Mukul S. Bansal

68 papers A 1B 5C 1Misc 1Journal 36Unranked 20
YearRankTypeTitle / Venue / Authors
2026 — ed.
Computational Advances in Bio and Medical Sciences - 13th International Conference, ICCABS 2025, Atlanta, GA, USA, January 12-14, 2025, Revised Selected Papers
ICCABS
Mohammed Alser, Mukul S. Bansal, Yury Khudyakov, Serghei Mangul, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Shibu Yooseph, Alexander Zelikovsky
2025 — ed.
Computational Advances in Bio and Medical Sciences - 12th International Conference, ICCABS 2023, Norman, OK, USA, December 11-13, 2023, Revised Selected Papers
ICCABS
Mukul S. Bansal, Wei Chen, Yury Khudyakov, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Sharma V. Thankachan, Alexander Zelikovsky
2025 J jnl
SISTEM: simulation of tumor evolution, metastasis, and DNA-seq data under genotype-driven selection.
Bioinform.
Samson Weiner, Mukul S. Bansal
2024 — conf
Assessing the Potential of Gene Tree Parsimony for Microbial Phylogenomics.
RECOMB-CG
Samson Weiner, Yutian Feng, J. Peter Gogarten, Mukul S. Bansal
2023 J jnl
CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors.
Bioinform.
Samson Weiner, Mukul S. Bansal
2023 J jnl
DaTeR: error-correcting phylogenetic chronograms using relative time constraints.
Bioinform.
Abhijit Mondal, Luiz Thibério Rangel, Jack G. Payette, Gregory Fournier, Mukul S. Bansal
2023 J jnl
Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains.
IEEE ACM Trans. Comput. Biol. Bioinform.
Abhijit Mondal, Mukul S. Bansal
2023 — conf
Reducing the Impact of Domain Rearrangement on Sequence Alignment and Phylogeny Reconstruction.
ISBRA
Sumaira Zaman, Mukul S. Bansal
2023 J jnl
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021).
J. Comput. Biol.
Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
2023 J jnl
virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.
J. Comput. Biol.
Sumaira Zaman, Samuel Sledzieski, Bonnie Berger, Yi-Chieh Wu, Mukul S. Bansal
2022 — ed.
Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Haifa, Israel, November 14-17, 2022, Proceedings
ISBRA
Mukul S. Bansal, Zhipeng Cai, Serghei Mangul
2022 — ed.
Computational Advances in Bio and Medical Sciences: 11th International Conference, ICCABS 2021, Virtual Event, December 16-18, 2021, Revised Selected Papers
ICCABS
Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
2022 — conf
On Partial Gene Transfer and Its Impact on Gene Tree Reconstruction.
RECOMB-CG
Sumaira Zaman, Mukul S. Bansal
2022 J jnl
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.
Saurav Dhar, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal
2021 J jnl
Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages.
Algorithms
Samson Weiner, Mukul S. Bansal
2021 B conf
Optimal Completion and Comparison of Incomplete Phylogenetic Trees Under Robinson-Foulds Distance.
CPM
Keegan Yao, Mukul S. Bansal
2021 Misc conf
TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference.
PSB
Samuel Sledzieski, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal
2020 — conf
A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene Transfers.
BCB
Abhijit Mondal, Misagh Kordi, Mukul S. Bansal
2020 J jnl
Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance.
Algorithms Mol. Biol.
Mukul S. Bansal
2020 — conf
TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity.
ISBRA
Saurav Dhar, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal
2020 — conf
TreeSolve: Rapid Error-Correction of Microbial Gene Trees.
AlCoB
Misagh Kordi, Mukul S. Bansal
2019 J jnl
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution.
IEEE ACM Trans. Comput. Biol. Bioinform.
Lei Li, Mukul S. Bansal
2019 J jnl
Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
IEEE ACM Trans. Comput. Biol. Bioinform.
Misagh Kordi, Mukul S. Bansal
2019 — conf
On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation.
BCB
Misagh Kordi, Soumya Kundu, Mukul S. Bansal
2019 J jnl
SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution.
Bioinform.
Soumya Kundu, Mukul S. Bansal
2019 — conf
Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model.
ISBRA
Lei Li, Mukul S. Bansal
2018 — conf
An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem.
BCB
Lei Li, Mukul S. Bansal
2018 — conf
Linear-Time Algorithms for Some Phylogenetic Tree Completion Problems Under Robinson-Foulds Distance.
RECOMB-CG
Mukul S. Bansal
2018 J jnl
On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation.
BMC Bioinform.
Soumya Kundu, Mukul S. Bansal
2018 J jnl
RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss.
Bioinform.
Mukul S. Bansal, Manolis Kellis, Misagh Kordi, Soumya Kundu
2018 J jnl
RecPhyloXML: a format for reconciled gene trees.
Bioinform.
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
2017 — conf
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution.
BCB
Lei Li, Mukul S. Bansal
2017 — conf
Assessing the Impact of Uncertain Gene Tree Rooting on Phylogenetic Reconciliation Using a Simulation Framework.
BCB
Soumya Kundu, Mukul S. Bansal
2017 J jnl
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
IEEE ACM Trans. Comput. Biol. Bioinform.
Misagh Kordi, Mukul S. Bansal
2016 — conf
Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
BCB
Misagh Kordi, Mukul S. Bansal
2016 — conf
Phylogenetic uncertainty and transmission network inference: Lessons from phylogenetic reconciliation.
ICCABS
Mukul S. Bansal
2015 J jnl
Improved gene tree error correction in the presence of horizontal gene transfer.
Bioinform.
Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis
2015 J jnl
Integrative analysis of 111 reference human epigenomes Open.
Nat.
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
2015 — conf
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees.
ISBRA
Misagh Kordi, Mukul S. Bansal
2014 J jnl
Pareto-optimal phylogenetic tree reconciliation.
Bioinform.
Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis
2013 J jnl
Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mukul S. Bansal, Oliver Eulenstein
2013 B conf
Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss.
RECOMB
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
2013 J jnl
Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss.
J. Comput. Biol.
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
2013 J jnl
Systematic inference of highways of horizontal gene transfer in prokaryotes.
Bioinform.
Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten, Ron Shamir
2012 J jnl
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.
Bioinform.
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
2011 J jnl
A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mukul S. Bansal, Ron Shamir
2011 J jnl
Comparing and aggregating partially resolved trees.
Theor. Comput. Sci.
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
2011 J jnl
Detecting Highways of Horizontal Gene Transfer.
J. Comput. Biol.
Mukul S. Bansal, Guy Banay, J. Peter Gogarten, Ron Shamir
2010 — conf
Detecting Highways of Horizontal Gene Transfer.
RECOMB-CG
Mukul S. Bansal, J. Peter Gogarten, Ron Shamir
2010 J jnl
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.
BMC Bioinform.
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein
2010 — conf
Inferring species trees from gene duplication episodes.
BCB
J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision
2010 — conf
Property-aware program sampling.
PASTE
Harish Narayanappa, Mukul S. Bansal, Hridesh Rajan
2010 J jnl
Robinson-Foulds Supertrees.
Algorithms Mol. Biol.
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca
2010 J jnl
iGTP: A software package for large-scale gene tree parsimony analysis.
BMC Bioinform.
Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein
2009 J jnl
Comparing and Aggregating Partially Resolved Trees
CoRR
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
2009 J jnl
Computing distances between partial rankings.
Inf. Process. Lett.
Mukul S. Bansal, David Fernández-Baca
2009 — conf
Generalized Binary Tanglegrams: Algorithms and Applications.
BICoB
Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca
2009 J jnl
Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants.
J. Comput. Biol.
John Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein
2009 J jnl
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mukul S. Bansal, Oliver Eulenstein, André Wehe
2008 J jnl
An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mukul S. Bansal, Oliver Eulenstein
2008 B conf
Comparing and Aggregating Partially Resolved Trees.
LATIN
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
2008 J jnl
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
Bioinform.
André Wehe, Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein
2008 B conf
Locating Multiple Gene Duplications through Reconciled Trees.
RECOMB
J. Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein
2008 — conf
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches.
ISBRA
Mukul S. Bansal, Oliver Eulenstein
2008 A conf
The multiple gene duplication problem revisited.
ISMB
Mukul S. Bansal, Oliver Eulenstein
2007 C conf
An
WABI
Mukul S. Bansal, Oliver Eulenstein
2007 B conf
Heuristics for the Gene-Duplication Problem: A
RECOMB
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, André Wehe
2005 J jnl
A note on finding a maximum clique in a graph using BDDs.
Australas. J Comb.
Mukul S. Bansal, V. Ch. Venkaiah