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Russell Schwartz

Department of Biological Sciences and School of Computer Science
Carnegie Mellon University

Email: russells@andrew.cmu.edu
Phone: (412) 268-3971
Fax: (412) 268-7129
Office: 654B Mellon Institute

First created 11/4/02.
Last updated 1/30/10.

My research interests are in the area of computational molecular biology and the modeling and simulation of biological systems. My group is currently working most actively on three topics: simulation methods for macromolecular assembly systems, with special focus on more realistic models of assembly in cellular environments; methods for analysis of human genetic variation data, most recently focused on phylogenetics and population substructure analysis; and application of phylogenetic methods to study cancer progression.

Links

• My Biological Sciences homepage

Teaching

Spring 2010: 03-310/03-311 Introduction to Computational Molecular Biology

• This is a substantially redesigned class introduction to major computational ideas, tools, and data sets for biological research aimed at biology students with little or no prior computational experience. The class can be taken either as a full-semester version, 03-310, that covers genomics, modeling, and image informatics, or as either of two half-semester mini-classes, 03-311 for the genomics material or 03-312 for modeling and image informatics. Students with prior training in programming, algorithms, and data structures should instead consider 03-511.

Fall 2009: 03-512/03-712/15-507/15-871 Computational Methods for Biological Modeling and Simulation

• This is a class on models, algorithms, and numerical methods used in modeling and simulating biological systems. The class is aimed at graduate students and advanced undergraduates interested in developing new methods and tools for computational biology. It assumes introductory knowledge of biology, algorithms and data structures, and computer programming. See the course web page for more information.

• I recently converted the course notes for this class into a textbook Biological Modeling and Simulation available from the MIT Press.

Past Classes

• I previously developed 03-101C, Computational Resources for Biology, a first-year mini class for biology students devoted to hands-on work with on-line tools and databases for genomics. The material of this class was subsumed and expanded to create 03-311.

• I also co-developed 02-730, Cell and Systems Modeling, a core class of our n Ph.D. Program in Computational Biology jointly run by the University of Pittsburgh and Carnegie Mellon. I co-taught this class with Joel Stiles and Ivan Maly in Spring 2007 and Spring 2007. It is now taught by Joel Stiles and James Faeder.

• I also previously taught 03-311, the non-programming version of Introduction to Computational Biology. This was a 6-unit mini class intended to provide an introduction to major computational ideas, tools, and data sets aimed primarily at Biological Sciences students with little or no prior computational experience. This class was intended as a small-scale pilot for the material comprising the new 03-311, described above.

Software

• CLEAX package for inferring population substructure, history, and admixture events.

• HapMotif package for analyzing conserved segments of haploid sequences.

• DESSA discrete event self-assembly simulation software, a package for fast simulation of self-assembly systems.

• SCIMP web server implementing methods for finding maximum parsimony imperfect phylogenies on haplotype or genotype data.

Selected Recent Publications:  (Full Publication List)

• N. Misra, R. Ravi, and R. Schwartz. "Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny." International Conference on Research in Computational Molecular Biology (RECOMB), accepted for publication, 2010.

• R. Schwartz and S. Shackney. "Applying unmixing to gene expression data for tumor phylogeny inference." BMC Bioinformatics, 11:42, 2010.

• H. Gong, Y. Guo, A. D. Linstedt, and R. Schwartz. "Discrete, continuous, and stochastic models of protein sorting in the Golgi." Physical Review E, 81(1):011914, 2010.

• H. J. Greenberg, A. J. Holder, M.-Y. Leung, and R. Schwartz. "Computational biology and medical applications." OR/MS Today, 36(3): 36-41, 2009.

• B. Lee, P. R. LeDuc, and R. Schwartz. "Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model." Physical Review E, 80:041918, 2009.

• Y. Park, S. Shackney, and R. Schwartz. "Network-based inference of cancer progression from microarray data." IEEE Transactions on Computational Biology and Bioinformatics, 6(2):200-212, 2009.

• N. Misra and R. Schwartz. "Efficient stochastic sampling of first-passage times with applications to self-assembly simulations." Journal of Chemical Physics, 129:204109, 2008.

• S. Sridhar and R. Schwartz. "A human genome-wide library of local phylogeny predictions for whole-genome inference problems." BMC Genomics, 9:389, 2008.

• B. Lee, P. R. LeDuc, and R. Schwartz. "Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Greens function reaction dynamics." Physical Review E, 78:031911, 2008.

• N. Misra, D. Lees, T. Zhang, and R. Schwartz. "Pathway complexity of model virus capsid assembly systems." Computational and Mathematical Methods in Medicine, 9(3):277-293, 2008.

• H. Gong, D. Sengupta, A. D. Linstedt, and R. Schwartz. "Simulated de novo assembly of Golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion." Biophysical Journal, 95:1674-1688, 2008.

• S. Sridhar, F. Lam, G. E. Blelloch, R. Ravi, and R. Schwartz. "Mixed integer linear programming for maximum parsimony phylogeny inference." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(3):323-331, 2008.

• B. Sweeney, T. Zhang. and R. Schwartz. "Exploring the parameter space of complex self-assembly through virus capsid models." Biophysical Journal, 94:772-783 2008.

• P. LeDuc and R. Schwartz. "Computational models of molecular self-organization in cellular environments." Cell Biochemistry and Biophysics, 48(1):16-31, 2007

• S. Sridhar, F. Lam, G. E. Blelloch, R. Ravi, and R. Schwartz. "Direct maximum parsimony phylogeny reconstruction from genotype data." BMC Bioinformatics, 8:472, 2007.

• S. Sridhar, K. Dhamdhere, G. E. Blelloch, E. Halperin, R. Ravi, and R. Schwartz. "Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(4):561-571, 2007.

• K.M. Puskar, A. Parisi-Amon, S. Ta'asan, R. Schwartz, and P.R. LeDuc. "Modeling molecular interactions to understand spatial crowding effects on heterodimer formations." Physical Review E, 76:e041904, 2007.

• T. Zhang, W. Kim, and R. Schwartz. "Investigating scaling effects on virus capsid-like self-assembly using discrete event simulations." IEEE Transactions on Nanobioscience, 6(3):235-241, 2007.

• G. Pennington, C. E. Smith, S. Shackney, and R. Schwartz. "Reconstructing tumor phylogenies from single-cell data." Journal of Bioinformatics and Computational Biology, 5(02A):407-427, 2007.

• A. P. Pfenning, R. Schwartz, and A. Barth. "A comparative genomics approach to identifying the plasticity transcriptome." BMC Neuroscience, 3:20, 2007.