Convergence of Machine Learning and Translational Genomics for Prostate Cancer Precision Medicine

2020 Emerging Leader Award - Arnold J. Levine Fellow

Eliezer Van Allen, MD, Dana-Farber Cancer Institute

Eliezer Van Allen, MD

Dr. Van Allen is developing machine-learning algorithms to analyze genomic, imaging, and clinical data from over 3000 prostate cancer patients that can be used to predict clinical outcomes, inform care decisions, and accelerate new biological discoveries. This work will create a clinical and translational discovery engine in prostate cancer that will ultimately be translated into an open source platform that can be used by both clinicians and researchers. These efforts will also lay a foundation for innovative data science efforts across cancer types. Originally from Los Angeles, Dr. Van Allen studied Symbolic Systems at Stanford University, obtained his MD from UCLA, and completed a residency in internal medicine at UCSF before completing a medical oncology fellowship at the Dana-Farber/Partners CancerCare program.


Berchuck JE, Zhang Z, Silver R, Kwak L, Xie W, Lee GM, Freedman ML, Kibel AS, Van Allen EM, McKay RR, Taplin ME. Impact of Pathogenic Germline DNA Damage Repair alterations on Response to Intense Neoadjuvant Androgen Deprivation Therapy in High-risk Localized Prostate Cancer. Eur Urol. 2021.

He MX, Cuoco MS, Crowdis J, Bosma-Moody A, Zhang Z, Bi K, Kanodia A, Su MJ, Ku SY, Garcia MM, Sweet AR, Rodman C, DelloStritto L, Silver R, Steinharter J, Shah P, Izar B, Walk NC, Burke KP, Bakouny Z, Tewari AK, Liu D, Camp SY, Vokes NI, Salari K, Park J, Vigneau S, Fong L, Russo JW, Yuan X, Balk SP, Beltran H, Rozenblatt-Rosen O, Regev A, Rotem A, Taplin ME, Van Allen EM. Transcriptional mediators of treatment resistance in lethal prostate cancer. Nat Med. 2021.

Tewari AK, Cheung ATM, Crowdis J, Conway JR, Camp SY, Wankowicz SA, Livitz DG, Park J, Lis RT, Bosma-Moody A, He MX, AlDubayan SH, Zhang Z, McKay RR, Leshchiner I, Brown M, Balk SP, Getz G, Taplin ME, Van Allen EM. Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer. Cell Rep. 2021.

Elmarakeby HA, Hwang J, Arafeh R, Crowdis J, Gang S, Liu D, AlDubayan SH, Salari K, Kregel S, Richter C, Arnoff TE, Park J, Hahn WC, Van Allen EM. Biologically informed deep neural network for prostate cancer discovery. Nature. 2021.

Reardon B, Moore ND, Moore NS, Kofman E, AlDubayan SH, Cheung ATM, Conway J, Elmarakeby H, Imamovic A, Kamran SC, Keenan T, Keliher D, Konieczkowski DJ, Liu D, Mouw KW, Park J, Vokes NI , Dietlein F, Van Allen EMIntegrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. Nat. Cancer. 2021.

Hwang JH, Arafeh R, Seo JH, Baca SC, Ludwig M, Arnoff TE, Sawyer L, Richter C, Tape S, Bergom HE, McSweeney S, Rennhack JP, Klingenberg SA, Cheung ATM, Kwon J, So J, Kregel S, Van Allen EM, Drake JM, Freedman ML, Hahn WC. CREB5 reprograms FOXA1 nuclear interactions to promote resistance to androgen receptor-targeting therapies. Elife. 2022.

Crowdis J, Balch S, Sterlin L, Thomas BS, Camp SY, Dunphy M, Anastasio E, Shah S, Damon AL, Ramos R, Sosa DM, Small IK, Tomson BN, Nguyen CM, McGillicuddy M, Chastain PS, He MX, Cheung ATM, Wankowicz S, Tewari AK, Kim D, AlDubayan SH, Dowdye A, Zola B, Nowak J, Manarite J, Gunn IH, Olson B, Lander ES, Painter CA, Wagle N, Van Allen EM. A patient-driven clinicogenomic partnership for metastatic prostate cancer. Cell Genom. 2022.

Schneider AC, Chandrasekar T, Bowler N, Fogg R, Leong JY, Gusev A, Rodgers LH, McCormick SR, Dahl DM, Efstathiou JA, Blute ML, Zietman AL, Wu CL, Smith MR, Van Allen EM, Feldman AS, Salari K. Impact of an Expanded Definition of Family History on Outcomes of Active Surveillance for Prostate Cancer. J Urol. 2023.

Elmarakeby HA, Trukhanov PS, Arroyo VM, Riaz IB, Schrag D, Van Allen EM, Kehl KL. Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports. BMC Bioinformatics. 2023.

Hantel A, Walsh TP, Marron JM, Kehl KL, Sharp R, Van Allen E, Abel GA. Perspectives of Oncologists on the Ethical Implications of Using Artificial Intelligence for Cancer Care. JAMA Netw Open. 2024.