Skip to nav Skip to content
Steven  Eschrich

Steven Eschrich, PhD

Program: Biostatistics and Bioinformatics

Research Program: Molecular Medicine Program

Google Scholar Profile

Contact

  • Overview

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

    Associations

    • Biostatistics and Bioinformatics
    • Lung Cancer Center of Excellence
    • Systems Medicine Working Group
    • Molecular Medicine Program
    • Experimental Therapeutics Program
    • Melanoma & Skin Cancer Center of Excellence

    Education & Training

    Graduate:

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

    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

    • Ionescu F, Nguyen J, Segura CM, Paravathaneni M, Grass GD, Johnstone P, Zacharias NM, Pettaway CA, Lu X, Kim Y, Whiting J, Dhillon J, Eschrich SA, Chadha J, Gullapalli K, Roman Souza G, Miyagi H, Manley BJ, Spiess PE, Chahoud J. Multiplex Immunofluorescence Captures Progressive Immune Exhaustion with Advancing Penile Squamous Cell Cancer Stage. Cancers (Basel). 2024 Jan.16(2). Pubmedid: 38275860. Pmcid: PMC10814242.
    • Torres-Roca JF, Eschrich SA, Kattan MW, Scott JG. Response to Mistry: Radiosensitivity index is not fit to be used for dose adjustments: A pan-cancer analysis. Clin Oncol (R Coll Radiol). 2023 Sep.35(9):621-623. Pubmedid: 37210320.
    • Ho E, De Cecco L, Cavalieri S, Sedor G, Hoebers F, Brakenhoff RH, Scheckenbach K, Poli T, Yang K, Scarborough JA, Campbell S, Koyfman S, Eschrich SA, Caudell JJ, Kattan MW, Licitra L, Torres-Roca JF, Scott JG. A clinicogenomic model including GARD predicts outcome for radiation treated patients with HPV+ oropharyngeal squamous cell carcinoma. medRxiv. 2023 Sep. Pubmedid: 37745365. Pmcid: PMC10516067.
    • Grass GD, Chahoud J, Lopez A, Dhillon J, Eschrich SA, Johnstone PAS, Spiess PE. An Analysis of Nectin-4 (PVRL4) in Penile Squamous Cell Carcinoma. Eur Urol Open Sci. 2023 Mar.49:1-5. Pubmedid: 36660545. Pmcid: PMC9843170.
    • Obermayer A, Chang D, Nobles G, Teng M, Tan AC, Wang X, Eschrich S, Rodriguez P, Grass GD, Meshinchi S, Tarhini A, Chen DT, Shaw T. DRPPM-PATH-SURVEIOR: Plug-and-Play Survival Analysis of Pathway-level Signatures and Immune Components. Res Sq. 2023 Mar. Pubmedid: 36993526. Pmcid: PMC10055629.
    • Obermayer AN, Chang D, Nobles G, Teng M, Tan AC, Wang X, Chen YA, Eschrich S, Rodriguez PC, Grass GD, Meshinchi S, Tarhini A, Chen DT, Shaw TI. PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing. BMC Bioinformatics. 2023 Jun.24(1):266. Pubmedid: 37380943. Pmcid: PMC10303868.
    • Putty Reddy S, Alontaga AY, Welsh EA, Haura EB, Boyle TA, Eschrich SA, Koomen JM. Deciphering Phenotypes from Protein Biomarkers for Translational Research with PIPER. J Proteome Res. 2023 Jun.22(6):2055-2066. Pubmedid: 37171072.
    • Grass GD, Ercan D, Obermayer AN, Shaw T, Stewart PA, Chahoud J, Dhillon J, Lopez A, Johnstone PAS, Rogatto SR, Spiess PE, Eschrich SA. An Assessment of the Penile Squamous Cell Carcinoma Surfaceome for Biomarker and Therapeutic Target Discovery. Cancers (Basel). 2023 Jul.15(14). Pubmedid: 37509297. Pmcid: PMC10377392.
    • Parza K, Mustasam A, Ionescu F, Paravathaneni M, Sandstrom R, Safa H, Grass GD, Johnstone PA, Eschrich SA, Chadha J, Zacharias N, Pettaway CA, Spiess PE, Chahoud J. The Prognostic Role of Human Papillomavirus and p16 Status in Penile Squamous Cell Carcinoma-A Systematic Review. Cancers (Basel). 2023 Jul.15(14). Pubmedid: 37509374. Pmcid: PMC10378259.
    • Heine J, Fowler EEE, Berglund A, Schell MJ, Eschrich S. Techniques to produce and evaluate realistic multivariate synthetic data. Sci Rep. 2023 Jul.13(1):12266. Pubmedid: 37507387. Pmcid: PMC10382509.
    • Torres-Roca JF, Grass GD, Scott JG, Eschrich SA. Towards Data Driven RT Prescription: Integrating Genomics into RT Clinical Practice. Semin Radiat Oncol. 2023 Jul.33(3):221-231. Pubmedid: 37331777.
    • Eschrich SA, Yu X, Teer JK. Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow. BMC Bioinformatics. 2023 Apr.24(1):164. Pubmedid: 37095442. Pmcid: PMC10124007.
    • Scarborough JA, Eschrich SA, Torres-Roca J, Dhawan A, Scott JG. Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature. NPJ Precis Oncol. 2023 Apr.7(1):38. Pubmedid: 37076665. Pmcid: PMC10115855.
    • Daniel Grass G, Alfonso JCL, Welsh E, Ahmed KA, Teer JK, Pilon-Thomas S, Harrison LB, Cleveland JL, Mulé JJ, Eschrich SA, Enderling H, Torres-Roca JF. The Radiosensitivity Index Gene Signature Identifies Distinct Tumor Immune Microenvironment Characteristics Associated With Susceptibility to Radiation Therapy. Int J Radiat Oncol Biol Phys. 2022 Jul.113(3):635-647. Pubmedid: 35289298. Pmcid: PMC9250625.
    • Rivera-Rivera Y, Vargas G, Jaiswal N, Núñez-Marrero A, Li J, Chen DT, Eschrich S, Rosa M, Johnson JO, Dutil J, Chellappan SP, Saavedra HI. Ethnic and racial-specific differences in levels of centrosome-associated mitotic kinases, proliferative and epithelial-to-mesenchymal markers in breast cancers. Cell Div. 2022 Dec.17(1):6. Pubmedid: 36494865. Pmcid: PMC9733043.
    • Berglund A, Muenyi C, Siegel EM, Ajidahun A, Eschrich SA, Wong D, Hendrick LE, Putney RM, Kim S, Hayes DN, Shibata D. Characterization of Epigenomic Alterations in HPV16+ Head and Neck Squamous Cell Carcinomas. Cancer Epidemiol Biomarkers Prev. 2022 Apr.31(4):858-869. Pubmedid: 35064062. Pmcid: PMC8983563.
    • Pérez-Morales J, Lu H, Mu W, Tunali I, Kutuk T, Eschrich SA, Balagurunathan Y, Gillies RJ, Schabath MB. Volume doubling time and radiomic features predict tumor behavior of screen-detected lung cancers. Cancer Biomark. 2022 Apr.33(4):489-501. Pubmedid: 35491768. Pmcid: PMC9310661.
    • Scott JG, Sedor G, Ellsworth P, Scarborough JA, Ahmed KA, Oliver DE, Eschrich SA, Kattan MW, Torres-Roca JF. Pan-cancer prediction of radiotherapy benefit using genomic-adjusted radiation dose (GARD): a cohort-based pooled analysis. Lancet Oncol. 2021 Sep.22(9):1221-1229. Pubmedid: 34363761.
    • Alfonso JCL, Grass GD, Welsh E, Ahmed KA, Teer JK, Pilon-Thomas S, Harrison LB, Cleveland JL, Mulé JJ, Eschrich SA, Torres-Roca JF, Enderling H. Tumor-immune ecosystem dynamics define an individual Radiation Immune Score to predict pan-cancer radiocurability. Neoplasia. 2021 Nov.23(11):1110-1122. Pubmedid: 34619428. Pmcid: PMC8502777.
    • Eschrich SA, Teer JK, Reisman P, Siegel E, Challa C, Lewis P, Fellows K, Malpica E, Carvajal R, Gonzalez G, Cukras S, Betin-Montes M, Aden-Buie G, Avedon M, Manning D, Tan AC, Fridley BL, Gerke T, Van Looveren M, Blake A, Greenman J, Rollison D. Enabling Precision Medicine in Cancer Care Through a Molecular Data Warehouse: The Moffitt Experience. JCO Clin Cancer Inform. 2021 May.5:561-569. Pubmedid: 33989014. Pmcid: PMC8240785.
    • Scott JG, Sedor G, Scarborough JA, Kattan MW, Peacock J, Grass GD, Mellon EA, Thapa R, Schell M, Waller A, Poppen S, Andl G, Teer J, Eschrich SA, Dilling TJ, Dalton WS, Harrison LB, Fox T, Torres-Roca JF. Personalizing Radiotherapy Prescription Dose Using Genomic Markers of Radiosensitivity and Normal Tissue Toxicity in NSCLC. J Thorac Oncol. 2021 Mar.16(3):428-438. Pubmedid: 33301984. Pmcid: PMC8549863.
    • Grove O, Berglund AE, Schabath MB, Aerts HJWL, Dekker A, Wang H, Velazquez ER, Lambin P, Gu Y, Balagurunathan Y, Eikman E, Gatenby RA, Eschrich S, Gillies RJ. Correction: Quantitative Computed Tomographic Descriptors Associate Tumor Shape Complexity and Intratumor Heterogeneity with Prognosis in Lung Adenocarcinoma. PLoS One. 2021 Mar.16(3):e0248541. Pubmedid: 33684181. Pmcid: PMC7939347.
    • Gordian E, Welsh EA, Gimbrone N, Siegel EM, Shibata D, Creelan BC, Cress WD, Eschrich SA, Haura EB, Muñoz-Antonia T. Correction: Transforming growth factor β-induced epithelial-to-mesenchymal signature predicts metastasis-free survival in non-small cell lung cancer. Oncotarget. 2021 Jun.12(13):1325. Pubmedid: 34194632. Pmcid: PMC8238243.
    • Koomen DC, Meads MB, Magaletti DM, Guingab-Cagmat JD, Oliveira PS, Fang B, Liu M, Welsh EA, Meke LE, Jiang Z, Hampton OA, Tungesvik A, De Avila G, Alugubelli RR, Nishihori T, Silva AS, Eschrich SA, Garrett TJ, Koomen JM, Shain KH. Metabolic Changes Are Associated with Melphalan Resistance in Multiple Myeloma. J Proteome Res. 2021 Jun.20(6):3134-3149. Pubmedid: 34014671.
    • Dash S, Yoder S, Mesa T, Smith A, Cen L, Eschrich S, Armaiz-Pena GN, Monteiro ANA. Effects of long-term norepinephrine treatment on normal immortalized ovarian and fallopian tube cells. Sci Rep. 2021 Jul.11(1):14334. Pubmedid: 34253763. Pmcid: PMC8275603.
    • Siegel EM, Ajidahun A, Berglund A, Guerrero W, Eschrich S, Putney RM, Magliocco A, Riggs B, Winter K, Simko JP, Ajani JA, Guha C, Okawara GS, Abdalla I, Becker MJ, Pizzolato JF, Crane CH, Brown KD, Shibata D. Genome-wide host methylation profiling of anal and cervical carcinoma. PLoS One. 2021 Dec.16(12):e0260857. Pubmedid: 34882728. Pmcid: PMC8659695.
    • Tunali I, Tan Y, Gray JE, Katsoulakis E, Eschrich SA, Saller J, Aerts HJWL, Boyle T, Qi J, Guvenis A, Gillies RJ, Schabath MB. Hypoxia-Related Radiomics and Immunotherapy Response: A Multicohort Study of Non-Small Cell Lung Cancer. JNCI Cancer Spectr. 2021 Aug.5(4). Pubmedid: 34409252. Pmcid: PMC8363765.
    • Stewart PA, Welsh EA, Fang B, Izumi V, Mesa T, Zhang C, Yoder S, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Avedon M, Wloch M, Fournier M, Fellows KM, Francis JM, Saller JJ, Boyle TA, Chen YA, Haura EB, Teer JK, Eschrich SA, Koomen JM. Managing a Large-Scale Multiomics Project: A Team Science Case Study in Proteogenomics. Methods Mol Biol. 2020 Sep.2194:187-221. Pubmedid: 32926368. Pmcid: PMC7771375.
    • Taylor NJ, Gaynanova I, Eschrich SA, Welsh EA, Garrett TJ, Beecher C, Sharma R, Koomen JM, Smalley KSM, Messina JL, Kanetsky PA. Metabolomics of primary cutaneous melanoma and matched adjacent extratumoral microenvironment. PLoS One. 2020 Oct.15(10):e0240849. Pubmedid: 33108391. Pmcid: PMC7591037.
    • Darville LNF, Cline JK, Rozmeski C, Martinez YC, Rich S, Eschrich SA, Egan KM, Yaghjyan L, Koomen JM. LC-HRMS of derivatized urinary estrogens and estrogen metabolites in postmenopausal women. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Oct.1154:122288. Pubmedid: 32769047. Pmcid: PMC7882395.
    • Fowler EE, Berglund A, Schell MJ, Sellers TA, Eschrich S, Heine J. Empirically-derived synthetic populations to mitigate small sample sizes. J Biomed Inform. 2020 May.105:103408. Pubmedid: 32173502. Pmcid: PMC7839232.
    • Mohammadi H, Prince A, Figura NB, Peacock JS, Fernandez DC, Montejo ME, Chon HS, Wenham RM, Eschrich SA, Torres-Roca JF, Ahmed KA. Using the Radiosensitivity Index (RSI) to Predict Pelvic Failure in Endometrial Cancer Treated With Adjuvant Radiation Therapy. Int J Radiat Oncol Biol Phys. 2020 Mar.106(3):496-502. Pubmedid: 31759077. Pmcid: PMC7050205.
    • Pérez-Morales J, Tunali I, Stringfield O, Eschrich SA, Balagurunathan Y, Gillies RJ, Schabath MB. Peritumoral and intratumoral radiomic features predict survival outcomes among patients diagnosed in lung cancer screening. Sci Rep. 2020 Jun.10(1):10528. Pubmedid: 32601340. Pmcid: PMC7324394.
    • Li Q, Fisher K, Meng W, Fang B, Welsh E, Haura EB, Koomen JM, Eschrich SA, Fridley BL, Chen YA. GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. Bioinformatics. 2020 Jan.36(1):257-263. Pubmedid: 31199438. Pmcid: PMC6956786.
    • Grisaru-Tal S, Itan M, Grass DG, Torres-Roca J, Eschrich SA, Gordon Y, Dolitzky A, Hazut I, Avlas S, Jacobsen EA, Ziv-Baran T, Munitz A. Primary tumors from mucosal barrier organs drive unique eosinophil infiltration patterns and clinical associations. Oncoimmunology. 2020 Dec.10(1):1859732. Pubmedid: 33457078. Pmcid: PMC7781846.
    • Sumi NJ, Ctortecka C, Hu Q, Bryant AT, Fang B, Remsing Rix LL, Ayaz M, Kinose F, Welsh EA, Eschrich SA, Lawrence HR, Koomen JM, Haura EB, Rix U. Divergent Polypharmacology-Driven Cellular Activity of Structurally Similar Multi-Kinase Inhibitors through Cumulative Effects on Individual Targets. Cell Chem Biol. 2019 Sep.26(9):1240-1252.e11. Pubmedid: 31257184. Pmcid: PMC6754293.
    • Saller J, Seydafkan S, Shahid M, Gadara M, Cives M, Eschrich SA, Boulware D, Strosberg JR, Aejaz N, Coppola D. EPB41L5 is Associated With the Metastatic Potential of Low-grade Pancreatic Neuroendocrine Tumors. Cancer Genomics Proteomics. 2019 Sep.16(5):309-318. Pubmedid: 31467225. Pmcid: PMC6727072.
    • Koomen DC, Guingab-Cagmat JD, Oliveira PS, Fang B, Liu M, Welsh EA, Meads MB, Nguyen T, Meke L, Eschrich SA, Shain KH, Garrett TJ, Koomen JM. Proteometabolomics of Melphalan Resistance in Multiple Myeloma. Methods Mol Biol. 2019 May.1996:273-296. Pubmedid: 31127562. Pmcid: PMC7771550.
    • Gordian E, Welsh EA, Gimbrone N, Siegel EM, Shibata D, Creelan BC, Cress WD, Eschrich SA, Haura EB, Muñoz-Antonia T. Transforming growth factor β-induced epithelial-to-mesenchymal signature predicts metastasis-free survival in non-small cell lung cancer. Oncotarget. 2019 Jan.10(8):810-824. Pubmedid: 30783512. Pmcid: PMC6368226.
    • Ahmed KA, Liveringhouse CL, Mills MN, Figura NB, Grass GD, Washington IR, Harris EE, Czerniecki BJ, Blumencranz PW, Eschrich SA, Scott JG, Diaz R, Torres-Roca JF. Utilizing the genomically adjusted radiation dose (GARD) to personalize adjuvant radiotherapy in triple negative breast cancer management. EBioMedicine. 2019 Aug.47:163-169. Pubmedid: 31416721. Pmcid: PMC6796536.
    • Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB. Proteogenomic landscape of squamous cell lung cancer. Nat Commun. 2019 Aug.10(1):3578. Pubmedid: 31395880. Pmcid: PMC6687710.
    • Dutil J, Chen Z, Monteiro AN, Teer JK, Eschrich SA. An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines. Cancer Res. 2019 Apr.79(7):1263-1273. Pubmedid: 30894373. Pmcid: PMC6445675.
    • Hayes KE, Batsomboon P, Chen WC, Johnson BD, Becker A, Eschrich S, Yang Y, Robart AR, Dudley GB, Geldenhuys WJ, Hazlehurst LA. Inhibition of the FAD containing ER oxidoreductin 1 (Ero1) protein by EN-460 as a strategy for treatment of multiple myeloma. Bioorg Med Chem. 2019 Apr.27(8):1479-1488. Pubmedid: 30850265. Pmcid: PMC6554731.
    • 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. 2018 Sep.26(8):552-556. Pubmedid: 27941559. Pmcid: PMC5466515.
    • Ahmed KA, Scott JG, Arrington JA, Naghavi AO, Grass GD, Perez BA, Caudell JJ, Berglund AE, Welsh EA, Eschrich SA, Dilling TJ, Torres-Roca JF. Radiosensitivity of Lung Metastases by Primary Histology and Implications for Stereotactic Body Radiation Therapy Using the Genomically Adjusted Radiation Dose. J Thorac Oncol. 2018 Aug.13(8):1121-1127. Pubmedid: 29733909. Pmcid: PMC7810135.
    • Teer JK, Zhang Y, Chen L, Welsh EA, Cress WD, Eschrich SA, Berglund AE. Evaluating somatic tumor mutation detection without matched normal samples. Hum Genomics. 2017 Sep.11(1):22. Pubmedid: 28870239. Pmcid: PMC5584341.
    • Strom T, Harrison LB, Giuliano AR, Schell MJ, Eschrich SA, Berglund A, Fulp W, Thapa R, Coppola D, Kim S, Frakes J, Foekens J, Mulé JJ, Torres-Roca JF. Tumour radiosensitivity is associated with immune activation in solid tumours. Eur J Cancer. 2017 Oct.84:304-314. Pubmedid: 28863385. Pmcid: PMC5822441.
    • 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. Pmcid: PMC5606153.
    • 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.
    • 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.
    • 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.
    • 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. Pmcid: PMC7771305.
    • 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 Aug.19(8):1145-1146. Pubmedid: 28379582. Pmcid: PMC5570253.
    • 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. Pmcid: PMC7771284.
    • 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.
    • 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.
    • 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.
    • 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 Jul.17(4):271-278. Pubmedid: 26712103. Pmcid: PMC4887405.
    • 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.
    • 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.
    • 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.
    • 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. Pmcid: PMC7771381.
    • 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):e0159880. Pubmedid: 27509046. Pmcid: PMC4980050.
    • 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. Pmcid: PMC7771365.
    • 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. Pmcid: PMC5811194.
    • 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.
    • 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.
    • 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.
    • Caudell JJ, Eschrich SA, Torres-Roca JF. Personalized medicine for radiation therapy. Per Med. 2013 Mar.10(2):107-110. Pubmedid: 29758841.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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 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.
    • 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.
    • Kamath V, Yeatman TJ, Eschrich SA. Toward a measure of classification complexity in gene expression signatures. Annu Int Conf IEEE Eng Med Biol Soc. 2008 Oct.2008:5704-5707. Pubmedid: 19164012.
    • 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.
    • 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. 2008 Dec.24(23):2801-2802. Pubmedid: 18842605.
    • 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.
    • 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.
    • Eschrich SA, Hoerter AM, Bloom GC, Fenstermacher DA. Tissue-specific RMA models to incrementally normalize Affymetrix GeneChip data. Annu Int Conf IEEE Eng Med Biol Soc. 2008.2008:2419-2422. Pubmedid: 19163190.
    • 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.
    • Eschrich SA, Hoerter AM. Libaffy: software for processing Affymetrix GeneChip data. Bioinformatics. 2007 Jun.23(12):1562-1564. Pubmedid: 17463032.
    • 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.
    • 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.
    • Eschrich S, Yeatman T. DNA microarrays and data analysis: an overview. Surgery. 2004 Sep.136(3):500-503. Pubmedid: 15349092.
    • 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.
    • Hall L, Bowyer K, Banfield R, Eschrich S, Collins R. Is Error-Based Pruning Redeemable?. Int J Artif Intell Tools. 2003 Sep.12(3):249-264.
    • Eschrich S, Ke J, Hall LO, Goldgof DB. Fast Accurate Fuzzy Clustering through Data Reduction. Ieee Trans Fuzzy Systems. 2003 Apr.11(2):262-270.
    • Eschrich S, Chawla N, Hall L. Learning to predict in complex biological domains. J System Stimulation. 2002 Nov.14(11):1464-1471.
  • Grants

    • Title: Tampa Bay Life Sciences Computing Commons (TBLSCC)
      Sponsor: Nat Institutes of Health
      PI: Eschrich, S.

Find a Researcher Search