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Journal Articles
- 2023
[j33]Abhijit Mondal, Luiz Thibério Rangel, Jack G. Payette, Gregory Fournier, Mukul S. Bansal
:
DaTeR: error-correcting phylogenetic chronograms using relative time constraints. Bioinform. 39(2) (2023)- [j32]Sumaira Zaman, Samuel Sledzieski, Bonnie Berger, Yi-Chieh Wu, Mukul S. Bansal:
virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. J. Comput. Biol. 30(1): 3-20 (2023) - [j31]Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021). J. Comput. Biol. 30(4): 363-365 (2023) - [j30]Abhijit Mondal, Mukul S. Bansal:
Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains. IEEE ACM Trans. Comput. Biol. Bioinform. 20(6): 3511-3522 (2023) - 2022
- [j29]Saurav Dhar, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal:
TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 230-242 (2022) - 2021
- [j28]Samson Weiner, Mukul S. Bansal:
Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages. Algorithms 14(8): 231 (2021) - 2020
- [j27]Mukul S. Bansal:
Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance. Algorithms Mol. Biol. 15(1): 6 (2020) - 2019
- [j26]Soumya Kundu, Mukul S. Bansal:
SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution. Bioinform. 35(18): 3496-3498 (2019) - [j25]Lei Li, Mukul S. Bansal:
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution. IEEE ACM Trans. Comput. Biol. Bioinform. 16(1): 63-76 (2019) - [j24]Misagh Kordi, Mukul S. Bansal:
Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 16(4): 1077-1090 (2019) - 2018
- [j23]Mukul S. Bansal, Manolis Kellis, Misagh Kordi, Soumya Kundu:
RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss. Bioinform. 34(18): 3214-3216 (2018) - [j22]Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S. Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A. Davín, Christophe Dessimoz, David Dylus, Damir Hasic, Diego Mallo, Rémi Planel, David Posada, Céline Scornavacca, Gergely J. Szöllosi, Louxin Zhang, Eric Tannier, Vincent Daubin:
RecPhyloXML: a format for reconciled gene trees. Bioinform. 34(21): 3646-3652 (2018) - [j21]Soumya Kundu, Mukul S. Bansal:
On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation. BMC Bioinform. 19-S(9): 105-115 (2018) - 2017
- [j20]Misagh Kordi, Mukul S. Bansal:
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 14(3): 587-599 (2017) - 2015
- [j19]Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis:
Improved gene tree error correction in the presence of horizontal gene transfer. Bioinform. 31(8): 1211-1218 (2015) - [j18]Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi Moussavi, Pouya Kheradpour, ZhiZhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis:
Integrative analysis of 111 reference human epigenomes Open. Nat. 518(7539): 317-330 (2015) - 2014
- [j17]Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis:
Pareto-optimal phylogenetic tree reconciliation. Bioinform. 30(12): 87-95 (2014) - 2013
- [j16]Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten, Ron Shamir:
Systematic inference of highways of horizontal gene transfer in prokaryotes. Bioinform. 29(5): 571-579 (2013) - [j15]Mukul S. Bansal, Eric J. Alm, Manolis Kellis:
Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. J. Comput. Biol. 20(10): 738-754 (2013) - [j14]Mukul S. Bansal, Oliver Eulenstein:
Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony. IEEE ACM Trans. Comput. Biol. Bioinform. 10(4): 939-956 (2013) - 2012
- [j13]Mukul S. Bansal, Eric J. Alm, Manolis Kellis:
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinform. 28(12): 283-291 (2012) - 2011
- [j12]Mukul S. Bansal, Guy Banay, J. Peter Gogarten, Ron Shamir:
Detecting Highways of Horizontal Gene Transfer. J. Comput. Biol. 18(9): 1087-1114 (2011) - [j11]Mukul S. Bansal, Ron Shamir:
A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 8(3): 848-850 (2011) - [j10]Mukul S. Bansal, Jianrong Dong, David Fernández-Baca:
Comparing and aggregating partially resolved trees. Theor. Comput. Sci. 412(48): 6634-6652 (2011) - 2010
- [j9]Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca:
Robinson-Foulds Supertrees. Algorithms Mol. Biol. 5: 18 (2010) - [j8]Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein:
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. BMC Bioinform. 11(S-1): 42 (2010) - [j7]Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein:
iGTP: A software package for large-scale gene tree parsimony analysis. BMC Bioinform. 11: 574 (2010) - 2009
- [j6]Mukul S. Bansal, David Fernández-Baca:
Computing distances between partial rankings. Inf. Process. Lett. 109(4): 238-241 (2009) - [j5]John Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein:
Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants. J. Comput. Biol. 16(8): 1071-1083 (2009) - [j4]Mukul S. Bansal, Oliver Eulenstein, André Wehe:
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches. IEEE ACM Trans. Comput. Biol. Bioinform. 6(2): 221-231 (2009) - 2008
- [j3]André Wehe, Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein:
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinform. 24(13): 1540-1541 (2008) - [j2]Mukul S. Bansal, Oliver Eulenstein:
An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 5(4): 514-524 (2008) - 2005
- [j1]Mukul S. Bansal, V. Ch. Venkaiah:
A note on finding a maximum clique in a graph using BDDs. Australas. J Comb. 32: 253-258 (2005)
Conference and Workshop Papers
- 2024
- [c28]Samson Weiner, Yutian Feng, J. Peter Gogarten, Mukul S. Bansal:
Assessing the Potential of Gene Tree Parsimony for Microbial Phylogenomics. RECOMB-CG 2024: 129-149 - 2023
- [c27]Sumaira Zaman, Mukul S. Bansal:
Reducing the Impact of Domain Rearrangement on Sequence Alignment and Phylogeny Reconstruction. ISBRA 2023: 337-350 - 2022
- [c26]Sumaira Zaman, Mukul S. Bansal:
On Partial Gene Transfer and Its Impact on Gene Tree Reconstruction. RECOMB-CG 2022: 168-186 - 2021
- [c25]Keegan Yao, Mukul S. Bansal:
Optimal Completion and Comparison of Incomplete Phylogenetic Trees Under Robinson-Foulds Distance. CPM 2021: 25:1-25:23 - [c24]Samuel Sledzieski, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal:
TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. PSB 2021 - 2020
- [c23]Misagh Kordi, Mukul S. Bansal:
TreeSolve: Rapid Error-Correction of Microbial Gene Trees. AlCoB 2020: 125-139 - [c22]Abhijit Mondal, Misagh Kordi, Mukul S. Bansal:
A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene Transfers. BCB 2020: 16:1-16:11 - [c21]Saurav Dhar, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal:
TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity. ISBRA 2020: 203-216 - 2019
- [c20]Misagh Kordi, Soumya Kundu, Mukul S. Bansal:
On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation. BCB 2019: 514-523 - [c19]Lei Li, Mukul S. Bansal:
Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model. ISBRA 2019: 73-86 - 2018
- [c18]Lei Li, Mukul S. Bansal:
An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem. BCB 2018: 386-397 - [c17]Mukul S. Bansal:
Linear-Time Algorithms for Some Phylogenetic Tree Completion Problems Under Robinson-Foulds Distance. RECOMB-CG 2018: 209-226 - 2017
- [c16]Lei Li, Mukul S. Bansal:
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution. BCB 2017: 611 - [c15]Soumya Kundu, Mukul S. Bansal:
Assessing the Impact of Uncertain Gene Tree Rooting on Phylogenetic Reconciliation Using a Simulation Framework. BCB 2017: 612 - 2016
- [c14]Misagh Kordi, Mukul S. Bansal:
Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. BCB 2016: 297-306 - [c13]Mukul S. Bansal:
Phylogenetic uncertainty and transmission network inference: Lessons from phylogenetic reconciliation. ICCABS 2016: 1 - 2015
- [c12]Misagh Kordi, Mukul S. Bansal:
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees. ISBRA 2015: 187-198 - 2013
- [c11]Mukul S. Bansal, Eric J. Alm, Manolis Kellis:
Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss. RECOMB 2013: 1-13 - 2010
- [c10]J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision:
Inferring species trees from gene duplication episodes. BCB 2010: 198-203 - [c9]Harish Narayanappa, Mukul S. Bansal, Hridesh Rajan:
Property-aware program sampling. PASTE 2010: 45-52 - [c8]Mukul S. Bansal, J. Peter Gogarten, Ron Shamir:
Detecting Highways of Horizontal Gene Transfer. RECOMB-CG 2010: 109-120 - 2009
- [c7]Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca:
Generalized Binary Tanglegrams: Algorithms and Applications. BICoB 2009: 114-125 - 2008
- [c6]Mukul S. Bansal, Oliver Eulenstein:
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches. ISBRA 2008: 14-25 - [c5]Mukul S. Bansal, Oliver Eulenstein:
The multiple gene duplication problem revisited. ISMB 2008: 132-138 - [c4]Mukul S. Bansal, Jianrong Dong, David Fernández-Baca:
Comparing and Aggregating Partially Resolved Trees. LATIN 2008: 72-83 - [c3]J. Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein:
Locating Multiple Gene Duplications through Reconciled Trees. RECOMB 2008: 273-284 - 2007
- [c2]Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, André Wehe:
Heuristics for the Gene-Duplication Problem: A Theta ( n ) Speed-Up for the Local Search. RECOMB 2007: 238-252 - [c1]Mukul S. Bansal, Oliver Eulenstein:
An Omega(n2/log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem. WABI 2007: 124-135
Editorship
- 2022
- [e2]Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Computational Advances in Bio and Medical Sciences: 11th International Conference, ICCABS 2021, Virtual Event, December 16-18, 2021, Revised Selected Papers. Lecture Notes in Computer Science 13254, Springer International Publishing 2022, ISBN 978-3-031-17530-5 [contents] - [e1]Mukul S. Bansal, Zhipeng Cai, Serghei Mangul:
Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Haifa, Israel, November 14-17, 2022, Proceedings. Lecture Notes in Computer Science 13760, Springer 2022, ISBN 978-3-031-23197-1 [contents]
Informal and Other Publications
- 2009
- [i1]Mukul S. Bansal, Jianrong Dong, David Fernández-Baca:
Comparing and Aggregating Partially Resolved Trees. CoRR abs/0906.5089 (2009)
Coauthor Index
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