Publications
Copyright notice: The material here is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author’s copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.
Disclaimer for NSF-funded work: Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Publications (in reverse chronological order)
- Assessing the potential of gene tree parsimony for microbial phylogenomics
Samson Weiner, Yutian Feng, J. Peter Gogarten, Mukul S. Bansal
RECOMB Comparative Genomics Conference (RECOMB-CG) 2024; to appear. - Reducing the impact of domain rearrangement on sequence alignment and phylogeny reconstruction
Sumaira Zaman, Mukul S. Bansal
International Symposium on Bioinformatics Research and Applications (ISBRA) 2023; LNBI 14248: 337–350. - CNAsim: Improved simulation of single-cell copy number profiles and DNA-seq data from tumors
Samson Weiner, Mukul S. Bansal
Bioinformatics; 39(7), btad434, 2023. - Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains
Abhijit Mondal, Mukul S. Bansal
IEEE/ACM Transactions on Computational Biology and Bioinformatics; 20(6): 3511-3522, 2023. - DaTeR: Error-Correcting Phylogenetic Chronograms Using Relative Time Constraints
Abhijit Mondal, L. Thiberio Rangel, Jack G. Payette, Gregory P. Fournier, Mukul S. Bansal
Bioinformatics, 39(2), btad084, 2023. - virDTL: Viral recombination analysis through phylogenetic reconciliation and its application to sarbecoviruses and SARS-CoV-2
Sumaira Zaman, Samuel Sledzieski, Bonnie Berger, Yi-Chieh Wu, Mukul S. Bansal
Journal of Computational Biology, 30(1): 3-20, 2023.
→ A preliminary version of this paper is available on bioRxiv: https://doi.org/10.1101/2021.08.12.456131 - On Partial Gene Transfer and its Impact on Gene Tree Reconstruction
Sumaira Zaman, Mukul S. Bansal
RECOMB Comparative Genomics Conference (RECOMB-CG) 2022; LNBI 13234: 168–186. - Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL
Mukul S. Bansal
In: Luo, H. (eds) Environmental Microbial Evolution. Methods in Molecular Biology, vol 2569, 2022. Humana, New York, NY. - TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread
Saurav Dhar, Chengchen Zhang, Ion Mandoiu, Mukul S. Bansal
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(1): 230-242, 2022. (Published online in July 2021)
→ The global COVID-19 dataset used in this paper is available from the Datasets Page
→ Acknowledgement tables for COVID-19 sequences used in our analysis: Global sequences and US sequences. - Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages
Samson Weiner, Mukul S. Bansal
Algorithms, 14(8): 231, 2021. - Optimal Completion and Comparison of Incomplete Phylogenetic Trees Under Robinson-Foulds Distance
Keegan Yao, Mukul S. Bansal
Combinatorial Pattern Matching (CPM) 2021; Leibniz International Proceedings in Informatics (LIPIcs), Vol. 191, No. 25.
→ This paper won the best student paper award at CPM 2021. - Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, J. Peter Gogarten, Mukul S. Bansal
Molecular Biology and Evolution, 38(6): 2639–2659, 2021. - TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference
Samuel Sledzieski, Chengchen Zhang, Ion Mandoiu, Mukul S. Bansal
Pacific Symposium on Biocomputing (PSB) 2021: Proceedings, pages 119-130.
→ A preliminary version of this paper was posted to bioRxiv and is available here
→ Slides from the PSB 2021 presentation are available from https://doi.org/10.7490/f1000research.1118422.1 - A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene Transfers
Abhijit Mondal, Misagh Kordi, Mukul S. Bansal
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2020; Proceedings, Article No.: 16, Pages 1–11. - Assessing the Accuracy of Phylogenetic Rooting Methods on Prokaryotic Gene Families
Taylor Wade, L. Thiberio Rangel, Soumya Kundu, Gregory P. Fournier, Mukul S. Bansal
PLOS One, 15(5): e0232950, 2020.
→ All datasets used in this paper are available from the Datasets Page - Linear-Time Algorithms for Phylogenetic Tree Completion Under Robinson-Foulds Distance
Mukul S. Bansal
Algorithms for Molecular Biology, 15:6, 2020.
→ A preliminary version of this paper appeared in RECOMB-CG 2018. - TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity
Saurav Dhar, Chengchen Zhang, Ion Mandoiu, Mukul S. Bansal
International Symposium on Bioinformatics Research and Applications (ISBRA) 2020, LNCS 12304: 203-216. - TreeSolve: Rapid Error-Correction of Microbial Gene Trees
Misagh Kordi, Mukul S. Bansal
Algorithms for Computational Biology (AlCoB) 2020, LNCS 12099: 125-139. - On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation
Misagh Kordi, Soumya Kundu, Mukul S. Bansal
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2019; Proceedings, pages 514-523.
→ The full version of this paper (with all proofs) is available from bioRxiv at https://doi.org/10.1101/2020.03.27.010785.
→ Simulated datasets used in this paper are available from the Datasets Page - Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model
Lei Li, Mukul S. Bansal
International Symposium on Bioinformatics Research and Applications (ISBRA) 2019, LNCS 11490: 73-86. - SaGePhy: An improved phylogenetic simulation framework for gene and subgene evolution
Soumya Kundu, Mukul S. Bansal
Bioinformatics, 35(18): 3496-3498, 2019.
→ A recorded talk describing SaGePhy is available from https://youtu.be/P8P_yDeInN4. - Linear-Time Algorithms for some Phylogenetic Tree Completion Problems Under Robinson-Foulds Distance
Mukul S. Bansal.
RECOMB Comparative Genomics Conference (RECOMB-CG) 2018; LNCS 11183: 209-226. - An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem
Lei Li, Mukul S. Bansal
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2018; Proceedings, pages 386-397.
→ This paper won the best student paper award at ACM-BCB 2018. - RecPhyloXML – a format for reconciled gene trees
W. Duchemin, G. Gence, A. Arigon-Chiffoleau, L. Arvestad, M. S. Bansal, V. Berry, B. Boussau, F. Chevenet, N. Comte, A. A. Davin, C. Dessimoz, D. Dylus, D. Hasic, D. Mallo, R. Planel, D. Posada, C. Scornavacca, G. Szollosi, L. Zhang, E. Tannier, and V. Daubin
Bioinformatics, 34(21): 3646–3652, 2018. - RANGER-DTL 2.0: Rigorous Reconstruction of Gene-Family Evolution by Duplication, Transfer, and Loss
Mukul S. Bansal, Manolis Kellis, Misagh Kordi, Soumya Kundu
Bioinformatics, 34(18): 3214–3216, 2018.
→ Supplementary material for this paper is available here. - On the Impact of Uncertain Gene Tree Rooting on Duplication-Transfer-Loss Reconciliation
Soumya Kundu, Mukul S. Bansal
BMC Bioinformatics, 19(Suppl 9):290, 2018. - An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution
Lei Li, Mukul S. Bansal
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB); 16(1): 63-76, 2019. (Published online in June 2018.)
→ Supplementary material for this paper is available here. - Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees
Misagh Kordi, Mukul S. Bansal
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB); 16(4): 1077-1090, 2019. (Published online in June 2017.)
→ A preliminary version of this paper appeared in ACM-BCB 2016. - On the Impact of Uncertain Gene Tree Rooting on Duplication-Transfer-Loss Reconciliation
Soumya Kundu, Mukul S. Bansal
International Symposium on Bioinformatics Research and Applications (ISBRA) 2017, LNCS 10330: L-LI. (2-page abstract) - On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees
Misagh Kordi, Mukul S. Bansal
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 14(3): 587-599, 2017.
→ A preliminary version of this paper appeared in ISBRA 2015. - Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees
Misagh Kordi, Mukul S. Bansal
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2016; Proceedings, pages 297-306.
http://dx.doi.org/10.1145/2975167.2975198. - On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees
Misagh Kordi, Mukul S. Bansal
International Symposium on Bioinformatics Research and Applications (ISBRA) 2015, LNCS 9096: 187-198.
→ Note: There is a slight error in the published version of this paper. The PDF of the paper available here includes an erratum page that corrects this error. - Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, A. Kundaje, W. Meuleman, J. Ernst, M. Bilenky, A. Yen, A. Heravi-Moussavi, P. Kheradpour, Z. Zhang, J. Wang, M. J. Ziller, V. Amin, J. W. Whitaker, M. D. Schultz, L. D. Ward, A. Sarkar, G. Quon, R. S. Sandstrom, M. L. Eaton, Y. Wu, A. R. Pfenning, X. Wang, M. Claussnitzer, Y. Liu, C. Coarfa, R. A. Harris, N. Shoresh, C. B. Epstein, E. Gjoneska, D. Leung, W. Xie, R. D. Hawkins, R. Lister, C. Hong, P. Gascard, A. J. Mungal, R. Moore, E. Chuah, A. Tam, T. K. Canfield, R. S. Hansen, R. Kaul, P. J. Sabo, M. S. Bansal, A. Carles, J. R. Dixon, K. Farh, S. Feizi, R. Karlic, A. Kim, A. Kulkarni, D. Li, R. Lowdon, T. R. Mercer, S. J. Neph, V. Onuchic, P. Polak, N. Rajagopa, P. Ray, R. C. Sallari, K. T. Siebenthall, N. A. Sinnott-Armstrong, M. Stevens, R. E. Thurman, J. Wu, B. Zhang, X. Zhou, A. E. Beaudet, L. Boyer, P. De Jager, P. J. Farnham, S. J. Fisher, D. Haussler, S. Jones, W. Li, M. Marra, M. T. McManus, S. Sunyaev, J. A. Thomson, T. D. Tlsty, L. Tsai, W. Wang, R. A. Waterland, M. Zhang, L. H. Chadwick, B. E. Bernstein, J. F. Costello, J. R. Ecker, M. Hirst, A. Meissner, A. Milosavljevic, B. Ren, J. A. Stamatoyannopoulos, T. Wang, and M. Kellis
Nature 518: 317-330, 2015. - Improved Gene Tree Error Correction in the Presence of Horizontal Gene Transfer
Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis
Bioinformatics, 31(8): 1211-1218, 2015.
→ Supplementary material for this paper is available here. - A Comparative Encyclopedia of DNA Elements in the Mouse Genome
F. Yue, Y. Cheng, A. Breschi, J. Vierstra, W. Wu, T. Ryba, R. Sandstrom, Z. Ma, C. Davis, B. Pope, Y. Shen, D. Pervouchine, S. Djebali, R. E. Thurman, R. Kaul, E. Rynes, A. Kirilusha, G. K. Marinov, B. A. Williams, D. Trout, H. Amrhein, K. Fisher-Aylor, I. Antoshechkin, G. DeSalvo, L. H. See, M. Fastuca, J. Drenkow, C. Zaleski, A. Dobin, P. Prieto, J. Lagarde, G. Bussotti, A. Tanzer, O. Denas, K. Li, M. A. Bender, M. Zhang, R. Byron, M. T. Groudine, D. McCleary, L. Pham, Z. Ye, S. Kuan, L. Edsall, Y. Wu, M. D. Rasmussen, M. S. Bansal, M. Kellis, C. A. Keller, C. S. Morrissey, T. Mishra, D. Jain, N. Dogan, R. S. Harris, P. Cayting, T. Kawli, A. P. Boyle, G. Euskirchen, A. Kundaje, S. Lin, Y. Lin, C. Jansen, V. S. Malladi, M. S. Cline, D. T. Erickson, V. M. Kirkup, K. Learned, C. A. Sloan, K. R. Rosenbloom, B. L. de Sousa, K. Beal, M. Pignatelli, P. Flicek, J. Lian, T. Kahveci, D. Lee, W. J. Kent, M. R. Santos, J. Herrero, C. Notredame, A. Johnson, S. Vong, K. Lee, D. Bates, F. Neri, M. Diegel, T. Canfield, P. J. Sabo, M. S. Wilken, T. A. Reh, E. Giste, A. Shafer, T. Kutyavin, E. Haugen, D. Dunn, A. P. Reynolds, S. Neph, R. Humbert, R. S. Hansen, M. De Bruijn, L. Selleri, A. Rudensky, S. Josefowicz, R. Samstein, E. E. Eichler, S. H. Orkin, D. Levasseur, T. Papayannopoulou, K. H. Chang, A. Skoultchi, S. Gosh, C. Disteche, P. Treuting, Y. Wang, M. J. Weiss, G. A. Blobel, X. Cao, S. Zhong, T. Wang, P. J. Good, R. F. Lowdon, L. B. Adams, X. Q. Zhou, M. J. Pazin, E. A. Feingold, B. Wold, J. Taylor, A. Mortazavi, S. M. Weissman, J. A. Stamatoyannopoulos, M. P. Snyder, R. Guigo, T. R. Gingeras, D. M. Gilbert, R. C. Hardison, M. A. Beer, B. Ren; Mouse ENCODE Consortium
Nature, 515: 355-365, 2014. - Pareto-Optimal Phylogenetic Tree Reconciliation
Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis
ISMB 2014; Bioinformatics, 30: i87-i95, 2014.
→ Supplementary material for this paper is available from here. - Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and Worm
Yi-Chieh Wu, Mukul S. Bansal, Matthew D. Rasmussen, Javier Herrero, Manolis Kellis
Technical report; bioRxiv, 2014. - Most Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep Coalescence Using Labeled Coalescent Trees
Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis
Genome Research, 24: 475-486, 2014.
→ Supplementary material for this paper is available here. - Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
Journal of Computational Biology (JCB), 20(10): 738-754, 2013.
→ A preliminary version of this paper appeared in RECOMB 2013. - Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony
Mukul S. Bansal, Oliver Eulenstein
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 10(4): 939-956, 2013.
→ Preliminary versions of parts of this paper appeared in RECOMB 2007 and APBC 2010. - Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
RECOMB 2013, LNCS 7821: 1-13. - Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes
Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten, Ron Shamir
Bioinformatics, 29(5): 571-579, 2013.
→ Supplementary material for this paper is available here. - TreeFix: statistically informed gene tree error correction using species trees
Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis
Systematic Biology, 62(1): 110-120, 2013.
→ Supplementary material for this paper is available here. - Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
ISMB 2012; Bioinformatics, 28: i283-i291, 2012.
→ Supplementary material for this paper is available here.
→ A recording of a talk describing this work is available on YouTube at https://youtu.be/Z30z9xAh8_U - Detecting Highways of Horizontal Gene Transfer
Mukul S. Bansal, Guy Banay, J. Peter Gogarten, Ron Shamir
Journal of Computational Biology (JCB), 18(9): 1087-1114, 2011.
→ A preliminary version of this paper appeared in RECOMB-CG 2010. - Comparing and Aggregating Partially Resolved Trees
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
Theoretical Computer Science (TCS), 412: 6634-6652, 2011.
→ A preliminary version of this paper appeared in LATIN 2008. - A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem
Mukul S. Bansal, Ron Shamir
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 8(3): 848-850, 2011. - Genome-scale phylogenetics: Inferring the plant tree of life from 18,896 gene trees
J. G. Burleigh, M. S. Bansal, O. Eulenstein, S. Hartmann, A. Wehe, and T. J. Vision
Systematic Biology, 60(2): 117-125, 2011. - Detecting Highways of Horizontal Gene Transfer
Mukul S. Bansal, J. Peter Gogarten, Ron Shamir
RECOMB-CG 2010; LNCS 6398: 109-120. - iGTP: A software package for large-scale gene tree parsimony analysis
Ruchi Chaudhary, Mukul S. Bansal, Andre Wehe, David Fernández-Baca, Oliver Eulenstein.
BMC Bioinformatics, 11:574, 2010. - Inferring Species Trees From Gene Duplication Episodes
J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision
Proceedings of ACM-BCB 2010, pages 198-203. - Robinson-Foulds Supertrees
Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein, David Fernández-Baca
Algorithms for Molecular Biology (AMB), 5:18, 2010. - Property-Aware Program Sampling
Harish Narayanappa, Mukul S. Bansal, Hridesh Rajan
Proceedings of PASTE 2010, pages 45-52. - Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein
APBC 2010; BMC Bioinformatics, 11(Suppl 1):S42, 2010. - The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches
Mukul S. Bansal, Oliver Eulenstein, Andre Wehe
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 6(2): 221-231, 2009.
→ A preliminary version of this paper appeared in ISBRA 2008. - Locating Large-Scale Gene Duplication Events Through Reconciled Trees: Implications For Identifying Ancient Polyploidy Events In Plants
J. G. Burleigh, Mukul S. Bansal, Andre Wehe, Oliver Eulenstein
Journal of Computational Biology (JCB), 16(8): 1071-1083, 2009.
→ A preliminary version of this paper appeared in RECOMB 2008. - Generalized Binary Tanglegrams: Algorithms and Applications
Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca
BICoB 2009, LNCS 5462: 114-125.
→ This paper won the best paper award at BICoB.
→ Note: The brief discussion on the fixed parameter tractability, approximability, and existence of planar layout of the GTL problem (page 8) that appears in the LNCS version of this paper contains some incorrect explanations. The version available here (above) contains a corrected version of this discussion. - Computing Distances Between Partial Rankings
Mukul S. Bansal, David Fernández-Baca
Information Processing Letters, 109: 238-241, 2009.
doi:10.1016/j.ipl.2008.10.010 - An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem
Mukul S. Bansal, Oliver Eulenstein
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 5(4): 514-524, 2008.
→ A preliminary version of this paper appeared in WABI 2007. - The Multiple Gene Duplication Problem Revisited
Mukul S. Bansal, Oliver Eulenstein
ISMB 2008; Bioinformatics, 24(13): i132-i138, 2008. - DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
Andre Wehe, Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein
Bioinformatics, 24(13): 1540-1541, 2008. - The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches
Mukul S. Bansal, Oliver Eulenstein
ISBRA 2008, LNCS 4983: 14-25. - Comparing and Aggregating Partially Resolved Trees
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
LATIN 2008, LNCS 4957: 72-83. - Locating Multiple Gene Duplications Through Reconciled Trees
J. G. Burleigh, Mukul S. Bansal, Andre Wehe, Oliver Eulenstein
RECOMB 2008, LNCS 4955: 273-284. - PhyloFinder: An intelligent search engine for phylogenetic tree databases
Duhong Chen, J.G. Burleigh, Mukul S. Bansal, David Fernández-Baca.
BMC Evolutionary Biology, 8:90, 2008. - An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem
Mukul S. Bansal, Oliver Eulenstein
WABI 2007, LNCS 4645: 124-135.
→ Note: Lemma 5 in the LNCS version of this paper is incorrectly stated. The version available here (above) contains the correctly stated version of this Lemma. - Heuristics for the gene-duplication problem: A Θ(n) speed-up for the local search
Mukul S. Bansal, J.G. Burleigh, Oliver Eulenstein, Andre Wehe
RECOMB 2007, LNCS 4453: 238-252. - Improved Fully Polynomial Time Approximation Scheme for the 0-1 Multiple-choice Knapsack Problem
Mukul S. Bansal, V.Ch.Venkaiah
Technical Report; # IIIT/TR/2004/3, International Institute of Information Technology, India; 2004.
Manuscipts under review
- Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes
Lina Kloub, Sophia Gosselin, Joerg Graf, J. Peter Gogarten, Mukul S. Bansal
Under review. - DICE: Fast and Accurate Distance-Based Reconstruction of Single-Cell Copy Number Phylogenies
Samson Weiner, Mukul S. Bansal
Under review.
Last updated: March 2024