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Jonathan Chen

Undergraduate
UCLA
Year of Entry into UCI MSTP
2002
Research Interests
Organic reaction expert systems. Just as human experts can solve problems with a pen & paper and a little expert intuition, these systems have the inherent ability to solve many of those same problems in organic chemistry. These will be applied in tasks ranging from drug discovery to broad explorations of chemical space. Refer to the link below for a much richer description and updated list of publications, presentations, etc.


Hobbies and Interests
Hometown
Hacienda Heights
Website

 

Lab Rotations Completed
Lab Advisor
Richard Lathrop
Department
ICS
Academic Quarter
Summer 2003
Project Topic
Prediction of p53 Cancer Mutant Function by Protein Surface Analysis
Project Abstract

Lab Advisor
Pierre Baldi
Department
ICS
Academic Quarter
Summer 2004
Project Topic
CombiCDB: Combinatorial Reaction Processing Extends the Utility of the UCI ChemDB
Project Abstract
High-throughput screening of small molecules, discovery of important chemical properties and in silico chemical synthesis and design can be greatly facilitated with large databases of small molecule information. Examples of this exploration to understand chemical space include screening drug candidate molecules by molecular docking or applying machine-learning techniques to predict chemical toxicity. Such databases enable this by allowing massive in silico chemical processing that would be impractical or impossible in a traditional in vitro setting. The UCI ChemDB has on the order of 107 compounds consolidated from multiple public and private sources. We hypothesize that the library’s size, and thus its utility, can be expanded even further from known available chemicals to theoretical compounds that are easily synthesized given those readily available sources. This can be achieved by applying in silico reactions to the current data set.

 

 

PUBLICATIONS
Jonathan Chen, S. Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, Pierre Baldi. , ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources. Bioinformatics(2005), 21(22):4133-4139.

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(2005), 21, Supplement 1, i359-368.

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), .

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(2007), 47(3):965-974.

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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