The Justin Jee Lab

Research

Justin Jee
Justin Jee, MD, PhD
Assistant Member, Department of Medicine and Co-Director, Thoracic Liquid Biopsy Program

AI and real-world data are alluring tools, which may transform the practice of oncology. But the integration and application of these tools to cancer research and clinical care has to improve at every step before they can meaningfully improve the lives of patients. 

To develop useful biomarkers, we need clinical data to study key outcomes and patient characteristics. But deploying either manual curators to annotate such data from millions of records is resource intensive and so seldom done at scale. To create predictive AI biomarkers that are as informative as histopathologic or genomic ones for guiding treatment, researchers must choose clinically actionable situations and test the impact of different treatment actions based on biomarker results; this is also seldom done. AI predictive biomarkers must be validated with interventional, prospective trials; because of gaps in training and culture, this is seldom done. 

As a thoracic medical oncologist with graduate training in computational biology, I lead a team of talented scientists, clinicians, engineers, and trainees in the Digital Oncology Program at MSK to bridge these gaps. To fulfill the promise of AI to improve cancer care, we tackle these obstacles with three intersecting approaches: 1. the development and clinical deployment of AI NLP for clinical data extraction at scale, 2. the quantitative modeling of clinically relevant cancer outcomes under different treatment regimes, and 3. the validation of AI biomarkers with prospective, interventional trials. 

Projects

  • AI natural language processing for clinicogenomic data (MSK-CHORD)
  • Liquid biopsies to inform lung cancer care
  • AI liquid biopsy clinical trials to guide cancer thrombosis management

Publications Highlights

Jee J*, Fong C*, Pichotta K*, Tran T*, Luthra A*, Waters M, Fu C, Altoe M, Liu S-Y, Maron S, Ahmed M, Shen R, Kim S, Pirun M, Chatila W, Brannon AR, Mastrogiacomo B, Aprati, TJ, Liu D, Gao JJ, Capelletti M, Pekala K, Loudon L, Perry M, Bandlamudi C, Donoghue M, Martin A, Chang J, Braunstein L, Li A, Pike L, Safonov A, Miller A, Stonestrom A, Sanchez-Vela P, Wilhelm C, Robson M, Scher H, Ladanyi M, Reis-Filho JS, Solit D, Gomez D, Yu H, de Bruijn I, Chakravarty D, Yaeger R, Abida W, Park W, O’Reilly E, Garcia-Aguilad J, Levine R, Socci N, Sanchez Vega F, Carrot-Zhang J, Rudin CM, Berger MF, Shah SP, Stetson PD, Schrag D, Razavi P, Kehl K, Li BT, Riely GJ, Schultz N. Automated real-world data integration improves cancer outcome prediction. Nature. 2024. https://doi.org/10.1038/s41586-024-08167-5

Jee J, Brannon AR, Fong C, Lee A, Pichotta, K, Luthra A, Derkach, A, Diosdado M, Haque M Guo J, Hernandez J, Garg K, Derkach A, Wilhelm C, Singh R, Arcila ME, Pavlakis N, Clarke S, Shah SP, Razavi R, Reis-Filho J, Ladanyi M, Schultz N, Zwicker J, Berger MF, Li, BT, Mantha, S. DNA liquid biopsy-based prediction of cancer-associated thromboembolism. Nature Medicine. 2024. https://doi.org/10.1038/s41591-024-03195-0

Jee, J, Lebow, ES, Yeh, R, Ras, JP, Namakydoust, A, Paik, P, Chaft, JE, Jayakumaran, G, Brannon, AR, Ryma B, Zehir A, Donoghue M, Schultz N, Chakravarty D, Kundra R, Madupuri R, Murciano-Goroff YR, Tu H, Xu C, Martinez A, Wilhelm C, Galle J, Daly B, Yu HA, Offin M, Hellmann MD, Lito P, Arbour KC, Zauderer MG, Kris MG, Ng KK, Eng J, Preeshagul I, Lai WV, Fiore JJ, Iqbal A, Molena D, Rocco G, Park BJ, Lim LP, Li M, Tong-Li C, De Silva M, Chan DL, Diakos CI, Itchins M, Clarke S, Pavlakis N, Lee A, Rekhtman N, Chang J, Travis WD, Riely GJ, Solit DB, Gonen M, Rusch VW, Rimner A, Gomez D, Drilon A, Scher HI, Shah SP, Berger MF, Arcila ME, Ladanyi M, Levine R, Shen R, Razavi P, Reis-Filho JS, Jones DR, Rudin CM, Isbell JM, Li BT. Overall Survival and Liquid Biopsy-Guided Therapy in Advanced Non-Small Cell Lung Cancer. Nature Medicine. 2022. doi:10.1038/s41591-022-02047-z

Jee, J.; Rasouly, A.; Shamovsky, I.; Akivis, Y.; Steinman, S.; Mishra, B.*; Nudler, E*. Rates and Mechanisms of Bacterial Mutagenesis from Maximum-Depth Sequencing. Nature. 2016. doi: 10.1038/nature18313

Jee, J.*; Foote, M.*; Lumish, M.*; Stonestrom, A.J.*; Wills, B.*; Narendra, V.*; Avutu, V.; Murciano-Goroff, Y.R.; Chan, J.E.; Derkach, A.; Philip, J.; Belenkaya, R.; Kerpelev, M.; Maloy, M.; Watson, A.; Fong, C.; Janjigian, Y.; Diaz Jr., L.A.; Bolton, K.; Pessin, M. Chemotherapy and Covid-19 outcomes in cancer patients. Journal of Clinical Oncology. 2020 doi:10.1200/JCO.20.01307.

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People

Justin Jee

Justin Jee, MD, PhD

Assistant Member, Department of Medicine and Co-Director, Thoracic Liquid Biopsy Program

  • We take real-world data, clean it and use it to discover new predictive biomarkers to guide cancer management (often with AI), and then implement these findings in clinical practice.
jeej@mskcc.org
Email Address

Members

Chris Fong

Computational Biologist, Lead Engineer, Clinical Data Mining

Chenlian (Tom) Fu
Chenlian (Tom) Fu

PhD Student

Ramzi Homsi

Research Associate

Yuxi (Jaden) Long

PhD Student

Karl Pichotta

Senior Computational Biologist

Mono Pirun

Bioinformatician

Michele Waters, PhD
Michele Waters

Senior Computational Biologist

Jie (Jenny) Yu

PhD Student

Thinh Tran

PhD Graduate

Achievements

  • K08 Career Development Award (NCI/NIH)
  • K12 Paul Calabresi Career Development Award for Clinical Oncology
  • Jill Soffer Young Investigator Award, (ASCO/Conquer Cancer Foundation)

Open Positions

To learn more about available postdoctoral opportunities, please visit our Career Center

To learn more about compensation and benefits for postdoctoral researchers at MSK, please visit Resources for Postdocs

Get in Touch

Disclosures

Doctors and faculty members often work with pharmaceutical, device, biotechnology, and life sciences companies, and other organizations outside of MSK, to find safe and effective cancer treatments, to improve patient care, and to educate the health care community.

MSK requires doctors and faculty members to report (“disclose”) the relationships and financial interests they have with external entities. As a commitment to transparency with our community, we make that information available to the public.

Justin Jee discloses the following relationships and financial interests:

  • MDSeq Inc
    Intellectual Property Rights

The information published here is a complement to other publicly reported data and is for a specific annual disclosure period. There may be differences between information on this and other public sites as a result of different reporting periods and/or the various ways relationships and financial interests are categorized by organizations that publish such data.

This page and data include information for a specific MSK annual disclosure period (January 1, 2023 through disclosure submission in spring 2024). This data reflects interests that may or may not still exist. This data is updated annually.

Learn more about MSK’s COI policies here. For questions regarding MSK’s COI-related policies and procedures, email MSK’s Compliance Office at ecoi@mskcc.org.


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