Featured Publications

EwyRaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.. Zhang B, Hu S, Baskin E, Patt A, Siddiqui JK, Mathé EA. Metabolites. 2018 Feb 22;8(1). pii: E16. doi:10.3390/metabo8010016. PubMed PMID: 29470400.

 

EwyALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data. Elizabeth Baskin, Rick Farouni, Ewy A. Mathe. Bioinformatics. 2016 Dec 22. pii: btw688. doi: 10.1093/bioinformatics/btw688.

 

EwyInteractome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Kieffer-Kwon KR *, Tang Z *, Mathe E *, Qian J *, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R. * equal contribution authors. Cell. 2013 Dec 19.

indexNoninvasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer. Mathé EA *, Patterson AD *, Haznadar M *, Manna SK, Krausz KW, Bowman ED, Shields PG, Idle JR, Smith PB, Anami K, Kazandjian DG, Hatzakis E, Gonzalez FJ, Harris CC. * equal contribution authors. Cancer Res. 2014 Jun 15.

 

Other Publications

Zhang B, Hu S, Baskin E, Patt A, Siddiqui JK, Mathé EA. RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites. Metabolites. 2018 Feb 22;8(1). pii: E16. doi:10.3390/metabo8010016. PubMed PMID: 29470400.

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. Accepted in BMC Bioinformatics Feb 2018. Preprint at arXiv:1802.10588.

Ozer HG, El-Gamal D, Powell B, Hing ZA, Blachly JS, Harrington B, Mitchell S, Grieselhuber NR, Williams K, Lai TH, Alinari L, Baiocchi RA, Brinton L, Baskin E, Cannon M, Beaver L, Goettl VM, Lucas DM, Woyach JA, Sampath D, Lehman AM, Yu L, Zhang J, Ma Y, Zhang Y, Spevak W, Shi S, Severson P, Shellooe R, Carias H, Tsang G, Dong K, Ewing T, Marimuthu A, Tantoy C, Walters J, Sanftner L, Rezaei H, Nespi M, Matusow B, Habets G, Ibrahim P, Zhang C, Mathé EA, Bollag G, Byrd JC, Lapalombella R. BRD4 profiling identifies critical Chronic Lymphocytic Leukemia oncogenic circuits and reveals sensitivity to PLX51107, a novel structurally distinct BET inhibitor. Cancer Discov. 2018 Jan 31. pii: CD-17-0902. doi: 10.1158/2159-8290.CD-17-0902. [Epub ahead of print] PubMed PMID: 29386193.

Haznadar M, Mathé EA. Experimental and Study Design Considerations for Uncovering Oncometabolites. Methods Mol Biol. 2017;1513:37-47. PMID: 27807829

Haznadar M, Cai Q, Krausz KW, Bowman ED, Margono E, Noro R, Thompson MD, Mathé EA, Munro HM, Steinwandel MD, Gonzalez FJ, Blot WJ, Harris CC. Urinary Metabolite Risk Biomarkers of Lung Cancer: A Prospective Cohort Study. Cancer Epidemiol Biomarkers Prev. 2016 Mar 24. pii: cebp.1191.2015.

Robles AI, Kanai Y, Mathé E, Okayama H, Schetter A, Brown D, Petersen D, Bowman ED, Noro R, Welsh J, Edelman D, Stevenson H, Tsuchiya N, Kohno T, Skaug V Mollerup S, Haugen A, Meltzer P, Yokota J, Harris . An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers.  J Thorac Oncol. 2015 Jul; Jul;10(7):1037-48.

Qian J*, Wang Q*, Dose M*, Pruett N*, Kieffer-Kwon K*, Resch W, Liang G, Tang Z, Mathé E, Benner C, Dubois W, Nelson S, Vian L, Oliveira TY, Jankovic M, Hakim O, Gazumyan A, Pavri R, Awasthi P, Song B, Liu G, Chen L, Zhu S, Feigenbaum L, Staudt L, Murre C, Ruan Y, Robbiani DF, Pan-Hammarstrom Q, Nussenzweig MC, Casellas R. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell. 2014 Dec 3. * Equal contribution authors.

Trauma A, Putluri N, Mishra1 P, Mathé EA, Dorsey TH, Yi M, Wallace TA, Issaq HJ, Zhou M, Killian JK, Stevenson HS, Karoly ED, Chan K, Samanta S, Prieto D, Hsu TY.T., Kurley SJ, Putluri V, Sonavane R, Edelman DC, Wulff J, Starks AM, Yang Y, Kittles RA, Yfantis HG, Lee DH, Ioffe OB, Schiff R, Stephens RM, Meltzer PS, Veenstra TD, Westbrook TF, Sreekumar A, and Stefan Ambs S. MYC-driven 2-hydroxyglutarate associates with poor prognosis in breast cancer. J Clin Invest. 2014 Jan 2;124(1):398-412.

Zhao Y, Schetter AJ, Yang GB, Nguyen G, Mathé EA, Li P, Cai H, Yu L, Liu F, Hang D, Yang H, Wang XW, Ke Y, Harris CC. microRNA and inflammatory gene expression as prognostic marker for overall survival in esophageal squamous cell carcinoma. Int J Cancer. 2013 Jun 15;132(12):2901-9.

Mathé E, Nguyen GH, Funamizu N, He P, Moake M, Croce CM, Hussain SP. Inflammation regulates microRNA expression in cooperation with p53 and nitric oxide. Int J Cancer. 2012 Aug 1;131(3):760-5.

Hakim O, Resch W, Yamane A, Klein I, Kieffer-Kwon KR, Jankovic M, Oliveira T, Bothmer A, Voss TC, Ansarah-Sobrinho C, Mathe E, Liang G, Cobell J, Nakahashi H, Robbiani DF, Nussenzweig A, Hager GL, Nussenzweig MC, Casellas R. DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature. 2012 Feb 7;484(7392):69-74

Saito M, Schetter AJ, Mollerup S, Kohno T, Skaug V, Bowman ED, Mathé EA, Takenoshita S, Yokota J, Haugen A, Harris CC. The association of microRNA expression with prognosis and progression in early-stage, non-small cell lung adenocarcinoma: a retrospective analysis of three cohorts. Clin Cancer Res. 2011 Apr 1;17(7):1875-82.

Nguyen GH, Schetter AJ, Chou DB, Bowman ED, Zhao R, Hawkes JE, Mathé E, Kumamoto K, Zhao Y, Budhu A, Hagiwara N, Wang XW, Miyashita M, Casson AG, Harris CC. Inflammatory and microRNA Gene Expression as Prognostic Classifiers of Barrett’s Associated Esophageal Adenocarcinoma. Clin Cancer Res. 2010 December; 16 5824-5834.

Mathé EA, Nguyen GH, Bowman ED, Zhao Y, Budhu A, Schetter AJ, Braun R, Reimers M, Kumamoto K, Hughes D, Altorki NK, Casson AG, Liu C-G, Wang XW, Yanaihara N, Hagiwara N, Dannenberg AJ, Miyashita M, Croce CM, Harris CC. MiRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus and associations with survival. Clin Cancer Res. 2009 Oct 1;15(19):6192-200. Epub 2009 Sep 29.

Fujita K, Mondal AM, Horikawa I, Nguyen GH, Kumamoto K, Sohn JJ, Bowman ED, Mathe EA, Schetter AJ, Pine SR, Ji H, Vojtesek B, Bourdon J-C, Lane DP, Harris CC. p53 isoforms, Δ133p53 and p53β, are endogenous regulators of replicative cellular senescence. Nat Cell Biol. 2009 Sep;11(9):1135-42. Epub 2009 Aug 23.

Seike M, Goto A, Okano T, Bowman ED, Schetter AJ, Horikawa I, Mathe EA, Jen J, Yang P, Sugimura H, Gemma A, Kudoh S, Croce CM, Harris CC. MiR-21 is an EGFR-regulated anti-apoptotic factor in lung cancer from never-smokers. Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12085-90. Epub 2009 Jul 13.

Schetter AJ, Nguyen GH, Bowman ED, Mathe E, Yuen ST, Hawkes J, Croce CM, Leung SY, Harris CC. Association of inflammation-related and microRNA gene expression with cancer specific mortality of colon adenocarcinoma. Clin Cancer Res. 2009 Sep 15;15(18):5878-87. Epub 2009 Sep 8.

Masso M, Mathe E, Parvez N, Hijazi K, and Vaisman II. Modeling the functional consequences of single residue replacements in Bacteriophage f1 Gene V Protein. Protein Eng Des Sel. 2009 Nov; 22(11):665-71.

Hussain SP, He P, Subleski J, Hofseth LJ, Trivers GE, Mechanic L, Hofseth AB, Bernard M, Schwank J, Nguyen G, Mathe E, Djurickovic D, Haines D, Weiss J, Back T, Gruys E, Laubach VE, Wiltrout RH, Harris CC. Nitric oxide is a key component in inflammation-accelerated tumorigenesis. Cancer Res. 2008 Sep 1; 68(17):7130-6.

Petitjean A, Mathe E, Kato S, Ishioka C, Tavtigian SV, Hainaut P, Olivier M. Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Hum Mutat. 2007 Jun; 28(6): 622-629.

Mathe E, Olivier M, Kato S, Ishioka C, Vaisman I, Hainaut P. Predicting the transactivation activity of p53 missense mutants using a four-body potential score derived from Delaunay tessellations. Hum Mutat. 2006 Jun; 28(6):622-9.

Mathe E, Olivier M, Kato S, Ishioka C, Hainaut P, Tavtigian SV. Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of 3 sequence analysis based methods. Nucleic Acids Res. 2006 Mar; 6;34(5):1317-25.

Mathe E, Grefenstette J. Polyoptimizing Genetic Algorithm for Feature Subset Selection; 36th SYMPOSIUM ON THE INTERFACE: Computational Biology and Bioinformatics Proceedings, Baltimore, MD. 2004.