Peer-Reviewed Journal Papers

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.

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.

2008

• 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.

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.

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.

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

2005

• F. Jamalyaria, R. Rohlfs, and R. Schwartz. "Queue-based method for efficient simulation of biological self-assembly systems." Journal of Computational Physics, 204(1):100-120, 2005.

2004

• R. Schwartz. "Haplotype parsing: methods for extracting information from human genetic variations." Applied Bioinformatics (special issue devoted to work presented at the First Biological Language Conference, 2003), 3:181-191, 2004.

• 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 Academies of Science USA, 101:13268-13272, 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.

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.

2002

• 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.

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.

• J. C. Venter, M. A. Adams, E. W. Myers, et al. "The sequence of the human genome." Science, 291(5507):1304-1351, 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.

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.

1999

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

1998

• 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.

Peer-Reviewed Conference Papers

2010

• 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.

2008

• Y. Park, S. Shackney, and R. Schwartz. "Network-based inference of cancer progression from microarray data." International Symposium of Bioinformatics Research and Applications (ISBRA08), pp. 268-279, 2008.

2007

• S. Sridhar, F. Lam, G. E. Blelloch, R. Ravi, and R. Schwartz. "Efficiently finding the most parsimonious phylogenetic tree via linear programming." Lecture Notes in Bioinformatics vol. 4463 (Proceedings of the International Symposium on Bioinformatics Research and Applications), 37-48, 2007.

2006

• G. E. Blelloch, K. Dhamdhere, E. Halperin, R. Ravi, R. Schwartz, and S. Sridhar. "Fixed parameter tractability of binary near-perfect phylogenetic tree reconstruction." Proceedings of the International Colloquium on Automata, Languages, and Computability (ICALP), pp. 667-678, 2006.

• S. Sridhar, G. E. Blelloch, R. Ravi, and R. Schwartz. "Optimal imperfect phylogeny reconstruction and haplotyping." Proceedings of the Computational Systems Bioinformatics Conference (CSB06), pp.199-210, 2006.

• G. Pennington, C. A. Smith, S. Shackney, and R. Schwartz. "Expectation-maximization method for the reconstruction of tumor phylogenies from single-cell data." Proceedings of the Computational Systems Bioinformatics Conference (CSB06), pp. 371-380, 2006.

• S. Sridhar, K. Dhamdhere, G. E. Blelloch, E. Halperin, R. Ravi, and R. Schwartz. "Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees." International Workshop on Bioinformatics Research and Applications (IWBRA06), 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), pp. 454-466, 2006.

2005

• T. Zhang, R. Rohlfs, and R. Schwartz. "Implementation of a discrete event simulator for biological self-assembly systems." Proceedings of the INFORMS Winter Simulation Conference, pp. 2223-2231, 2005.

2004

• R. Schwartz. "Algorithms for association study design using a generalized model of haplotype conservation." Proceedings of the 3rd IEEE Computational Systems Biotechnology Conference, 90-97, 2004.

• R. Schwartz, A. G. Clark, and S. Istrail. "Inferring piecewise ancestral history from haploid sequences." Proceedings of the 2002 DIMACS/RECOMB Satellite Workshop on SNPs and Haplotype Assembly (published as Lecture Notes in Bioinformatics 2983), pp.62-73, 2004.

2003

• L. Florea, B. Halldorsson, O. Kohlbacher, R. Schwartz, S. Hoffman, and S. Istrail. "Epitope prediction algorithms for peptide-based vaccine design." Proceedings of the Second IEEE Computer Society Bioinformatics Conference, pp. 17-26, 2003.

• 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.

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

2002

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

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

2001

• R. J. Turner, K. Chaturvedi, N. J. Edwards, D. Fasulo, A. L. Halpern, D. H. Huson, O. Kohlbacher, J. R. Miller, K. Reinert, K. A. Remington, R. Schwartz, B. Walenz, S. Yooseph, and S. Istrail. "Visualization Challenges for a New Cyberpharmaceutical Computing Paradigm." In Proceedings of the IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics, 2001.

1999

• L. W. Hobbs, C. E. Jesurum, A. Coventry, V. Pulim, R. Schwartz, and B. Berger. "Towards a topological description of poorly-crystalline networks." In Advances in Materials for the 21st Century: The 1999 Julia R. Weertman Symposium, 1999.

1998

• R. Schwartz and B. Berger. "Applying multithreaded programming to the simulation of virus shell self-assembly." Proceedings of the Yale Multithreaded Programming Workshop, 1998.

Books and Book Chapters

• R. Schwartz. Biological Modeling and Simulation: A Survey of Practical Models, Algorithms, and Numerical Methods. MIT Press: Cambridge, MA, 2008.

• S. Shackney, D. R. Emlet, R. Schwartz, K. A. Brown, A. A. Pollice, and C.A. Smith. "Expression of HER-2 and epidermal growth factor receptor as clinical markers for response to targeted therapy." in M.A. Hayat, ed. Methods of Cancer Diagnosis, Therapy, and Prognosis: vol. 1, Breast Carcinoma. Springer: Netherlands, 2008.

Review Articles

• R. Schwartz. "Theory and algorithms for the haplotype assembly problem." Communications in Information Systems, in press, 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.

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

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

Unrefereed Reports

• N. Misra and R. Schwartz. "Efficient stochastic sampling of first passage times for fracturing bond networks." arXiv:0804.0448v1, 2008.

• G. Pennington, S. Shackney, and R. Schwartz. "Cancer phylogenetics from single-cell assays." CMU Computer Science Department Technical Report CMU-CS-06-103, 2006.

• 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 Department Technical Report CMU-CS-05-119, 2005.

• S. Sridhar, K. Dhamdhere, G. E. Blelloch, E. Halperin, R. Ravi, and R. Schwartz. "FPT algorithms for binary near-perfect phylogenetic trees." CMU Computer Science Department Technical Report CMU-CS-05-181, 2005.

• 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 Department Technical Report CMU-CS-04-166, 2004.

• R. Schwartz. "The local rules dynamics model for self-assembly simulation." MIT Laboratory for Computer Science Technical Report 800, 2000.

• R. Schwartz, P. E. Prevelige, Jr., and B. Berger. "Local rules modeling of nucleation-limited virus capsid assembly." MIT Laboratory for Computer Science Technical Memo 584, 1998.