Steven <span>Allen</span> Eschrich
Researcher

Steven Allen Eschrich

Academic Rank: Assistant Member

Overview

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

Discipline

    • Biostatistics and Bioinformatics
    • Systems Medicine Working Group
    • Chemical Biology and Molecular Medicine Program
    • Lung Cancer Center of Excellence

Education & Training

    • Florida State University, MS - Computer Science
    • University of South Florida, PhD - Computer Science
Research

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.

Publications

  • Ahmed KA, Berglund AE, Welsh EA, Naghavi AO, Kim Y, Yu M, Robinson TJ, Eschrich SA, Johnstone PA, Torres-Roca JF. The radiosensitivity of brain metastases based upon primary histology utilizing a multigene index of tumor radiosensitivity. Neurooncol. 2017 Mar. Pubmedid: 28379582.
  • Kamath VP, Torres-Roca JF, Eschrich SA. Integrating Biological Covariates into Gene Expression-Based Predictors of Radiation Sensitivity. Int J Genomics. 2017 Mar;2017:6576840. Pubmedid: 28280724. Pmcid: PMC5320380.
  • Li B, Eschrich SA, Berglund A, Mitchell M, Fenstermacher D, Danaee H, Dai H, Sullivan D, Trepicchio WL, Dalton WS. Use of the Total Cancer Care System to Enrich Screening for CD30-Positive Solid Tumors for Patient Enrollment Into a Brentuximab Vedotin Clinical Trial: A Pilot Study to Evaluate Feasibility. JMIR Res Protoc. 2017 Mar;6(3):e45. Pubmedid: 28320689. Pmcid: PMC5379017.
  • Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics. 2017 Mar;17(6). Pubmedid: 28195392.
  • Berglund AE, Welsh EA, Eschrich SA. Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures. Int J Genomics. 2017 Mar;2017:2354564. Pubmedid: 28265563. Pmcid: PMC5317117.
  • Scott JG, Berglund A, Schell MJ, Mihaylov I, Fulp WJ, Yue B, Welsh E, Caudell JJ, Ahmed K, Strom TS, Mellon E, Venkat P, Johnstone P, Foekens J, Lee J, Moros E, Dalton WS, Eschrich SA, McLeod H, Harrison LB, Torres-Roca JF. A genome-based model for adjusting radiotherapy dose (GARD): a retrospective, cohort-based study. Lancet Oncol. 2017 Feb;18(2):202-211. Pubmedid: 27993569.
  • Strom T, Torres-Roca JF, Parekh A, Naghavi AO, Caudell JJ, Oliver DE, Messina JL, Khushalani NI, Zager JS, Sarnaik A, Mulé JJ, Trotti AM, Eschrich SA, Sondak VK, Harrison LB. Regional Radiation Therapy Impacts Outcome for Node-Positive Cutaneous Melanoma. J Natl Compr Canc Ne. 2017 Apr;15(4):473-482. Pubmedid: 28404758.
  • Pimiento JM, Neill KG, Henderson-Jackson E, Eschrich SA, Chen DT, Husain K, Shibata D, Coppola D, Malafa MP. Knockdown of CSE1L Gene in Colorectal Cancer Reduces Tumorigenesis in Vitro. Am J Pathol. 2016 Oct;186(10):2761-2768. Pubmedid: 27521996. Pmcid: PMC5222983.
  • Scott JG, Torres-Roca JF, Harrison LB, Berglund AE, Schell M, Mihaylov IB, Fulp WJ, Yue B, Welsh EA, Caudell JJ, Ahmed KA, Strom T, Mellon EA, Venkat PS, Johnstone PA, Moros EG, Lee J, Foekens J, Dalton WS, Eschrich SA, McLeod HL. A Genomic Framework for Precision Radiation Therapy. Int J Radiat Oncol Biol Phys. 2016 Oct;96(2S):S215-S216. Pubmedid: 27675815.
  • Kim JY, Welsh EA, Fang B, Bai Y, Kinose F, Eschrich SA, Koomen JM, Haura EB. Phosphoproteomics Reveals MAPK Inhibitors Enhance MET- and EGFR-Driven AKT Signaling in KRAS-Mutant Lung Cancer. Mol Cancer Res. 2016 Oct;14(10):1019-1029. Pubmedid: 27422710. Pmcid: PMC5065770.
  • Grass GD, Teer J, Welsh EA, Eschrich SA, Torres-Roca JF. Multiscale Genomics to Model Functional Gene Networks Involved in Radiosensitivity. Int J Radiat Oncol Biol Phys. 2016 Oct;96(2S):E576. Pubmedid: 27675058.
  • Ahmed KA, Berglund AE, Welsh EA, Naghavi AO, Perez BA, Dilling TJ, Eschrich SA, Torres-Roca JF. Differences in the Radiosensitivity Index (RSI) Between Lung Metastases Based Upon Primary Histology. Int J Radiat Oncol Biol Phys. 2016 Oct;96(2S):S68. Pubmedid: 27675988.
  • Ahmed KA, Strom T, Scott JG, Welsh EA, McLeod HL, Harrison LB, Eschrich SA, Torres-Roca JF. The Radiosensitivity Index (RSI) and the Connectivity Map: A Genomically Guided Approach for the Identification of Novel Radiosensitizers. Int J Radiat Oncol Biol Phys. 2016 Oct;96(2S):S236. Pubmedid: 27675869.
  • Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Jun;4(2):16. Pubmedid: 28154798. Pmcid: PMC5217344.
  • Schabath MB, Welsh EA, Fulp WJ, Chen L, Teer JK, Thompson ZJ, Engel BE, Xie M, Berglund AE, Creelan BC, Antonia SJ, Gray JE, Eschrich SA, Chen DT, Cress WD, Haura EB, Beg AA. Differential association of STK11 and TP53 with KRAS mutation-associated gene expression, proliferation and immune surveillance in lung adenocarcinoma. Oncogene. 2016 Jun;35(24):3209-3216. Pubmedid: 26477306. Pmcid: PMC4837098.
  • Yoshida T, Song L, Bai Y, Kinose F, Li J, Ohaegbulam KC, Muñoz-Antonia T, Qu X, Eschrich S, Uramoto H, Tanaka F, Nasarre P, Gemmill RM, Roche J, Drabkin HA, Haura EB. ZEB1 Mediates Acquired Resistance to the Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancer. PLoS One. 2016 Jan;11(1):e0147344. Pubmedid: 26789630. Pmcid: PMC4720447.
  • Kuenzi BM, Borne AL, Li J, Haura EB, Eschrich SA, Koomen JM, Rix U, Stewart PA. APOSTL: An Interactive Galaxy Pipeline for Reproducible Analysis of Affinity Proteomics Data. J Proteome Res. 2016 Dec;15(12):4747-4754. Pubmedid: 27680298. Pmcid: PMC5231908.
  • Chen L, Kurtyka CA, Welsh EA, Rivera JI, Engel BE, Muñoz-Antonia T, Yoder SJ, Eschrich SA, Creelan BC, Chiappori AA, Gray JE, Ramirez JL, Rosell R, Schabath MB, Haura EB, Chen DT, Cress WD. Early2 factor (E2F) deregulation is a prognostic and predictive biomarker in lung adenocarcinoma. Oncotarget. 2016 Dec;7(50):82254-82265. Pubmedid: 27756884. Pmcid: PMC5347689.
  • Jiang K, Neill K, Cowden D, Klapman J, Eschrich S, Pimiento J, Malafa MP, Coppola D. Expression of CAS/CSE1L, the Cellular Apoptosis Susceptibility Protein, Correlates With Neoplastic Progression in Barrett's Esophagus. Appl Immunohistochem Mol Morphol. 2016 Dec. Pubmedid: 27941559. Pmcid: PMC5466515.
  • Schabath MB, Massion PP, Thompson ZJ, Eschrich SA, Balagurunathan Y, Goldof D, Aberle DR, Gillies RJ. Differences in Patient Outcomes of Prevalence, Interval, and Screen-Detected Lung Cancers in the CT Arm of the National Lung Screening Trial. PLoS One. 2016 Aug;11(8). Pubmedid: 27509046. Pmcid: PMC4980050.
  • Ahmed KA, Caudell JJ, El-Haddad G, Berglund AE, Welsh EA, Yue B, Hoffe SE, Naghavi AO, Abuodeh YA, Frakes JM, Eschrich SA, Torres-Roca JF. Radiosensitivity Differences Between Liver Metastases Based on Primary Histology Suggest Implications for Clinical Outcomes After Stereotactic Body Radiation Therapy. Int J Radiat Oncol Biol Phys. 2016 Aug;95(5):1399-1404. Pubmedid: 27319288.
  • Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Apr;4(2). Pubmedid: 28248226.
  • Wang H, Schabath MB, Liu Y, Stringfield O, Balagurunathan Y, Heine JJ, Eschrich SA, Ye Z, Gillies RJ. Association Between Computed Tomographic Features and Kirsten Rat Sarcoma Viral Oncogene Mutations in Patients With Stage I Lung Adenocarcinoma and Their Prognostic Value. Clin Lung Cancer. 2016 07;17(4):271-278. Pubmedid: 26712103. Pmcid: PMC4887405.
  • Ahmed KA, Chinnaiyan P, Fulp WJ, Eschrich S, Torres-Roca JF, Caudell JJ. The radiosensitivity index predicts for overall survival in glioblastoma. Oncotarget. 2015 Oct;6(33):34414-34422. Pubmedid: 26451615. Pmcid: PMC4741462.
  • Strom T, Hoffe SE, Fulp W, Frakes J, Coppola D, Springett GM, Malafa MP, Harris CL, Eschrich SA, Torres-Roca JF, Shridhar R. Radiosensitivity index predicts for survival with adjuvant radiation in resectable pancreatic cancer. Radiother Oncol. 2015 Oct;117(1):159-164. Pubmedid: 26235848.
  • Wang H, Schabath MB, Liu Y, Berglund AE, Bloom GC, Kim J, Stringfield O, Eikman EA, Klippenstein DL, Heine JJ, Eschrich SA, Ye Z, Gillies RJ. Semiquantitative Computed Tomography Characteristics for Lung Adenocarcinoma and Their Association With Lung Cancer Survival. Clin Lung Cancer. 2015 Nov;16(6):e141-e163. Pubmedid: 26077095. Pmcid: PMC4609593.
  • Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One. 2015 Nov;10(11):e0142162. Pubmedid: 26539827. Pmcid: PMC4634858.
  • Torres-Roca JF, Fulp WJ, Caudell JJ, Servant N, Bollet MA, van de Vijver M, Naghavi AO, Harris EE, Eschrich SA. Integration of a Radiosensitivity Molecular Signature Into the Assessment of Local Recurrence Risk in Breast Cancer. Int J Radiat Oncol Biol Phys. 2015 Nov;93(3):631-638. Pubmedid: 26461005.
  • Grove O, Berglund AE, Schabath MB, Aerts HJ, Dekker A, Wang H, Velazquez ER, Lambin P, Gu Y, Balagurunathan Y, Eikman E, Gatenby RA, Eschrich S, Gillies RJ. Quantitative computed tomographic descriptors associate tumor shape complexity and intratumor heterogeneity with prognosis in lung adenocarcinoma. PLoS One. 2015 Mar;10(3):e0118261. Pubmedid: 25739030. Pmcid: PMC4349806.
  • Pidala J, Bloom GC, Eschrich S, Sarwal M, Enkemann S, Betts BC, Beato F, Yoder S, Anasetti C. Tolerance associated gene expression following allogeneic hematopoietic cell transplantation. PLoS One. 2015 Mar;10(3):e0117001. Pubmedid: 25774806. Pmcid: PMC4361657.
  • Ahmed KA, Fulp WJ, Berglund AE, Hoffe SE, Dilling TJ, Eschrich SA, Shridhar R, Torres-Roca JF. Differences Between Colon Cancer Primaries and Metastases Using a Molecular Assay for Tumor Radiation Sensitivity Suggest Implications for Potential Oligometastatic SBRT Patient Selection. Int J Radiat Oncol Biol Phys. 2015 Jul;92(4):837-842. Pubmedid: 25838188. Pmcid: PMC4481172.
  • 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(9-10):783-795. Pubmedid: 24723328. Pmcid: PMC4302417.
  • Chen YA, Eschrich SA. Computational methods and opportunities for phosphorylation network medicine. Transl Cancer Res. 2014 Jun;3(3):266-278. Pubmedid: 25530950. Pmcid: PMC4271781.
  • Siegel EM, Berglund AE, Riggs BM, Eschrich SA, Putney RM, Ajidahun AO, Coppola D, Shibata D. Expanding epigenomics to archived FFPE tissues: an evaluation of DNA repair methodologies. Cancer Epidemiol Biomarkers Prev. 2014 Dec;23(12):2622-2631. Pubmedid: 25472669. Pmcid: PMC4256717.
  • 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 Dec;27(6):805-823. Pubmedid: 24990346. Pmcid: PMC4391075.
  • 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.
  • 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.
  • 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. 2013 Nov;9:705. Pubmedid: 24189400. Pmcid: PMC4039310.
  • 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.
  • Welsh EA, Eschrich SA, Berglund AE, Fenstermacher DA. Iterative rank-order normalization of gene expression microarray data. BMC Bioinformatics. 2013 May;14:153. Pubmedid: 23647742. Pmcid: PMC3651355.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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. Pmcid: PMC4638418.
  • 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. Pmcid: PMC4641440.
  • 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.
  • 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.
  • 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 Oct;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.
  • 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.
  • 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.
  • 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.
  • 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. 2011 Dec;141(6):2140-2153. Pubmedid: 21878201. Pmcid: PMC3395068.
  • 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. Proteom Clin Appl. 2011 Aug;5(7-8):383-396. Pubmedid: 21656910. Pmcid: PMC3530891.
  • 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.
  • 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. 2010 Oct;5(10):e13470. Pubmedid: 20976048. Pmcid: PMC2957407.
  • 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.
  • 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.
  • 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 Tr. 2010 Jun;16(6):729-738. Pubmedid: 19922809.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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. Pmcid: PMC2920750.
  • 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.
  • 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.
  • 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.
  • 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 Apr;1:13. Pubmedid: 18442402. Pmcid: PMC2408576.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Eschrich SA, Hoerter AM. Libaffy: software for processing Affymetrix GeneChip data. Bioinformatics. 2007 Aug;23(12):1562-1564. Pubmedid: 17463032.
  • 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;8(7):R131. Pubmedid: 17615082. Pmcid: PMC2323222.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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, Chawla N, Hall L. Learning to predict in complex biological domains. J System Stimulation. 2002;14(11):1464-1471. Pubmedid: noPMID.