Publications

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Publications (in reverse chronological order)

  1. Improved Duplication-Transfer-Loss Reconciliation with Extinct and Unsampled Lineages
    Samson Weiner, Mukul S. Bansal
    Algorithms, 14(8): 231, 2021.
  2. 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; 2021 (in press).
    → 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.
  3. 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.
  4. 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.
  5. 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
  6. 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.
  7. 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
  8. 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.
  9. 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.
  10. TreeSolve: Rapid Error-Correction of Microbial Gene Trees
    Misagh Kordi, Mukul S. Bansal
    Algorithms for Computational Biology (AlCoB) 2020, LNCS 12099: 125-139.
  11. 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
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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)
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. Detecting Highways of Horizontal Gene Transfer
    Mukul S. Bansal, J. Peter Gogarten, Ron Shamir
    RECOMB-CG 2010; LNCS 6398: 109-120.
  42. 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.
  43. 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.
  44. Robinson-Foulds Supertrees
    Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein, David Fernández-Baca
    Algorithms for Molecular Biology (AMB), 5:18, 2010.
  45. Property-Aware Program Sampling
    Harish Narayanappa, Mukul S. Bansal, Hridesh Rajan
    Proceedings of PASTE 2010, pages 45-52.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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
  51. 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.
  52. The Multiple Gene Duplication Problem Revisited
    Mukul S. Bansal, Oliver Eulenstein
    ISMB 2008; Bioinformatics, 24(13): i132-i138, 2008.
  53. 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.
  54. The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches
    Mukul S. Bansal, Oliver Eulenstein
    ISBRA 2008, LNCS 4983: 14-25.
  55. Comparing and Aggregating Partially Resolved Trees
    Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
    LATIN 2008, LNCS 4957: 72-83.
  56. Locating Multiple Gene Duplications Through Reconciled Trees
    J. G. Burleigh, Mukul S. Bansal, Andre Wehe, Oliver Eulenstein
    RECOMB 2008, LNCS 4955: 273-284.
  57. 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.
  58. 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.
  59. 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.
  60. 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.

Papers under review


Last updated on Juy 8, 2021