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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 7/31/09.

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

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.

Spring 2009: 03-311 Introduction to Computational Molecular Biology

• This is 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. Students with prior training in programming, algorithms, and data structures should instead consider 03-510.

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.

Software

• 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 Publications:  (Full Publication List)

• 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.

• 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.

• S. Sridhar, K. Dhamdhere, G. E. Blelloch, E. Halperin, R. Ravi, and R. Schwartz. "Fixed parameter tractability of binary near-perfect phylogenetic tree reconstruction." Proceedings of the International Colloquium on Automata, Languages, and Computability (ICALP), 2006.

• D. R. Emlet, R. Schwartz, K. Brown, A. A. Pollice, C. A. Smith, and S. E. Schackney. "HER2 expression as a potential marker for response to therapy targeted to the EGFR." British Journal of Cancer, 94(8):1144-1153, 2006.

• K. Puskar, S. Ta'asan, R. Schwartz, and P. LeDuc. "Evaluating spatial constraints in cellular assembly processes using a Monte Carlo approach." Cell Biochemistry and Biophysics, 45(2):195-202, 2006.

• T. Zhang and R. Schwartz. "Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics." Biophysical Journal, 90:57-64, 2006.

• N. Castellana, K. Dhamdhere, S. Sridhar, and R. Schwartz. "Relaxing haplotype block models for association testing." Proceedings of the Pacific Symposium on Biocomputing (PSB06), 2006.

• R. Schwartz and J. King. "Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure." Protein Science, 15:102-112, 2006.

• R. Schwartz, P. W. Shor, and B. Berger. "Local rule simulations of capsid assembly." Journal of Theoretical Medicine, 6:81-86, 2005.

• F. Jamalyaria, R. Rohlfs, and R. Schwartz. "Queue-based Method for Efficient Simulation of Biological Self-Assembly Systems." Journal of Computational Physics, 204:100-120, 2005.

• K. Dhamdhere, S. Sridhar, G.E. Blelloch, E. Halperin, R. Ravi, and R. Schwartz. "A New Algorithm for the Reconstruction of Near-Perfect Binary Phylogenetic Trees." CMU Computer Science Technical Report CMU-CS-05-119, 2005.

• S. Istrail, L. Florea, B. Halldorsson, O. Kohlbacher, R. Schwartz, J. Yewdell, and S. Hoffman. "Comparative immuno-peptidomics of humans and their pathogens." Proceedings of the National Academy of Sciences USA, 101:13268-13272, 2004.

• R. Schwartz. "Algorithms for association study design using a generalized model of haplotype conservation." Proceedings of the Third IEEE Computational Systems Biotechnology Conference, 90-97, 2004.

• S. Sridhar, K. Dhamdhere, G.E. Blelloch, R. Ravi, and R. Schwartz. "Evaluation of the Haplotype Motif Model using the Principle of Minimum Description." CMU Computer Science Technical Report CMU-CS-04-166, 2004.

• B. Halldorsson, V. Bafna, R. Lippert, R. Schwartz, F. De la Vega, A. Clark, and S. Istrail. "Optimal block-free selection of tagging SNPs for genome-wide association studies." Genome Research, 14:1633-1640, 2004.

• K. Puskar, L. Apeltsin, S. Ta'asan, R. Schwartz, and P. R. LeDuc. "Understanding actin organization in cell structure through lattice Monte Carlo simulations." Mechanics and Chemistry of Biosystems, 1:123-131, 2004.

• R. Schwartz. "Haplotype motifs: an algorithmic approach to locating evolutionarily conserved patterns in haploid sequences." Proceedings of the Second IEEE Computer Society Bioinformatics Conference, pp. 306-314, 2003.

• R. Schwartz, B. Halldorsson, V. Bafna, A. G. Clark, and S. Istrail. "Robustness of inference of haplotype block structure." Journal of Computational Biology, 10(1): 13-20, 2003.

• V. Bafna, B. Halldorsson, R. Schwartz, A. Clark, and S. Istrail. "Haplotypes and informative SNP selection algorithms." Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2003), 19-27, 2003.

• R. Lippert, R. Schwartz, G. Lancia, and S. Istrail. "Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem." Briefings in Bioinformatics, 3(1): 23-31, 2002.

• R. Schwartz, A. G. Clark, and S. Istrail. "Methods for inferring block-wise ancestral history from haploid sequences: the haplotype coloring problem." Lecture Notes in Computer Science 2452 (Proceedings of the Second Workshop on Algorithms in Bioinformatics), 44-59, 2002.

• G. Lancia, V. Bafna, S. Istrail, R. Lippert, and R. Schwartz. S"NPs problems, complexity, and algorithms." Lecture Notes in Computer Science 2161 (Proceedings of the Ninth Annual European Symposium on Algorithms): 182-183, 2001.

• R. Schwartz, C. Ting, and J. King. "Whole-proteome pI values correlate with sub-cellular localization for organisms in the three domains of life." Genome Research, 11(5):703-709, 2001.

• R. Schwartz, S. Istrail, and J. King. "Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues." Protein Science, 10(5):1023-1031, 2001.

• R. Schwartz. "The local rules dynamics model for self-assembly simulation." MIT Computer Science Ph.D. Thesis (Published as MIT-LCS TR-800), 2000.

• R. Schwartz, R. L. Garcea, and B. Berger. "`Local rules’ theory applied to polyomavirus polymorphic capsid assemblies." Virology, 268(2):461-470, 2000.

• B. Berger, J. A. King, R. Schwartz, and P. W. Shor. "Local rule mechanism for selecting icosahedral shell geometry." Discrete Applied Mathematics, 105:55-69, 2000.

• S. Istrail, R. Schwartz, and J. King. "Lattice simulations of aggregation funnels for protein folding." Journal of Computational Biology, 6(2):143-162, 1999.

• R. Schwartz, P. W. Shor, P. E. Prevelige, Jr., and B. Berger. "Local rules simulation of the kinetics of virus capsid self-assembly." Biophysical Journal, 75:2626-2636, 1998.