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Jonathan H. Chen
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UC Irvine MD/PhD Candidate, Chemoinformatics
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Research
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Current research interests focus on organic reaction expert systems
that can solve important problems in organic chemistry just as human experts can.
Underlying biology and medicine is the biochemistry of the cell,
which in turn is founded upon the reactivity of organic molecules.
Many organic molecules, such as those derived from natural products,
can thus be of great medicinal value, but they may have significant
costs or limitations to harvesting them from natural sources.
Synthetic organic chemistry can make such molecules accessible from
simpler building blocks, but reliable and efficient solutions
generally require substantial human chemical expertise.
An organic reaction expert system would thus be an invaluable tool to
provide retro-synthetic decision support,
validate synthesis plans with general reaction predictions,
and support chemical education in ways previously unrealized.
UCI ChemDB:
One of the flagship systems 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...
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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.
- Synthesis Explorer:
Organic chemistry education tool. Dynamically generates reaction and synthesis
problems, enabling students to learn through practice and experimentation.
- Mechanism Explorer:
Extension to Synthesis Explorer to enable dynamic generation and testing of
complete curved-arrow reaction mechanism diagrams.
- Mechanism Predictor:
Chemical reactivity predictor to predict the products for
given reactant combinations and reaction conditions. Furthermore, will generate
curved-arrow mechanism diagrams to illustrate feasible explanations for
how such reactions occur.
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Honors & Awards
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- UCI MSTP Research Presentation Award (2007, 2008)
Awarded for best presentation by a student of the Medical Scientist Training Program:
"Organic Reaction Expert Systems." Won 2 consecutive years.
- Orange County ARCS Foundation Scholarship (2005-2007)
- UCI IGB, Bioinformatics Training Grant (NIH/NLM) (2006-2008)
- UCI SOM, Educational Affairs Service Award (2004-2005)
For development of medical elective scheduling system
- UCI SOM, Basic Sciences Certificate of Excellence (2002-2003)
Awarded to ~15% of medical students, ranked academically
- UCI Medical Scientist Training Grant (NIH) (2002-Present)
- UCLA, Graduated with... (2000)
- College Honors
- Departmental Honors
- Summa Cum Laude
- UCLA, Dean’s List (1997-1998)
- CSULA, Dean’s List (1994-1995, 1995-1996)
- CSULA, Honor’s Student of the Year, Nominated (1994-1995)
- CSULA, Early Entrance Program (1994-1996)
Admitted to college, full-time, at age 13
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Extracurricular Projects
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| Medical Elective Scheduling System |
- 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 adminstrator 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.
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| MSP Exam Archive & Assignment System |
- Medical student cooperative learning system
- Enhanced previous exam archive system by adding
complete assignments workflow system
- Allowed coordinators to seamlessly assign questions to
students for explanation and cooperative learning
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| Clinica Carino Patient Tracking DB |
- Developed patient information tracking system for
medical student free clinic community service program
- Convenient MS Access database and form input system
for non-technical users
- Allowed for better follow up for repeat patients
and facilitated summary research analysis for students
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| Grade Analysis Worksheets |
- 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.
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| Personal Information |
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| Email |
chenjh (at) uci.edu
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| Cell / Voicemail |
(626) 840-4491 |
| AIM |
jonc101x |
| Office |
ICS2 - 247 |
| Campus Mail |
444 Computer Science
Irvine, CA 92697-3430
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| Personal Website |
http://jonc101.tripod.com |
| CV / Resume |
Resume Page |
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| Affiliations |
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| Publications |
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Synthesis Explorer: A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction
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Jonathan H. Chen, Pierre Baldi.
Synthesis Explorer: A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction,
Journal of Chemical Education,
(accepted June 2008)
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ChemDB Update - Full-Text Search and Virtual Chemical Space
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Jonathan H. Chen, Erik Linstead, S. Joshua Swamidass, Dennis Wang, and Pierre Baldi
ChemDB Update - Full-Text Search and Virtual Chemical Space,
Bioinformatics 2007 23(17):2348-2351
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One- to Four-Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties
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Chloé-Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass, Jonathan Chen, Liva Ralaivola, and Pierre Baldi.
One- to Four-Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties,
Journal of Chemical Informatics and Modeling, 47(3):965-974, (2007)
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ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources
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Jonathan Chen*, S. Joshua Swamidass*, Yimeng Dou, Jocelyne Bruand, Pierre Baldi.
ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources,
Bioinformatics, 21(22):4133-4139, (2005)
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Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity
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S. Joshua Swamidass*, Jonathan Chen*, Peter Phung, Jocelyne Bruand, Liva Ralaivola, and Pierre Baldi.
Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.
Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05.
Bioinformatics, 21, Supplement 1, i359-368, (2005).
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Functional census of mutation sequence spaces: The example of p53 cancer rescue mutants
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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.
Functional census of mutation sequence spaces: The example of p53 cancer rescue mutants.
IEEE Transactions on Computational Biology and Bioinformatics, (2005).
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* These authors contributed equally
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Presentations
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Reaction prediction, classification, and retro-synthesis using a rule-based reaction expert system
[Demo Screenshots]
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Jonathan H. Chen, Qian-Nan Hu, Pierre Baldi
ACS National Meeting, New Orleans, LA, Spring 2008
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Synthesis Explorer: Organic chemistry tutorial system for multistep synthesis design and reaction mechanism prediction
[Demo Screenshots]
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Jonathan H. Chen, Pierre Baldi
ACS National Meeting, New Orleans, LA, Spring 2008
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| Organic Reaction Expert Systems (including Mechanism Explorer) |
UC Irvine MSTP Retreat 2008 (Winner of Best Presentation Award)
UC Irvine Bioinformatics Training Program Symposium 2008
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| Organic Reaction Expert Systems Proposal |
| UC Irvine Computer Science PhD Advancement to Candidacy, Summer 2007 |
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| Organic Reaction Expert Systems |
UC Irvine MSTP Retreat 2007 (Winner of Best Presentation Award)
UC Irvine Bioinformatics Training Program Symposium 2007
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| 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
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| 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
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| 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 |
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| Chemical Informatics: Database Searching, Similarity Measures and Property Prediction (1.3 MB) |
| National Library of Medicine Training Conference, Vanderbilt University, Spring 2006 |
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| Chemical Fingerprints and Retro-Synthetic Search (350KB) |
| UC Irvine, ICS 273A - Machine Learning, Winter 2006 |
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| Combinatorial Reactions, Applications and Discovery (2MB) |
| UC Irvine MSTP Retreat 2006 |
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| Chemical Toxicity Prediction |
| UC Irvine MSTP Retreat 2005 |
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| Chemical Informatics, The Importance of 3D Structure (2MB) |
| UC Irvine, ICS 277B - Probabilistic Modeling of Biological Data, Winter 2005 |
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| Chemical Toxicity Prediction, String Kernel Methods (200KB) |
| UC Irvine, ICS 277A - Algorithms and Representations in Molecular Biology, Fall 2004 |
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| p53 Surface Analysis (8MB) |
| UC Irvine MSTP Retreat 2004 |
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Please do not use the contents of these presentations without express permission.
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