title: Functional proteomics of human breast tumors

K. Coombes, A. Børresen-Dale, W. Kuo, 2008 .

Immunohistochemical detection of ZAP70 in chronic lymphocytic leukemia predicts immunoglobulin heavy chain gene mutation status and time to progression

K. Coombes, L. Medeiros, L. Abruzzo, 2010, Modern Pathology.

Cross platform comparison of multigene predictors of response to neoadjuvant paclitaxel/FAC chemotherapy in breast cancer generated by cDNA arrays and Affymetrix GeneChips.

K. Coombes, J. Stec, M. Ayers, 2004, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Concomitant inhibition of DNA methyltransferase and BCL-2 protein function synergistically induce mitochondrial apoptosis in acute myelogenous leukemia cells

K. Coombes, M. Konopleva, M. Andreeff, 2012, Annals of Hematology.

Role of peroxisome proliferator-activated receptor-gamma and its coactivator DRIP205 in cellular responses to CDDO (RTA-401) in acute myelogenous leukemia.

Kevin R Coombes, Zhenlin Ju, Marina Konopleva, 2010, Cancer research.

MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia.

George A Calin, Steven M Kornblau, Muller Fabbri, 2008, Blood.

Relevance of the immunoglobulin VH somatic mutation status in patients with chronic lymphocytic leukemia treated with fludarabine, cyclophosphamide, and rituximab (FCR) or related chemoimmunotherapy regimens.

K. Coombes, L. Rassenti, T. Kipps, 2009, Blood.

Role of Peroxisome Proliferator-Activated Receptor- γ and Its Coactivator DRIP205 in Cellular Responses to CDDO (RTA-401) in Acute Myelogenous Leukemia

K. Coombes, M. Konopleva, M. Andreeff, 2010 .

Atorvastatin for the Prophylaxis of Acute Graft-versus-Host Disease in Patients Undergoing HLA-Matched Related Donor Allogeneic Hematopoietic Stem Cell Transplantation (allo-HCT).

K. Coombes, C. Hofmeister, R. Garzon, 2016, Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation.

Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration

K. Coombes, Sara Goodwin, F. Sedlazeck, 2022, bioRxiv.

Human papillomavirus and the landscape of secondary genetic alterations in oral cancers

Anne-Katrin Emde, K. Coombes, Heather Geiger, 2018, Genome research.

Investigation of PARP1 as a therapeutic target in small cell lung cancer.

J. Weinstein, K. Coombes, Jing Wang, 2012 .

Survivin is highly expressed in CD34 (cid:1) 38 (cid:2) leukemic stem/progenitor cells and predicts poor clinical outcomes in AML

K. Coombes, G. Mills, Nianxiang Zhang, 2012 .

Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers

Anne-Katrin Emde, K. Coombes, Heather Geiger, 2021, bioRxiv.

Transglutaminase 2 expression in acute myeloid leukemia: Association with adhesion molecule expression and leukemic blast motility

K. Coombes, Nianxiang Zhang, G. Borthakur, 2013, Proteomics.

Multi-Data Correlation in Papillary Thyroid Cancer THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By

K. Coombes, Kun Huang, P. Wakely, 2017 .

Data Enrichment : Multitask Learning in High Dimension with Theoretical Guarantees

Amir H. Asiaee, A. Banerjee, K. Coombes, 2019 .

Simulation-derived best practices for clustering clinical data

Guy N. Brock, Kevin R. Coombes, Zachary B. Abrams, 2021, J. Biomed. Informatics.

DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia

C. Bloomfield, J. Byrd, K. Coombes, 2021, Genome research.

Unsupervised machine learning and prognostic factors of survival in chronic lymphocytic leukemia

Kevin R Coombes, Zachary B. Abrams, Caitlin E. Coombes, 2020, J. Am. Medical Informatics Assoc..

Thresher: determining the number of clusters while removing outliers

Min Wang, Kevin R. Coombes, Zachary B. Abrams, 2018, BMC Bioinformatics.

Histone Modification Patterns Using RPPA‐Based Profiling Predict Outcome in Acute Myeloid Leukemia Patients

Chenyue W. Hu, K. Coombes, A. Qutub, 2018, Proteomics.

Co-occurring genomic alterations define major subsets of KRAS-mutant lung adenocarcinoma with distinct biology, immune profiles, and therapeutic vulnerabilities.

Michael Peyton, Humam Kadara, Murim Choi, 2015, Cancer discovery.

Erk Negative Feedback Control Enables Pre-B Cell Transformation and Represents a Therapeutic Target in Acute Lymphoblastic Leukemia.

K. Coombes, Nianxiang Zhang, A. Melnick, 2015, Cancer cell.

Preclinical Evaluation of the Novel BTK Inhibitor Acalabrutinib in Canine Models of B-Cell Non-Hodgkin Lymphoma

J. Byrd, K. Coombes, A. Johnson, 2016, PloS one.

Loss of TRIM62 expression is an independent adverse prognostic factor in acute myeloid leukemia.

K. Coombes, C. Creighton, Nianxiang Zhang, 2015, Clinical lymphoma, myeloma & leukemia.

Zonal heterogeneity for gene expression in human pancreatic carcinoma.

K. Coombes, I. Fidler, Toru Nakamura, 2007, Cancer research.

Patterns of CTCF and ZFHX3 Mutation and Associated Outcomes in Endometrial Cancer.

K. Coombes, P. Goodfellow, R. Bundschuh, 2015, Journal of the National Cancer Institute.

microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival.

George A Calin, Kevin R Coombes, Muller Fabbri, 2010, Blood.

The Bimodality Index: A Criterion for Discovering and Ranking Bimodal Signatures from Cancer Gene Expression Profiling Data

Kevin R. Coombes, Jing Wang, Sijin Wen, 2009, Cancer informatics.

Time-to-progression after front-line fludarabine, cyclophosphamide, and rituximab chemoimmunotherapy for chronic lymphocytic leukaemia: a retrospective, multicohort study.

Zachary B. Abrams, K. Coombes, B. Czerniak, 2019, The Lancet. Oncology.

Developmental subtypes assessed by DNA methylation-iPLEX forecast the natural history of chronic lymphocytic leukemia.

J. Byrd, K. Coombes, Yue-zhong Wu, 2019, Blood.

Genomic variation by whole-genome SNP mapping arrays predicts time-to-event outcome in patients with chronic lymphocytic leukemia: a comparison of CLL and HapMap genotypes.

K. Coombes, B. Czerniak, Tadeusz Majewski, 2013, The Journal of molecular diagnostics : JMD.

LDOC1 mRNA is differentially expressed in chronic lymphocytic leukemia and predicts overall survival in untreated patients.

K. Coombes, B. Czerniak, Tadeusz Majewski, 2011, Blood.

Independent validation of a model using cell line chemosensitivity to predict response to therapy.

K. Coombes, K. Baggerly, S. Knudsen, 2013, Journal of the National Cancer Institute.

Individualized molecular medicine: linking functional proteomics to select therapeutics targeting the PI3K pathway for specific patients.

Yiling Lu, Gordon B Mills, Kevin R Coombes, 2008, Advances in experimental medicine and biology.

High expression of activation-induced cytidine deaminase (AID) and splice variants is a distinctive feature of poor-prognosis chronic lymphocytic leukemia.

Kevin R Coombes, Jing Wang, Lynne V Abruzzo, 2003, Blood.

A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition

Jaime Rodriguez-Canales, Pan Tong, Kevin R. Coombes, 2015, Clinical Cancer Research.

Chemistry-First Approach for Nomination of Personalized Treatment in Lung Cancer

Michael Peyton, John D. Minna, Donna M. Muzny, 2018, Cell.

targetHub: a programmable interface for miRNA-gene interactions

Kevin R. Coombes, George A. Calin, Ganiraju Manyam, 2013, Bioinform..

Oncogenetic Network Estimation with Disjunctive Bayesian Networks

Kevin R. Coombes, Amir H. Asiaee, Oksana A. Chkrebtii, 2020, bioRxiv.

HOX expression patterns identify a common signature for favorable AML

K. Coombes, S. Kornblau, M. Andreeff, 2008, Leukemia.

Molecular analysis of anoikis resistance in oral cavity squamous cell carcinoma.

K. Coombes, Jing Wang, M. Mandal, 2007, Oral oncology.

Prognostic impact and targeting of CRM1 in acute myeloid leukemia.

R. Davis, K. Coombes, Nianxiang Zhang, 2012, Blood.

Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma

Michael F. Sharpnack, K. Coombes, J. Sharpnack, 2018, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

A Pooled Analysis

K. Coombes, D. Carbone, K. Shilo, 2015 .

Genomic Characterization of Non-Small-Cell Lung Cancer in African Americans by Targeted Massively Parallel Sequencing.

K. Coombes, D. Carbone, K. Shilo, 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Genes suppressed by DNA methylation in non-small cell lung cancer reveal the epigenetics of epithelial–mesenchymal transition

J. Weinstein, K. Coombes, Jing Wang, 2014, BMC Genomics.

Taxane-Platin-Resistant Lung Cancers Co-develop Hypersensitivity to JumonjiC Demethylase Inhibitors.

Milind B. Suraokar, K. Coombes, B. Garcia, 2017, Cell reports.

BAYESIAN SPARSE GRAPHICAL MODELS FOR CLASSIFICATION WITH APPLICATION TO PROTEIN EXPRESSION DATA.

Yuan Ji, Yiling Lu, Veerabhadran Baladandayuthapani, 2014, The annals of applied statistics.

A novel model to label delirium in an intensive care unit from clinician actions

Kevin R. Coombes, Naleef Fareed, Caitlin E. Coombes, 2021, BMC Medical Informatics and Decision Making.

Non-parametric quantification of protein lysate arrays

Xuming He, Kevin R. Coombes, Keith A. Baggerly, 2007, Bioinform..

Explaining Gene Expression Using Twenty-One MicroRNAs

Amir H. Asiaee, Zachary B. Abrams, K. Coombes, 2019, J. Comput. Biol..

RefSeq Refinements of UniGene-Based Gene Matching Improve the Correlation of Expression Measurements Between Two Microarray Platforms

Kevin Coombes, Sijin Wen, W. Fraser Symmans, 2006, Applied bioinformatics.

Statistical contributions to proteomic research.

Jeffrey S. Morris, Kevin R Coombes, Jeffrey S Morris, 2010, Methods in molecular biology.

Identification of Cell Cycle Regulatory Genes as Principal Targets of p53-mediated Transcriptional Repression*

K. Coombes, D. Gold, T. McDonnell, 2006, Journal of Biological Chemistry.

drexplorer: A tool to explore dose-response relationships and drug-drug interactions

Pan Tong, Kevin R. Coombes, Lixia Diao, 2015, Bioinform..

Gene expression profile of metastatic human pancreatic cancer cells depends on the organ microenvironment.

Kevin R Coombes, K. Coombes, I. Fidler, 2007, Cancer research.

Biostatistics and Bioinformatics in Clinical Trials

Donald A. Berry, Kevin R. Coombes, D. Berry, 2020, Abeloff's Clinical Oncology.

Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1.

Michael Peyton, Li Shen, John N Weinstein, 2012, Cancer discovery.

Ovarian cancer: linking genomics to new target discovery and molecular markers--the way ahead.

Yiling Lu, Gordon B Mills, Kevin R Coombes, 2008, Advances in experimental medicine and biology.

eIF2β, a subunit of translation‐initiation factor EIF2, is a potential therapeutic target for non‐small cell lung cancer

K. Coombes, J. Minna, L. Girard, 2018, Cancer science.

Identification of proteasomal catalytic subunit PSMA6 as a therapeutic target for lung cancer

K. Coombes, J. Minna, L. Girard, 2017, Cancer science.

Real-Time Gene Expression: Statistical Challenges in Design and Inference

Bani K. Mallick, Kevin R. Coombes, David L. Gold, 2008, J. Comput. Biol..

Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cells

K. Coombes, Z. Estrov, R. Kurzrock, 2008, Molecular Cancer Therapeutics.

Biomarker expression patterns that correlate with high grade features in treatment naive, organ-confined prostate cancer

Kim-Anh Do, Kevin Coombes, Shawn Brisbay, 2008, BMC Medical Genomics.

cells and predicts poor clinical outcomes in AML leukemic stem/progenitor - 38 + Survivin is highly expressed in CD34

K. Coombes, G. Mills, Nianxiang Zhang, 2013 .

Sequence verification as quality-control step for production of cDNA microarrays.

D Cogdell, K. Coombes, D. Cogdell, 2001, BioTechniques.

Variable slope normalization of reverse phase protein arrays

Kevin R. Coombes, Keith A. Baggerly, Steven M. Kornblau, 2009, Bioinform..

Akt isoform-specific effects on thyroid cancer development and progression in a murine thyroid cancer model

K. Coombes, K. L. La Perle, P. Tsichlis, 2020, Scientific Reports.

Tissue-Specific Function of Lymph Node Fibroblastic Reticulum Cells

K. Coombes, V. Thomazy, W. Lang, 2006, Pathobiology.

The BATTLE-2 Study: A Biomarker-Integrated Targeted Therapy Study in Previously Treated Patients With Advanced Non-Small-Cell Lung Cancer.

Li Shen, John V Heymach, Kevin R Coombes, 2016, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

KEAP1-dependent synthetic lethality induced by AKT and TXNRD1 inhibitors in lung cancer.

K. Coombes, J. Minna, J. Roth, 2013, Cancer research.

Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer.

Kevin R Coombes, Keith A Baggerly, K. Coombes, 2008, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments

Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, 2004, Bioinform..

integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory

Pan Tong, Kevin R. Coombes, K. Coombes, 2012, Bioinform..

Prognostic Biomarkers for Esophageal Adenocarcinoma Identified by Analysis of Tumor Transcriptome

K. Coombes, Kenneth K Wang, J. Ajani, 2010, PloS one.

Monitoring the Quality of Microarray Experiments

Jing Wang, Kevin R. Coombes, K. Coombes, 2004 .

Identifying Differentially Expressed Genes in cDNA Microarray Experiments

Kevin R. Coombes, Wei Zhang, Keith A. Baggerly, 2001, J. Comput. Biol..

Proteomic biomarkers apolipoprotein A1, truncated transthyretin and connective tissue activating protein III enhance the sensitivity of CA125 for detecting early stage epithelial ovarian cancer.

K. Coombes, R. Bast, E. Fung, 2011, Gynecologic oncology.

Therapeutic Target for Overcoming EGFR Inhibitor Resistance Resistance to EGFR and PI 3 K Inhibitors and Identifies Axl as a Mesenchymal Transition Gene Signature Predicts

Edward S. Kim, J. Weinstein, K. Coombes, 2012 .

Recurrent expression signatures of cytokines and chemokines are present and are independently prognostic in acute myelogenous leukemia and myelodysplasia.

K. Coombes, Z. Estrov, S. Kornblau, 2010, Blood.

Identification and comparison of genes differentially regulated by transcription factors and miRNAs

Amir H. Asiaee, Zachary B. Abrams, K. Coombes, 2019, bioRxiv.

SIBER: systematic identification of bimodally expressed genes using RNAseq data

Yong Chen, Xiao Su, Pan Tong, 2013, Bioinform..

PrepMS: TOF MS data graphical preprocessing tool

Jeffrey S. Morris, Jonas S. Almeida, Kevin R. Coombes, 2007, Bioinform..

Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum

Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, 2005, Bioinform..

Statistical Considerations in the Assessment of cDNA Microarray Data Obtained Using Amplification

K. Coombes, K. Baggerly, Wei Zhang, 2006 .

Research Report RNA Amplification Strategies for cDNA Microarray Experiments

K. Coombes, J. Wang, L. Hu, 2003 .

Increased VEGFR-2 gene copy is associated with chemoresistance and shorter survival in patients with non-small-cell lung carcinoma who receive adjuvant chemotherapy.

K. Coombes, Jing Wang, J. Minna, 2011, Cancer research.

MLL-Rearranged Acute Lymphoblastic Leukemias Activate BCL-2 through H3K79 Methylation and Are Sensitive to the BCL-2-Specific Antagonist ABT-199

K. Coombes, A. Letai, Nianxiang Zhang, 2015, Cell reports.

lymphocytic leukemia splice variants is a distinctive feature of poor-prognosis chronic High expression of activation-induced cytidine deaminase ( AID ) and

K. Coombes, K. Elenitoba-Johnson, Jing Wang, 2003 .

The long noncoding RNA, treRNA, decreases DNA damage and is associated with poor response to chemotherapy in chronic lymphocytic leukemia

M. Grever, K. Coombes, I. Flinn, 2017, OncoTarget.

Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays

Kevin R. Coombes, Keith A. Baggerly, Lynne V. Abruzzo, 2002, J. Comput. Biol..

Chemoprevention of Skin Carcinogenesis by Phenylretinamides: Retinoid Receptor–Independent Tumor Suppression

Satish Cheepala, John L. Clifford, Kevin Coombes, 2006, Clinical Cancer Research.

Stem cell-ness: a "magic marker" for cancer.

Gordon B Mills, Kevin R Coombes, K. Coombes, 2005, The Journal of clinical investigation.

Development of a robust classifier for quality control of reverse-phase protein arrays

John N. Weinstein, Wenbin Liu, Kevin R. Coombes, 2015, Bioinform..

Microarrays: handling the deluge of data and extracting reliable information.

K R Hess, W Zhang, K A Baggerly, 2001, Trends in biotechnology.

miRNA expression profiles in head and neck squamous cell carcinoma and adjacent normal tissue

K. Coombes, L. Ramdas, M. Story, 2009, Head & neck.

Applications of beta-mixture models in bioinformatics

Yuan Ji, Chunlei Wu, Ping Liu, 2005, Bioinform..

MLN0128, a novel mTOR kinase inhibitor, disrupts survival signaling and triggers apoptosis in AML and AML stem/ progenitor cells

K. Coombes, M. Konopleva, M. Andreeff, 2016, Oncotarget.

Biological validation of differentially expressed genes in chronic lymphocytic leukemia identified by applying multiple statistical methods to oligonucleotide microarrays.

Kevin R Coombes, Jing Wang, Lynne V Abruzzo, 2005, The Journal of molecular diagnostics : JMD.

Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data

Veerabhadran Baladandayuthapani, Kevin R. Coombes, Karl B. Gregory, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

LC-FACSeq is a method for detecting rare clones in leukemia.

J. Byrd, K. Coombes, G. Lozanski, 2020, JCI insight.

BCL-2 family proteins as 5-Azacytidine-sensitizing targets and determinants of response in myeloid malignancies

James M. Bogenberger, K. Coombes, G. Ahmann, 2014, Leukemia.

LGALS3 is connected to CD74 in a previously unknown protein network that is associated with poor survival in patients with AML

Chenyue W. Hu, K. Coombes, M. Andreeff, 2019, EBioMedicine.

Merging microarray data, robust feature selection, and predicting prognosis in prostate cancer

Jing Wang, Kevin R. Coombes, Spyros Tsavachidis, 2006, Cancer informatics.

Upregulation of c-MYC in WT1-mutant tumors: assessment of WT1 putative transcriptional targets using cDNA microarray expression profiling of genetically defined Wilms' tumors

K. Coombes, V. Huff, Sang-Joon Lee, 2003, Oncogene.

Analysis of dose-response effects on gene expression data with comparison of two microarray platforms

Kevin R. Coombes, Wei Zhang, Jianhua Hu, 2005, Bioinform..

Role of Peroxisome Proliferator-Activated Receptor-γ and Its Coactivator DRIP 205 in Cellular Responses to CDDO ( RTA-401 ) in Acute Myelogenous Leukemia

K. Coombes, Z. Ju, M. Konopleva, 2010 .

Pattern recognition in lymphoid malignancies using CytoGPS and Mercator

Philip R. O. Payne, Kevin R. Coombes, Zachary B. Abrams, 2021, BMC Bioinform..

Array CGH Analysis of Chronic Lymphocytic Leukemia Reveals Frequent Cryptic Monoallelic and Biallelic Deletions of Chromosome 22q11.

K. Coombes, S. Gunn, L. Abruzzo, 2008 .

Host lung gene expression patterns predict infectious etiology in a mouse model of pneumonia

K. Coombes, Jiexin Zhang, B. Dickey, 2010, Respiratory research.

Targeting The Mitochondrial ClpP As a Novel Therapeutic Strategy For Acute Myeloid Leukemia

K. Coombes, M. Minden, Nianxiang Zhang, 2013 .

Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing

Kevin R Coombes, Zachary B. Abrams, Mark R Zucker, 2019, Bioinform..

Inter-Gene Correlation on Oligonucleotide Arrays

Kevin R Coombes, David L Gold, Jing Wang, 2005, American journal of pharmacogenomics : genomics-related research in drug development and clinical practice.

Expression profiling stratifies mesothelioma tumors and signifies deregulation of spindle checkpoint pathway and microtubule network with therapeutic implications.

K. Coombes, I. Wistuba, J. Lee, 2014, Annals of oncology : official journal of the European Society for Medical Oncology.

plasma: Partial LeAst Squares for Multiomics Analysis

K. Coombes, Lianbo Yu, C. Oakes, 2023, bioRxiv.

Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry

Kelly K. Hunt, Kevin R. Coombes, Lajos Pusztai, 2004, Breast Cancer Research and Treatment.

IntLIM: integration using linear models of metabolomics and gene expression data

Mingrui Liu, Bofei Zhang, Kevin R. Coombes, 2018, BMC Bioinformatics.

Sources of nonlinearity in cDNA microarray expression measurements

Kevin R Coombes, Wei Zhang, Latha Ramdas, 2001, Genome Biology.

Serum amyloid A as a tumor marker in sera of nude mice with orthotopic human pancreatic cancer and in plasma of patients with pancreatic cancer.

Kevin R Coombes, John Koomen, David Hawke, 2005, International journal of oncology.

Simulating Gene Expression Data To Estimate Sample Size For Class and Biomarker Discovery

Kevin R. Coombes, Paul L. Roebuck, K. Coombes, 2012 .

Umpire 2.0: Simulating realistic, mixed-type, clinical data for machine learning

Kevin R. Coombes, Guy N. Brock, Zachary B. Abrams, 2020, F1000Research.

Mutation of TGFβ-RII eliminates NSAID cancer chemoprevention

K. Coombes, C. Croce, P. Gasparini, 2017, Oncotarget.

Genetic variants in thyroid cancer distant metastases.

K. Coombes, T. Giordano, C. Croce, 2016, Endocrine-related cancer.

Serum proteomics profiling—a young technology begins to mature

Jeffrey S. Morris, Kevin R Coombes, Jianhua Hu, 2005, Nature Biotechnology.

Reproducibility of SELDI Spectra Across Time and Laboratories

Jeffrey S. Morris, Kevin R. Coombes, Robert C. Bast, 2011, Cancer informatics.

Co‐Expression Analysis Reveals Mechanisms Underlying the Varied Roles of NOTCH1 in NSCLC

K. Coombes, D. Carbone, Ferdinando Cerciello, 2019, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

and determinants of response in myeloid malignancies

James M. Bogenberger, K. Coombes, G. Ahmann, 2014 .

Thresher: determining the number of clusters while removing outliers

Zachary B. Abrams, K. Coombes, S. Kornblau, 2018, BMC Bioinformatics.

Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies

Kevin R. Coombes, Lynne V. Abruzzo, Jing Wang, 2004, Bioinform..

Characterizing the Molecular Spatial and Temporal Field of Injury in Early-Stage Smoker Non–Small Cell Lung Cancer Patients after Definitive Surgery by Expression Profiling

Edward S. Kim, K. Coombes, Jing Wang, 2012, Cancer Prevention Research.

Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups

Jiexin Zhang, Kevin R. Coombes, K. Coombes, 2012, BMC Bioinformatics.

Abnormal expression of FLI1 protein is an adverse prognostic factor in acute myeloid leukemia.

Steven M Kornblau, Kevin R Coombes, K. Coombes, 2011, Blood.

Application of protein lysate microarrays to molecular marker verification and quantification

Zhenlin Ju, Kevin Coombes, Rahul Mitra, 2005, Proteome Science.

Biological properties of ligand-dependent activation of the MET receptor kinase in acute myeloid leukemia

K. Coombes, A. Look, A. Kentsis, 2014, Leukemia.

BIOLOGY-DRIVEN CLUSTERING OF MICROARRAY DATA

H. Sung, K. Coombes, K. Baggerly, 2002 .

University of Groningen Epidermal growth factor receptor is expressed and active in a subset of acute myeloid leukemia

K. Coombes, S. Kornblau, Y. Qiu, 2017 .

The arithmetic of zero cycles on surfaces with geometric genus and irregularity zero

K. Coombes, 1991 .

Motifs,L-functions, and theK-cohomology of rational surfaces over finite fields

K. Coombes, 1987 .

Every rational surface is separably split

Kevin R. Coombes, K. Coombes, 1988 .

Zero cycles on del Pezzo surfaces over local fields

K. Coombes, D. Muder, 1985 .

On SK1 of curves and kahler differentials

K. Coombes, 1985 .

RelativeK-theory and vector bundles on certain singular varieties

K. Coombes, V. Srinivas, 1982 .

On the K-theory of curves over finite fields

K. Coombes, 1988 .

Hurwitz families and arithmetic Galois groups

Kevin R. Coombes, David Harbater, K. Coombes, 1985 .

Genes suppressed by DNA methylation in non-small cell lung cancer reveal the epigenetics of epithelial–mesenchymal transition

J. Weinstein, K. Coombes, Jing Wang, 2014, BMC Genomics.

Perifosine plus docetaxel in patients with platinum and taxane resistant or refractory high-grade epithelial ovarian cancer.

K. Coombes, G. Mills, R. Bast, 2012, Gynecologic oncology.

A protocol to evaluate RNA sequencing normalization methods

Philip R. O. Payne, Kun Huang, Travis S. Johnson, 2019, BMC Bioinformatics.

Differential correlation across subpopulations of single cells in subtypes of acute myeloid leukemia

K. Coombes, G. Behbehani, Reginald L. McGee, 2022, bioRxiv.

Serial dilution curve: a new method for analysis of reverse phase protein array data

Li Zhang, Wenbin Liu, Li Mao, 2009, Bioinform..

Get Training Numbers

K. Coombes, K. Baggerly, 2008 .

Genomic signatures based on the NCI 60 cell lines do not predict patient response to chemotherapy

K. Coombes, K. Baggerly, Jing Wang, 2007 .

Bayesian Analysis of Mass Spectrometry Proteomic Data Using Wavelet‐Based Functional Mixed Models

Jeffrey S. Morris, Kevin R Coombes, Jeffrey S Morris, 2008, Biometrics.

High Expression of Autophagy Related Proteins Negatively Impacts Clinical Outcomes in Acute Myelogenous Leukemia–Time to Target Autophagy to Improve Therapy Outcomes?

K. Coombes, Nianxiang Zhang, M. Konopleva, 2011 .

Use of reverse phase protein microarrays to study protein expression in leukemia: technical and methodological lessons learned.

Steven M Kornblau, Kevin R Coombes, K. Coombes, 2011, Methods in molecular biology.

Proteomic Profiling of 150 Proteins in 511 Acute Myelogenous Leukemia (AML) Patient Samples Using Reverse Phase Proteins Arrays (RPPA) Reveals Recurrent Proteins Expression Signatures with Prognostic Implications

K. Coombes, Z. Ju, Nianxiang Zhang, 2008 .

Decomposing the Apoptosis Pathway Into Biologically Interpretable Principal Components

Min Wang, Kevin R. Coombes, Steven M. Kornblau, 2017, bioRxiv.

Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups

K. Coombes, Jiexin Zhang, 2012, BMC Bioinformatics.

Transcriptome Complexity Disentangled: A Regulatory Molecules Approach

Amir H. Asiaee, Zachary B. Abrams, K. Coombes, 2023, bioRxiv.

Molecular pathogenesis of lung cancer with translation to the clinic: M10-01

K. Coombes, S. Lam, J. Minna, 2007 .

Polychrome: Creating and Assessing Qualitative Palettes With Many Colors

Kevin R. Coombes, Guy N. Brock, Zachary B. Abrams, 2018, bioRxiv.

The Palaemonoid Shrimp Fauna (Crustacea: Decapoda: Caridea) of the Cobourg Peninsula, Northern Territory

K. Coombes, A. Bruce, 1995, The Beagle : Records of the Museums and Art Galleries of the Northern Territory.

Erratum: Stem cell-ness: A "magic marker" for cancer (Journal of Clinical Investigation (2005) 115 (1463-1467) DOI: 10.1172/JCI25455)

K. Coombes, G. Mills, John P. Lahad, 2005 .

Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays

Katerina Kechris, Ru-Fang Yeh, Yee Hwa Yang, 2008, BMC Genomics.

Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology

K. Coombes, K. Baggerly, 2009, 1010.1092.

Organ-Specific Differences in Gene Expression and Unigene Annotations Describing Source Material

Kevin R. Coombes, Gary L. Rosner, Jing Wang, 2004 .

Functional proteomic profiling of AML predicts response and survival *

K. Coombes, G. Mills, M. Andreeff, 2008 .

Biomarker expression patterns that correlate with high grade features in treatment naive, organ-confined prostate cancer.

K. Coombes, T. McDonnell, G. Prendergast, 2008 .

Malachite: A Gene Enrichment Meta-Analysis (GEM) Tool for ToppGene

Kevin R. Coombes, Zachary B. Abrams, Caitlin E. Coombes, 2019, bioRxiv.

Understanding the characteristics of mass spectrometry data through the use of simulation

Jeffrey S. Morris, K. Coombes, K. Baggerly, 2007, Cancer Informatics.

Analysis of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models

Jeffrey S. Morris, Kevin R. Coombes, Philip J. Brown, 2006 .

Use of a panel of proteomic markers to improve the sensitivity of CA125 for detecting stage I epithelial ovarian cancer

K. Coombes, R. Bast, E. Fung, 2008 .

Epidermal growth factor receptor is expressed and active in a subset of acute myeloid leukemia

K. Coombes, S. Kornblau, Y. Qiu, 2016, Journal of Hematology & Oncology.

Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia.

K. Coombes, M. Odenthal, K. Elenitoba-Johnson, 2023, Blood.

Alternative Probeset Definitions for Combining Microarray Data Across Studies Using Different Versions of Affymetrix Oligonucleotide Arrays

Jeffrey S. Morris, Chunlei Wu, Kevin R. Coombes, 2006 .

RNAi Screening Identifies BCL-XL As An Erythroid Lineage-Specific 5-Azacytidine Sensitizer While the BCL-2/BCL-XL/BCL-W Inhibitor ABT-737 Results in More Universal Sensitization in Leukemia Cells,

K. Coombes, S. Kornblau, R. Mesa, 2011 .

High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient pdf

Arindam Banerjee, Samet Oymak, Kevin R. Coombes, 2018, ArXiv.

Intratumoral heterogeneity and clonal evolution induced by HPV integration 1

K. Coombes, Sara Goodwin, F. Sedlazeck, 2023 .

K. Coombes, L. Rassenti, T. Kipps, 2009, Blood.

Characterizing the Molecular Spatial and Temporal Field of Injury in Early-Stage Smoker Non–Small Cell Lung Cancer Patients after Definitive Surgery by Expression Profiling

Edward S. Kim, K. Coombes, Jing Wang, 2012, Cancer Prevention Research.

Cardiomyocyte PDGFR-beta signaling is an essential component of the mouse cardiac response to load-induced stress.

K. Coombes, Lawrence Buja, M. Entman, 2010, The Journal of clinical investigation.

Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer.

K. Coombes, G. Mills, R. Akbani, 2016, Seminars in oncology.

Sequences of Events from the Electronic Medical Record and the Onset of Infection

Caitlin E. Coombes, K. Coombes, Naleef Fareed, 2022, Chemistry & biodiversity.

integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory

K. Coombes, P. Tong, 2012, Bioinform..

VEGF/VEGFR-2 Upregulates EZH2 Expression in Lung Adenocarcinoma Cells and EZH2 Depletion Enhances the Response to Platinum-Based and VEGFR-2–Targeted Therapy

Milind B. Suraokar, K. Coombes, Jing Wang, 2014, Clinical Cancer Research.

Individualized molecular medicine: linking functional proteomics to select therapeutics targeting the PI3K pathway for specific patients.

K. Coombes, G. Mills, Yiling Lu, 2008, Advances in experimental medicine and biology.

Survivin is highly expressed in CD34(+)38(-) leukemic stem/progenitor cells and predicts poor clinical outcomes in AML.

K. Coombes, G. Mills, Nianxiang Zhang, 2012, Blood.

On Heterogeneous Spaces

K. Coombes, David Grant, 1989 .

Reproducibility of SELDI Spectra Across Time and Laboratories

Jeffrey S. Morris, K. Coombes, K. Baggerly, 2011, Cancer informatics.

From the Selectedworks of Jeffrey S. Morris the Importance of Experimental Design in Proteomic Mass Spectrometry Experiments: Some Cautionary Tales the Importance of Experimental Design in Proteomic Mass Spectrometry Experiments: Some Cautionary Tales

Jeffrey S. Morris, K. Coombes, K. Baggerly, 2022 .

Proteomic Profiling of 128 Proteins In 194 Acute Lymphocytic Leukemia (ALL) Patients Using Reverse Phase Proteins Arrays (RPPA) Reveals Recurrent Proteins Expression Signatures with Prognostic Implications

K. Coombes, Nianxiang Zhang, H. Kantarjian, 2010 .

Survival Prediction In High Dimensional Datasets – Comparative Evaluation Of Lasso Regularization and Random Survival Forests

K. Coombes, Nianxiang Zhang, E. Bernstam, 2013 .

Genetic Algorithms for Feature Selection

K. Coombes, 2018 .

Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL

Bani K. Mallick, Kevin R. Coombes, David L. Gold, 2007, Briefings Bioinform..

Overexpression of HIF1 Alpha Predicts Worse Overall and Event-Free Survival in Patients with Philadelphia Chromosome-Negative Precursor B-Lymphoblastic Leukemia

K. Coombes, Nianxiang Zhang, M. Konopleva, 2008 .

Latent feature decompositions for integrative analysis of diverse high-throughput genomic data

Michael Peyton, John D. Minna, Veerabhadran Baladandayuthapani, 2012, Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

SITH: an R package for visualizing and analyzing a spatial model of intratumor heterogeneity

Kevin R. Coombes, Amir H. Asiaee, Phillip B. Nicol, 2020, bioRxiv.