Skip to content. | Skip to navigation

National Cancer Institute U.S. National Institutes of Health


Personal tools

You are here: Home / Sites / The University of Texas MD Anderson Cancer Center / Farley, Paul Joseph

Farley, Paul Joseph (B.S.)

Staff, The University of Texas MD Anderson Cancer Center, 206-667-1961

Contact Information

Fax: 206-667-2537

To update contact information, please visit the Data Management and Coordinating Center.

Open Protocols

Protocol Name Biomarkers Datasets
Pancreatic Reference Set Application: Samir Hanash-MD Anderson (2017) 0 0
A Biomarker Bakeoff in Early Stage Pancreatic Cancer 0 0
Affinity-based strategies to fast track development of colon cancer biomarkers 0 0
Biomarkers of Risk for Colorectal Neoplasia (Team Project #2) 0 0
Identification of biomarkers for lung cancer in never smokers 0 29

Closed Protocols

Protocol Name Biomarkers Datasets
EDRN-WHI Pre-Clinical Colon Ca Specimens 0 9
Validation of Protein Markers for Lung Cancer Using CARET Sera and Proteomics Techniques 6 1
Preliminary Validation of Biomarkers for the Detection of Colorectal Adenomas (Team Project #1) 1 0
Standard Specimen Reference Set: Lung 0 0


Publication Name PubMed ID Journal
Identification of a Specific Vimentin Isoform That Induces an Antibody Response in Pancreatic Cancer. 18769604 Biomark Insights
Identification of beta-tubulin isoforms as tumor antigens in neuroblastoma. 11051243 Clin. Cancer Res.
Integrated mass spectrometry-based analysis of plasma glycoproteins and their glycan modifications. 21372808 Nat Protoc
Operomics: molecular analysis of tissues from DNA to RNA to protein. 11097332 Clin. Chem. Lab. Med.
Proteomics in early detection of cancer. 11568117 Clin. Chem.
A proteomic approach to the identification of lung cancer markers. 11790896 Dis. Markers
Biomedical applications of two-dimensional electrophoresis using immobilized pH gradients: current status. 10786892 Electrophoresis
A meeting of minds in proteomics. 11822353 Proteomics
Operomics: integrated genomic and proteomic profiling of cells and tissues. 15251063 Brief Funct Genomic Proteomic
2-D or not 2-D--is there a future for 2-D gels in proteomics? Insights from the York proteomics meeting. 11678032 Proteomics
Global profiling of gene expression in cancer using genomics and proteomics. 11804268 Curr. Opin. Mol. Ther.
Proteomic approaches within the NCI early detection research network for the discovery and identification of cancer biomarkers. 11708463 Ann. N. Y. Acad. Sci.
Integrating cancer genomics and proteomics in the post-genome era. 11788993 Proteomics
Proteomics approaches to uncover the repertoire of circulating biomarkers for breast cancer. 12882525 J Mammary Gland Biol Neoplasia
Contributions of proteome profiling to the molecular analysis of cancer. 12625782 Technol. Cancer Res. Treat.
Identification of tumor-associated antigens using proteomics. 12625784 Technol. Cancer Res. Treat.
Harnessing immunity for cancer marker discovery. 12511908 Nat. Biotechnol.
Multi-dimensional liquid phase based separations in proteomics. 12659729 J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.
The Human Proteome Organization: a mission to advance proteome knowledge. 12169681 Mol. Cell Proteomics
Molecular analysis of cancer using DNA and protein microarrays. 12908549 Adv. Exp. Med. Biol.
Disease proteomics. 12634796 Nature
Isoform analysis of LC-MS/MS data from multidimensional fractionation of the serum proteome. 18419151 J. Proteome Res.
Plasma proteome profiling of a mouse model of breast cancer identifies a set of up-regulated proteins in common with human breast cancer cells. 18311905 J. Proteome Res.
Innovative proteomic approaches for cancer biomarker discovery. 17907570 BioTechniques
Mining the plasma proteome for cancer biomarkers. 18385731 Nature
High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy. 17184556 Breast Cancer Res.
A mouse to human search for plasma proteome changes associated with pancreatic tumor development. 18547137 PLoS Med.
Evaluation of known oncoantibodies, HER2, p53, and cyclin B1, in prediagnostic breast cancer sera. 22715141 Cancer Prev Res (Phila)
Increased throughput and reduced carryover of mass spectrometry-based proteomics using a high-efficiency nonsplit nanoflow parallel dual-column capillary HPLC system. 18512973 J. Proteome Res.
A mouse plasma peptide atlas as a resource for disease proteomics. 18522751 Genome Biol.
Mouse model of human ovarian endometrioid adenocarcinoma based on somatic defects in the Wnt/beta-catenin and PI3K/Pten signaling pathways. 17418409 Cancer Cell
Cleavage of endoplasmic reticulum proteins in hepatocellular carcinoma: Detection of generated fragments in patient sera. 16762624 Gastroenterology
Ubiquitin COOH-terminal hydrolase 1: a biomarker of renal cell carcinoma associated with enhanced tumor cell proliferation and migration. 17200335 Clin. Cancer Res.
Proteomic approaches for cancer biomarker discovery in plasma. 17941811 Expert Rev Proteomics
Unraveling the complex proteome for biomarker discovery in gastrointestinal and liver diseases. 17064703 Gastroenterology
Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. 17696519 J. Proteome Res.
Discovery of cancer biomarkers through the use of mouse models. 17320282 Cancer Lett.
Microparticles from ovarian carcinomas are shed into ascites and promote cell migration. 22315094 Int. J. Gynecol. Cancer
Integration of proteomics into systems biology of cancer. 22407608 Wiley Interdiscip Rev Syst Biol Med
Comprehensive proteomic profiling of aldehyde dehydrogenases in lung adenocarcinoma cell lines. 22110949 Int J Proteomics
Plasma proteome profiles associated with inflammation, angiogenesis, and cancer. 21589862 PLoS ONE
Isoelectric focusing nonporous RP HPLC: a two-dimensional liquid-phase separation method for mapping of cellular proteins with identification using MALDI-TOF mass spectrometry. 10740846 Anal. Chem.
Protein based microarrays: a tool for probing the proteome of cancer cells and tissues. 11721639 Proteomics
Targets of the tumor suppressor miR-200 in regulation of the epithelial-mesenchymal transition in cancer. 21987723 Cancer Res.
Tumor microenvironment-derived proteins dominate the plasma proteome response during breast cancer induction and progression. 21653680 Cancer Res.
Virtual genome scan: a tool for restriction landmark-based scanning of the human genome. 11483587 Genome Res.
Application of proteomics to cancer early detection. 22157286 Cancer J
A minimal critical region of the 8p22-23 amplicon in esophageal adenocarcinomas defined using sequence tagged site-amplification mapping and quantitative polymerase chain reaction includes the GATA-4 gene. 10728696 Cancer Res.
Concordant release of glycolysis proteins into the plasma preceding a diagnosis of ER+ breast cancer. 22367215 Cancer Res.
Emerging molecular biomarkers--blood-based strategies to detect and monitor cancer. 21364687 Nat Rev Clin Oncol
Profiling of the cell surface proteome. 14625857 Proteomics
Harnessing the immune response for cancer detection. 21454417 Cancer Epidemiol. Biomarkers Prev.
Making sense of microarray data to classify cancer. 14597962 Pharmacogenomics J.
Gene-expression profiles predict survival of patients with lung adenocarcinoma. 12118244 Nat. Med.
Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function. 12493773 J. Biol. Chem.
Gene expression patterns define pathways correlated with loss of differentiation in lung adenocarcinomas. 12681502 FEBS Lett.
Profiling of pathway-specific changes in gene expression following growth of human cancer cell lines transplanted into mice. 12844362 Genome Biol.
Accurate molecular classification of human cancers based on gene expression using a simple classifier with a pathological tree-based framework. 14578198 Am. J. Pathol.
Microarrays of tumor cell derived proteins uncover a distinct pattern of prostate cancer serum immunoreactivity. 14595819 Proteomics
Molecular profiling of pancreatic adenocarcinoma and chronic pancreatitis identifies multiple genes differentially regulated in pancreatic cancer. 12750293 Cancer Res.
Global and specific translational control by rapamycin in T cells uncovered by microarrays and proteomics. 11943782 J. Biol. Chem.
Discordant protein and mRNA expression in lung adenocarcinomas. 12096112 Mol. Cell Proteomics
Mining gene expression databases for association rules. 12499296 Bioinformatics
Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS. 16889424 J. Proteome Res.
The gene for the axonal cell adhesion molecule TAX-1 is amplified and aberrantly expressed in malignant gliomas. 11280781 Cancer Res.
Proteomic analysis of cytokeratin isoforms uncovers association with survival in lung adenocarcinoma. 12192603 Neoplasia
Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. 16396501 J. Proteome Res.
Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. 16525410 Nat. Biotechnol.
Proteomic analysis of lung adenocarcinoma: identification of a highly expressed set of proteins in tumors. 12114434 Clin. Cancer Res.
Identification of androgen-regulated genes in the prostate cancer cell line LNCaP by serial analysis of gene expression and proteomic analysis. 11721644 Proteomics
A database of protein expression in lung cancer. 11721642 Proteomics
Two messenger RNAs and five isoforms for Po66-CBP, a galectin-8 homolog in a human lung carcinoma cell line. 11675018 Gene
The major CD9 and CD81 molecular partner. Identification and characterization of the complexes. 11278880 J. Biol. Chem.
A distinct repertoire of autoantibodies in hepatocellular carcinoma identified by proteomic analysis. 12096119 Mol. Cell Proteomics
Transforming properties of a Q18-->E mutation of the microtubule regulator Op18. 12242154 Cancer Cell
A wide range of protein isoforms in serum and plasma uncovered by a quantitative intact protein analysis system. 16047307 Proteomics
Expression of matrix metalloproteinase 9 (MMP-9/gelatinase B) in adenocarcinomas strongly correlated with expression of immune response genes. 12954092 In Silico Biol. (Gedrukt)
Proteomic analysis of eIF-5A in lung adenocarcinomas. 12687616 Proteomics
Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. 16104056 Proteomics
A functional annotation of subproteomes in human plasma. 16104058 Proteomics
The hepatocyte nuclear factor 3 alpha gene, HNF3alpha (FOXA1), on chromosome band 14q13 is amplified and overexpressed in esophageal and lung adenocarcinomas. 12234996 Cancer Res.
Protein profiles associated with survival in lung adenocarcinoma. 14573703 Proc. Natl. Acad. Sci. U.S.A.
Overexpression of oncoprotein 18 correlates with poor differentiation in lung adenocarcinomas. 12644570 Mol. Cell Proteomics
Increased C-CRK proto-oncogene expression is associated with an aggressive phenotype in lung adenocarcinomas. 12970743 Oncogene
RANTES expression is a predictor of survival in stage I lung adenocarcinoma. 12473593 Clin. Cancer Res.
A proteomics platform combining depletion, multi-lectin affinity chromatography (M-LAC), and isoelectric focusing to study the breast cancer proteome. 21513341 Anal. Chem.
Confounding effects of hormone replacement therapy in protein biomarker studies. 21037107 Cancer Epidemiol. Biomarkers Prev.
Intact-protein analysis system for discovery of serum-based disease biomarkers. 21468941 Methods Mol. Biol.
Mining the plasma proteome for disease applications across seven logs of protein abundance. 21062094 J. Proteome Res.

To update protocols, publications, biomarkers, or science data, please contact the Informatics Center.


1100 Fairview Avenue North ,M5-A864
Fred Hutchinson Cancer Research Center

To update addresses, please visit the Data Management and Coordinating Center.

Announcement 6/2/2018
Thank you to everyone to made the 10th EDRN Scientific Workshop a success. The next event is the 33rd EDRN Steering Committee Meeting from September 5-6, 2018 in Boston, MA. Details will be available soon.

Announcement 6/1/2018

Dr. Sudhir Srivastava was honored with the 2017 Human Proteome Organization (HUPO) Award for a Distinguished Scientist in Clinical and Translational Proteomics. Please join us in congratulating him on his accomplishments and contributions. The awards were presented at HUPO 2017 in Dublin, Ireland and the winners were present to provide a small talk during the Awards Ceremony and HUPO Lectures.