Computational Biology Research Laboratory

Publications

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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; LNCS 14616: 129-149.
• 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: May 2024