- 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.

- 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.

- C. Tan, R. Schwartz, L. You. "Phenotypic signatures arising from unbalanced bacterial growth," PLoS Computational Biology, 10(8):e1003751, 2014.

- 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.

- 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.

- 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.

- 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)

- 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)

- 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.

- 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.

- 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.

- 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.

- L. Xie, G. Smith, X. Feng, and R. Schwartz. "Surveying capsid assembly pathways through simulation-based data fitting." Biophysical Journal, 103:1545-1554, 2012.

- 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.

- 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)

- 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.

- 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.

- 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.

- B. Lee, P. R. LeDuc, and R. Schwartz. "Unified regression model of binding equilibria in crowded environments" Scientific Reports, 1:97, 2011.

- 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.

- 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)

- 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)

- 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.

- 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)

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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, 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

- 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.

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

- 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.

- 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.

- 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.

- 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.