Our Science

Leveraging clinical and molecular data, interpreted through sophisticated data science, to help researchers find the answers to their most pressing questions

M2GEN’s Integrated Clinical and Molecular Data Platform

  1. icon-discovery

    Discovery

    Biomarker studies, Target Discovery, Identification of Unmet Need

  2. icon-translational-medicine

    Translational Medicine

    In Silico Trial Design, Combination Strategies, Basket Trial Design

  3. icon-post-market-analysis

    Post-Market Analysis

    Comparative Effectiveness, Pharmacovigilance

Bringing New Insights Into Cancer Research With Cutting-Edge Science

Data is what drives cancer research forward, providing novel insights that enable the creation of life-saving diagnostic tools and therapies. Through our extensive partnerships and specialized bioinformatics services, M2GEN is revolutionizing the way oncology data is collected and analyzed, making the future of cancer research brighter than ever.

M2GEN leverages the power of data collected through the Oncology Research Information Exchange Network® (ORIEN), an alliance of the nation’s top cancer centers. The unique Total Cancer Care® (TCC) protocol powers the ORIEN network’s operations, allowing for the collection of longitudinal clinical and molecular data over the lifetime of consenting patients who agree to be re-contacted. To date, more than 300,000 patients have enrolled, making it one of the most comprehensive registries in the world. By eliminating the barriers between patients, physicians, and researchers, these partnerships serve as a powerful engine, generating a robust cache of raw data on many different cancer types in a wide array of patient cohorts.

ORIEN Intermember Projects

Researchers and doctors collaborating around a table with laptops

Aligning with the ORIEN Mission of accelerating cancer discovery and delivering hope through collaborative learning and partnerships, ORIEN Intermember Projects encourage research opportunities between ORIEN member institutions, and are inclusive of nonmember and industry partners.  ORIEN Intermember Projects provide a forum for clinical and scientific experts to exchange ideas and identify areas for collaboration to address unmet needs; advancing cancer research and patient care.

ORIEN Members are currently collaborating on nearly 50 Intermember Projects providing a forum for clinical and scientific experts to address unmet needs; advancing cancer research and patient care. Learn more about this research by visiting the ORIEN website. 

ORIEN Research Highlights:

Landscape of ALK Fusions in Soft-Tissue Sarcomas (STS)

Ex Vivo Drug Sensitivity and Functional Genomics Platform Identifies Novel Combinations Targeting Intrinsic and Extrinsic Apoptotic Signaling Pathways in Multiple Myeloma

DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden

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Orien_logo_4C_2ndLOGOS_ORIEN CLINICAL

Using the Total Cancer Care® Protocol as a master trial-screening protocol, M2GEN was able to dramatically accelerate enrollment for an otherwise challenging biomarker-driven clinical trial in gastric and pancreatic cancers. M2GEN is collaborating with leading biopharmaceutical companies in the development of “synthetic control arms.” One such example is a Phase 2 CAR-T clinical trial. Enrollment of patients in the TCC protocol offers patients increased probability of being matched to effective clinical trial. Additionally, the pace of clinical trial development can be accelerated by taking a proactive approach to rapidly identify eligible patients for the trial using the ORIEN Avatar data.  This approach improves clinical trial efficiency by reducing study timeline and overall costs. Centrally managed by M2GEN, the ORIEN Clinical Trials Network (OCTN) provides the ability to identify patients for target-based clinical trials. In addition to the rapid patient identification process, OCTN further enhances trial efficiency through a centralized protocol review and approval process. 

Publications

Our ecosystem is scientifically rooted and believes meaningful advancements for patients come from data-driven decisions. See how we are already contributing to the fight against cancer. The following publications were developed by ORIEN Members based on Total Cancer Care data. 

2022

  1. Racial and ethnic differences in clonal hematopoiesis, tumor markers, and outcomes of patients with multiple myeloma Peres LC, Colin-Leitzinger C, Teng M, et al. [published online ahead of print, 2022 May 2]. Blood Adv. 2022;bloodadvances.2021006652. doi:10.1182/bloodadvances.2021006652

  2. Replicative Instability Drives Cancer Progression. Biomolecules 12, no. 11: 1570. https://doi.org/10.3390/biom12111570 Morris, Benjamin B., Jason P. Smith, Qi Zhang, Zhijie Jiang, Oliver A. Hampton, Michelle L. Churchman, Susanne M. Arnold, Dwight H. Owen, Jhanelle E. Gray, Patrick M. Dillon, Hatem H. Soliman, Daniel G. Stover, Howard Colman, Arnab Chakravarti, Kenneth H. Shain, Ariosto S. Silva, John L. Villano, Michael A. Vogelbaum, Virginia F. Borges, Wallace L. Akerley, Ryan D. Gentzler, Richard D. Hall, Cindy B. Matsen, C. M. Ulrich, Andrew R. Post, David A. Nix, Eric A. Singer, James M. Larner, Peter Todd Stukenberg, David R. Jones, and Marty W. Mayo. 2022

2021

  1. Metabolic Changes Are Associated with Melphalan Resistance in Multiple Myeloma 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, Reddy Alugubelli RR, Nishihori T, Silva AS, Eschrich SA, Garrett TJ, Koomen JM, and Shain KH Journal of Proteome Research Article ASAP DOI: 10.1021/acs.jproteome.1c00022

  2. MYBL2-Driven Transcriptional Programs Link Replication Stress and Error-prone DNA Repair With Genomic Instability in Lung Adenocarcinoma. Morris Benjamin B., Wages Nolan A., Grant Patrick A., Stukenberg P. Todd, Gentzler Ryan D., Hall Richard D., Akerley Wallace L., Varghese Thomas K., Arnold Susanne M., Williams Terence M., Coppola Vincenzo, Jones David R., Auble David T., Mayo Marty W. (2021)  Frontiers in Oncology, 10 DOI: 10.3389/fonc.2020.585551 
  3. Real-World Evaluation of Universal Germline Screening for Cancer Treatment-Relevant Pharmacogenes. Hutchcraft, M. L., Lin, N., Zhang, S., Sears, C., Zacholski, K., Belcher, E. A., Durbin, E. B., Villano, J. L., Cavnar, M. J., Arnold, S. M., Ueland, F. R., & Kolesar, J. M. (2021).  Cancers, 13(18), 4524. https://doi.org/10.3390/cancers13184524 

  4. Plasma cell dependence on histone/protein deacetylase 11 reveals a therapeutic target in multiple myeloma Mostofa A, Distler A, Meads MB, et al. JCI Insight. 2021;6(24):e151713. Published 2021 Dec 22. doi:10.1172/jci.insight.151713

 

2020

  1. Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity. Seligson ND, Warner JL, Dalton WS, et al.  [published online ahead of print, 2020 Sep 4]. J Am Med Inform Assoc. 2020;ocaa159. doi:10.1093/jamia/ocaa159

  2. Genomic and immunologic correlates of LAG-3 expression in cancer. Panda A, Rosenfeld JA, Singer EA, Bhanot G & Ganesan S (2020), OncoImmunology, 9:1, DOI:10.1080/2162402X.2020.1756116

  3. Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease.

    Mason, M.J., Schinke, C., Eng, C.L.P. et al.  Leukemia (2020). https://doi.org/10.1038/s41375-020-0742-z

  4. Transcriptionally Active Androgen Receptor Splice Variants Promote Hepatocellular Carcinoma Progression.

    Dauki AM, Blachly JS, Kautto EA, Ezzat S, Abdel-Rahman MH, Coss CC. Cancer Res. 2020 Feb 1;80(3):561-575. doi:10.1158/0008-5472.CAN-19-1117. Epub 2019 Nov 4. PubMed PMID: 31685543; PubMed Central PMCID: PMC7002251.

  5. Effects of Tobacco Smoking on the Tumor Immune Microenvironment in Head and Neck Squamous Cell Carcinoma.

    de la Iglesia JV, Slebos RJC, Martin-Gomez L, Wang X, Teer JK, Tan AC, Gerke TA, Aden-Buie G, van Veen T, Masannat J, Chaudhary R, Song F, Fournier M, Siegel EM, Schabath MB, Wadsworth JT, Caudell J, Harrison L, Wenig BM, Conejo-Garcia J, Hernandez-Prera JC, Chung CH. Clin Cancer Res. 2020 Mar 15;26(6):1474-1485. doi: 10.1158/1078-0432.CCR-19-1769. Epub 2019 Dec 17. PubMed PMID: 31848186; PubMed Central PMCID: PMC7073297.

  6. DACH1 mutation frequency in endometrial cancer is associated with high tumor mutation burden. Riggs MJ, Lin N, Wang C, Piecoro DW, Miller RW, Hampton OA, et al. (2020) PLoS ONE 15(12): e0244558. https://doi.org/10.1371/journal.pone.0244558

2019

  1. Effects of tobacco smoking on the tumor immune microenvironment in head and neck squamous cell carcinoma.
    Janis V. de la Iglesia, Robbert C Slebos, Laura Martin-Gomez, Xuefeng Wang, Jamie K. Teer, Aik-Choon Tan, Travis A. Gerke, Garrick Aden-Buie, Tessa Van Veen, Jude Masannat, Ritu Chaudhary, Feifei Song, Michelle Fournier, Erin M. Siegel, Matthew B. Schabath, J. Trad Wadsworth, Jimmy J. Caudell, Louis B Harrison, Bruce Wenig, José R. Conejo-Garcia, Juan C. Hernandez-Prera and Christine H. Chung. Clin Cancer Res December 17 2019 DOI: 10.1158/1078-0432.CCR-19-1769 https://clincancerres.aacrjournals.org/content/early/2019/12/17/1078-0432.CCR-19-1769
  2. Prognostic significance of MYC oncoprotein expression on survival outcome in patients with acute myeloid leukemia with myelodysplasia related changes (AML-MRC).

    Yun S, Sharma R, Chan O, Vincelette ND, Sallman DA, Sweet K, Padron E, Komrokji R, Lancet JE, Abraham I, Moscinski LC, Cleveland JL, List AF, Zhang L. Leuk Res. 2019 Sep;84:106194. doi: 10.1016/j.leukres.2019.106194. Epub 2019 Jul 18. PubMed PMID: 31357093. https://www.ncbi.nlm.nih.gov/pubmed/31357093

  3. Proteogenomic landscape of squamous cell lung cancer.

    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. Nat Commun. 2019 Aug 8;10(1):3578. doi:10.1038/s41467-019-11452-x. PubMed PMID: 31395880; PubMed Central PMCID: PMC6687710. https://www.ncbi.nlm.nih.gov/pubmed/31395880

  4. Validation of the Khorana score in acute myeloid leukemia patients: a single-institution experience.

    Mirza AS, Yun S, Ali NA, Shin H, O'Neil JL, Elharake M, Schwartz D, Robinson K, Nowell E, Engle G, Badat I, Brimer T, Kuc A, Sequeira A, Mirza S, Sikaria D, Vera JD, Hackney N, Abusrur S, Jesurajan J, Kuang J, Patel S, Khalil S, Bhaskar S, Beard A, Abuelenen T, Ratnasamy K, Visweshwar N, Komrokji R, Jaglal M. Thromb J. 2019 Jul 2;17:13. doi: 1186/s12959-019-0202-z. eCollection 2019. PubMed PMID: 31303864; PubMed Central PMCID: PMC6604148. https://www.ncbi.nlm.nih.gov/pubmed/31303864

  5. A Molecular Epidemiological Analysis Of Programmed Cell Death Ligand-1 (PD-L1) Protein Expression, Mutations And Survival In Non-Small Cell Lung Cancer. Schabath MB, Dalvi TB, Dai HA, Crim AL, Midha A, Shire N, Gimbrone NT, Walker J, Greenawalt DM, Lawrence D,as JR Rig, Brody R, Potter D, Kumar NS, Huntsman SA, Gray JE. https://www.dovepress.com/a-molecular-epidemiological-analysis-of-programmed-cell-death-ligand-1-peer-reviewed-fulltext-article-CMAR
  6. Racial and ethnic disparities in a state-wide registry of patients with pancreatic cancer and an exploratory investigation of cancer cachexia as a contributor to observed inequities. Permuth JB, Clark Daly A, Jeong D, Choi JW, Cameron ME, Chen DT, Teer JK, Barnett TE, Li J, Powers BD, Kumar NB, George TJ, Ali KN, Huynh T, Vyas S, Gwede CK, Simmons VN, Hodul PJ, Carballido EM, Judge AR, Fleming JB, Merchant N, Trevino JG. Cancer Med. 2019 Jun;8(6):3314-3324. doi:10.1002/cam4.2180. Epub 2019 May 9. PubMed PMID: 31074202; PubMed Central PMCID: PMC6558500.
  7. Expression of the BAD pathway is a marker of triple-negative status and poor outcome.  Boac BM, Abbasi F, Ismail-Khan R, Xiong Y, Siddique A, Park H, Han M, Saeed-Vafa D, Soliman H, Henry B, Pena MJ, McClung EC, Robertson SE, Todd SL, Lopez A, Sun W, Apuri S, Lancaster JM, Berglund AE, Magliocco AM, Marchion DC. Sci Rep. 2019 Nov 25;9(1):17496. doi: 10.1038/s41598-019-53695-0. PubMed PMID: 31767884; PubMed Central PMCID: PMC6877530.

     

 

2018

  1. Patient Enrichment for Precision-Based Cancer Clinical Trials: Using Prospective Cohort Surveillance as an Approach to Improve Clinical Trials. Dalton WS, Sullivan D, Ecsedy J, Caligiuri MA. Clin Pharmacol Ther. 2018 Mar 23. doi: 10.1002/cpt.1051. PMID: 29570791. https://www.ncbi.nlm.nih.gov/pubmed/29570791
  2. Using Big Data in oncology to prospectively impact clinical patient care: A proof of concept study. Dougoud-Chauvin V, Lee JJ, Santos E, Williams VL, Battisti NML, Ghia K, Sehovic M, Croft C, Kim J, Balducci L, Kish JA, Extermann M. J Geriatr Oncol. 2018 Apr 17. pii: S1879-4068(18)30130-9. doi: 10.1016/j.jgo.2018.03.017. PMID: 29678669. https://www.ncbi.nlm.nih.gov/pubmed/29678669

  3. Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk. Lu Y, Beeghly-Fadiel A, Wu L, Guo X, Li B, Schildkraut JM, Im HK, Chen YA, Permuth JB, Reid BM, Teer JK, Moysich KB, Andrulis IL, Anton-Culver H, Arun BK, Bandera EV, Barkardottir RB, Barnes DR, Benitez J, Bjorge L, Brenton J, Butzow R, Caldes T, Caligo MA, Campbell I, Chang-Claude J, Claes KBM, Couch FJ, Cramer DW, Daly MB, deFazio A, Dennis J, Diez O, Domchek SM, Dörk T, Easton DF, Eccles DM, Fasching PA, Fortner RT, Fountzilas G, Friedman E, Ganz PA, Garber J, Giles GG, Godwin AK, Goldgar DE, Goodman MT, Greene MH, Gronwald J, Hamann U, Heitz F, Hildebrandt MAT, Høgdall CK, Hollestelle A, Hulick PJ, Huntsman DG, Imyanitov EN, Isaacs C, Jakubowska A, James P, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Kwong A, Le ND, Leslie G, Lesueur F, Levine DA, Mattiello A, May T, McGuffog L, McNeish IA, Merritt MA, Modugno F, Montagna M, Neuhausen SL, Nevanlinna H, Nielsen FC, Nikitina-Zake L, Nussbaum RL, Offit K, Olah E, Olopade OI, Olson SH, Olsson H, Osorio A, Park SK, Parsons MT, Peeters PHM, Pejovic T, Peterlongo P, Phelan CM, Pujana MA, Ramus SJ, Rennert G, Risch H, Rodriguez GC, Rodríguez-Antona C, Romieu I, Rookus MA, Rossing MA, Rzepecka IK, Sandler DP, Schmutzler RK, Setiawan VW, Sharma P, Sieh W, Simard J, Singer CF, Song H, Southey MC, Spurdle AB, Sutphen R, Swerdlow AJ, Teixeira MR, Teo SH, Thomassen M, Tischkowitz M, Toland AE, Trichopoulou A, Tung N, Tworoger SS, van Rensburg EJ, Vanderstichele A, Vega A, Edwards DV, Webb PM, Weitzel JN, Wentzensen N, White E, Wolk A, Wu AH, Yannoukakos D, Zorn KK, Gayther SA, Antoniou AC, Berchuck A, Goode EL, Chenevix-Trench G, Sellers TA, Pharoah PDP, Zheng W, Long J. A Cancer Res. 2018 Sep 15;78(18):5419-5430. doi: 10.1158/0008-5472.CAN-18-0951. Epub 2018 Jul 27. PubMed PMID: 30054336; PubMed Central PMCID: PMC6139053. https://www.ncbi.nlm.nih.gov/pubmed/30054336

  4. Quantification of Breast Cancer Protein Biomarkers at Different Expression Levels in Human Tumors. Chen Y, Britton D, Wood ER, Brantley S, Fournier M, Wloch M, Williams VL, Johnson J, Magliocco A, Pike I, Koomen JM. Methods Mol Biol. 2018;1788:251-268. doi: 10.1007/7651_2017_113. PubMed PMID: 29243084.

  5. Circulating T Cell Subpopulations Correlate With Immune Responses at the Tumor Site and Clinical Response to PD1 Inhibition in Non-Small Cell Lung Cancer. Manjarrez-Orduño N, Menard LC, Kansal S, Fischer P, Kakrecha B, Jiang C, Cunningham M, Greenawalt D, Patel V, Yang M, Golhar R, Carman JA, Lezhnin S, Dai H, Kayne PS, Suchard SJ, Bernstein SH, Nadler SG. Front Immunol. 2018 Aug 3;9:1613. doi: 10.3389/fimmu.2018.01613. eCollection 2018. PubMed PMID: 30123214; PubMed Central PMCID: PMC6085412.

2017

  1. Improved local and regional control with radiotherapy for Merkel cell carcinoma of the head and neck. Strom T, Naghavi AO, Messina JL, Kim S, Torres-Roca JF, Russell J, Sondak VK, Padhya TA, Trotti AM, Caudell JJ, Harrison LB. Head Neck. 2017 Jan;39(1):48-55. doi: 10.1002/hed.24527. PMID: 27300153. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27300153
  2. Clonal haemopoiesis and therapy-related myeloid malignancies in elderly patients: a proof-of-concept, case-control study. Gillis NK, Ball M, Zhang Q, Ma Z, Zhao Y, Yoder SJ, Balasis ME, Mesa TE, Sallman DA, Lancet JE, Komrokji RS, List AF, McLeod HL, Alsina M, Baz R, Shain KH, Rollison DE, Padron E. Lancet Oncol. 2017 Jan;18(1):112-121. doi: 10.1016/S1470-2045(16)30627-1. PMID: 27927582. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27927582 Details of the quality control criteria used for sequence analysis are available in appendix pp 1–2. When available, results from clinical genetic testing were incorporated into the analysis of cases.
  3. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Proteomics. 2017 Feb 14. doi: 10.1002/pmic.201600300. [Epub ahead of print]. PMID:  28195392. https://www-ncbi-nlm-nih-gov.moffitt.idm.oclc.org/pubmed/28195392
  4. Metabolic Activity by 18F-FDG-PET/CT Is Prognostic for Stage I and II Pancreatic Cancer. Pimiento JM, Davis-Yadley AH, Kim RD, Chen DT, Eikman EA, Berman CG, Malafa MP. Clin Nucl Med. 2016 Mar;41(3):177-81. doi: 10.1097/RLU.0000000000001098. PMID: 26673243. https://www-ncbi-nlm-nih-gov.moffitt.idm.oclc.org/pubmed/26673243
  5. Subsequent primary malignancies among multiple myeloma patients treated with or without lenalidomide. Rollison, D. E., Komrokji, R., Lee, J. H., Hampras, S., Fulp, W., Fisher, K., Baz, R., Nishihori, T., Xu, Q., Olesnyckyj, M., Kenvin, L., Knight, R., Sullivan, D., Alsina, M., Dalton, W., Shain, H.K. Leuk Lymphoma, 2017 Mar; 58(3), 560-568. doi:10.1080/10428194.2016.1207763. PMID: 27424609. https://www.ncbi.nlm.nih.gov/pubmed/?term=27424609
  6. Evaluation of invasive breast cancer samples using a 12-chemokine gene expression score: correlation with clinical outcomes. Prabhakaran S, Rizk VT, Ma Z, Cheng CH, Berglund AE, Coppola D, Khalil F, Mulé JJ, Soliman HH. Breast Cancer Res. 2017 Jun 19;19(1):71. doi: 10.1186/s13058-017-0864-z. PMID: 28629479. https://www.ncbi.nlm.nih.gov/pubmed/?term=28629479
  7. A genome-based model for adjusting radiotherapy dose (GARD): a retrospective, cohort-based study. 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. Lancet Oncol. 2017 Feb;18(2):202-211. doi: 10.1016/S1470-2045(16)30648-9. Epub 2016 Dec 18. PMID: 27993569. https://www.ncbi.nlm.nih.gov/pubmed/?term=torres-roca%2C+dalton+ws
  8. 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. Li B, Eschrich SA, Berglund A, Mitchell M, Fenstermacher D, Danaee H, Dai H, Sullivan D, Trepicchio WL, Dalton WS. JMIR Res Protoc. 2017 Mar 20;6(3):e45. doi: 10.2196/resprot.7289.  PMID: 28320689.
  9. Unification of de novo and acquired ibrutinib resistance in mantle cell lymphoma. Zhao X, Lwin T, Silva A, Shah B, Tao J, Fang B, Zhang L, Fu K, Bi C, Li J, Jiang H, Meads MB, Jacobson T, Silva M, Distler A, Darville L, Zhang L, Han Y, Rebatchouk D, Di Liberto M, Moscinski LC, Koomen JM, Dalton WS, Shain KH, Wang M, Sotomayor E, Tao J. Nat Commun. 2017 Apr 18;8:14920. doi: 10.1038/ncomms14920. PMID: 2841679.
  10. An Ex Vivo Platform for the Prediction of Clinical Response in Multiple Myeloma. Silva A, Silva MC, Sudalagunta P, Distler A, Jacobson T, Collins A, Nguyen T, Song J, Chen DT, Chen L, Cubitt C, Baz R, Perez L, Rebatchouk D, Dalton W, Greene J, Gatenby R, Gillies R, Sontag E, Meads MB, Shain KH. Cancer Res. 2017 Jun 15;77(12):3336-3351. doi: 10.1158/0008-5472.CAN-17-0502. PMID: 28400475.

2016

  1. From concept to clinic: Mathematically informed immunotherapy. Walker R, Engerling H. Curr Probl Cancer. 2016 Jan-Feb;40(1):68-83. doi: 10.1016/j.currproblcancer.2015.10.004. Epub 2015 Oct 8. PMID: 26645497. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26645497
  2. A Composite Gene Expression Signature Optimizes Prediction of Colorectal Cancer Metastasis and Outcome. Schell MJ, Yang M, Missiaglia E, Delorenzi M, Soneson C, Yue B, Nebozhyn MV, Loboda A, Bloom G, Yeatman TJ. Clin Cancer Res. 2016 Feb 1;22(3):734-45. doi: 10.1158/1078-0432.CCR-15-0143. PMID: 26446941. https://www.ncbi.nlm.nih.gov/pubmed/26446941
  3. A Sensitive NanoString-Based Assay to Score STK11 (LKB1) Pathway Disruption in Lung Adenocarcinoma. Chen L1, Engel BE2, Welsh EA3, Yoder SJ4, Brantley SG5, Chen DT3, Beg AA6, Cao C7, Kaye FJ7, Haura EB8, Schabath MB9, Cress WD10. J Thorac Oncol. 2016 Jun;11(6):838-49. doi: 10.1016/j.jtho.2016.02.009. Epub 2016 Feb 23.merlevede. PMID: 26917230. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26917230
  4. Partnering to advance early detection and prevention efforts for pancreatic cancer: the Florida Pancreas Collaborative. Permuth JB, Trevino J, Merchant N, Malafa M; Florida Pancreas Collaborative. Future Oncol. 2016;12(8):997-1000. doi: 10.2217/fon-2016-0045. No abstract available. PMID: 26863203. https://www.ncbi.nlm.nih.gov/pubmed/26863203
  5. STAT3 polymorphisms may predict an unfavorable response to first-line platinum-based therapy for women with advanced serous epithelial ovarian cancer. Permuth-Wey J, Fulp WJ, Reid BM, Chen Z, Georgeades C, Cheng JQ, Magliocco A, Chen DT, Lancaster JM. Int J Cancer. 2016 Feb 1;138(3):612-9. doi: 10.1002/ijc.29799. PMID: 26264211. https://www.ncbi.nlm.nih.gov/pubmed/26264211
  6. A genome-based model for adjusting radiotherapy dose (GARD): a retrospective, cohort-based study. 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. Lancet Oncol. 2016 Dec 18. pii: S1470-2045(16)30648-9. doi: 10.1016/S1470-2045(16)30648-9. [Epub ahead of print]. PMID: 27993569. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27993569
  7. Radiation Therapy is Associated with Improved Outcomes in Merkel Cell Carcinoma. Strom T, Carr M, Zager JS, Naghavi A, Smith FO, Cruse CW, Messina JL, Russell J, Rao NG, Fulp W, Kim S, Torres-Roca JF, Padhya TA, Sondak VK, Trotti AM, Harrison LB, Caudell JJ. Ann Surg Oncol. 2016 Oct;23(11):3572-8. doi: 10.1245/s10434-016-5293-1. PMID: 27251134. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27251134
  8. Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition. Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM. J Proteome Res. 2016 Dec 2;15(12):4476-4489. PMID: 27934295. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27934295
  9. Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics. Haake SM, Li J, Bai Y, Kinose F, Fang B, Welsh EA, Zent R, Dhillon J, Pow-Sang JM, Chen YA, Koomen JM, Rathmell WK, Fishman M, Haura EB. Clin Cancer Res. 2016 May 24. [Epub ahead of print]. PMID: 27220961. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27220961
  10. Subsequent primary malignancies and acute myelogenous leukemia transformation among myelodysplastic syndrome patients treated with or without lenalidomide. Rollison DE, Shain KH, Lee JH, Hampras SS, Fulp W, Fisher K, Al Ali NH, Padron E, Lancet J, Xu Q, Olesnyckyj M, Kenvin L, Knight R, Dalton W, List A, Komrokji RS. Cancer Med. 2016 Jul;5(7):1694-701. doi: 10.1002/cam4.721. PMID: 27098006. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27098006
  11. Increased Expression of the Glucose Transporter Type 1 Gene Is Associated With Worse Overall Survival in Resected Pancreatic Adenocarcinoma. Davis-Yadley AH, Abbott AM, Pimiento JM, Chen DT, Malafa MP. Pancreas. 2016 Aug;45(7):974-9. doi: 10.1097/MPA.0000000000000580. PMID: 26692443. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26692443
  12. Differential association of STK11 and TP53 with KRAS mutation-associated gene expression, proliferation and immune surveillance in lung adenocarcinoma. 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. Oncogene. 2016 Jun 16;35(24):3209-16. doi: 10.1038/onc.2015.375. PMID: 26477306. https://www.ncbi.nlm.nih.gov/pubmed/26477306
  13. Association Between Computed Tomographic Features and Kirsten Rat Sarcoma Viral Oncogene Mutations in Patients With Stage I Lung Adenocarcinoma and Their Prognostic Value. Wang H, Schabath MB, Liu Y, Stringfield O, Balagurunathan Y, Heine JJ, Eschrich SA, Ye Z, Gillies RJ. Clin Lung Cancer. 2016 Jul;17(4):271-8. doi: 10.1016/j.cllc.2015.11.002. PMID: 26712103. https://www.ncbi.nlm.nih.gov/pubmed/26712103
  14. Radiosensitivity Differences Between Liver Metastases Based on Primary Histology Suggest Implications for Clinical Outcomes After Stereotactic Body Radiation Therapy. 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. Int J Radiat Oncol Biol Phys. 2016 Aug 1;95(5):1399-404. doi: 10.1016/j.ijrobp.2016.03.050. PMID: 27319288. https://www.ncbi.nlm.nih.gov/pubmed/27319288
  15. Endosialin and Associated Protein Expression in Soft Tissue Sarcomas: A Potential Target for Anti-Endosialin Therapeutic Strategies. O'Shannessy, D. J., Dai, H., Mitchell, M., Huntsman, S., Brantley, S., Fenstermacher, D., Reed, D. R. Sarcoma, 2016 Jan 27; 5213628. doi:10.1155/2016/5213628. PMID: 27057137. https://www.ncbi.nlm.nih.gov/pubmed/?term=27057137
  16. Synchronous rectal adenocarcinoma and splenic marginal zone lymphoma. Srikumar, T., Markow, M., Centeno, B., Hoffe, S., Tao, J., Fernandez, H., Strosberg, J., and Shibata, D. Curr Oncol, 2016 Feb; 23(1), e70-74. doi:10.3747/co.23.2711. PMID: 26966416. https://www.ncbi.nlm.nih.gov/pubmed/?term=26966416
  17. Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents. Merlevede, J., Droin, N., Qin, T., Meldi, K., Yoshida, K., Morabito, M., Chautard, E., Auboeuf, D., Fenaux, P.,  Braun, T.,  Itzykson, R., de Botton, S., Quesnel, B., Commes, T., Jourdan, E., Vainchenker, W., Bernard, O., Pata-Merci, N., Solier, S., Gayevskiy, V., Dinger, M.E.,  Cowley, M.J.,  Selimoglu-Buet, D., Meyer, V.,   Artiguenave, F.,  Deleuze, J.F., Preudhomme, C., Stratton, M.R.,  Alexandrov, L.B., Padron, E., Ogawa, S., Koscielny, S.,  Figueroa, M., Solary, E. Nat Commun, 2016 Feb 4; 7, 10767. doi:10.1038/ncomms10767. PMID: 26908133. https://www.ncbi.nlm.nih.gov/pubmed/?term=26908133
  18. Patients with ClearCode34-identified molecular subtypes of clear cell renal cell carcinoma represent unique populations with distinct comorbidities. Haake, S. M., Brooks, S. A., Welsh, E., Fulp, W. J., Chen, D. T., Dhillon, J., Haura, E., Sexton, W., Spiess, P.E.,  Pow-Sang, J., Rathmell, W.K., Fishman, M. Urol Oncol, 2016 Mar 3; 34(3), 122.e121-127. doi:10.1016/j.urolonc.2015.09.015. PMID: 26546482. https://www.ncbi.nlm.nih.gov/pubmed/?term=26546482
  19. Outcomes of a Clinical Pathway for Borderline Resectable Pancreatic Cancer. Rashid, O. M., Pimiento, J. M., Gamenthaler, A. W., Nguyen, P., Ha, T. T., Hutchinson, T., Springett, G., Hoffe, S., Shridhar, R., Hodul,, P.J., Johnson, B.L.  Illig, K., Armstrong, P.A., Centeno, B.A.,  Fulp, W.J.,  Chen, D.T., Malafa, M.P. Ann Surg Oncol, 2016 Apr; 23(4), 1371-1379. doi:10.1245/s10434-015-5006-1. PMID: 26661409. https://www.ncbi.nlm.nih.gov/pubmed/?term=26661409
  20. Loss of H3K27me3 Expression Is a Highly Sensitive Marker for Sporadic and Radiation-induced MPNST. Prieto-Granada, C. N., Wiesner, T., Messina, J. L., Jungbluth, A. A., Chi, P.,  Antonescu, C. R. Am J Surg Pathol, 2016 Apr; 40(4), 479-489. doi:10.1097/PAS.0000000000000564. PMID: 26645727. https://www.ncbi.nlm.nih.gov/pubmed/?term=26645727
  21. Inactivation of RASA1 promotes melanoma tumorigenesis via R-Ras activation. Sung, H., Kanchi, K. L., Wang, X., Hill, K. S., Messina, J. L., Lee, J. H., Kim,Y., Dees, N. D., Ding, L.,Teer, J.K.,  Yang, S.,  Sarnaik, A.A.,  Sondak, V.K.,  Mule, J.J.,  Wilson, R.K., Weber, J.S., Kim, M. Oncotarget, 2016. Apr 26; 7(17), 23885-23896. doi:10.18632/oncotarget.8127. PMID: 26993606. https://www.ncbi.nlm.nih.gov/pubmed/?term=26993606
  22. Targeting PYK2 mediates microenvironment-specific cell death in multiple myeloma. Meads, M. B., Fang, B., Mathews, L., Gemmer, J., Nong, L., Rosado-Lopez, I.,  Nguyen, T., Ring, J.E., Matsui, W., MacLeod, W.A., Pachter, J.A.,  Hazlehurst, L.A.,  Koomen, J.M., Shain, K.H. Oncogene, 2016 May; 35(21), 2723-2734. doi:10.1038/onc.2015.334. PMID: 26387544. https://www.ncbi.nlm.nih.gov/pubmed/?term=26387544
  23. Subsequent primary malignancies and acute myelogenous leukemia transformation among myelodysplastic syndrome patients treated with or without lenalidomide. Rollison DE, Shain KH, Lee JH, Hampras SS, Fulp W, Fisher K, Al Ali NH, Padron E, Lancet J, Xu Q, Olesnyckyj M, Kenvin L, Knight R, Dalton W, List A, Komrokji RS. Cancer Med. 2016 Jul;5(7):1694-701. doi: 10.1002/cam4.721. PMID: 27098006. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+27098006
  24. Outcomes in patients with brain metastasis from esophageal carcinoma. Kothari, N., Mellon, E., Hoffe, S. E., Frakes, J., Shridhar, R., Pimiento, J., Meredith, K.,  Tran, N.D,  Saeed, N.,  Almhanna, K. J Gastrointest Oncol, 2016 Aug 7; 7(4), 562-569. doi:10.21037/jgo.2016.03.12. PMID: 27563446. https://www.ncbi.nlm.nih.gov/pubmed/?term=27563446
  25. Molecular evidence of viral DNA in non-small cell lung cancer and non-neoplastic lung. Robinson, L. A., Jaing, C. J., Pierce Campbell, C., Magliocco, A., Xiong, Y., Magliocco, G., Thissen, J.B., Antonia, S. Br J Cancer, 2016 Aug 9; 115(4), 497-504. doi:10.1038/bjc.2016.213. PMID: 27415011. https://www.ncbi.nlm.nih.gov/pubmed/?term=27415011
  26. Treatment of acquired drug resistance in multiple myeloma by combination therapy with XPO1 and topoisomerase II inhibitors. Turner, J. G., Dawson, J. L., Grant, S., Shain, K. H., Dalton, W. S., Dai, Y., Meads, M., Baz, R., Kauffman, M., Shacham, S., Sullivan, D.M. J Hematol Oncol, 2016 Aug 24; 9(1), 73. doi:10.1186/s13045-016-0304-z. PMID: 27557643. https://www.ncbi.nlm.nih.gov/pubmed/?term=27557643
  27. Expansion of tumor-infiltrating lymphocytes (TIL) from human pancreatic tumors. Hall, M., Liu, H., Malafa, M., Centeno, B., Hodul, P. J., Pimiento, J, Pilon-Thomas, S. Sarnaik, A.A. J Immunother Cancer, 2016 Oct 18; 4, 61. doi:10.1186/s40425-016-0164-7. PMID: 27777771. https://www.ncbi.nlm.nih.gov/pubmed/?term=27777771%5Buid%5D
  28. Treatment delays, race, and outcomes in head and neck cancer. Naghavi, A. O., Echevarria, M. I., Strom, T. J., Abuodeh, Y. A., Ahmed, K. A., Venkat, P. S., Trotti, A., Harrison, L.B., Green, B.L., Yamoah, K., Caudell, J.J. Cancer Epidemiol, 2016 Dec; 45, 18-25. doi:10.1016/j.canep.2016.09.005. PMID: 27664388. https://www.ncbi.nlm.nih.gov/pubmed/?term=27664388
  29. Genetic Investigation of Uterine Carcinosarcoma: Case Report and Cohort Analysis. Hembree, T. N., Teer, J. K., Hakam, A., Chiappori, A. A. Cancer Control, 2016 Jan; 23(1), 61-66. PMID: 27009459.https://www.ncbi.nlm.nih.gov/pubmed/?term=27009459
  30. Sensitivity of ovarian cancer cells to acetaminophen reveals biological pathways that affect patient survival. Bush, S. H., Tollin, S., Marchion, D. C., Xiong, Y., Abbasi, F., Ramirez, I. J., Zgheib, N.B.,  Boac, B., Judson, P.L., Chon, H.S.,  Wenham, R.H.,  Apte, S.M., Cubitt, C.L., Berglund, A. E., Havrilesky, L.J., Lancaster, J.M. Mol Clin Oncol, 2016 Mar; 4(3), 399-404. doi:10.3892/mco.2016.725. PMID: 26998291. https://www.ncbi.nlm.nih.gov/pubmed/?term=26998291
  31. Combining radiomic features with a miRNA classifier may improve prediction of malignant pathology for pancreatic intraductal papillary mucinous neoplasms. Permuth, J. B., Choi, J., Balarunathan, Y., Kim, J., Chen, D. T., Chen, L., Orcutt, S., Doepker, M.P., Gage, K., Zhang, G., Latifi, K.,  Hoffe, S., Jiang, K., Coppola, D., Centeno, B.A, Magliocco, A., Li, Q.,  Trevino, J., Merchant, N.,  Gillies, R., Malafa, M., Oncotarget, 2016 Dec 27; 7(52), 85785-85797. doi:10.18632/oncotarget.11768. PMID: 27589689. https://www.ncbi.nlm.nih.gov/pubmed/?term=27589689
  32. Increased incidence of FBXW7 and POLE proofreading domain mutations in young adult colorectal cancers. Kothari, N., Teer, J. K., Abbott, A. M., Srikumar, T., Zhang, Y., Yoder, S. J., Brohl, A.S., Kim, R.D., Reed, D.R., Shibata, D. Cancer. 2016 Sept 15; 122(18), 2828-35. doi:10.1002/cncr.30082. PMID: 27244218. https://www.ncbi.nlm.nih.gov/pubmed/?term=27244218

2015

  1. Overexpression of major CDKN3 transcripts is associated with poor survival in lung adenocarcinoma. Fan C, Chen L, Huang Q, Shen T, Welsh EA, Teer JK, Cai J, Cress WD, Wu J. Br J Cancer. 2015 Dec 22;113(12):1735-43. doi: 10.1038/bjc.2015.378. PMID: 26554648. https://www.ncbi.nlm.nih.gov/pubmed/26554648
  2. Cancer: Reshaping the cancer clinic. Schmidt C. Nature. 2015 Nov 5;527(7576):S10-1. doi: 10.1038/527S10a. No abstract available. PMID: 26536216. https://www.ncbi.nlm.nih.gov/pubmed/26536216
  3. Radiosensitivity index predicts for survival with adjuvant radiation in resectable pancreatic cancer. Strom T, Hoffe SE, Fulp W, Frakes J, Coppola D, Springett GM, Malafa MP, Harris CL, Eschrich SA, Torres-Roca JF, Shridhar R. Radiother Oncol. 2015 Oct;117(1):159-64. doi: 10.1016/j.radonc.2015.07.018. PMID: 26235848. https://www.ncbi.nlm.nih.gov/pubmed/26235848
  4. The PIM inhibitor AZD1208 synergizes with ruxolitinib to induce apoptosis of ruxolitinib sensitive and resistant JAK2-V617F-driven cells and inhibit colony formation of primary MPN cells. Mazzacurati L, Lambert QT, Pradhan A, Griner LN, Huszar D, Reuther GW. Oncotarget. 2015 Nov 24;6(37):40141-57. doi: 10.18632/oncotarget.5653. PMID: 26472029. https://www.ncbi.nlm.nih.gov/pubmed/26472029
  5. A proliferation saturation index to predict radiation response and personalize radiotherapy fractionation. Prokopiou S, Moros EG, Poleszczuk J, Caudell J, Torres-Roca JF, Latifi K, Lee JK, Myerson R, Harrison LB, Enderling H. Radiat Oncol. 2015 Jul 31;10:159. doi: 10.1186/s13014-015-0465-x. PMID: 26227259. https://www.ncbi.nlm.nih.gov/pubmed/26227259
  6. Prediction of Optimal Cytoreductive Surgery of Serous Ovarian Cancer With Gene Expression Data. Abdallah R, Chon HS, Bou Zgheib N, Marchion DC, Wenham RM, Lancaster JM, Gonzalez-Bosquet J. Int J Gynecol Cancer. 2015 Jul;25(6):1000-9. doi: 10.1097/IGC.0000000000000449. PMID: 26098088. https://www.ncbi.nlm.nih.gov/pubmed/26098088
  7. Integration of a Radiosensitivity Molecular Signature Into the Assessment of Local Recurrence Risk in Breast Cancer. Torres-Roca JF, Fulp WJ, Caudell JJ, Servant N, Bollet MA, van de Vijver M, Naghavi AO, Harris EE, Eschrich SA. Int J Radiat Oncol Biol Phys. 2015 Nov 1;93(3):631-8. doi: 10.1016/j.ijrobp.2015.06.021. PMID: 2646100. https://www.ncbi.nlm.nih.gov/pubmed/26461005
  8. Radiosensitivity index predicts for survival with adjuvant radiation in resectable pancreatic cancer. Strom T, Hoffe SE, Fulp W, Frakes J, Coppola D, Springett GM, Malafa MP, Harris CL, Eschrich SA, Torres-Roca JF, Shridhar R. Radiother Oncol. 2015 Oct;117(1):159-64. doi: 10.1016/j.radonc.2015.07.018. PMID: 26235848. https://www.ncbi.nlm.nih.gov/pubmed/26235848
  9. Overexpression of major CDKN3 transcripts is associated with poor survival in lung adenocarcinoma. Fan C, Chen L, Huang Q, Shen T, Welsh EA, Teer JK, Cai J, Cress WD, Wu J. Br J Cancer. 2015 Dec 22;113(12):1735-43. doi: 10.1038/bjc.2015.378. PMID: 26554648. https://www.ncbi.nlm.nih.gov/pubmed/26554648
  10. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. PLoS One. 2015 Nov 5;10(11):e0142162. doi: 10.1371/journal.pone.0142162. PMID: 26539827. https://www.ncbi.nlm.nih.gov/pubmed/26539827
  11. Impact of tobacco usage on disease outcome in myelodysplastic syndromes. Mishra A, Rollison DE, Brandon TH, Al Ali NH, Corrales-Yepez M, Padron E, Epling-Burnette PK, Lancet JE, List AF, Komrokji RS. Leuk Res. 2015 Jul;39(7):673-8. doi: 10.1016/j.leukres.2015.03.020. PMID: 25934048. https://www.ncbi.nlm.nih.gov/pubmed/25934048

2014

  1. Collaborative Biomedicine in the Age of Big Data: The Case of Cancer. Shaikh AR, Butte AJ, Schully SD, Dalton WS, Khoury MJ, Hesse BW, Journal of Medical Internet Research,  2014 Apr 7;16(4):e101. doi: 10.2196/jmir.2496. PMID: 24711045. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+24711045
  2. Evaluating melanoma drug response and therapeutic escape with quantitative proteomics. Rebecca VW, Wood E, Fedorenko IV, Paraiso KH, Haarberg HE, Chen Y, Xiang Y, Sarnaik A, Gibney GT, Sondak VK, Koomen JM, Smalley KS. Mol Cell Proteomics. 2014 Jul;13(7):1844-54. doi: 10.1074/mcp.M113.037424. PMID: 24760959. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+24760959
  3. Chemoprevention Trial Feasibility Using Botanicals in Exceptionally High Risk Populations for Lung Cancer. Kumar NB, Quinn GP, Alexandrow MG, Gray J, Schell M, Sutton S, Haura EB. J Clin Trials. 2014 Sep;4(4). pii: 180. PMID: 26101725. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+26101725
  4. Adaptive responses to dasatinib-treated lung squamous cell cancer cells harboring DDR2 mutations. Bai Y, Kim JY, Watters JM, Fang B, Kinose F, Song L, Koomen JM, Teer JK, Fisher K, Chen YA, Rix U, Haura EB. Cancer Res. 2014 Dec 15;74(24):7217-28. doi: 10.1158/0008-5472.CAN-14-0505. PMID: 25348954. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+25348954

2013

  1. Simulating the contribution of the biospecimen and clinical data repository in a phase II clinical trial: A value of information analysis. Craig BM, Gang H, Munkin MK, Fenstermacher D. Statistical Methods in Medical Research (SMMR), 2013 March 28. DOI : 10.1177/0962280213480282. PMID: 23503303. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+23503303
  2. Comparative Effectiveness Research in Cancer Genomics and Precision Medicine: Current Landscape and Future Prospects. Simonds NI, Khoury MJ, Schully SD, Armstrong K, Cohn WF, Fenstermacher DA, Ginsburg FS, Goddard KAB, Knaus WA, Lyman GH, Ramsey SD, Xu J, Freedman AN, JNCI, 2013 Jul 3;105(13):929-36. doi: 10.1093/jnci/djt108. Epub 2013 May 9. PMID: 23661804. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+23661804
  3. JAK1 truncating mutations in gynecologic cancer define new role of cancer-associated protein tyrosine kinase aberrations. Ren Y, Zhang Y, Liu RZ, Fenstermacher DA, Wright KL, Teer JK, Wu J. Sci Rep. 2013 Oct 24;3:3042. doi: 10.1038/srep03042. PMID: 24154688. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+24154688
  4. Development and application of a novel metric to assess effectiveness of biomedical data. Bloom GC, Eschrich S, Han G, Schabath MB, Bhansali N, Hoerter AM, Morgan S, Fenstermacher DA. BMJ Open. 2013 Aug 23;3(8):e003220. doi: 10.1136/bmjopen-2013-003220. PMID: 23975264. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+23975264
  5. A microenvironment-mediated c-Myc/miR-548m/HDAC6 amplification loop in non-Hodgkin B cell lymphomas. Lwin T, Zhao X, Cheng F, Zhang X, Huang A, Shah B, Zhang Y, Moscinski LC, Choi YS, Kozikowski AP, Bradner JE, Dalton WS, Sotomayor E, Tao J. J Clin Invest. 2013 Nov;123(11):4612-26. PMID: 24216476. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+24216476

2012

  1. A Phase II Study of RO4929097 in Metastatic Colorectal Cancer. Strosberg JR, Yeatman T, Weber J, Coppola D, Schell M, Han G, Almhanna K, Kim R, Valone T, Jump H, Sullivan D. European Journal of Cancer. 2012 May;48(7):997-1003. doi: 10.1016/j.ejca.2012.02.056. Epub 2012 Mar 23. PMID: 22445247. https://www.ncbi.nlm.nih.gov/pubmed/?term=22445247
  2. 12-Chemokine Gene Signature Identifies Lymph Node-like Structures in Melanoma: Potential for Patient Selection for Immunotherapy? Messina JL, Fenstermacher DA, Eschrich S, Qu X, Berglund AE, Lloyd MC, Schell MJ, Sondak VK, Weber JS, Mule JJ. Scientific Reports, 2012 October 24; 2:765 I DOI: 10.1038/srep0075. PMID: 23097687. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+23097687
  3. Phosphoproteomics identifies driver tyrosine kinases in sarcoma cell lines and tumors. Bai Y, Li J, Fang B, Edwards A, Zhang G, Bui M, Eschrich S, Altiok S, Koomen J, Haura EB. Cancer Res. 2012 May 15;72(10):2501-11. doi: 10.1158/0008-5472.CAN-11-3015. PMID: 22461510. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+22461510
  4. Validation of a radiosensitivity molecular signature in breast cancer. 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. Clin Cancer Res. 2012 Sep 15;18(18):5134-43. PMID: 22832933. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+22832933
  5. Coordinated silencing of MYC-mediated miR-29 by HDAC3 and EZH2 as a therapeutic target of histone modification in aggressive B-Cell lymphomas. Zhang X, Zhao X, Fiskus W, Lin J, Lwin T, Rao R, Zhang Y, Chan JC, Fu K, Marquez VE, Chen-Kiang S, Moscinski LC, Seto E, Dalton WS, Wright KL, Sotomayor E, Bhalla K, Tao J. Cancer Cell. 2012 Oct 16;22(4):506-23. doi: 10.1016/j.ccr.2012.09.003. PMID: 23079660. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+23079660
  6. Stemness of B-cell progenitors in multiple myeloma bone marrow. Boucher K, Parquet N, Widen R, Shain K, Baz R, Alsina M, Koomen J, Anasetti C, Dalton W, Perez LE. Clin Cancer Res. 2012 Nov 15;18(22):6155-68. doi: 10.1158/1078-0432.CCR-12-0531. PMID: 22988056. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+22988056

2011

  1. Implementing Personalized Medicine in a Cancer Center. Fenstermacher DA, Wenham RM, Rollison DE, Dalton WS. The Cancer Journal, 2011 Nov-Dec;17(6):528-36. doi: 10.1097/PPO.0b013e318238216e. PMID: 22157297. https://www.ncbi.nlm.nih.gov/pubmed/?term=22157297
  2. BAD phosphorylation determines ovarian cancer chemosensitivity and patient survival. 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. Clin Cancer Res. 2011 Oct 1;17(19):6356-66. doi: 10.1158/1078-0432.CCR-11-0735. PMID: 21849418. https://www.ncbi.nlm.nih.gov/pubmed/?term=21849418
  3. Monitoring a nuclear factor-κB signature of drug resistance in multiple myeloma. 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. Mol Cell Proteomics. 2011 Nov;10(11):M110.005520. doi: 10.1074/mcp.M110.005520. PMID: 21846842. https://www.ncbi.nlm.nih.gov/pubmed/?term=PMID%3A+21846842

2010

  1. The 2010 Health Care Reform Act: a potential opportunity to advance cancer research by taking cancer personally. Dalton WS, Sullivan DM, Yeatman TJ, Fenstermacher DA. Clin Cancer Res. 2010 Dec 15;16(24):5987-96  doi: 10.1158/1078-0432.CCR-10-1216. Review. PMID: 21169252. https://www.ncbi.nlm.nih.gov/pubmed/?term=21169252
  2. A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors. Loboda A, Nebozhyn M, Klinghoffer R, Frazier J, Chastain M, Arthur W, Roberts B, Zhang T, Chenard M, Haines B, Andersen J, Nagashima K, Paweletz C, Lynch B, Feldman I, Dai H, Huang P, Watters J. BMC Med Genomics. 2010 Jun 30;3:26. doi: 10.1186/1755-8794-3-26. PMID: 20591134. https://www.ncbi.nlm.nih.gov/pubmed/?term=20591134

2009

  1. A gene expression model of intrinsic tumor radiosensitivity: prediction of response and prognosis after chemoradiation. 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. Int J Radiat Oncol Biol Phys. 2009 Oct 1;75(2):489-96. doi: 10.1016/j.ijrobp.2009.06.014. PMID: 19735873. https://www.ncbi.nlm.nih.gov/pubmed/?term=19735873

2008

  1. Toward a measure of classification complexity in gene expression signatures. Kamath V, Yeatman TJ, Eschrich SA. Conf Proc IEEE Eng Med Biol Soc. 2008;2008:5704-7. doi: 10.1109/IEMBS.2008.4650509. PMID:19164012. https://www.ncbi.nlm.nih.gov/pubmed/?term=19164012
  2. Tissue-specific RMA models to incrementally normalize Affymetrix GeneChip data. Eschrich SA, Hoerter AM, Bloom GC, Fenstermacher DA. Conf Proc IEEE Eng Med Biol Soc. 2008;2008:2419-22. doi: 10.1109/IEMBS.2008.4649687. PMID:19163190. https://www.ncbi.nlm.nih.gov/pubmed/?term=19163190%5Buid%5D

2006

  1. Cancer biomarkers--an invitation to the table. Dalton WS, Friend SH. Science. 2006 May 26;312(5777):1165-8. https://www.ncbi.nlm.nih.gov/pubmed/16728629

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