Mukul S. Bansal

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 30

Top Topics

Supervised Machine Learning

Horizontal Gene Transfer

Exact Algorithms

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Samson Weiner, Yutian Feng, J. Peter Gogarten, Mukul S. Bansal
Assessing the Potential of Gene Tree Parsimony for Microbial Phylogenomics. RECOMB-CG (2024)
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) (2023)
Sumaira Zaman, Mukul S. Bansal
Reducing the Impact of Domain Rearrangement on Sequence Alignment and Phylogeny Reconstruction. ISBRA (2023)
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)
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) (2023)
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) (2023)
Sumaira Zaman, Mukul S. Bansal
On Partial Gene Transfer and Its Impact on Gene Tree Reconstruction. RECOMB-CG (2022)
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) (2022)
Keegan Yao, Mukul S. Bansal
Optimal Completion and Comparison of Incomplete Phylogenetic Trees Under Robinson-Foulds Distance. CPM (2021)
Samson Weiner, Mukul S. Bansal
Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages. Algorithms 14 (8) (2021)
Samuel Sledzieski, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal
TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. PSB (2021)
Misagh Kordi, Mukul S. Bansal
TreeSolve: Rapid Error-Correction of Microbial Gene Trees. AlCoB (2020)
Mukul S. Bansal
Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance. Algorithms Mol. Biol. 15 (1) (2020)
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)
Abhijit Mondal, Misagh Kordi, Mukul S. Bansal
A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene Transfers. BCB (2020)
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) (2019)
Lei Li, Mukul S. Bansal
Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model. ISBRA (2019)
Soumya Kundu, Mukul S. Bansal
SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution. Bioinform. 35 (18) (2019)
Misagh Kordi, Soumya Kundu, Mukul S. Bansal
On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation. BCB (2019)
Lei Li, Mukul S. Bansal
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Soumya Kundu, Mukul S. Bansal
On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation. BMC Bioinform. (9) (2018)
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) (2018)
Lei Li, Mukul S. Bansal
An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem. BCB (2018)
Mukul S. Bansal
Linear-Time Algorithms for Some Phylogenetic Tree Completion Problems Under Robinson-Foulds Distance. RECOMB-CG (2018)
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) (2018)
Soumya Kundu, Mukul S. Bansal
Assessing the Impact of Uncertain Gene Tree Rooting on Phylogenetic Reconciliation Using a Simulation Framework. BCB (2017)
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) (2017)
Lei Li, Mukul S. Bansal
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution. BCB (2017)
Misagh Kordi, Mukul S. Bansal
Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. BCB (2016)
Mukul S. Bansal
Phylogenetic uncertainty and transmission network inference: Lessons from phylogenetic reconciliation. ICCABS (2016)
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) (2015)
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) (2015)
Misagh Kordi, Mukul S. Bansal
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees. ISBRA (2015)
Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis
Pareto-optimal phylogenetic tree reconciliation. Bioinform. 30 (12) (2014)
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) (2013)
Mukul S. Bansal, Oliver Eulenstein
Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (4) (2013)
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss. RECOMB (2013)
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) (2013)
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinform. 28 (12) (2012)
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
Comparing and aggregating partially resolved trees. Theor. Comput. Sci. 412 (48) (2011)
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) (2011)
Mukul S. Bansal, Guy Banay, J. Peter Gogarten, Ron Shamir
Detecting Highways of Horizontal Gene Transfer. J. Comput. Biol. 18 (9) (2011)
Harish Narayanappa, Mukul S. Bansal, Hridesh Rajan
Property-aware program sampling. PASTE (2010)
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) (2010)
J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision
Inferring species trees from gene duplication episodes. BCB (2010)
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca
Robinson-Foulds Supertrees. Algorithms Mol. Biol. 5 (2010)
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 (2010)
Mukul S. Bansal, J. Peter Gogarten, Ron Shamir
Detecting Highways of Horizontal Gene Transfer. RECOMB-CG (2010)
Mukul S. Bansal, David Fernández-Baca
Computing distances between partial rankings. Inf. Process. Lett. 109 (4) (2009)
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) (2009)
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) (2009)
Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca
Generalized Binary Tanglegrams: Algorithms and Applications. BICoB (2009)
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
Comparing and Aggregating Partially Resolved Trees CoRR (2009)
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
Comparing and Aggregating Partially Resolved Trees. LATIN (2008)
Mukul S. Bansal, Oliver Eulenstein
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches. ISBRA (2008)
Mukul S. Bansal, Oliver Eulenstein
The multiple gene duplication problem revisited. ISMB (2008)
J. Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein
Locating Multiple Gene Duplications through Reconciled Trees. RECOMB (2008)
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) (2008)
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) (2008)
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, André Wehe
) Speed-Up for the Local Search. RECOMB (2007)
Mukul S. Bansal, Oliver Eulenstein
) Speed-Up of TBR Heuristics for the Gene-Duplication Problem. WABI (2007)
Mukul S. Bansal, V. Ch. Venkaiah
A note on finding a maximum clique in a graph using BDDs. Australas. J Comb. 32 (2005)