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
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).
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
NIH Big Data 2 Knowledge (BD2K) All Hands Meeting, November, 29, 2016 Pacific Symposium of Biocomputing, January 8, 2016 AMIA Joint Summits on Translational Science, San Francisco, CA, March 2017 (Student: Muthu Alaggapan)
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
UCSF Division of Hospital Medicine, November 21, 2016
University of Washington Department of Biomedical Informatics and Medical Education, February 7, 2017
Washington University of St. Louis, Institute for Informatics, February 14, 2017
Jonathan H. Chen, Mary K. Goldstein, Steven M. Asch, Russ B. Altman
Stanford Mobilize Center, October 27, 2016
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
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 for the concrete rewards of caring for real people and
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]
Reaction Explorer LLC, Founding Member (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 around 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
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.
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
Includes grade histograms, distribution statistics
Customized grade reports if user inputs their student ID number,
including exam rankings and percentiles
Illustrates results after final exam,
including predicted final course grade
Illustrates results mid-term,
including estimated scores required on future
exams to achieve final course grades.
Medical Calculation / Analysis Tools (2009-Present)
Web-based scripts / pages for calculation and analysis
of some common issues on medicine wards.
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.
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.
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.