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Mukul S. Bansal - Publications

Affiliations: 
School of Computer Science Tel Aviv University, Tel Aviv-Yafo, Tel Aviv District, Israel 
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30 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
2022 Zaman S, Sledzieski S, Berger B, Wu YC, Bansal MS. virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 36125448 DOI: 10.1089/cmb.2021.0507  0.55
2020 Wade T, Rangel LT, Kundu S, Fournier GP, Bansal MS. Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families. Plos One. 15: e0232950. PMID 32413061 DOI: 10.1371/Journal.Pone.0232950  0.41
2019 Kundu S, Bansal MS. SaGePhy: An improved phylogenetic simulation framework for gene and subgene evolution. Bioinformatics (Oxford, England). PMID 30715213 DOI: 10.1093/Bioinformatics/Btz081  0.396
2018 Kundu S, Bansal MS. On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation. Bmc Bioinformatics. 19: 290. PMID 30367593 DOI: 10.1186/S12859-018-2269-0  0.402
2018 Li L, Bansal MS. An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29994126 DOI: 10.1109/Tcbb.2018.2846253  0.375
2018 Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, et al. RecPhyloXML - a format for reconciled gene trees. Bioinformatics (Oxford, England). PMID 29762653 DOI: 10.1093/Bioinformatics/Bty389  0.403
2018 Bansal MS, Kellis M, Kordi M, Kundu S. RANGER-DTL 2.0: Rigorous Reconstruction of Gene-Family Evolution by Duplication, Transfer, and Loss. Bioinformatics (Oxford, England). PMID 29688310 DOI: 10.1093/Bioinformatics/Bty314  0.571
2017 Kordi M, Bansal MS. Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 28622673 DOI: 10.1109/Tcbb.2017.2710342  0.402
2015 Kordi M, Bansal M. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 28055898 DOI: 10.1109/Tcbb.2015.2511761  0.406
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Bansal MS, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.319
2015 Bansal MS, Wu YC, Alm EJ, Kellis M. Improved gene tree error correction in the presence of horizontal gene transfer. Bioinformatics (Oxford, England). 31: 1211-8. PMID 25481006 DOI: 10.1093/Bioinformatics/Btu806  0.578
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Bansal MS, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.792
2014 Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M. Pareto-optimal phylogenetic tree reconciliation. Bioinformatics (Oxford, England). 30: i87-95. PMID 24932009 DOI: 10.1093/Bioinformatics/Btu289  0.523
2014 Wu YC, Rasmussen MD, Bansal MS, Kellis M. Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees. Genome Research. 24: 475-86. PMID 24310000 DOI: 10.1101/Gr.161968.113  0.739
2013 Bansal MS, Eulenstein O. Algorithms for genome-scale phylogenetics using gene tree parsimony. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 939-56. PMID 24334388 DOI: 10.1109/Tcbb.2013.103  0.42
2013 Bansal MS, Alm EJ, Kellis M. Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 738-54. PMID 24033262 DOI: 10.1089/Cmb.2013.0073  0.588
2013 Bansal MS, Banay G, Harlow TJ, Gogarten JP, Shamir R. Systematic inference of highways of horizontal gene transfer in prokaryotes. Bioinformatics (Oxford, England). 29: 571-9. PMID 23335015 DOI: 10.1093/Bioinformatics/Btt021  0.4
2013 Wu YC, Rasmussen MD, Bansal MS, Kellis M. TreeFix: statistically informed gene tree error correction using species trees. Systematic Biology. 62: 110-20. PMID 22949484 DOI: 10.1093/Sysbio/Sys076  0.746
2012 Bansal MS, Alm EJ, Kellis M. Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics (Oxford, England). 28: i283-91. PMID 22689773 DOI: 10.1093/Bioinformatics/Bts225  0.593
2011 Bansal MS, Banay G, Gogarten JP, Shamir R. Detecting highways of horizontal gene transfer. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1087-114. PMID 21899418 DOI: 10.1089/Cmb.2011.0066  0.392
2011 Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ. Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Systematic Biology. 60: 117-25. PMID 21186249 DOI: 10.1093/Sysbio/Syq072  0.412
2011 Bansal MS, Shamir R. A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 848-50. PMID 20733245 DOI: 10.1109/Tcbb.2010.74  0.379
2010 Chaudhary R, Bansal MS, Wehe A, Fernández-Baca D, Eulenstein O. iGTP: a software package for large-scale gene tree parsimony analysis. Bmc Bioinformatics. 11: 574. PMID 21092314 DOI: 10.1186/1471-2105-11-574  0.464
2010 Bansal MS, Burleigh JG, Eulenstein O, Fernández-Baca D. Robinson-Foulds supertrees. Algorithms For Molecular Biology : Amb. 5: 18. PMID 20181274 DOI: 10.1186/1748-7188-5-18  0.304
2010 Bansal MS, Burleigh JG, Eulenstein O. Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. Bmc Bioinformatics. 11: S42. PMID 20122216 DOI: 10.1186/1471-2105-11-S1-S42  0.47
2009 Burleigh JG, Bansal MS, Wehe A, Eulenstein O. Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1071-83. PMID 19689214 DOI: 10.1089/Cmb.2009.0139  0.424
2009 Bansal MS, Eulenstein O, Wehe A. The gene-duplication problem: near-linear time algorithms for NNI-based local searches. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 6: 221-31. PMID 19407347 DOI: 10.1109/Tcbb.2009.7  0.327
2008 Bansal MS, Eulenstein O. An Omega(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 5: 514-24. PMID 18989039 DOI: 10.1109/Tcbb.2008.69  0.332
2008 Wehe A, Bansal MS, Burleigh JG, Eulenstein O. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics (Oxford, England). 24: 1540-1. PMID 18474508 DOI: 10.1093/Bioinformatics/Btn230  0.405
2008 Chen D, Burleigh JG, Bansal MS, Fernández-Baca D. PhyloFinder: an intelligent search engine for phylogenetic tree databases. Bmc Evolutionary Biology. 8: 90. PMID 18366717 DOI: 10.1186/1471-2148-8-90  0.323
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