Steven Allen Eschrich, PhD

Where You Are:
Steven Allen Eschrich, PhD

Associate Member

"Identifying relevant and novel connections within the context of the experiment is a crucial component of biomedical research in the high-throughput era.”"

Office  (813) 745-1303

Education And Training
  • PhD, University of South Florida, 2003 - Computer Science
  • MS, Florida State University, 1995 - Computer Science
  • BA, Florida State University, 1994 - Computer Science


My research interests can be broadly categorized into two areas. First, I am interested in developing and adapting technology to answer biomedical questions more precisely or more robustly. My work in this area includes the development of software tools and algorithms for more accurately quantifying gene expression from microarray experiments. This includes aspects such as normalization algorithms, image processing algorithms for the raw image generated from a microarray experiment. My interests do not center solely on gene expression; I have also begun working in developing more accurate peak detection within mass spec data and better quantification of variability within spectratyping technologies. Several of these systems are in use at Moffitt currently. This effort also includes developing software for easier end-user visualization of existing data.

A second area of research interest involves the use of computational tools to elucidate more knowledge from high-throughput biological assays. Methodological development in the analysis of noisy and redundant biological data is an important area of focus that can dramatically improve the biological leads provided in expression-based experiments. As more data is generated at the bench, increasingly the most difficult aspect of the experiment is the correct and complete interpretation of the results. For instance, gene expression experiments may generate a number of potential targets but at present there is little guidance on understanding how these targets may interact at the system level. This increase in the amount of data generated has eliminated manual inspection of raw data from most large experiments.

Intelligent systems that identify relevant connections and suggest new, novel connections within the context of the experiment performed is a crucial component to undertaking biomedical research in the high-throughput era. At present, little knowledge exists on the theoretical aspects of this biological data; however, machine learning provides a mechanism for developing empirically-justified algorithms for summarizing and mining large datasets for essentially leads that can be taken forward in further investigations within a laboratory setting.

  • Remily-Wood ER, Benson K, Baz RC, Chen YA, Hussein M, Hartley-Brown MA, Sprung RW, Perez B, Liu RZ, Yoder S, Teer J, Eschrich SA, Koomen JM. Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients. Proteom Clin Appl. 2014 Oct;8(10):783-795. Pubmedid: 24723328.
  • Siegel EM, Eschrich S, Winter K, Riggs B, Berglund A, Ajidahun A, Simko J, Moughan J, Ajani J, Magliocco A, Elahi A, Hoffe S, Shibata D. Epigenomic characterization of locally advanced anal cancer: a radiation therapy oncology group 98-11 specimen study. Dis Colon Rectum. 2014 Aug;57(8):941-957. Pubmedid: 25003289. Pmcid: PMC4100249.
  • Balagurunathan Y, Kumar V, Gu Y, Kim J, Wang H, Liu Y, Goldgof DB, Hall LO, Korn R, Zhao B, Schwartz LH, Basu S, Eschrich S, Gatenby RA, Gillies RJ. Test-Retest Reproducibility Analysis of Lung CT Image Features. J Digit Imaging. 2014 Jul. Pubmedid: 24990346.
  • Li J, Bennett K, Stukalov A, Fang B, Zhang G, Yoshida T, Okamoto I, Kim JY, Song L, Bai Y, Qian X, Rawal B, Schell M, Grebien F, Winter G, Rix U, Eschrich S, Colinge J, Koomen J, Superti-Furga G, Haura EB. Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Mol Syst Biol. 2014 Mar;9:705. Pubmedid: 24189400. Pmcid: PMC4039310.
  • Siegel E, Eschrich S, Winter K, Riggs B, Berglund A, Ajidahun A, Simko J, Ajani J, Magliocco A, Elahi A, Coppola D, Shibata D. Epigenomic profiling of anal cancer: does size matter? An RTOG 98-11 specimen study. Sex Health. 2013 Nov;10(6):590. Pubmedid: 24262262.
  • Welsh EA, Eschrich SA, Berglund AE, Fenstermacher DA. Iterative rank-order normalization of gene expression microarray data. BMC Bioinformatics. 2013 Sep;14:153. Pubmedid: 23647742. Pmcid: PMC3651355.
  • Bloom GC, Eschrich S, Hang G, Schabath MB, Bhansali N, Hoerter AM, Morgan S, Fenstermacher DA. Development and application of a novel metric to assess effectiveness of biomedical data. BMJ Open. 2013 Aug;3(8):e003220. Pubmedid: 23975264. Pmcid: PMC3753524.
  • Kim JY, Welsh EA, Oguz U, Fang B, Bai Y, Kinose F, Bronk C, Remsing Rix LL, Beg AA, Rix U, Eschrich SA, Koomen JM, Haura EB. Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells. Proc Natl Acad Sci U S A. 2013 Jul;110(30):12414-12419. Pubmedid: 23836654. Pmcid: PMC3725062.
  • Hernandez JM, Siegel EM, Riggs B, Eschrich S, Elahi A, Qu X, Ajidahun A, Berglund A, Coppola D, Grady WM, Giuliano AR, Shibata D. DNA methylation profiling across the spectrum of HPV-associated anal squamous neoplasia. PLoS One. 2013 May;7(11):e50533. Pubmedid: 23226306. Pmcid: PMC3511539.
  • Messina JL, Fenstermacher DA, Eschrich S, Qu X, Berglund AE, Lloyd MC, Schell MJ, Sondak VK, Weber JS, Mulé JJ. 12-Chemokine gene signature identifies lymph node-like structures in melanoma: potential for patient selection for immunotherapy?. Sci Rep. 2013 Mar;2:765. Pubmedid: 23097687. Pmcid: PMC3479449.
  • Levy MA, Freymann JB, Kirby JS, Fedorov A, Fennessy FM, Eschrich SA, Berglund AE, Fenstermacher DA, Tan Y, Guo X, Casavant TL, Brown BJ, Braun TA, Dekker A, Roelofs E, Mountz JM, Boada F, Laymon C, Oborski M, Rubin DL. Informatics methods to enable sharing of quantitative imaging research data. Magn Reson Imaging. 2012 Nov;30(9):1249-1256. Pubmedid: 22770688. Pmcid: PMC3466343.
  • Chinnaiyan P, Kensicki E, Bloom G, Prabhu A, Sarcar B, Kahali S, Eschrich S, Qu X, Forsyth P, Gillies R. The metabolomic signature of malignant glioma reflects accelerated anabolic metabolism. Cancer Res. 2012 Nov;72(22):5878-5888. Pubmedid: 23026133.
  • Kumar V, Gu Y, Basu S, Berglund A, Eschrich SA, Schabath MB, Forster K, Aerts HJ, Dekker A, Fenstermacher D, Goldgof DB, Hall LO, Lambin P, Balagurunathan Y, Gatenby RA, Gillies RJ. Radiomics: the process and the challenges. Magn Reson Imaging. 2012 Nov;30(9):1234-1248. Pubmedid: 22898692. Pmcid: PMC3563280.
  • Eschrich SA, Fulp WJ, Pawitan Y, Foekens JA, Smid M, Martens JW, Echevarria M, Kamath V, Lee JH, Harris EE, Bergh J, Torres-Roca JF. Validation of a radiosensitivity molecular signature in breast cancer. Clin Cancer Res. 2012 Sep;18(18):5134-5143. Pubmedid: 22832933. Pmcid: PMC3993974.
  • Bai Y, Li J, Fang B, Edwards A, Zhang G, Bui M, Eschrich S, Altiok S, Koomen J, Haura EB. Phosphoproteomics identifies driver tyrosine kinases in sarcoma cell lines and tumors. Cancer Res. 2012 May;72(10):2501-2511. Pubmedid: 22461510.
  • Haviland R, Eschrich S, Bloom G, Ma Y, Minton S, Jove R, Cress WD. Necdin, a negative growth regulator, is a novel STAT3 target gene down-regulated in human cancer. PLoS One. 2012 Mar;6(10):e24923. Pubmedid: 22046235. Pmcid: PMC3203112.
  • Freeman TJ, Smith JJ, Chen X, Washington MK, Roland JT, Means AL, Eschrich SA, Yeatman TJ, Deane NG, Beauchamp RD. Smad4-mediated signaling inhibits intestinal neoplasia by inhibiting expression of β-catenin. Gastroenterology. 2012 Mar;142(3):562-571.e2. Pubmedid: 22115830. Pmcid: PMC3343368.
  • Singh AB, Sharma A, Smith JJ, Krishnan M, Chen X, Eschrich S, Washington MK, Yeatman TJ, Beauchamp RD, Dhawan P. Claudin-1 up-regulates the repressor ZEB-1 to inhibit E-cadherin expression in colon cancer cells. Gastroenterology. 2012 Feb;141(6):2140-2153. Pubmedid: 21878201. Pmcid: PMC3395068.
  • Xiang Y, Remily-Wood ER, Oliveira V, Yarde D, He L, Cheng JQ, Mathews L, Boucher K, Cubitt C, Perez L, Gauthier TJ, Eschrich SA, Shain KH, Dalton WS, Hazlehurst L, Koomen JM. Monitoring a nuclear factor-κB signature of drug resistance in multiple myeloma. Mol Cell Proteomics. 2011 Nov;10(11):M110.005520. Pubmedid: 21846842. Pmcid: PMC3226396.
  • Williams CS, Zhang B, Smith JJ, Jayagopal A, Barrett CW, Pino C, Russ P, Presley SH, Peng D, Rosenblatt DO, Haselton FR, Yang JL, Washington MK, Chen X, Eschrich S, Yeatman TJ, El-Rifai W, Beauchamp RD, Chang MS. BVES regulates EMT in human corneal and colon cancer cells and is silenced via promoter methylation in human colorectal carcinoma. J Clin Invest. 2011 Nov;121(10):4056-4069. Pubmedid: 21911938. Pmcid: PMC3195453.
  • Marchion DC, Cottrill HM, Xiong Y, Chen N, Bicaku E, Fulp WJ, Bansal N, Chon HS, Stickles XB, Kamath SG, Hakam A, Li L, Su D, Moreno C, Judson PL, Berchuck A, Wenham RM, Apte SM, Gonzalez-Bosquet J, Bloom GC, Eschrich SA, Sebti S, Chen DT, Lancaster JM. BAD phosphorylation determines ovarian cancer chemosensitivity and patient survival. Clin Cancer Res. 2011 Oct;17(19):6356-6366. Pubmedid: 21849418. Pmcid: PMC3186862.
  • Remily-Wood ER, Liu RZ, Xiang Y, Chen Y, Thomas CE, Rajyaguru N, Kaufman LM, Ochoa JE, Hazlehurst L, Pinilla-Ibarz J, Lancet J, Zhang G, Haura E, Shibata D, Yeatman T, Smalley KS, Dalton WS, Huang E, Scott E, Bloom GC, Eschrich SA, Koomen JM. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics Clin Appl. 2011 Aug;5(7-8):383-396. Pubmedid: 21656910. Pmcid: PMC3530891.
  • Dhawan P, Ahmad R, Chaturvedi R, Smith JJ, Midha R, Mittal MK, Krishnan M, Chen X, Eschrich S, Yeatman TJ, Harris RC, Washington MK, Wilson KT, Beauchamp RD, Singh AB. Claudin-2 expression increases tumorigenicity of colon cancer cells: role of epidermal growth factor receptor activation. Oncogene. 2011 Jul;30(29):3234-3247. Pubmedid: 21383692.
  • Machida K, Eschrich S, Li J, Bai Y, Koomen J, Mayer BJ, Haura EB. Characterizing tyrosine phosphorylation signaling in lung cancer using SH2 profiling. PLoS One. 2011 Mar;5(10):e13470. Pubmedid: 20976048. Pmcid: PMC2957407.
  • Zhang G, Fang B, Liu RZ, Lin H, Kinose F, Bai Y, Oguz U, Remily-Wood ER, Li J, Altiok S, Eschrich S, Koomen J, Haura EB. Mass spectrometry mapping of epidermal growth factor receptor phosphorylation related to oncogenic mutations and tyrosine kinase inhibitor sensitivity. J Proteome Res. 2011 Jan;10(1):305-319. Pubmedid: 21080693. Pmcid: PMC3050523.
  • Fang B, Haura EB, Smalley KS, Eschrich SA, Koomen JM. Methods for investigation of targeted kinase inhibitor therapy using chemical proteomics and phosphorylation profiling. Biochem Pharmacol. 2010 Sep;80(5):739-747. Pubmedid: 20361944. Pmcid: PMC2995952.
  • Chen Y, Gruidl M, Remily-Wood E, Liu RZ, Eschrich S, Lloyd M, Nasir A, Bui MM, Huang E, Shibata D, Yeatman T, Koomen JM. Quantification of beta-catenin signaling components in colon cancer cell lines, tissue sections, and microdissected tumor cells using reaction monitoring mass spectrometry. J Proteome Res. 2010 Aug;9(8):4215-4227. Pubmedid: 20590165. Pmcid: PMC2924816.
  • Pidala J, Bloom GC, Enkemann S, Eschrich S, Lancaster J, Anasetti C. Biomarkers to discern transplantation tolerance after allogeneic hematopoietic cell transplantation. Biol Blood Marrow Transplant. 2010 Jun;16(6):729-738. Pubmedid: 19922809.
  • Melis M, Hernandez J, Siegel EM, McLoughlin JM, Ly QP, Nair RM, Lewis JM, Jensen EH, Alvarado MD, Coppola D, Eschrich S, Bloom GC, Yeatman TJ, Shibata D. Gene expression profiling of colorectal mucinous adenocarcinomas. Dis Colon Rectum. 2010 Jun;53(6):936-943. Pubmedid: 20485009.
  • Li J, Rix U, Fang B, Bai Y, Edwards A, Colinge J, Bennett KL, Gao J, Song L, Eschrich S, Superti-Furga G, Koomen J, Haura EB. A chemical and phosphoproteomic characterization of dasatinib action in lung cancer. Nat Chem Biol. 2010 Apr;6(4):291-299. Pubmedid: 20190765. Pmcid: PMC2842457.
  • Smith JJ, Deane NG, Wu F, Merchant NB, Zhang B, Jiang A, Lu P, Johnson JC, Schmidt C, Bailey CE, Eschrich S, Kis C, Levy S, Washington MK, Heslin MJ, Coffey RJ, Yeatman TJ, Shyr Y, Beauchamp RD. Experimentally derived metastasis gene expression profile predicts recurrence and death in patients with colon cancer. Gastroenterology. 2010 Mar;138(3):958-968. Pubmedid: 19914252. Pmcid: PMC3388775.
  • Krishnan M, Singh AB, Smith JJ, Sharma A, Chen X, Eschrich S, Yeatman TJ, Beauchamp RD, Dhawan P. HDAC inhibitors regulate claudin-1 expression in colon cancer cells through modulation of mRNA stability. Oncogene. 2010 Jan;29(2):305-312. Pubmedid: 19881542. Pmcid: PMC3388773.
  • Jorissen RN, Gibbs P, Christie M, Prakash S, Lipton L, Desai J, Kerr D, Aaltonen LA, Arango D, Kruhøffer M, Orntoft TF, Andersen CL, Gruidl M, Kamath VP, Eschrich S, Yeatman TJ, Sieber OM. Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer. Clin Cancer Res. 2009 Dec;15(24):7642-7651. Pubmedid: 19996206.
  • Lu AT, Salpeter SR, Reeve AE, Eschrich S, Johnston PG, Barrier AJ, Bertucci F, Buckley NS, Salpeter EE, Lin AY. Gene expression profiles as predictors of poor outcomes in stage II colorectal cancer: A systematic review and meta-analysis. Clin Colorectal Cancer. 2009 Oct;8(4):207-214. Pubmedid: 19822511.
  • Eschrich S, Zhang H, Zhao H, Boulware D, Lee JH, Bloom G, Torres-Roca JF. Systems biology modeling of the radiation sensitivity network: a biomarker discovery platform. Int J Radiat Oncol Biol Phys. 2009 Oct;75(2):497-505. Pubmedid: 19735874. Pmcid: PMC2762403.
  • Eschrich SA, Pramana J, Zhang H, Zhao H, Boulware D, Lee JH, Bloom G, Rocha-Lima C, Kelley S, Calvin DP, Yeatman TJ, Begg AC, Torres-Roca JF. A gene expression model of intrinsic tumor radiosensitivity: prediction of response and prognosis after chemoradiation. Int J Radiat Oncol Biol Phys. 2009 Oct;75(2):489-496. Pubmedid: 19735873. Pmcid: PMC3038688.
  • Gopalappa C, Das TK, Enkemann S, Eschrich S. Removal of hybridization and scanning noise from microarrays. IEEE Trans Nanobioscience. 2009 Sep;8(3):210-218. Pubmedid: 20051337.
  • Lu D, Liu RZ, Izumi V, Fenstermacher D, Haura EB, Koomen J, Eschrich SA. IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry. Bioinformatics. 2009 Jan;24(23):2801-2802. Pubmedid: 18842605.
  • Coppola D, Khalil F, Eschrich SA, Boulware D, Yeatman T, Wang HG. Down-regulation of Bax-interacting factor-1 in colorectal adenocarcinoma. Cancer. 2008 Nov;113(10):2665-2670. Pubmedid: 18833585. Pmcid: PMC2614910.
  • Shedden K, Taylor JM, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Giordano TJ, Misek DE, Chang AC, Zhu CQ, Strumpf D, Hanash S, Shepherd FA, Ding K, Seymour L, Naoki K, Pennell N, Weir B, Verhaak R, Ladd-Acosta C, Golub T, Gruidl M, Sharma A, Szoke J, Zakowski M, Rusch V, Kris M, Viale A, Motoi N, Travis W, Conley B, Seshan VE, Meyerson M, Kuick R, Dobbin KK, Lively T, Jacobson JW, Beer DG. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med. 2008 Aug;14(8):822-827. Pubmedid: 18641660. Pmcid: PMC2667337.
  • Li CG, Gruidl M, Eschrich S, McCarthy S, Wang HG, Alexandrow MG, Yeatman TJ. Insig2 is associated with colon tumorigenesis and inhibits Bax-mediated apoptosis. Int J Cancer. 2008 Jul;123(2):273-282. Pubmedid: 18464289. Pmcid: PMC2650850.
  • Kamath V, Yeatman TJ, Eschrich SA. Toward a measure of classification complexity in gene expression signatures. Conf Proc IEEE Eng Med Biol Soc. 2008;2008:5704-5707. Pubmedid: 19164012.
  • Eschrich SA, Hoerter AM, Bloom GC, Fenstermacher DA. Tissue-specific RMA models to incrementally normalize Affymetrix GeneChip data. Conf Proc IEEE Eng Med Biol Soc. 2008;2008:2419-2422. Pubmedid: 19163190.
  • Chen DT, Schell MJ, Chen JJ, Fulp WJ, Eschrich S, Yeatman T. A predictive risk probability approach for microarray data with survival as an endpoint. J Biopharm Stat. 2008;18(5):841-852. Pubmedid: 18781520. Pmcid: PMC2717790.
  • Riker AI, Enkemann SA, Fodstad O, Liu S, Ren S, Morris C, Xi Y, Howell P, Metge B, Samant RS, Shevde LA, Li W, Eschrich S, Daud A, Ju J, Matta J. The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis. BMC Med Genomics. 2008;1:13-. Pubmedid: 18442402. Pmcid: PMC2408576.
  • McCarthy S, Caporali A, Enkemann S, Scaltriti M, Eschrich S, Davalli P, Corti A, Lee A, Sung J, Yeatman TJ, Bettuzzi S. Green tea catechins suppress the DNA synthesis marker MCM7 in the TRAMP model of prostate cancer. Mol Oncol. 2007 Sep;1(2):196-204. Pubmedid: 18521193. Pmcid: PMC2408886.
  • Eschrich SA, Hoerter AM. Libaffy: software for processing Affymetrix GeneChip data. Bioinformatics. 2007 Aug;23(12):1562-1564. Pubmedid: 17463032.
  • Lee J, Eschrich S, Beam C. An exact test for detecting inconsistency in readers interpretation over time in screening mammograms. Biom J. 2007 Aug;49(5):672-681. Pubmedid: 17638286.
  • Kaiser S, Park YK, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, Chen X, Haigis K, Jegga AG, Kong S, Sakthivel B, Xu H, Reichling T, Azhar M, Boivin GP, Roberts RB, Bissahoyo AC, Gonzales F, Bloom GC, Eschrich S, Carter SL, Aronow B, Kleimeyer J, Kleimeyer M, Ramaswamy V, Settle SH, Boone B, Levy S, Graff JM, Doetschman T, Groden J, Dove WF, Threadgill DW, Yeatman T, Coffey RJ, Aronow BJ. Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol. 2007 Jul;8(7): R131- . Pubmedid: 17615082.
  • Li J, Yu B, Song L, Eschrich S, Haura E. Effects of IFN-gamma and Stat1 on gene expression, growth, and survival in non-small cell lung cancer cells. J Interferon Cytokine Res. 2007 Mar;27(3):209-220. Pubmedid: 17348819.
  • Bloom GC, Eschrich S, Zhou J, Coppola D, Yeatman TJ. Elucidation of a protein signature discriminating six common types of adenocarcinoma. Int J Cancer. 2007 Feb;120(4):769-775. Pubmedid: 17131332.
  • Gritsko T, Williams A, Turkson J, Kaneko S, Bowman T, Huang M, Nam S, Eweis I, Diaz N, Sullivan D, Yoder S, Enkemann S, Eschrich S, Lee JH, Beam CA, Cheng J, Minton S, Muro-Cacho CA, Jove R. Persistent activation of stat3 signaling induces survivin gene expression and confers resistance to apoptosis in human breast cancer cells. Clin Cancer Res. 2006 Jan;12(1):11-19. Pubmedid: 16397018.
  • Torres-Roca JF, Eschrich S, Zhao H, Bloom G, Sung J, McCarthy S, Cantor AB, Scuto A, Li C, Zhang S, Jove R, Yeatman T. Prediction of radiation sensitivity using a gene expression classifier. Cancer Res. 2005 Aug;65(16):7169-7176. Pubmedid: 16103067.
  • Eschrich S, Yang I, Bloom G, Kwong K, Boulware D, Cantor A, Coppola D, Kruhoffer M, Aaltonen L, Orntoft T, Quackenbush J, Yeatman T. Molecular staging for survival prediction of colorectal cancer patients. J Clin Oncol. 2005 May;23(15):3526-3535. Pubmedid: 15908663.
  • Bloom G, Yang IV, Boulware D, Kwong KY, Coppola D, Eschrich S, Quackenbush J, Yeatman TJ. Multi-platform, multi-site, microarray-based human tumor classification. Am J Pathol. 2004 Jan;164(1):9-16. Pubmedid: 14695313. Pmcid: PMC1602228.
  • Eschrich S, Yeatman T. DNA microarrays and data analysis: an overview. Surgery. 2004;136(3):500-503. Pubmedid: 15349092.
  • Hall L, Bowyer K, Banfield R, Eschrich S, Collins R. Is Error-Based Pruning Redeemable?. Int J Artif Intell Tools. 2003;12(3):249-264. Pubmedid: noPMID.
  • Eschrich S, Ke J, Hall LO, Goldgof DB. Fast Accurate Fuzzy Clustering through Data Reduction. Ieee Trans Fuzzy Systems. 2003;11(2):262-270. Pubmedid: noPMID.
  • Eschrich S, Chawla N, Hall L. Learning to predict in complex biological domains. J System Stimulation. 2002;14(11):1464-1471. Pubmedid: noPMID.
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