Russell Schwartz - Publications

Affiliations: 
Biological Sciences Carnegie Mellon University, Pittsburgh, PA 

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Eaton J, Wang J, Schwartz R. Deconvolution and phylogeny inference of structural variations in tumor genomic samples. Bioinformatics (Oxford, England). 34: i357-i365. PMID 29950001 DOI: 10.1093/bioinformatics/bty270  0.32
2017 Roman T, Xie L, Schwartz R. Automated deconvolution of structured mixtures from heterogeneous tumor genomic data. Plos Computational Biology. 13: e1005815. PMID 29059177 DOI: 10.1371/journal.pcbi.1005815  0.56
2016 Gertz EM, Chowdhury SA, Lee WJ, Wangsa D, Heselmeyer-Haddad K, Ried T, Schwartz R, Schäffer AA. FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe. Plos One. 11: e0158569. PMID 27362268 DOI: 10.1371/journal.pone.0158569  0.56
2016 Smith GR, Xie L, Schwartz R. Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation. Plos One. 11: e0156547. PMID 27244559 DOI: 10.1371/journal.pone.0156547  0.56
2016 Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, et al. Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). Plos Computational Biology. 12: e1004943. PMID 27175996 DOI: 10.1371/journal.pcbi.1004943  0.56
2016 Xie L, Smith G, Schwartz R. Derivative-free optimization of rate parameters of capsid assembly models from bulk in vitro data. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 27168601 DOI: 10.1109/TCBB.2016.2563421  0.56
2016 Roman T, Xie L, Schwartz R. Medoidshift clustering applied to genomic bulk tumor data. Bmc Genomics. 17: 6. PMID 26817708 DOI: 10.1186/s12864-015-2302-x  0.56
2015 Subramanian A, Schwartz R. Reference-free inference of tumor phylogenies from single-cell sequencing data. Bmc Genomics. 16: S7. PMID 26576947 DOI: 10.1186/1471-2164-16-S11-S7  0.56
2015 Chowdhury SA, Gertz EM, Wangsa D, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R. Inferring models of multiscale copy number evolution for single-tumor phylogenetics. Bioinformatics (Oxford, England). 31: i258-67. PMID 26072490 DOI: 10.1093/bioinformatics/btv233  0.56
2015 Costa-Silva B, Aiello NM, Ocean AJ, Singh S, Zhang H, Thakur BK, Becker A, Hoshino A, Mark MT, Molina H, Xiang J, Zhang T, Theilen TM, García-Santos G, Williams C, ... ... Schwartz RE, et al. Pancreatic cancer exosomes initiate pre-metastatic niche formation in the liver. Nature Cell Biology. 17: 816-26. PMID 25985394 DOI: 10.1038/ncb3169  1
2015 Rasmussen TL, Ma Y, Park CY, Harriss J, Pierce SA, Dekker JD, Valenzuela N, Srivastava D, Schwartz RJ, Stewart MD, Tucker HO. Smyd1 facilitates heart development by antagonizing oxidative and ER stress responses. Plos One. 10: e0121765. PMID 25803368 DOI: 10.1371/journal.pone.0121765  0.32
2015 Kang J, Puskar KM, Ehrlicher AJ, LeDuc PR, Schwartz RS. Structurally governed cell mechanotransduction through multiscale modeling. Scientific Reports. 5: 8622. PMID 25722249 DOI: 10.1038/srep08622  0.56
2015 Simmons O, Snider P, Wang J, Schwartz RJ, Chen Y, Conway SJ. Persistent Noggin arrests cardiomyocyte morphogenesis and results in early in utero lethality. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 244: 457-67. PMID 25428115 DOI: 10.1002/dvdy.24233  0.32
2015 Ashktorab H, Daremipouran M, Devaney J, Varma S, Rahi H, Lee E, Shokrani B, Schwartz R, Nickerson ML, Brim H. Identification of novel mutations by exome sequencing in African American colorectal cancer patients. Cancer. 121: 34-42. PMID 25250560 DOI: 10.1002/cncr.28922  0.56
2014 Guo N, Schwartz RS, Qian J, Jia P, Deng Y. Network and pathway analysis of cancer susceptibility (a). Cancer Informatics. 13: 125-7. PMID 25861212 DOI: 10.4137/CIN.S24095  0.56
2014 Heselmeyer-Haddad KM, Berroa Garcia LY, Bradley A, Hernandez L, Hu Y, Habermann JK, Dumke C, Thorns C, Perner S, Pestova E, Burke C, Chowdhury SA, Schwartz R, Schäffer AA, Paris PL, et al. Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis. The American Journal of Pathology. 184: 2671-86. PMID 25131421 DOI: 10.1016/j.ajpath.2014.06.030  0.68
2014 Tan C, Smith RP, Tsai MC, Schwartz R, You L. Phenotypic signatures arising from unbalanced bacterial growth. Plos Computational Biology. 10: e1003751. PMID 25101949 DOI: 10.1371/journal.pcbi.1003751  0.56
2014 Chowdhury SA, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R. Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics. Plos Computational Biology. 10: e1003740. PMID 25078894 DOI: 10.1371/journal.pcbi.1003740  0.56
2014 Batzoglou S, Schwartz R. Computational biology and bioinformatics. Bioinformatics (Oxford, England). 30: i1-2. PMID 24931972 DOI: 10.1093/bioinformatics/btu304  0.56
2014 Tan C, Saurabh S, Bruchez MP, Schwartz R, LeDuc P. Reply to 'Complexity of molecular crowding in cell-free enzymatic reaction networks'. Nature Nanotechnology. 9: 407-8. PMID 24894472 DOI: 10.1038/nnano.2014.111  0.56
2014 Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV. Bioinformatics curriculum guidelines: toward a definition of core competencies. Plos Computational Biology. 10: e1003496. PMID 24603430 DOI: 10.1371/journal.pcbi.1003496  0.56
2014 Smith GR, Xie L, Lee B, Schwartz R. Applying molecular crowding models to simulations of virus capsid assembly in vitro. Biophysical Journal. 106: 310-20. PMID 24411263 DOI: 10.1016/j.bpj.2013.11.022  0.56
2013 Tsai MC, Blelloch G, Ravi R, Schwartz R. Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 1137-49. PMID 23959633  0.56
2013 Tan C, Saurabh S, Bruchez MP, Schwartz R, Leduc P. Molecular crowding shapes gene expression in synthetic cellular nanosystems. Nature Nanotechnology. 8: 602-8. PMID 23851358 DOI: 10.1038/nnano.2013.132  0.56
2013 Chowdhury SA, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R. Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. Bioinformatics (Oxford, England). 29: i189-98. PMID 23812984 DOI: 10.1093/bioinformatics/btt205  0.56
2013 Catanzaro D, Ravi R, Schwartz R. A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion. Algorithms For Molecular Biology : Amb. 8: 3. PMID 23343437 DOI: 10.1186/1748-7188-8-3  0.56
2012 Heselmeyer-Haddad K, Berroa Garcia LY, Bradley A, Ortiz-Melendez C, Lee WJ, Christensen R, Prindiville SA, Calzone KA, Soballe PW, Hu Y, Chowdhury SA, Schwartz R, Schäffer AA, Ried T. 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. The American Journal of Pathology. 181: 1807-22. PMID 23062488 DOI: 10.1016/j.ajpath.2012.07.012  0.56
2012 Xie L, Smith GR, Feng X, Schwartz R. Surveying capsid assembly pathways through simulation-based data fitting. Biophysical Journal. 103: 1545-54. PMID 23062347 DOI: 10.1016/j.bpj.2012.08.057  0.56
2012 Ruder WC, Hsu CP, Edelman BD, Schwartz R, Leduc PR. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid. Applied Physics Letters. 101: 63701. PMID 22952408 DOI: 10.1063/1.4742329  0.56
2012 Welch LR, Schwartz R, Lewitter F. A report of the Curriculum Task Force of the ISCB Education Committee. Plos Computational Biology. 8: e1002570. PMID 22761560 DOI: 10.1371/journal.pcbi.1002570  0.56
2012 Wren NS, Zhong Z, Schwartz RS, Dahl KN. Modeling nuclear blebs in a nucleoskeleton of independent filament networks. Cellular and Molecular Bioengineering. 5: 73-81. PMID 22523521 DOI: 10.1007/s12195-011-0196-5  0.56
2012 Lee B, LeDuc PR, Schwartz R. Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments. Plos One. 7: e30131. PMID 22272286 DOI: 10.1371/journal.pone.0030131  0.56
2011 Lee B, Leduc PR, Schwartz R. Unified regression model of binding equilibria in crowded environments. Scientific Reports. 1: 97. PMID 22355615 DOI: 10.1038/srep00097  0.56
2011 Misra N, Blelloch G, Ravi R, Schwartz R. An optimization-based sampling scheme for phylogenetic trees. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1599-609. PMID 21951054 DOI: 10.1089/cmb.2011.0164  0.56
2011 Misra N, Blelloch G, Ravi R, Schwartz R. Generalized buneman pruning for inferring the most parsimonious multi-state phylogeny. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 445-57. PMID 21385046 DOI: 10.1089/cmb.2010.0254  0.56
2011 Tsai MC, Blelloch G, Ravi R, Schwartz R. A consensus tree approach for reconstructing human evolutionary history and detecting population substructure. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 918-28. PMID 21282863 DOI: 10.1109/TCBB.2011.23  0.56
2011 Kang J, Steward RL, Kim Y, Schwartz RS, LeDuc PR, Puskar KM. Response of an actin filament network model under cyclic stretching through a coarse grained Monte Carlo approach. Journal of Theoretical Biology. 274: 109-19. PMID 21241710 DOI: 10.1016/j.jtbi.2011.01.011  0.56
2010 Gong H, Guo Y, Linstedt A, Schwartz R. Discrete, continuous, and stochastic models of protein sorting in the Golgi apparatus. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 81: 011914. PMID 20365406 DOI: 10.1103/PhysRevE.81.011914  0.56
2009 Lee B, LeDuc PR, Schwartz R. Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 041918. PMID 19905353 DOI: 10.1103/PhysRevE.80.041918  0.56
2008 Misra N, Schwartz R. Efficient stochastic sampling of first-passage times with applications to self-assembly simulations. The Journal of Chemical Physics. 129: 204109. PMID 19045854 DOI: 10.1063/1.3026595  0.56
2008 Lee B, Leduc PR, Schwartz R. Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Green's function reaction dynamics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 78: 031911. PMID 18851069 DOI: 10.1103/PhysRevE.78.031911  0.56
2008 Sridhar S, Schwartz R. A human genome-wide library of local phylogeny predictions for whole-genome inference problems. Bmc Genomics. 9: 389. PMID 18710563 DOI: 10.1186/1471-2164-9-389  1
2008 Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R. Mixed integer linear programming for maximum-parsimony phylogeny inference. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 5: 323-31. PMID 18670037 DOI: 10.1109/TCBB.2008.26  0.56
2008 Gong H, Sengupta D, Linstedt AD, Schwartz R. Simulated de novo assembly of golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion. Biophysical Journal. 95: 1674-88. PMID 18469086 DOI: 10.1529/biophysj.107.127498  0.56
2008 Sweeney B, Zhang T, Schwartz R. Exploring the parameter space of complex self-assembly through virus capsid models. Biophysical Journal. 94: 772-83. PMID 17921216 DOI: 10.1529/biophysj.107.107284  1
2007 Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R. Direct maximum parsimony phylogeny reconstruction from genotype data. Bmc Bioinformatics. 8: 472. PMID 18053244 DOI: 10.1186/1471-2105-8-472  0.56
2007 Sridhar S, Dhamdhere K, Blelloch G, Halperin E, Ravi R, Schwartz R. Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 4: 561-71. PMID 17975268 DOI: 10.1109/TCBB.2007.1070  0.56
2007 Zhang T, Kim WT, Schwartz R. Investigating scaling effects on virus capsid-like self-assembly using discrete event simulations. Ieee Transactions On Nanobioscience. 6: 235-41. PMID 17926782  1
2007 Pfenning AR, Schwartz R, Barth AL. A comparative genomics approach to identifying the plasticity transcriptome. Bmc Neuroscience. 8: 20. PMID 17355637 DOI: 10.1186/1471-2202-8-20  0.56
2006 Sridhar S, Blelloch GE, Ravi R, Schwartz R. Optimal imperfect phylogeny reconstruction and haplotyping (IPPH). Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 199-210. PMID 17369638  0.56
2006 Castellana N, Dhamdhere K, Sridhar S, Schwartz R. Relaxing haplotype block models for association testing. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 454-66. PMID 17094260  0.56
2006 Puskar K, Ta 'asan S, Schwartz R, LeDuc PR. Evaluating spatial constraints in cellular assembly processes using a monte carlo approach. Cell Biochemistry and Biophysics. 45: 195-201. PMID 16757820 DOI: 10.1385/CBB:45:2:195  0.56
2006 Zhang T, Schwartz R. Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics. Biophysical Journal. 90: 57-64. PMID 16214864 DOI: 10.1529/biophysj.105.072207  1
2004 Puskar K, Apeltsin L, Ta'asan S, Schwartz R, LeDuc PR. Understanding actin organization in cell structure through lattice based Monte Carlo simulations. Mechanics & Chemistry of Biosystems : McB. 1: 123-31. PMID 16783938  0.56
2004 Schwartz R. Algorithms for association study design using a generalized model of haplotype conservation. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 90-7. PMID 16448003  0.56
2004 Istrail S, Florea L, Halldórsson BV, Kohlbacher O, Schwartz RS, Yap VB, Yewdell JW, Hoffman SL. Comparative immunopeptidomics of humans and their pathogens. Proceedings of the National Academy of Sciences of the United States of America. 101: 13268-72. PMID 15326311 DOI: 10.1073/pnas.0404740101  0.56
2004 Halldórsson BV, Bafna V, Lippert R, Schwartz R, De La Vega FM, Clark AG, Istrail S. Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Research. 14: 1633-40. PMID 15289481 DOI: 10.1101/gr.2570004  0.56
2003 Florea L, Halldórsson B, Kohlbacher O, Schwartz R, Hoffman S, Istrail S. Epitope prediction algorithms for peptide-based vaccine design. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 2: 17-26. PMID 16826643 DOI: 10.1109/CSB.2003.1227293  0.56
2003 Schwartz R. Haplotype motifs: an algorithmic approach to locating evolutionarily conserved patterns in haploid sequences. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 2: 306-14. PMID 16452806  0.56
2003 Schwartz R, Halldórsson BV, Bafna V, Clark AG, Istrail S. Robustness of inference of haplotype block structure. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 13-9. PMID 12676048 DOI: 10.1089/106652703763255642  0.56
2002 Lippert R, Schwartz R, Lancia G, Istrail S. Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Briefings in Bioinformatics. 3: 23-31. PMID 12002221  0.56
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