UC Irvine Medical Scientist Training Program

S Joshua Swamidass

Undergraduate	UC Irvine
Year of Entry into UCI MSTP	2001
Graduation Year	2009
Department	Information and Computer Sciences
Ph.D Advisor	Pierre Baldi
Thesis	Chemical databases, data structures, and algorithms
Postgraduate Training	Resident in Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University; Visiting scientist at the Broad Institute.
Last Known Position	Resident in Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University; Visiting scientist at the Broad Institute.
Website
Research Interests	Bioinformatics

PUBLICATIONS

L. Ralaivola, S. J. Swamidass, H. Saigo, and P. Baldi., Graph Kernels for Chemical Informatics.. Neural Networks(2006), 18:1093-110.
S. J. Swamidass, J. Chen, P. Phung, J. Bruand, L. Ralaivola, and P. 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. (2005), Bioinformatics, 21, Supplement 1, i359-368.
J. Chen, S. J. Swamidass, Y. Dou, J. Bruand, and P. Baldi., ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources. . Bioinformatics;(2005), 15;21:4133-9.
T. Lin, M. Melgar, S. J. Swamidass, J. Purdon, T. Tseng, G. Gago, D. Kurth, P. Baldi, H. Gramajo, and S. Tsai., Structure-Based Inhibitor Design of AccD5, an Essential acyl-CoA Carboxylase Carboxyltransferase Domain of Mycobacterium tuberculosis. . Proceedings of the National Academy of Sciences (2006), .
S. J. Swamidass and P. Baldi., Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sub-Linear Time. . The Journal of Chemical Informatics and Modeling.(2006), .
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, R. K. Brachmann, and R. H. Lathrop., Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants. . IEEE/ACM Trans Comput Biol Bioinform(2006), 3(2):114-125.
C.-A. Azencott, A. Ksikes, S. J. Swamidass, J. H. Chen, L. Ralaivola, and P. Baldi, One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties. J Chem Inf Model(2007), 47(3):965-974.
S. J. Swamidass and P. Baldi., Mathematical correction for fingerprint similarity measures to improve chemical retrieval.. J Chem Inf Model(2007), 47(3):952-964.
J. Chen, E. Linstead, S. J. Swamidass, D. Wang, and P. F. Baldi, ChemDB update - full-text search and virtual chemical space. . Bioinformatics(2007), .
P. F. Baldi, R. W. Benz, D. S. Hirschberg, S. J. Swamidass , Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval. J Chem Inf Model(2007), .
R. Benz. S. J. Swamidass, and P. F. Baldi, The discovery of Power-law distributions in chemistry. J Chem Inf Model(2008), Submitted.

GRANTS

The Mustard Seed Foundation Harvey Fellowship: , , .