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Mukul S. Bansal
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2020 – today
- 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
- [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) - [c27]Sumaira Zaman, Mukul S. Bansal
:
Reducing the Impact of Domain Rearrangement on Sequence Alignment and Phylogeny Reconstruction. ISBRA 2023: 337-350 - 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) - [c26]Sumaira Zaman, Mukul S. Bansal
:
On Partial Gene Transfer and Its Impact on Gene Tree Reconstruction. RECOMB-CG 2022: 168-186 - [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] - 2021
- [j28]Samson Weiner, Mukul S. Bansal
:
Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages. Algorithms 14(8): 231 (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
- [j27]Mukul S. Bansal
:
Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance. Algorithms Mol. Biol. 15(1): 6 (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
2010 – 2019
- 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) - [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
- [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) - [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
- [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) - [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
- [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) - [c12]Misagh Kordi, Mukul S. Bansal
:
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees. ISBRA 2015: 187-198 - 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) - [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 - 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) - [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
2000 – 2009
- 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) - [c7]Mukul S. Bansal
, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca:
Generalized Binary Tanglegrams: Algorithms and Applications. BICoB 2009: 114-125 - [i1]Mukul S. Bansal, Jianrong Dong, David Fernández-Baca:
Comparing and Aggregating Partially Resolved Trees. CoRR abs/0906.5089 (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) - [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 - 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)
Coauthor Index
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