Publications: Mukul Bansal

• 2023

• CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors.
  Weiner S, Bansal MS
  Bioinformatics (Oxford, England) (2023) 39(7): PMC3966983 10.1093/bioinformatics/btad434
• Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021).
  Bansal MS, Măndoiu II, Moussa M, Patterson M, Rajasekaran S, Skums P, Zelikovsky A
  Journal of computational biology : a journal of computational molecular cell biology (2023) 30(4):363-365 10.1089/cmb.2023.29085.msb
• DaTeR: error-correcting phylogenetic chronograms using relative time constraints.
  Mondal A, Rangel LT, Payette JG, Fournier GP, Bansal MS
  Bioinformatics (Oxford, England) (2023) 39(2): PMC7056644 10.1093/bioinformatics/btad084

• 2022

• virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.
  Zaman S, Sledzieski S, Berger B, Wu YC, Bansal MS
  Journal of computational biology : a journal of computational molecular cell biology (2022) 30(1):3-20 PMC7095418 10.1089/cmb.2021.0507
• Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL.
  Bansal MS
  Methods in molecular biology (Clifton, N.J.) (2022) 2569:233-252 10.1109/TCBB.2018.2846253
• Comparison of knowledge and awareness of infection control practices among nurses in India: A cross-sectional survey.
  Sodhi K, Arya M, Chanchalani G, Sinha V, Dominic Savio R, Ak AK, Ahmed A, Jagiasi B, Agarwal D, Jagathkar G, Khasne R, Sahasrabudhe SS, Jha SK, Sahoo TK, Mittal V, Hr H, Bansal S, Agarwal C, Kumar M
  American journal of infection control (2022) : 10.1016/j.ajic.2022.02.014

• 2021

• TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread.
  Dhar S, Zhang C, Mandoiu II, Bansal MS
  IEEE/ACM transactions on computational biology and bioinformatics (2021) 19(1):230-242 PMC5850600 10.1109/TCBB.2021.3096455
• TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference.
  Sledzieski S, Zhang C, Mandoiu I, Bansal MS
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2021) 26:119-130

• 2020

• Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families.
  Wade T, Rangel LT, Kundu S, Fournier GP, Bansal MS
  PloS one (2020) 15(5):e0232950 PMC7228096 10.1371/journal.pone.0232950
• Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance.
  Bansal MS
  Algorithms for molecular biology : AMB (2020) 15:6 PMC7155338 10.1186/s13015-020-00166-1

• 2019

• SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution.
  Kundu S, Bansal MS
  Bioinformatics (Oxford, England) (2019) 35(18):3496-3498 10.1093/bioinformatics/btz081

• 2018

• On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation.
  Kundu S, Bansal MS
  BMC Bioinformatics (2018) 19(Suppl 9):290 (PMC6101088) 10.1186/s12859-018-2269-0
• An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution.
  Li L, Bansal MS
  IEEE/ACM transactions on computational biology and bioinformatics (2018) 16(1):63-76 10.1109/TCBB.2018.2846253
• RecPhyloXML: a format for reconciled gene trees.
  Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V
  Bioinformatics (2018) 34(21):3646-3652 (PMC6198865) 10.1093/bioinformatics/bty389
• RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss.
  Bansal MS, Kellis M, Kordi M, Kundu S
  Bioinformatics (2018) 34(18):3214-3216 (PMC6137995) 10.1093/bioinformatics/bty314

• 2017

• Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
  Kordi M, Bansal MS
  IEEE/ACM transactions on computational biology and bioinformatics (2017) 16(4):1077-1090 10.1109/TCBB.2017.2710342
• On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.
  Kordi M, Bansal MS
  IEEE/ACM Trans Comput Biol Bioinform (2017) 14(3):587-599

• 2015

• Integrative analysis of 111 reference human epigenomes.
  Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning A, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Abdennur N, Adli M, Akerman M, Barrera L, Antosiewicz-Bourget J, Ballinger T, Barnes MJ, Bates D, Bell RJ, Bennett DA, Bianco K, Bock C, Boyle P, Brinchmann J, Caballero-Campo P, Camahort R, Carrasco-Alfonso MJ, Charnecki T, Chen H, Chen Z, Cheng JB, Cho S, Chu A, Chung WY, Cowan C, Athena Deng Q, Deshpande V, Diegel M, Ding B, Durham T, Echipare L, Edsall L, Flowers D, Genbacev-Krtolica O, Gifford C, Gillespie S, Giste E, Glass IA, Gnirke A, Gormley M, Gu H, Gu J, Hafler DA, Hangauer MJ, Hariharan M, Hatan M, Haugen E, He Y, Heimfeld S, Herlofsen S, Hou Z, Humbert R, Issner R, Jackson AR, Jia H, Jiang P, Johnson AK, Kadlecek T, Kamoh B, Kapidzic M, Kent J, Kim A, Kleinewietfeld M, Klugman S, Krishnan J, Kuan S, Kutyavin T, Lee AY, Lee K, Li J, Li N, Li Y, Ligon KL, Lin S, Lin Y, Liu J, Liu Y, Luckey CJ, Ma YP, Maire C, Marson A, Mattick JS, Mayo M, McMaster M, Metsky H, Mikkelsen T, Miller D, Miri M, Mukamel E, Nagarajan RP, Neri F, Nery J, Nguyen T, O'Geen H, Paithankar S, Papayannopoulou T, Pelizzola M, Plettner P, Propson NE, Raghuraman S, Raney BJ, Raubitschek A, Reynolds AP, Richards H, Riehle K, Rinaudo P, Robinson JF, Rockweiler NB, Rosen E, Rynes E, Schein J, Sears R, Sejnowski T, Shafer A, Shen L, Shoemaker R, Sigaroudinia M, Slukvin I, Stehling-Sun S, Stewart R, Subramanian SL, Suknuntha K, Swanson S, Tian S, Tilden H, Tsai L, Urich M, Vaughn I, Vierstra J, Vong S, Wagner U, Wang H, Wang T, Wang Y, Weiss A, Whitton H, Wildberg A, Witt H, Won KJ, Xie M, Xing X, Xu I, Xuan Z, Ye Z, Yen CA, Yu P, Zhang X, Zhang X, Zhao J, Zhou Y, Zhu J, Zhu Y, Ziegler S, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M
  Nature (2015) 518(7539):317-30 (PMC4530010)

• 2014

• Improved gene tree error correction in the presence of horizontal gene transfer.
  Bansal MS, Wu YC, Alm EJ, Kellis M
  Bioinformatics (2014) 31(8):1211-8 (PMC4393519)
• A comparative encyclopedia of DNA elements in the mouse genome.
  Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B
  Nature (2014) 515(7527):355-64 (PMC4266106)
• Pareto-optimal phylogenetic tree reconciliation.
  Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M
  Bioinformatics (2014) 30(12):i87-95 (PMC4058917)

• 2013

• Algorithms for genome-scale phylogenetics using gene tree parsimony.
  Bansal MS, Eulenstein O
  IEEE/ACM Trans Comput Biol Bioinform (2013) 10(4):939-56
• Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.
  Wu YC, Rasmussen MD, Bansal MS, Kellis M
  Genome Res. (2013) 24(3):475-86 (PMC3941112)
• Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss.
  Bansal MS, Alm EJ, Kellis M
  J. Comput. Biol. (2013) 20(10):738-54 (PMC3791060)
• Systematic inference of highways of horizontal gene transfer in prokaryotes.
  Bansal MS, Banay G, Harlow TJ, Gogarten JP, Shamir R
  Bioinformatics (2013) 29(5):571-9

• 2012

• TreeFix: statistically informed gene tree error correction using species trees.
  Wu YC, Rasmussen MD, Bansal MS, Kellis M
  Syst. Biol. (2012) 62(1):110-20 (PMC3526801)
• Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.
  Bansal MS, Alm EJ, Kellis M
  Bioinformatics (2012) 28(12):i283-91 (PMC3371857)

• 2011

• Detecting highways of horizontal gene transfer.
  Bansal MS, Banay G, Gogarten JP, Shamir R
  J. Comput. Biol. (2011) 18(9):1087-114

• 2010

• Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.
  Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ
  Syst. Biol. (2010) 60(2):117-25 (PMC3038350)
• iGTP: a software package for large-scale gene tree parsimony analysis.
  Chaudhary R, Bansal MS, Wehe A, Fernández-Baca D, Eulenstein O
  BMC Bioinformatics (2010) 11:574 (PMC3002902)
• A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem.
  Bansal MS, Shamir R
  IEEE/ACM Trans Comput Biol Bioinform (2010) 8(3):848-50
• Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.
  Bansal MS, Burleigh JG, Eulenstein O
  BMC Bioinformatics (2010) 11 Suppl 1:S42 (PMC3009515)
• Robinson-Foulds supertrees.
  Bansal MS, Burleigh JG, Eulenstein O, Fernández-Baca D
  Algorithms Mol Biol (2010) 5:18 (PMC2846952)

• 2009

• Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants.
  Burleigh JG, Bansal MS, Wehe A, Eulenstein O
  J. Comput. Biol. (2009) 16(8):1071-83
• The gene-duplication problem: near-linear time algorithms for NNI-based local searches.
  Bansal MS, Eulenstein O, Wehe A
  IEEE/ACM Trans Comput Biol Bioinform (2009) 6(2):221-31

• 2008

• An Omega(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem.
  Bansal MS, Eulenstein O
  IEEE/ACM Trans Comput Biol Bioinform (2008) 5(4):514-24
• The multiple gene duplication problem revisited.
  Bansal MS, Eulenstein O
  Bioinformatics (2008) 24(13):i132-8 (PMC2718628)
• DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
  Wehe A, Bansal MS, Burleigh JG, Eulenstein O
  Bioinformatics (2008) 24(13):1540-1
• PhyloFinder: an intelligent search engine for phylogenetic tree databases.
  Chen D, Burleigh JG, Bansal MS, Fernández-Baca D
  BMC Evol. Biol. (2008) 8:90 (PMC2362120)

• 0

• 
  
  (0) :