| Year |
Citation |
Score |
| 2023 |
Bristy NA, Fu X, Schwartz R. Sc-TUSV-ext: Single-cell clonal lineage inference from single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV). Biorxiv : the Preprint Server For Biology. PMID 38106049 DOI: 10.1101/2023.12.07.570724 |
0.305 |
|
| 2022 |
Tao Y, Ma X, Palmer D, Schwartz R, Lu X, Osmanbeyoglu HU. Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers. Nucleic Acids Research. PMID 36243974 DOI: 10.1093/nar/gkac881 |
0.663 |
|
| 2022 |
Lei H, Guo XA, Tao Y, Ding K, Fu X, Oesterreich S, Lee AV, Schwartz R. Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer. Bioinformatics (Oxford, England). 38: i386-i394. PMID 35758822 DOI: 10.1093/bioinformatics/btac262 |
0.668 |
|
| 2022 |
Fu X, Lei H, Tao Y, Schwartz R. Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations. Bioinformatics (Oxford, England). 38: i125-i133. PMID 35758777 DOI: 10.1093/bioinformatics/btac253 |
0.667 |
|
| 2022 |
Ren S, Tao Y, Yu K, Xue Y, Schwartz R, Lu X. De novo Prediction of Cell-Drug Sensitivities Using Deep Learning-based Graph Regularized Matrix Factorization. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27: 278-289. PMID 34890156 |
0.637 |
|
| 2021 |
Fu X, Lei H, Tao Y, Heselmeyer-Haddad K, Torres I, Dean M, Ried T, Schwartz R. Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 34612714 DOI: 10.1089/cmb.2021.0255 |
0.687 |
|
| 2021 |
Lei H, Gertz EM, Schäffer AA, Fu X, Tao Y, Heselmeyer-Haddad K, Torres I, Li G, Xu L, Hou Y, Wu K, Shi X, Dean M, Ried T, Schwartz R. Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. Bioinformatics (Oxford, England). PMID 34289030 DOI: 10.1093/bioinformatics/btab504 |
0.677 |
|
| 2021 |
Tao Y, Rajaraman A, Cui X, Cui Z, Chen H, Zhao Y, Eaton J, Kim H, Ma J, Schwartz R. Assessing the contribution of tumor mutational phenotypes to cancer progression risk. Plos Computational Biology. 17: e1008777. PMID 33711014 DOI: 10.1371/journal.pcbi.1008777 |
0.652 |
|
| 2020 |
Tao Y, Lei H, Lee AV, Ma J, Schwartz R. Neural Network Deconvolution Method for Resolving Pathway-Level Progression of Tumor Clonal Expression Programs With Application to Breast Cancer Brain Metastases. Frontiers in Physiology. 11: 1055. PMID 33013452 DOI: 10.3389/Fphys.2020.01055 |
0.693 |
|
| 2020 |
Tao Y, Lei H, Fu X, Lee AV, Ma J, Schwartz R. Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis. Bioinformatics (Oxford, England). 36: i407-i416. PMID 32657393 DOI: 10.1093/Bioinformatics/Btaa396 |
0.698 |
|
| 2020 |
Lei H, Lyu B, Gertz EM, Schäffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R. Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 32181683 DOI: 10.1089/Cmb.2019.0302 |
0.422 |
|
| 2019 |
Lei H, Lyu B, Gertz EM, Schaeffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R. Abstract 1650: Deconvolution of copy number alterations combining bulk and single-cell genomic data Cancer Research. 79: 1650-1650. DOI: 10.1158/1538-7445.Am2019-1650 |
0.416 |
|
| 2018 |
Kang J, Rancati T, Lee S, Oh JH, Kerns SL, Scott JG, Schwartz R, Kim S, Rosenstein BS. Machine Learning and Radiogenomics: Lessons Learned and Future Directions. Frontiers in Oncology. 8: 228. PMID 29977864 DOI: 10.3389/Fonc.2018.00228 |
0.324 |
|
| 2018 |
Thomas M, Schwartz R. A method for efficient Bayesian optimization of self-assembly systems from scattering data. Bmc Systems Biology. 12: 65. PMID 29884203 DOI: 10.1186/S12918-018-0592-8 |
0.465 |
|
| 2017 |
Oltmann J, Heselmeyer-Haddad K, Hernandez LS, Meyer R, Torres I, Hu Y, Doberstein N, Killian JK, Petersen D, Zhu YJ, Edelman DC, Meltzer PS, Schwartz R, Gertz EM, Schäffer AA, et al. Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients. Genes, Chromosomes & Cancer. PMID 29181861 DOI: 10.1002/Gcc.22515 |
0.347 |
|
| 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 |
0.433 |
|
| 2017 |
Thomas M, Schwartz R. Quantitative computational models of molecular self-assembly in systems biology. Physical Biology. 14: 035003. PMID 28535149 DOI: 10.1088/1478-3975/Aa6Cdc |
0.425 |
|
| 2017 |
Schwartz R, Schäffer AA. The evolution of tumour phylogenetics: principles and practice. Nature Reviews. Genetics. PMID 28190876 DOI: 10.1038/Nrg.2016.170 |
0.343 |
|
| 2017 |
Roman T, Xiao B, Schwartz R. Abstract 974: Automating deconvolution of heterogeneous bulk tumor genomic data Cancer Research. 77: 974-974. DOI: 10.1158/1538-7445.Am2017-974 |
0.428 |
|
| 2017 |
Torres IM, Hernandez L, Tzeng J, Schwartz R, Schaffer A, Gertz E, Brower S, Sanchez M, Auer G, Heselmeyer-Haddad K, Thomas R. Abstract 2908: Single-cell genetic analysis of ductal carcinoma in situ with and without synchronous invasive breast cancer by multiplex FISH delineates specific patterns of tumor clonality and heterogeneity Cancer Research. 77: 2908-2908. DOI: 10.1158/1538-7445.Am2017-2908 |
0.303 |
|
| 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 |
0.399 |
|
| 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 |
0.696 |
|
| 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 |
0.687 |
|
| 2016 |
Subramanian A, Schwartz R. Erratum to: 'Reference-free inference of tumor phylogenies from single-cell sequencing data'. Bmc Genomics. 17: 348. PMID 27164840 DOI: 10.1186/S12864-016-2609-2 |
0.308 |
|
| 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 |
0.412 |
|
| 2016 |
Wangsa D, Chowdhury SA, Ryott M, Gertz EM, Elmberger G, Auer G, Åvall Lundqvist E, Küffer S, Ströbel P, Schäffer AA, Schwartz R, Munck-Wikland E, Ried T, Heselmeyer-Haddad K. Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis. International Journal of Cancer. Journal International Du Cancer. 138: 98-109. PMID 26175310 DOI: 10.1002/Ijc.29691 |
0.327 |
|
| 2016 |
Roman T, Xie L, Schwartz R. Abstract 849: Improved geometric deconvolution of bulk tumor genomic data Cancer Research. 76: 849-849. DOI: 10.1158/1538-7445.Am2016-849 |
0.419 |
|
| 2015 |
Kang J, Schwartz R, Flickinger J, Beriwal S. Machine Learning Approaches for Predicting Radiation Therapy Outcomes: A Clinician's Perspective. International Journal of Radiation Oncology, Biology, Physics. 93: 1127-35. PMID 26581149 DOI: 10.1016/J.Ijrobp.2015.07.2286 |
0.311 |
|
| 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 |
0.369 |
|
| 2015 |
Catanzaro D, Shackney S, Schaffer A, Schwartz R. Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 26353381 DOI: 10.1109/Tcbb.2015.2476808 |
0.365 |
|
| 2015 |
Roman T, Nayyeri A, Fasy BT, Schwartz R. A simplicial complex-based approach to unmixing tumor progression data. Bmc Bioinformatics. 16: 254. PMID 26264682 DOI: 10.1186/S12859-015-0694-X |
0.378 |
|
| 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 |
0.407 |
|
| 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 |
0.303 |
|
| 2015 |
Chowdhury SA, Gertz EM, Wangsa D, Heselmeyer-Haddad K, Ried T, Schaeffer A, Schwartz R. Abstract 2182: Reconstructing evolutionary models of tumor progression from single-cell heterogeneity data Cancer Research. 75: 2182-2182. DOI: 10.1158/1538-7445.Am2015-2182 |
0.37 |
|
| 2015 |
Roman T, Schwartz R. Abstract 1934: Improved deconvolution of heterogeneous tumor data to reconstruct clonal evolution from bulk genomic samples Cancer Research. 75: 1934-1934. DOI: 10.1158/1538-7445.Am2015-1934 |
0.445 |
|
| 2015 |
Xie L, Smith G, Schwartz R. Applying Derivative-Free Optimization to Fit Kinetic Parameters of Viral Capsid Self-Assembly Models from Multi-Source Bulk in vitro Data Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.2572 |
0.707 |
|
| 2015 |
Smith GR, Xie L, Schwartz R. Computationally Projecting the Influence of Nucleic Acid on Pathways of Nucleation-Limited Virus Capsid Assembly Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.1734 |
0.713 |
|
| 2014 |
Shackney SE, Chowdhury SA, Schwartz R. A Novel Subset of Human Tumors That Simultaneously Overexpress Multiple E2F-responsive Genes Found in Breast, Ovarian, and Prostate Cancers. Cancer Informatics. 13: 89-100. PMID 25392696 DOI: 10.4137/Cin.S14062 |
0.309 |
|
| 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 |
0.436 |
|
| 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 |
0.677 |
|
| 2014 |
Chowdhury SA, Subramanian A, Schäffer AA, Shackney SE, Wangsa D, Heselmeyer-Haddad K, Ried T, Schwartz R. Abstract 5338: Inferring evolutionary models of tumor progression from single-cell heterogeneity data Cancer Research. 74: 5338-5338. DOI: 10.1158/1538-7445.Am2014-5338 |
0.434 |
|
| 2014 |
Smith GR, Xie L, Lee B, Schwartz R. Evaluating the Influence of Environment on Virus Capsid Assembly Pathways through Stochastic Simulation Biophysical Journal. 106: 61a. DOI: 10.1016/J.Bpj.2013.11.417 |
0.701 |
|
| 2013 |
Subramanian A, Shackney S, Schwartz R. Novel multisample scheme for inferring phylogenetic markers from whole genome tumor profiles. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 1422-31. PMID 24407301 DOI: 10.1109/Tcbb.2013.33 |
0.407 |
|
| 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 DOI: 10.1109/Tcbb.2013.98 |
0.358 |
|
| 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 |
0.415 |
|
| 2013 |
Subramanian A, Shackney S, Schwartz R. Abstract 5133: Inference of tumor phylogenetic markers from large copy number datasets. Cancer Research. 73: 5133-5133. DOI: 10.1158/1538-7445.Am2013-5133 |
0.383 |
|
| 2013 |
Chowdhury SA, Schäffer AA, Shackney SE, Wangsa D, Heselmeyer-Haddad K, Ried T, Schwartz R. Abstract 2895: Phylogenetic models of tumor progression from fluorescence in situ hybridization (FISH) data on many single cells of a solid tumor. Cancer Research. 73: 2895-2895. DOI: 10.1158/1538-7445.Am2013-2895 |
0.413 |
|
| 2013 |
Xie L, Smith GR, Schwartz R. Improving Inference of Rate Parameters for Viral Capsid Assembly Systems Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.2302 |
0.697 |
|
| 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 |
0.33 |
|
| 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 |
0.675 |
|
| 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 |
0.312 |
|
| 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 |
0.328 |
|
| 2012 |
Subramanian A, Schwartz R, Shackney S. Abstract 3964: Inference of robust tumor phylogenetic markers from multi-sample data Cancer Research. 72: 3964-3964. DOI: 10.1158/1538-7445.Am2012-3964 |
0.422 |
|
| 2012 |
Smith GR, Xie L, Feng X, Lee B, Schwartz R. Translating Bulk Measures of Capsid Assembly Progress into Insights on Fine-Scale Kinetics and Pathways Biophysical Journal. 102: 640a. DOI: 10.1016/J.Bpj.2011.11.3485 |
0.707 |
|
| 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 |
0.366 |
|
| 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 |
0.309 |
|
| 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 |
0.368 |
|
| 2011 |
Tsourakakis CE, Peng R, Tsiarli MA, Miller GL, Schwartz R. Approximation algorithms for speeding up dynamic programming and denoising aCGH data Acm Journal of Experimental Algorithms. 16. DOI: 10.1145/1963190.2063517 |
0.318 |
|
| 2011 |
Lee B, LeDuc PR, Schwartz R. Toward a Unified Model of Molecular Crowding: A Regression Approach to Predict Equilibria and Kinetics of Assembly Systems in Crowded Environments Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3532 |
0.392 |
|
| 2011 |
Kumar MS, Smith G, Xie L, Khandpur RP, Schwartz R. Learning Physical Parameters of Capsid Assembly Systems from Indirect Measures of Assembly Progress Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.2391 |
0.48 |
|
| 2010 |
Kumar MS, Schwartz R. A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly. Physical Biology. 7: 045005. PMID 21149973 DOI: 10.1088/1478-3975/7/4/045005 |
0.356 |
|
| 2010 |
Tolliver D, Tsourakakis C, Subramanian A, Shackney S, Schwartz R. Robust unmixing of tumor states in array comparative genomic hybridization data. Bioinformatics (Oxford, England). 26: i106-14. PMID 20529894 DOI: 10.1093/Bioinformatics/Btq213 |
0.385 |
|
| 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 |
0.553 |
|
| 2010 |
Schwartz R. Theory and Algorithms for the Haplotype Assembly Problem Communications in Information and Systems. 10: 23-38. DOI: 10.4310/Cis.2010.V10.N1.A2 |
0.372 |
|
| 2010 |
Lee B, LeDuc PR, Schwartz R. Simulation Study of Binding Chemistry in Crowded Conditions Using Two- and Three-Dimensional Stochastic Off-Lattice Models Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.331 |
0.376 |
|
| 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 |
0.369 |
|
| 2009 |
Park Y, Shackney S, Schwartz R. Network-based inference of cancer progression from microarray data. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 6: 200-12. PMID 19407345 DOI: 10.1109/Tcbb.2008.126 |
0.605 |
|
| 2009 |
Lee B, LeDuc PR, Schwartz R. Parameter Effects Of Crowding On Binding Chemistry Using Stochastic Off-lattice Simulations Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.344 |
0.402 |
|
| 2009 |
Misra N, Schwartz R. Multiscale Simulation of Nucleation-limited Viral Capsid Assembly Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.2056 |
0.475 |
|
| 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 |
0.399 |
|
| 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 |
0.449 |
|
| 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 |
0.578 |
|
| 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 |
0.567 |
|
| 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 |
0.548 |
|
| 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 |
0.77 |
|
| 2008 |
Misra N, Lees D, Zhang T, Schwartz R. Pathway Complexity of Model Virus Capsid Assembly Systems Computational and Mathematical Methods in Medicine. 9: 277-293. DOI: 10.1080/17486700802168379 |
0.773 |
|
| 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 |
0.567 |
|
| 2007 |
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Schwartz R, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.656 |
|
| 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 |
0.548 |
|
| 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 DOI: 10.1109/Tnb.2007.903484 |
0.771 |
|
| 2007 |
LeDuc P, Schwartz R. Computational models of molecular self-organization in cellular environments. Cell Biochemistry and Biophysics. 48: 16-31. PMID 17703065 DOI: 10.1007/S12013-007-0012-Y |
0.331 |
|
| 2007 |
Pennington G, Smith CA, Shackney S, Schwartz R. Reconstructing tumor phylogenies from heterogeneous single-cell data. Journal of Bioinformatics and Computational Biology. 5: 407-27. PMID 17589968 DOI: 10.1142/S021972000700259X |
0.302 |
|
| 2007 |
Schwartz R. Stochastic Modelling for Systems Biology.Darren J. Wilkinson Briefings in Bioinformatics. 8: 204-205. DOI: 10.1093/Bib/Bbm001 |
0.309 |
|
| 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 |
0.512 |
|
| 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 |
0.564 |
|
| 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 |
0.419 |
|
| 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 |
0.768 |
|
| 2005 |
Schwartz R, Shor PW, Berger B. Local rule simulations of capsid assembly Journal of Theoretical Medicine. 6: 81-85. DOI: 10.1080/10273660500149257 |
0.6 |
|
| 2005 |
Jamalyaria F, Rohlfs R, Schwartz R. Queue-based method for efficient simulation of biological self-assembly systems Journal of Computational Physics. 204: 100-120. DOI: 10.1016/J.Jcp.2004.10.004 |
0.427 |
|
| 2004 |
Schwartz R. Haplotype parsing: methods for extracting information from human genetic variations. Applied Bioinformatics. 3: 181-91. PMID 15693743 DOI: 10.2165/00822942-200403020-00012 |
0.352 |
|
| 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 DOI: 10.1093/Bib/3.1.23 |
0.378 |
|
| 2001 |
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, ... ... Schwartz R, et al. The sequence of the human genome. Science (New York, N.Y.). 291: 1304-51. PMID 11181995 DOI: 10.1126/Science.1058040 |
0.358 |
|
| 2000 |
Schwartz R, Garcea RL, Berger B. "Local rules" theory applied to polyomavirus polymorphic capsid assemblies. Virology. 268: 461-70. PMID 10704354 DOI: 10.1006/Viro.1999.0180 |
0.584 |
|
| 2000 |
Berger B, King J, Schwartz R, Shor P. Local rule mechanism for selecting icosahedral shell geometry Discrete Applied Mathematics. 104: 97-111. DOI: 10.1016/S0166-218X(00)00187-6 |
0.544 |
|
| 1999 |
Istrail S, Schwartz R, King J. Lattice simulations of aggregation funnels for protein folding Journal of Computational Biology. 6: 143-162. PMID 10421520 DOI: 10.1089/Cmb.1999.6.143 |
0.325 |
|
| 1998 |
Schwartz R, Shor PW, Prevelige PE, Berger B. Local rules simulation of the kinetics of virus capsid self-assembly Biophysical Journal. 75: 2626-2636. PMID 9826587 DOI: 10.1016/S0006-3495(98)77708-2 |
0.619 |
|
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