Mukul S Bansal

Mukul S Bansal

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Mukul S Bansal

Mukul S Bansal

Publications by authors named "Mukul S Bansal"

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28Publications

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

Bioinformatics 2019 Sep;35(18):3496-3498

Department of Computer Science & Engineering, Storrs, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz081DOI Listing
September 2019

An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution.

IEEE/ACM Trans Comput Biol Bioinform 2019 Jan-Feb;16(1):63-76. Epub 2018 Jun 12.

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http://dx.doi.org/10.1109/TCBB.2018.2846253DOI Listing
August 2019

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

Bioinformatics 2018 09;34(18):3214-3216

Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137995PMC
September 2018

On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation.

BMC Bioinformatics 2018 Aug 13;19(Suppl 9):290. Epub 2018 Aug 13.

Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-018-2269-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101088PMC
August 2018

On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

IEEE/ACM Trans Comput Biol Bioinform 2017 May-Jun;14(3):587-599. Epub 2015 Dec 23.

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http://dx.doi.org/10.1109/TCBB.2015.2511761DOI Listing
March 2018

Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

IEEE/ACM Trans Comput Biol Bioinform 2019 Jul-Aug;16(4):1077-1090. Epub 2017 Jun 1.

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http://dx.doi.org/10.1109/TCBB.2017.2710342DOI Listing
June 2017

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

Bioinformatics 2015 Apr 5;31(8):1211-8. Epub 2014 Dec 5.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393519PMC
April 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Algorithms for genome-scale phylogenetics using gene tree parsimony.

IEEE/ACM Trans Comput Biol Bioinform 2013 Jul-Aug;10(4):939-56

Iowa State University, Ames.

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http://dx.doi.org/10.1109/TCBB.2013.103DOI Listing
August 2014

Pareto-optimal phylogenetic tree reconciliation.

Bioinformatics 2014 Jun;30(12):i87-95

Department of Computer Science, Harvey Mudd College, Claremont, CA 91711, Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 and Broad Institute, Cambridge, MA 02142, USADepartment of Computer Science, Harvey Mudd College, Claremont, CA 91711, Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 and Broad Institute, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058917PMC
June 2014

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.

Genome Res 2014 Mar 5;24(3):475-86. Epub 2013 Dec 5.

Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;

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http://genome.cshlp.org/cgi/doi/10.1101/gr.161968.113
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http://dx.doi.org/10.1101/gr.161968.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941112PMC
March 2014

Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss.

J Comput Biol 2013 Oct 14;20(10):738-54. Epub 2013 Sep 14.

1 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts.

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http://dx.doi.org/10.1089/cmb.2013.0073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791060PMC
October 2013

Systematic inference of highways of horizontal gene transfer in prokaryotes.

Bioinformatics 2013 Mar 17;29(5):571-9. Epub 2013 Jan 17.

The Blavatnik School of Computer Science, Tel-Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1093/bioinformatics/btt021DOI Listing
March 2013

TreeFix: statistically informed gene tree error correction using species trees.

Syst Biol 2013 Jan 4;62(1):110-20. Epub 2012 Sep 4.

Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/sysbio/sys076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526801PMC
January 2013

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

Bioinformatics 2012 Jun;28(12):i283-91

Computer Science and Artificial Intelligence Laboratory, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371857PMC
June 2012

Detecting highways of horizontal gene transfer.

J Comput Biol 2011 Sep;18(9):1087-114

The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1089/cmb.2011.0066DOI Listing
September 2011

A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem.

IEEE/ACM Trans Comput Biol Bioinform 2011 May-Jun;8(3):848-50

School of Computer Science, Schreiber Bldg., Tel-Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1109/TCBB.2010.74DOI Listing
August 2011

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.

Syst Biol 2011 Mar 24;60(2):117-25. Epub 2010 Dec 24.

Department of Biology, University of Florida, Gainesville, FL 32609, USA.

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http://dx.doi.org/10.1093/sysbio/syq072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038350PMC
March 2011

iGTP: a software package for large-scale gene tree parsimony analysis.

BMC Bioinformatics 2010 Nov 23;11:574. Epub 2010 Nov 23.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1471-2105-11-574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002902PMC
November 2010

Robinson-Foulds supertrees.

Algorithms Mol Biol 2010 Feb 24;5:18. Epub 2010 Feb 24.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1186/1748-7188-5-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846952PMC
February 2010

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

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S42. Epub 2010 Jan 18.

School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1186/1471-2105-11-S1-S42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009515PMC
January 2010

The gene-duplication problem: near-linear time algorithms for NNI-based local searches.

IEEE/ACM Trans Comput Biol Bioinform 2009 Apr-Jun;6(2):221-31

Department of Computer Science, Iowa StateUniversity, Ames, IA 50011, USA.

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http://dx.doi.org/10.1109/TCBB.2009.7DOI Listing
August 2009

An Omega(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem.

IEEE/ACM Trans Comput Biol Bioinform 2008 Oct-Dec;5(4):514-24

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1109/TCBB.2008.69DOI Listing
January 2009

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

Bioinformatics 2008 Jul 12;24(13):1540-1. Epub 2008 May 12.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn230DOI Listing
July 2008

The multiple gene duplication problem revisited.

Bioinformatics 2008 Jul;24(13):i132-8

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718628PMC
July 2008

PhyloFinder: an intelligent search engine for phylogenetic tree databases.

BMC Evol Biol 2008 Mar 21;8:90. Epub 2008 Mar 21.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1471-2148-8-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2362120PMC
March 2008