Mukul S. Bansal

Orcid: 0000-0003-0039-2596

According to our database1, Mukul S. Bansal authored at least 56 papers between 2005 and 2024.

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Bibliography

2024
Assessing the Potential of Gene Tree Parsimony for Microbial Phylogenomics.
Proceedings of the Comparative Genomics - 21st International Conference, 2024

2023
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021).
J. Comput. Biol., April, 2023

DaTeR: error-correcting phylogenetic chronograms using relative time constraints.
Bioinform., February, 2023

Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains.
IEEE ACM Trans. Comput. Biol. Bioinform., 2023

virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.
J. Comput. Biol., 2023

Reducing the Impact of Domain Rearrangement on Sequence Alignment and Phylogeny Reconstruction.
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

2022
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., 2022

On Partial Gene Transfer and Its Impact on Gene Tree Reconstruction.
Proceedings of the Comparative Genomics - 19th International Conference, 2022

2021
Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages.
Algorithms, 2021

TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference.
Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021

Optimal Completion and Comparison of Incomplete Phylogenetic Trees Under Robinson-Foulds Distance.
Proceedings of the 32nd Annual Symposium on Combinatorial Pattern Matching, 2021

2020
Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance.
Algorithms Mol. Biol., 2020

TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity.
Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene Transfers.
Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

TreeSolve: Rapid Error-Correction of Microbial Gene Trees.
Proceedings of the Algorithms for Computational Biology, 2020

2019
Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution.
Bioinform., 2019

Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model.
Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018
On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation.
BMC Bioinform., 2018

RecPhyloXML: a format for reconciled gene trees.
Bioinform., 2018

RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss.
Bioinform., 2018

Linear-Time Algorithms for Some Phylogenetic Tree Completion Problems Under Robinson-Foulds Distance.
Proceedings of the Comparative Genomics - 16th International Conference, 2018

An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017
On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017

Assessing the Impact of Uncertain Gene Tree Rooting on Phylogenetic Reconciliation Using a Simulation Framework.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016
Phylogenetic uncertainty and transmission network inference: Lessons from phylogenetic reconciliation.
Proceedings of the 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2016

2015
Integrative analysis of 111 reference human epigenomes Open.
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Nat., 2015

Improved gene tree error correction in the presence of horizontal gene transfer.
Bioinform., 2015

2014
Pareto-optimal phylogenetic tree reconciliation.
Bioinform., 2014

2013
Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss.
J. Comput. Biol., 2013

Systematic inference of highways of horizontal gene transfer in prokaryotes.
Bioinform., 2013

2012
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.
Bioinform., 2012

2011
Comparing and aggregating partially resolved trees.
Theor. Comput. Sci., 2011

A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Detecting Highways of Horizontal Gene Transfer.
J. Comput. Biol., 2011

2010
iGTP: A software package for large-scale gene tree parsimony analysis.
BMC Bioinform., 2010

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.
BMC Bioinform., 2010

Robinson-Foulds Supertrees.
Algorithms Mol. Biol., 2010

Detecting Highways of Horizontal Gene Transfer.
Proceedings of the Comparative Genomics - International Workshop, 2010

Property-aware program sampling.
Proceedings of the 9th ACM SIGPLAN-SIGSOFT Workshop on Program Analysis for Software Tools and Engineering, 2010

Inferring species trees from gene duplication episodes.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants.
J. Comput. Biol., 2009

Computing distances between partial rankings.
Inf. Process. Lett., 2009

Generalized Binary Tanglegrams: Algorithms and Applications.
Proceedings of the Bioinformatics and Computational Biology, 2009

2008
An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
Bioinform., 2008

Locating Multiple Gene Duplications through Reconciled Trees.
Proceedings of the Research in Computational Molecular Biology, 2008

The multiple gene duplication problem revisited.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches.
Proceedings of the Bioinformatics Research and Applications, 2008

2007
An <i>Omega</i>(<i>n</i><sup>2</sup>/log <i>n</i>) Speed-Up of TBR Heuristics for the Gene-Duplication Problem.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Heuristics for the Gene-Duplication Problem: A <i>Theta</i> ( <i>n</i> ) Speed-Up for the Local Search.
Proceedings of the Research in Computational Molecular Biology, 2007

2005
A note on finding a maximum clique in a graph using BDDs.
Australas. J Comb., 2005


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