Our Science

Delivering health informatics solutions to biopharmaceutical companies and providers

M2Gen’s Integrated Clinical and Molecular Data Platform

  1. icon-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

Case Studies

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 also currently collaborating with leading biopharmaceutical companies in the development of “synthetic control arms.” One such example is a Phase 2 CAR-T clinical trial.

This powerful platform allows biopharmaceutical companies to discover new targets and biomarkers, supplement clinical trial design and enrollment, and secure post-market analysis over time. We work with research groups to provide targeted datasets. If you would like to find out if M2Gen has your dataset of interest, please complete our query form.

Biopharmaceutical Partners

Researchers and doctors collaborating around a table with laptops

Biopharmaceutical companies play a vital role in the fight against cancer, from researching new targets to developing innovative clinical trials and ultimately bringing new medicines to the market. By leveraging our Oncology Research Information Exchange Network®  (ORIEN) database to support their efforts, we help our pharma partners reduce research and discovery costs, perform more effective clinical trials, and accelerate drug development timelines.

We provide biopharmaceutical companies unparalleled insights into patients' clinical and molecular data that extends beyond the treatment window, giving broader context to health and outcomes and a unique view into how cancer impacts people differently. This accelerates cancer research and helps companies make more informed decisions around clinical trial structuring and development, maximizing the value of the data in our network.



In consultation with our pharma partners and ORIEN Members, M2Gen has identified cohorts of “high risk” patients, i.e., those with advanced primary or metastatic disease, who have limited treatment options, and those patients who are likely to develop progressive disease. Through development of a comprehensive genotypic and phenotypic profile of patients who have consented to being studied, we can identify their in silico “avatar,” i.e., patients like them. We can use this information to accelerate research, e.g., to match patients to clinical trials and develop real-world comparator cohorts. The depth and breadth of the ORIEN Avatar clinical and molecular data enables study of a wide array of clinically relevant markers, including emerging biomarkers associated with response to immuno-oncology agents.


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. 


  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


  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.


  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


  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


  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


  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


  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


  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


  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


  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


  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


  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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