Peer-Reviewed Journal Papers
2014
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S. E. Shackney, S. A. Chowdhury, R. Schwartz. "A novel subset of human tumors that simultaneously overexpress multiple E2F responsive genes found in breast, ovarian, and prostate cancer." Cancer Informatics, 13(S5):89, 2014.
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K. Heselmeyer-Haddad, L.Y. Berroa Garcia, A. Bradley, L. Hernandez, Y. Hu, J.K. Habermann, C. Dumke, C. Thorns, S. Perner, E. Pestova, C. Burke, S.A. Chowdhury, R. Schwartz, A.A. Schaffer, P. Paris, T. Ried. "Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis", American Journal of Pathology, 184(10):2671-2686, 2014.
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C. Tan, R. Schwartz, L. You. "Phenotypic signatures arising from unbalanced bacterial growth," PLoS Computational Biology, 10(8):e1003751, 2014.
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H. Ashktorab, M. Daremipouran, J. Devaney, S. Varma, H. Rahi, E., Lee, B. Shokrani, R. Schwartz, M. Nickerson, H. Brim. "Identification of novel mutations by exome sequencing in African American colorectal cancer patients", Cancer, 121(1):34-42, 2014.
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S.A. Chowdhury, S.E. Shackney, K. Heselmeyer-Haddad, T. Ried, A. Schaffer, R. Schwartz. "Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics," PLoS Computational Biology, 10(7):e1003740, 2014.
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G.R. Smith, L. Xie, B. Lee, and R. Schwartz. "Applying cellular crowding models to simulations of capsid assembly in vitro." Biophysical Journal, 106(1):310-320, 2014.
2013
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M.-C. Tsai, G. Blelloch, R. Ravi, and R. Schwartz. "Coalescent-based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(5):1137-1149, 2013. (extended version of ACM-BCB conference paper)
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A. Subramanian, S. Shackney, and R. Schwartz. "Novel multi-sample scheme for inferring phylogenetic markers from whole genome tumor profiles." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(6):1422-1431, 2013. (extended version of ISBRA conference paper)
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C. Tan, S. Saurabh, M. Bruchez, R. Schwartz, and P. LeDuc. "Molecular crowding shapes gene expression in synthetic cellular nanosystems." Nature Nanotechnology, 8(8):602-608, 2013.
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S. A. Chowdhury, S. E. Shackney, K. Heselmeyer-Haddad, T. Ried, A. A. Schffer, R. Schwartz. "Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations." Bioinformatics (proceedings issue for ISMB 2013), 29(13):i189-i198, 2013.
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D. Catanzaro, R. Ravi, and R. Schwartz. "A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion." Algorithms for Molecular Biology, 8:3, 2013.
2012
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K. Heselmeyer-Haddad, L. Y. Berroa Garcia, A. Bradley, C. Ortiz-Melendez, W.-J. Lee, R. Christensen, S. A. Prindiville, K. A. Calzone, P. W. Soballe, Y. Hu, S. A. Chowdhury, R. Schwartz, A. A. Schffer, and T. Ried. "Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity, yet conserved genomic imbalances and gain of MYC during progression." American Journal of Pathology, 181(11):1807-1822, 2012.
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L. Xie, G. Smith, X. Feng, and R. Schwartz. "Surveying capsid assembly pathways through simulation-based data fitting." Biophysical Journal, 103:1545-1554, 2012.
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W. C. Ruder, C.-P. D. Hsu, B. D. Edelman, R. Schwartz, and P. R. LeDuc "Biological colloid engineering: self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid." Applied Physics Letters, 101:063701, 2012.
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A. Subramanian, S. Shackney, and R. Schwartz. "Inference of tumor phylogenies from genomic assays on heterogeneous samples." Journal of Biomedicine and Biotechnology, 2012:798812, 2012. (extended version of 2011 ACM/BCB conference paper below)
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H. Kuwahara and R. Schwartz. "Stochastic steady state gain in a gene expression process with mRNA degradation control." Journal of the Royal Society Interface, 9:1589-1598, 2012.
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B. Lee, P. R. LeDuc, and R. Schwartz. "Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments." PLoS One, 7(1): e30131, 2012.
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N. S. Wren, R. Schwartz, and K. N. Dahl. "Modeling nuclear blebs in a nucleoskeleton of independent filament networks." Cellular and Molecular Bioengineering, 5(1):73-81, 2012.
2011
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B. Lee, P. R. LeDuc, and R. Schwartz. "Unified regression model of binding equilibria in crowded environments" Scientific Reports, 1:97, 2011.
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C. E. Tsourakakis, R. Peng, M. A. Tsiarli, G. L. Miller, and R. Schwartz. "Approximation algorithms for speeding up dynamic programming and denoising aCGH data." Journal of Experimental Algorithmics, 16:1.8, 2011.
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N. Misra, G. Blelloch, R. Ravi, and R. Schwartz. "An optimization-based sampling scheme for phylogenetic trees." Journal of Computational Biology, 18(11):1599-1609, 2011. (extended version of RECOMB conference paper)
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M.-C. Tsai, G. Blelloch, R. Ravi, and R. Schwartz. "A consensus-tree approach for reconstructing human evolutionary history and identifying population substructure." IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8(4):918-928, 2011. (extended version of Tsai et al. (2010) conference paper below)
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J. Kang, R. Steward, R. Schwartz, P. R. Leduc, and K. Puskar. "Controlled response of actin filament networks under cyclic stress through a coarse grained Monte Carlo model." Journal of Theoretical Biology, 274:109-119, 2011.
2010
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N. Misra, G. Blelloch, R. Ravi, and R. Schwartz. "Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny." Journal of Computational Biology, 18(3):445-457, 2011. (extended version of RECOMB 2010 paper, Lecture Notes in Bioinformatics, 6044:369-383, 2010)
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M. S. Kumar and R. Schwartz. "A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly." Physical Biology, 7:045005, 2010.
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G. Lancia, R. Rizzi, and R. Schwartz. "Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms." Proceedings of the Prague Stringology Conference (PSC 2010), pp. 89-102, 2010.
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M.-C. Tsai, G. Blelloch, R. Ravi, and R. Schwartz. "A consensus-tree approach for reconstructing human evolutionary history and identifying population substructure." Lecture Notes in Bioinformatics (Proc. International Symposium on Bioinformatics Research and Applications (ISBRA 2010)), 6053:167-178, 2010.
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R. Schwartz and S. Shackney. "Applying unmixing to gene expression data
for tumor phylogeny inference." BMC Bioinformatics, 11:42, 2010.
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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
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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.
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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.
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S. Sridhar and R. Schwartz. "A human genome-wide library of local
phylogeny predictions for whole-genome inference problems." BMC
Genomics, 9:389, 2008.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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A. P. Pfenning, R. Schwartz, and A. Barth. "A comparative genomics
approach to identifying the plasticity transcriptome." BMC
Neuroscience, 3:20, 2007.
2006
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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.
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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.
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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
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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
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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.
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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.
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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.
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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
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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
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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.
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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.
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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
2013
-
S. A. Chowdhury, S. E. Shackney, K. Heselmeyer-Haddad, T. Ried, A. A. Schffer, R. Schwartz. "Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations." Bioinformatics (proceedings issue for ISMB 2013), 29(13):i189-i198, 2013.
2012
-
M.-C. Tsai, G. Blelloch, R. Ravi, and R. Schwartz. "Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data." ACM Conference on Computational Biology and Biomedicine (ACM-BCB), 90-97, 2012.
-
A. Subramanian, S. Shackney, and R. Schwartz. "Novel multi-sample scheme for inferring phylogenetic markers from whole genome tumor profiles." Lecture Notes in Computer Science 7292 (Proc. International Symposium on Bioinformatics Research and Applications), 250-262, 2012.
2011
-
A. Subramanian, S. Shackney, and R. Schwartz. "Inference of tumor phylogenies from genomic assays on heterogeneous samples." Proceedings of the ACM Conference on Bioinformatics and Computational Biology, 2011.
-
N. Misra, G. Blelloch, R. Ravi, and R. Schwartz. "An optimization-based sampling scheme for phylogenetic trees." Proc. International Conference on Research in Computational Molecular Biology (RECOMB 2011), 252-266, 2011.
-
G. L. Miller, R. Peng, R. Schwartz, and C. Tsourakakis. "Approximate dynamic programming using halfspace queries and multiscale Monge decomposition." ACM Symposium on Discrete Algorithms (SODA2011), 1675-1682, 2011.
2010
-
D. Tolliver, C. Tsourakakis, A. Subramanian, S. Shackney, and R. Schwartz. "Robust unmixing of tumor states in array comparative genomic hybridization data." Bioinformatics (Proceedings Issue for Intelligent Systems for Molecular Biology (ISMB 2010)), 26(12):i106-i114, 2010.
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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), 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
-
A. Subramanian, S. Shackney, and R. Schwartz. "Tumor phylogenetics in the NGS era: strategies, challenges, and future prospects," Applications of Next Generation Sequencing in Cancer Research, Wei Wu and Hani Choudhry, eds., Springer, pp. 335-357, 2013.
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L. Bleris, I. Mandoiu, R. Schwartz, and J. Wang, eds. "Proc. International Symposium on Bioinformatics Research and Applications." Lecture Notes in Bioinformatics vol. 7292, Springer, 2012.
-
R. Schwartz. "Regulatory network inference." In Bioinformatics for Biologists, R. Shamir and P. Pevzner, eds., Cambridge University Press, 2011.
-
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
-
L. Welch, F. Lewitter, R. Schwartz, C. Brooksbank. P. Radivojac, B. Gaeta, M.V. Schneider. "Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies," PLoS Computational Biology, 10(3): e1003496, 2014.
-
L. Welch, R. Schwartz, and F. Lewitter. "A Report of the Curriculum Task Force of the ISCB Education Committee." PLoS Computational Biology, 8(6): e1002570, 2012.
-
C. Tsourakakis, D. Tolliver, M. A. Tsiarli, S. Shackney, and R. Schwartz. "CGHTrimmer: Discretizing noisy array CGH data." arXiv:1002.4438v1, 2010.
-
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.