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Items: 17

1.

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

Siddiqui JK, Baskin E, Liu M, Cantemir-Stone CZ, Zhang B, Bonneville R, McElroy JP, Coombes KR, Mathé EA.

BMC Bioinformatics. 2018 Mar 5;19(1):81. doi: 10.1186/s12859-018-2085-6.

2.

RaMP: 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.

3.

BRD4 Profiling Identifies Critical Chronic Lymphocytic Leukemia Oncogenic Circuits and Reveals Sensitivity to PLX51107, a Novel Structurally Distinct BET Inhibitor.

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.

Cancer Discov. 2018 Apr;8(4):458-477. doi: 10.1158/2159-8290.CD-17-0902. Epub 2018 Jan 31.

4.

ALTRE: workflow for defining ALTered regulatory elements using chromatin accessibility data.

Baskin E, Farouni R, Mathé EA.

Bioinformatics. 2017 Aug 15;33(16):2609. doi: 10.1093/bioinformatics/btx386. No abstract available.

5.

ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data.

Baskin E, Farouni R, Mathé EA.

Bioinformatics. 2017 Mar 1;33(5):740-742. doi: 10.1093/bioinformatics/btw688. Erratum in: Bioinformatics. 2017 Aug 15;33(16):2609.

6.

Experimental and Study Design Considerations for Uncovering Oncometabolites.

Haznadar M, Mathé EA.

Methods Mol Biol. 2017;1513:37-47. Review.

PMID:
27807829
7.

Urinary Metabolite Risk Biomarkers of Lung Cancer: A Prospective Cohort Study.

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.

Cancer Epidemiol Biomarkers Prev. 2016 Jun;25(6):978-86. doi: 10.1158/1055-9965.EPI-15-1191. Epub 2016 Mar 24.

8.

An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers.

Robles AI, Arai E, Mathé EA, Okayama H, Schetter AJ, Brown D, Petersen D, Bowman ED, Noro R, Welsh JA, Edelman DC, Stevenson HS, Wang Y, Tsuchiya N, Kohno T, Skaug V, Mollerup S, Haugen A, Meltzer PS, Yokota J, Kanai Y, Harris CC.

J Thorac Oncol. 2015 Jul;10(7):1037-48. doi: 10.1097/JTO.0000000000000560.

9.

Noninvasive 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.

Cancer Res. 2014 Jun 15;74(12):3259-70. doi: 10.1158/0008-5472.CAN-14-0109. Epub 2014 Apr 15.

10.

MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis.

Terunuma A, Putluri N, Mishra 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, 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, Ambs S.

J Clin Invest. 2014 Jan;124(1):398-412. doi: 10.1172/JCI71180. Epub 2013 Dec 9.

11.

microRNA and inflammatory gene expression as prognostic marker for overall survival in esophageal squamous cell carcinoma.

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.

Int J Cancer. 2013 Jun 15;132(12):2901-9. doi: 10.1002/ijc.27954. Epub 2012 Dec 17.

12.

The association of microRNA expression with prognosis and progression in early-stage, non-small cell lung adenocarcinoma: a retrospective analysis of three cohorts.

Saito M, Schetter AJ, Mollerup S, Kohno T, Skaug V, Bowman ED, Mathé EA, Takenoshita S, Yokota J, Haugen A, Harris CC.

Clin Cancer Res. 2011 Apr 1;17(7):1875-82. doi: 10.1158/1078-0432.CCR-10-2961. Epub 2011 Feb 24.

13.

Inflammatory and microRNA gene expression as prognostic classifier of Barrett's-associated esophageal adenocarcinoma.

Nguyen GH, Schetter AJ, Chou DB, Bowman ED, Zhao R, Hawkes JE, Mathé EA, Kumamoto K, Zhao Y, Budhu A, Hagiwara N, Wang XW, Miyashita M, Casson AG, Harris CC.

Clin Cancer Res. 2010 Dec 1;16(23):5824-34. doi: 10.1158/1078-0432.CCR-10-1110. Epub 2010 Oct 14.

14.

MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: associations with survival.

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 CG, Wang XW, Yanaihara N, Hagiwara N, Dannenberg AJ, Miyashita M, Croce CM, Harris CC.

Clin Cancer Res. 2009 Oct 1;15(19):6192-200. doi: 10.1158/1078-0432.CCR-09-1467. Epub 2009 Sep 29.

15.

Association of inflammation-related and microRNA gene expression with cancer-specific mortality of colon adenocarcinoma.

Schetter AJ, Nguyen GH, Bowman ED, Mathé EA, Yuen ST, Hawkes JE, Croce CM, Leung SY, Harris CC.

Clin Cancer Res. 2009 Sep 15;15(18):5878-87. doi: 10.1158/1078-0432.CCR-09-0627. Epub 2009 Sep 8.

16.

p53 isoforms Delta133p53 and p53beta are endogenous regulators of replicative cellular senescence.

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 JC, Lane DP, Harris CC.

Nat Cell Biol. 2009 Sep;11(9):1135-42. doi: 10.1038/ncb1928. Epub 2009 Aug 23.

17.

MiR-21 is an EGFR-regulated anti-apoptotic factor in lung cancer in never-smokers.

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.

Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12085-90. doi: 10.1073/pnas.0905234106. Epub 2009 Jul 13.

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