Jonathan H. Chen, MD, PhD, Medical Informatics
 Personal Information
Email     jonc101 (at) stanford.edu
Phone     (626) 840-4491 (cell / voicemail)
  (650) 736-6700 (clinic / ClickWell)
  (650) 721-6669 (office)
Office     1265 Welch Rd
  MSOB X338
  Stanford, CA 94305
Skype     jonc101x
Personal Website     http://jonc101.tripod.com
CV / Resume     Resume Page
Stanford Affiliations
  • Department of Medicine
  • ClickWell Care
  • General Medical Disciplines
  • Hospitalist Group
  • Veteran Affairs (VA) Affiliations (Previous)
  • Medical Informatics Fellowship
  • Center for Innovation to Implementation (Ci2i)
  • Stanford Affiliations (Previous)
  • Altman Research Group
  • Primary Care and Outcome Research (CHP/PCOR)
  • Internal Medicine Residency
  • Translational Research and Applied Medicine
  • Resident Informatics Council
  • Clinical Investigator Pathway
  • Stanford University Hospital
  • Society of Physician Scholars
  • UC Irvine Affiliations (Previous)
  • Baldi Research Group
  • Information & Computer Science (ICS)
  • School of Medicine (SOM)
  • Medical Scientist Training Program (MSTP)
  • UC Irvine (UCI)
  • Institute for Genomics and Bioinformatics (IGB)

  •  Peer-Reviewed Publications
    Effect of Opioid Prescribing Guidelines in Primary Care
    Chen, J.H., Hom, J., Richman, I., Asch, S.M., Podchiyska, T., Atwan Johansen, N. Medicine (2016)
    Predicting Inpatient Clinical Order Patterns with Probabilistic Topic Models vs. Conventional Order Sets
    Chen, J.H., Goldstein, M.K., Asch, S.M., Mackey, L., Altman, R.B. Journal of the American Medical Informatics Association (2016)
    Use of Opioid Agonist Therapy for Medicare Patients in 2013
    Lembke, A., Chen, J.H. JAMA Psychiatry (2016)
    Related Press: [Medscape] [Pacific Standard] [Kaiser Health] [US News] [Healio] [Med Page Today] [Clincial Advisor] [Pew Trusts]
    Fulfilling Outpatient Medicine Responsibilities During Internal Medicine Residency: A Quantitative Study of Housestaff Participation with Between Visit Tasks
    Hom, J., Richman, I., Chen, J.H., Singh, B., Crump, C., Chi, J. BMC Med. Educ. 2016;16(1):139. doi:10.1186/s12909-016-0665-6.
    Patient Outcomes When Housestaff Exceed Eighty Hours per Week
    Ouyang, D., Chen, J.H., Krishnan, G., Hom, J., Witteles, R., Chi, J. American Journal of Medicine (2016)
    The Patient You Least Want To See [A Piece of My Mind]
    Chen, J.H. JAMA (2016)
    Related Press: [Health Affairs] [Scope]
    Dynamically Evolving Clinical Practices and Implications For Predicting Medical Decisions
    Chen, J.H., Goldstein, M.K., Asch, S.M., Altman, R.B. Pacific Symposium of Biocomputing (2016)
    Distribution of Opioids by Different Types of Medicare Providers
    Chen, J.H., Humphreys K., Shah, N.H., Lembke, A. JAMA Internal Medicine (2015)
    Related Press: [NY Times 1] [NY Times 2] [Washington Post] [USA Today] [NBC] [HuffPost Live] [Medscape] [Kaiser Health 1] [Kaiser Health 2] [Kaiser Health 3] [STAT 1] [STAT 2] [Pacific Standard Magazine] [UPI] [Philly] [Medical Daily] [Pain Medicine] [Science News] [Stanford Medicine]
    Internal Medicine Resident Computer Usage: An Electronic Audit of an Inpatient Service
    Ouyang, D., Chen, J. H., Hom, J. & Chi, J. JAMA Internal Medicine (2015)
    Related Press: [MedPage Today] [MedicalResearch.com]
    OrderRex: Clinical Order Decision Support and Outcome Predictions by Data-Mining Electronic Medical Records
    Chen, J. H., Podchiyska, T. & Altman, R. B. Journal of the American Medical Informatics Association ocv091 (2015). doi:10.1093/jamia/ocv091
    Improving and Sustaining a Reduction in Iatrogenic Pneumothorax through a Multifaceted Quality Improvement Approach
    Shieh, L., Go, M., Gessner, D., Chen, J.H., Hopkins, J., Maggio, P. Journal of Hospital Medicine 2015;10(9):599-607. doi:10.1002/jhm.2388
    Data-Mining Electronic Medical Records for Clinical Order Recommendations: Wisdom of the Crowd or Tyranny of the Mob?
    Jonathan H. Chen, Russ B. Altman. AMIA Joint Summits on Translational Science Proceedings (2015)
    (Best Student Paper Award, Finalist)
    Development and Evaluation of an Electronic Medical Record–Based Best-Practice Discharge Checklist for Hospital Patients
    Garg, T., Lee, J. Y., Evans, K. H., Chen, J., & Shieh, L. (2015). The Joint Commission Journal on Quality and Patient Safety. 41, 126 (2015).
    Why providers transfuse blood products outside recommended guidelines in spite of integrated electronic best practice alerts
    Chen, J. H., Fang, D. Z., Tim Goodnough, L., Evans, K. H., Lee Porter, M., & Shieh, L. (2014). Journal of Hospital Medicine : An Official Publication of the Society of Hospital Medicine. doi:10.1002/jhm.2236
    Automated Physician Order Recommendations and Outcome Predictions by Data-Mining Electronic Medical Records
    Jonathan H. Chen, Russ B. Altman. AMIA Joint Summits on Translational Science Proceedings (2014)
    (Winner of Best Student Paper Award)
    Mining for Clinical Expertise in (Undocumented) Order Sets to Power an Order Suggestion System
    Chen, J. H., & Altman, R. B. (2013). AMIA Joint Summits on Translational Science Proceedings (2013), 34–8.
    Learning to Predict Chemical Reactions
    Matthew A. Kayala, Chloe-Agathe Azencott, Jonathan H. Chen, and Pierre Baldi. Journal of Chemical Information and Modeling 2011 51 (9), 2209-2222 (2011)
    Reaction Explorer: Towards a Knowledge Map of Organic Chemistry To Support Dynamic Assessment and Personalized Instruction
    Jonathan H. Chen, Matthew A. Kayala, Pierre Baldi. Enhancing Learning with Online Resources, Social Networking, and Digital Libraries, American Chemical Society. p. 191-209, (2010)
    No Electron Left-Behind: A Rule-based Expert System to Predict Chemical Reactions and Reaction Mechanisms
    Jonathan H. Chen, Pierre Baldi. Journal of Chemical Informatics and Modeling 49(9): 2034-2043, (2009)
    Synthesis Explorer: A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction
    Jonathan H. Chen, Pierre Baldi. Journal of Chemical Education 2008(85):1699, (2008)
    ChemDB Update - Full-Text Search and Virtual Chemical Space
    Jonathan H. Chen, Erik Linstead, S. Joshua Swamidass, Dennis Wang, and Pierre Baldi. Bioinformatics 2007 23(17):2348-2351
    One- to Four-Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties
    Chloe-Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass, Jonathan Chen, Liva Ralaivola, and Pierre Baldi. Journal of Chemical Informatics and Modeling, 47(3):965-974, (2007)
    ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources
    Jonathan Chen*, S. Joshua Swamidass*, Yimeng Dou, Jocelyne Bruand, Pierre Baldi. Bioinformatics, 21(22):4133-4139, (2005)
    Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity
    S. Joshua Swamidass*, Jonathan Chen*, Peter Phung, Jocelyne Bruand, Liva Ralaivola, and Pierre Baldi. Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05. Bioinformatics, 21, Supplement 1, i359-368, (2005).
    Functional census of mutation sequence spaces: The example of p53 cancer rescue mutants
    S. A. Danziger, S. J. Swamidass, J. Zeng, L. R. Dearth, Q. Lu, J. H. Chen, J. Cheng, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, Rainer K. Brachmann, and Richard H. Lathrop. IEEE-ACM Transactions on Computational Biology and Bioinformatics 2006, 3, (2), 114-125
    * These authors contributed equally

    Oral Presentations
    Wisdom of the Crowd or Tyranny of the Mob? Data-Mining Electronic Health Records for Clinical Decision Support
    Stanford Center for Biomedical Informatics Research, September 6, 2016
    Columbia University Department of Biomedical Informatics, September 13, 2016
    University of Pittsburgh Department of Biomedical Informatics, October 10, 2016
    Stanford Mobilize Center, October 27, 2016
    Opioid Prescibing Distribution: What if it's not just a few bad apples?
    NIH/NIDA Clinical Trials Network Invited Webinar, April 5, 2016
    Automated Organization of Electronic Health Record Data by Probabilistic Topic Modeling to Inform Clinical Decision Making
    Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Lester Mackey, Russ B. Altman
    AMIA Joint Summits on Translational Science, San Francisco, CA, 2016
    Data-Mining Electronic Health Records for Clinical Decision Support [Video]
    Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman
    OCHIN Research, May 2016
    Kaiser Permanente Division of Research, March 2016
    Stanford Department of Medicine Grand Rounds, February 2016
    Chapman University, Invited Talk, October 2015
    Stanford Primary Care and Outcomes Research (PCOR), September 2015
    Veteran Affairs Palo Alto, Center for Innovation to Implementation (Ci2i), April 2015
    OrderRex: Data-Mining Clinical Decision Support from Electronic Medical Records, Wisdom of the Crowd or Tyranny of the Mob?
    Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman
    Stanford Medicine X, September 2016
    National Library of Medicine Training Conference, NIH, June 2015
    Data-Mining Electronic Medical Records for Clinical Order Recommendations, Wisdom of the Crowd or Tyranny of the Mob?
    Jonathan H. Chen, Russ B. Altman
    AMIA Joint Summits on Translational Science, San Francisco, CA, 2015
    (Finalist for Best Student Paper Award)
    Preparing for Scholarly Presentations for AMIA Annual Symposium
    AMIA Student Working Group, Webinar, Invited Presenter, August 2014
    Automated Physician Order Recommendations and Outcome Predictions by Data-Mining Electronic Medical Records
    Jonathan H. Chen, Russ B. Altman
    AMIA Joint Summits on Translational Science, San Francisco, CA, 2014
    (Winner of Best Student Paper Award)
    Mining for Clinical Expertise in (Undocumented) Electronic Order Sets
    Jonathan H. Chen, Russ B. Altman
    AMIA Joint Summits on Translational Science, San Francisco, CA, 2013
    Physician Order Suggestions Powered by Clinical Expertise Mined from (Undocumented) Order Sets
    Jonathan H. Chen, Russ B. Altman
    UC Irvine, Institute for Genomics and Bioinformatics, Invited Talk, November 2012
    Reaction Explorer: Organic chemistry online tutorial system for multistep synthesis and mechanism problems adapted to engage students through gaming interfaces
    Jonathan H. Chen, Pierre Baldi
    ACS National Meeting, Anaheim, CA, Spring 2011
    Reaction simulation expert system for synthetic organic chemistry
    Jonathan H. Chen, Pierre Baldi
    ACS National Meeting, Salt Lake City, UT, Spring 2009
    (Winner of CINF Scholarship for Scientific Excellence [Poster Version])
    Synthesis Explorer: Organic chemistry tutorial system for multistep synthesis and mechanism problems with personalized assessment and adaptive problem generation
    Jonathan H. Chen, Pierre Baldi
    ACS National Meeting, Salt Lake City, UT, Spring 2009
    Artificial Intelligence in Chemistry: An Expert Computer System for Predicting Organic Chemistry Reactions
    Jonathan H. Chen, Pierre Baldi
    National Library of Medicine Board of Regents Meeting, February 2009
    (One of only two student speakers invited to present before the board)
    Reaction mechanism prediction by transformation rules and general principles
    Jonathan H. Chen, Pierre Baldi
    ACS National Meeting, Philadelphia, PA, Fall 2008
    (Winner of CINF Scholarship for Scientific Excellence [Poster Version])
    Organic Reaction Expert Systems
    Jonathan H. Chen, Pierre Baldi
    National Library of Medicine Training Conference, NIH, Summer 2008
    Reaction prediction, classification, and retro-synthesis using a rule-based reaction expert system
    Jonathan H. Chen, Qian-Nan Hu, Pierre Baldi
    ACS National Meeting, New Orleans, LA, Spring 2008
    Synthesis Explorer: Organic chemistry tutorial system for multistep synthesis design and reaction mechanism prediction [Video]
    Jonathan H. Chen, Pierre Baldi
    ACS National Meeting, New Orleans, LA, Spring 2008
    Organic Reaction Expert Systems (including Mechanism Explorer)
    UC Irvine MSTP Retreat 2008 (Winner of Best Presentation Award)
    UC Irvine Bioinformatics Training Program Symposium 2008
    Organic Reaction Expert Systems Proposal
    UC Irvine Computer Science PhD Advancement to Candidacy, Summer 2007
    Organic Reaction Expert Systems
    UC Irvine MSTP Retreat 2007 (Winner of Best Presentation Award)
    UC Irvine Bioinformatics Training Program Symposium 2007
    Synthesis Explorer: Dynamically generated reaction and synthesis problems for organic chemistry education
    Jonathan H. Chen, Peter Phung, Pierre Baldi
    ACS National Meeting, Chicago, IL, Spring 2007
    ChemDB: A public database of small molecules and related chemoinformatics resources
    Jonathan H. Chen, Erik Linstead, S. Joshua Swamidass, Dennis Wang, Yimeng Dou, Pierre Baldi
    ACS National Meeting, Chicago, IL, Spring 2007
    Chemical Informatics Tutorial (Representations, Reactions sections) (18 MB, several files)
    ISMB 2006, Fortaleza, Brazil. Presented by Prof. Pierre Baldi. Jonathan produced primary content of "Representations" and "Reactions" sections
    Chemical Informatics: Database Searching, Similarity Measures and Property Prediction (1.3 MB)
    National Library of Medicine Training Conference, Vanderbilt University, Spring 2006
    Chemical Fingerprints and Retro-Synthetic Search (350KB)
    UC Irvine, ICS 273A - Machine Learning, Winter 2006
    Combinatorial Reactions, Applications and Discovery (2MB)
    UC Irvine MSTP Retreat 2006
    Chemical Toxicity Prediction
    UC Irvine MSTP Retreat 2005
    Chemical Informatics, The Importance of 3D Structure (2MB)
    UC Irvine, ICS 277B - Probabilistic Modeling of Biological Data, Winter 2005
    Chemical Toxicity Prediction, String Kernel Methods (200KB)
    UC Irvine, ICS 277A - Algorithms and Representations in Molecular Biology, Fall 2004
    p53 Surface Analysis (8MB)
    UC Irvine MSTP Retreat 2004
    Please do not use the contents of these presentations without express permission.
    Jonathan H. Chen, M.D.,Ph.D.
    Medical Informatics (Internal Medicine + Computer Science)
    I am a physician-scientist with professional software development experience and graduate training in computer science. I continue to practice Internal Medicine to inspire my research focused on mining clinical data sources to inform medical decision making.


    A current focus is automated generation of personalized content and design of fluid interfaces for decision support, analogous to Netflix or Amazon's "Customer's who bought A also bought B" recommender systems. Such a system anticipates what a doctor wants for their patient, even before they ask for it, by tapping in to the collective experience of previous doctors caring for similar patients.

    With the support of an NIH Big Data 2 Knowledge K01 Career Development Award, I will develop this approach to systematically extract and disseminate the undocumented collective wisdom of practicing clinicians. This will translate endpoint clinical data into a reproducible and executable form of expertise. Deploying this right at the point-of-care will close the loop of a continuously learning health system.
    [Stanford Health Policy News] [Scope Blog]

    Honors & Awards

     Extracurricular Projects
    Reaction Explorer LLC, Chief Executive Officer (2010-Present)
    • Founding partner of startup company based on a unique system for teaching complex problem-solving in organic chemistry with the aid of expert system technology.
    • Original inventor of the technology from graduate research project
    • Carried the concept through from original invention to formation of the company and translation of the technology into a profitable commercial application.
    • In partnership with John Wiley & Sons, Inc., global leader in higher education publishing, the application is now being distributed to schools and students across the nation and the world so that they may benefit from its unique learning advantages.
    Stanford Resident Informatics Council (2012-2014)
    • Resident representative to develop and support efficient training and usage of hospital electronic medical record systems by the housestaff
    • Developed multiple documentation templates for efficiency as well as teaching of common medicine problems, widely used by the housestaff
    • Revived as principal editor of [Wiki] knowledge sharing site to persist and distribute housestaff survival strategies
    Medical Elective Scheduling System (2005-2010)
    • Self-initiated design and development of a Web-accessible 3rd & 4th year medical student rotation scheduling system.
    • Directly addressed years of student complaints of manual system requiring scheduled administrator meeting for every action.
    • [Screenshot] Illustrates intuitive "time block" layout for schedule planning, including color-coded scheme to represent available, filled, wait-listed and unavailable (blackout) slots.
    Grade Analysis Worksheets (2002-2003)
    • Excel spreadsheets to analyze cumulative class grade distributions
    • Includes grade histograms, distribution statistics
    • Customized grade reports if user inputs their student ID number, including exam rankings and percentiles
    • [Example1]: Illustrates results after final exam, including predicted final course grade
    • [Example2]: Illustrates results mid-term, including estimated scores required on future exams to achieve final course grades.
    Medical Calculation / Analysis Tools (2009-Present)

    Graduate Research
    My current research is based on work from my previous VA Research Fellowship in Medical Informatics completed in 2015 and clinical training within the Stanford Internal Medicine residency program in 2014. Prior to this, I completed the Medical Scientist Training Program (MSTP) and Biomedical Informatics Training (BIT) program at the University of California, Irvine in 2011, where my research interests focused on organic reaction expert systems. Besides contributing to applications in drug discovery and design, I translated my research technology into a practical education tool and co-founded a start-up company, Reaction Explorer, LLC, to partner with Wiley Publishing and distribute the software to students across the world.

    Reaction Explorer: Advanced organic chemistry learning tool built upon an expert system with inherent predictive power. Core functional components include:

    • Synthesis Explorer: Dynamically generates reaction and synthesis problems, enabling students to learn through practice and experimentation.
    • Mechanism Explorer: Enables dynamic generation and testing of complete curved-arrow reaction mechanism diagrams.

    UCI ChemDB: Flagship system developed and maintained by Jonathan and the Baldi research group to collect a repository of chemical data and facilitate rapid search and exploration through that chemical space. Key modules and sub-projects include...

    • Virtual Chemical Space: Retro-synthetic analysis and combinatorial library design to explore the space of chemicals which may not be directly available, but could be synthesized from available building blocks.
    • Machine Learning Based Mechanistic Reaction Predictor Produced by the Baldi group, built upon much of the above infrastructure. Working towards an overall chemical reactivity predictor. Generates curved-arrow mechanism diagrams to illustrate feasible explanations for how such reactions occur.