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List of works by Kevin R. Coombes

A Semantic Web management model for integrative biomedical informatics

scientific article

A Technical Assessment of the Utility of Reverse Phase Protein Arrays for the Study of the Functional Proteome in Non-microdissected Human Breast Cancers

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A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays

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A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples

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A comprehensive assessment of p53-responsive genes following adenoviral-p53 gene transfer in Bcl-2-expressing prostate cancer cells

scientific article published on March 2004

A two-gene signature, SKI and SLAMF1, predicts time-to-treatment in previously untreated patients with chronic lymphocytic leukemia

scientific article

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

scientific article published on 13 September 2011

An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance

scientific article published on 22 October 2012

Analysis of Mass Spectrometry Profiles of the Serum Proteome

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

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Application of protein lysate microarrays to molecular marker verification and quantification

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Applications of beta-mixture models in bioinformatics

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

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Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer

Bayesian analysis of mass spectrometry proteomic data using wavelet-based functional mixed models

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Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE.

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Blasted cell line names

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

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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

scientific article published on 19 October 2012

Chemoprevention of skin carcinogenesis by phenylretinamides: retinoid receptor-independent tumor suppression

scientific article published in February 2006

Clinical evaluation of chemotherapy response predictors developed from breast cancer cell lines

scientific article

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

scientific article published on 15 August 2012

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

scientific article

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

scientific article published on 10 July 2019

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

scientific article published in July 2004

Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery

scientific article published in May 2005

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

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

scientific article published on 31 October 2006

Exploratory analysis of the copy number alterations in glioblastoma multiforme

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

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Expression of autotaxin and lysophosphatidic acid receptors increases mammary tumorigenesis, invasion, and metastases

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

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Functional characterization of CLPTM1L as a lung cancer risk candidate gene in the 5p15.33 locus

scientific article published in 2012

Functional proteomic analysis of advanced serous ovarian cancer using reverse phase protein array: TGF-beta pathway signaling indicates response to primary chemotherapy

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Functional proteomic profiling of AML predicts response and survival

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Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer

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

scientific article published on January 2007

Gene sequence signatures revealed by mining the UniGene affiliation network

scientific article published on 8 December 2005

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

scientific article published on 27 December 2012

HOX expression patterns identify a common signature for favorable AML.

scientific article published on 31 July 2008

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

scientific article published on 13 February 2003

High-resolution serum proteomic patterns for ovarian cancer detection

scientific article published in December 2004

Highly phosphorylated FOXO3A is an adverse prognostic factor in acute myeloid leukemia

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

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

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Identification of cell cycle regulatory genes as principal targets of p53-mediated transcriptional repression

scientific article published on 23 June 2006

Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays

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Identifying differentially expressed genes in cDNA microarray experiments.

scientific article published in January 2001

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

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Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform

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

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Independent Validation of a Model Using Cell Line Chemosensitivity to Predict Response to Therapy ⬇️

scientific article published on August 20, 2013

KEAP1-Dependent Synthetic Lethality Induced by AKT and TXNRD1 Inhibitors in Lung Cancer ⬇️

scientific article published on July 3, 2013

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

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Low expression of PP2A regulatory subunit B55α is associated with T308 phosphorylation of AKT and shorter complete remission duration in acute myeloid leukemia patients

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

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

scientific article published on 04 July 2016

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

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MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia

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Microarrays: handling the deluge of data and extracting reliable information

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Microarrays: retracing steps

scientific article published on 01 November 2007

Modeling significance and reproducibility on high-density cDNA microarrays

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

scientific article published on 15 September 2006

Molecular signatures associated with clinical outcome in patients with high-risk head-and-neck squamous cell carcinoma treated by surgery and radiation

scientific article published on 10 November 2005

Monte Carlo calculations and measurements of absorbed dose per monitor unit for the treatment of uveal melanoma with proton therapy.

scientific article published on 25 February 2008

Non-parametric quantification of protein lysate arrays

scientific article published on 28 June 2007

Obtaining reliable information from minute amounts of RNA using cDNA microarrays

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

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PKCδRegulates Translation Initiation through PKR and eIF2αin Response to Retinoic Acid in Acute Myeloid Leukemia Cells ⬇️

scientific article published on July 15, 2012

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

scientific article published on 06 April 2012

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

scientific article

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

scientific article published in February 2005

PrepMS: TOF MS data graphical preprocessing tool

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Prognostic biomarkers for esophageal adenocarcinoma identified by analysis of tumor transcriptome

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Prognostic role of a multigene reverse transcriptase-PCR assay in patients with node-negative breast cancer not receiving adjuvant systemic therapy.

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

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Proteomic profiling identifies distinct protein patterns in acute myelogenous leukemia CD34+CD38- stem-like cells

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

scientific article published on 6 September 2012

Proteomic profiling identifies pathways dysregulated in non-small cell lung cancer and an inverse association of AMPK and adhesion pathways with recurrence

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Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization

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RPPAML/RIMS: a metadata format and an information management system for reverse phase protein arrays

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Real-time gene expression: statistical challenges in design and inference

scientific article published in July 2008

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

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RefSeq refinements of UniGene-based gene matching improve the correlation of expression measurements between two microarray platforms

scientific article published in January 2006

Relax with CouchDB--into the non-relational DBMS era of bioinformatics

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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

scientific article published on 02 December 2008

Reproducibility of SELDI Spectra Across Time and Laboratories

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

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Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients

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

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SIBER: systematic identification of bimodally expressed genes using RNAseq data

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

scientific article published in 2022

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

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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.

scientific article

Serum proteomics profiling—a young technology begins to mature

scientific article published on 01 March 2005

Signal in Noise: Evaluating Reported Reproducibility of Serum Proteomic Tests for Ovarian Cancer

scientific article published on 01 February 2005

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

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

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Statistical contributions to proteomic research

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

scientific article published on June 2005

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

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The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales

scientific article published in February 2005

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

scientific article

Thirty biologically interpretable clusters of transcription factors distinguish cancer type

scientific article published on 11 October 2018

Tissue-Specific Function of Lymph Node Fibroblastic Reticulum Cells

scientific article published on 01 January 2006

Transformation of human mesenchymal cells and skin fibroblasts into hematopoietic cells

scientific article

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

scientific article published on January 2011

Variable slope normalization of reverse phase protein arrays

scientific article published on 31 March 2009

What Information Should Be Required to Support Clinical "Omics" Publications?

scientific article published on 01 May 2011

Zonal heterogeneity for gene expression in human pancreatic carcinoma

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

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

scientific article published on May 2009

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

scientific article published on 14 April 2010

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