Home Page for Russell Schwartz

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 3/27/07.

My research interests are in the area of computational molecular biology and the modeling and simulation of biological systems.

Links

My Biological Sciences homepage

Teaching

Last term, I taught a Mellon College of Science freshman mini class on Web-based tools and database for biology research.

This term, I am teaching 03-512/03-712, a class on computational methods for biological modeling and simulation. This class is intended to teach graduate students and advanced undergraduates the major algorithms, data structures, and design methodologies needed for modeling and simulation in biology. See the course web page for more information.

Next term, I will be co-teaching 02-730, Cell and Systems Modeling, a core class of our new Ph.D. Program in Computational Biology jointly run by the University of Pittsburgh and Carnegie Mellon.

Software

HapMotif package for analyzing conserved segments of haploid sequences.

We have released version 1.2.0 of our Discrete-Event Self-Assembly Simulator software, a package for fast simulation of self-assembly systems.

We have recently added a web server implementing methods we have developed for finding imperfect phylogenies on genetic data.

Selected Publications:

S. Sridhar, F. Lam, G. E. Blelloch, R. Ravi, and R. Schwartz. "Efficiently finding the most parsimonious phylogenetic tree via linear programming." International Symposium on Bioinformatics Research and Applications, accepted for publication, 2007.

P. LeDuc and R. Schwartz. "Computational models of molecular self-organization in cellular environments." Cell Biochemistry and Biophysics, accepted for publication, 2007.

G. Pennington, C. E. Smith, S. Shackney, and R. Schwartz. "Reconstructing tumor phylogenies from single-cell data." Journal of Bioinformatics and Computational Biology, accepted for publication, 2007.

S. Sridhar, K. Dhamdhere, G. E. Blelloch, E. Halperin, R. Ravi, and R. Schwartz. "Simple reconstruction of binary near-perfect phylogenetic trees." IEEE/ACM Transactions on Computational Biology and Bioinformatics, accepted for publication, 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, accepted for publication, 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.