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Mukul S. Bansal

Contact Information

Massachusetts Institute of Technology 32 Vassar Street, D.510 Cambridge, MA, USA Phone: (+1) 617-335-6163 Email : [email protected] Webpage: http://people.csail.mit.edu/mukul

Research Interests

Computational biology and bioinformatics, with a focus on computational molecular evolution. I develop new computational methods, efficient algorithms, and powerful software tools to help answer fundamental questions in molecular evolution. I am especially interested in problems related to understanding gene family and genome evolution, and accurately reconstructing organismal phylogenies.

Education

Postdoctoral Associate, January 2011 ­ Present Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology, Cambridge, USA Postdoc Advisors: Prof. Manolis Kellis and Prof. Eric J. Alm Postdoctoral Fellow, July 2009 ­ December 2010 The Blavatnik School of Computer Science Tel Aviv University, Tel Aviv, Israel Postdoc Advisor : Prof. Ron Shamir M.S. and Ph.D. in Computer Science, Fall 2004 ­ Summer 2009 Department of Computer Science Iowa State University, Ames, Iowa, USA Advisors: Prof. David Fern´ndez-Baca and Prof. Oliver Eulenstein a Dissertation Title: Algorithms for efficient phylogenetic tree construction B.Tech. in Computer Science, 2000 ­ 2004 Department of Computer Science and Engineering International Institute of Information Technology, Hyderabad, India

Journal Publications

[1] M. S. Bansal, G. Banay, T. J. Harlow, J. P. Gogarten, and R. Shamir, "Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes", Bioinformatics 2013, 29(5): 571­579. [2] Y. Wu, M. D. Rasmussen, M. S. Bansal, and M. Kellis, "TreeFix: statistically informed gene tree error correction using species trees", Systematic Biology 2013, 62(1): 110­120. [3] M. S. Bansal, G. Banay, J. P. Gogarten, and R. Shamir, "Detecting Highways of Horizontal Gene Transfer", Journal of Computational Biology 2011, 18(9): 1087-1114. [4] M. S. Bansal, J. Dong, and D. Fern´ndez-Baca, "Comparing and Aggregating Partially Resolved a Trees", Theoretical Computer Science 2011, 412: 6634­6652. [5] M. S. Bansal and R. Shamir, "A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem", IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011, 8(3): 848­ 850.

[6] J. G. Burleigh, M. S. Bansal, O. Eulenstein, S. Hartmann, A. Wehe, and T. J. Vision, "Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees", Systematic Biology 2011, 60(2): 117­125. a [7] R. Chaudhary, M. S. Bansal, A. Wehe, D. Fern´ndez-Baca, and O. Eulenstein, "iGTP: A software application for large-scale gene tree parsimony analysis", BMC Bioinformatics 2010, 11:574. [8] M. S. Bansal, J. G. Burleigh, O. Eulenstein, and D. Fern´ndez-Baca, "Robinson-Foulds Supertrees", a Algorithms for Molecular Biology 2010, 5:18. [9] M. S. Bansal, O. Eulenstein, and A. Wehe, "The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches", IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009, 6(2): 221­231. [10] J. G. Burleigh, M. S. Bansal, A. Wehe, and O. Eulenstein, "Locating Large-Scale Gene Duplication Events Through Reconciled Trees: Implications For Identifying Ancient Polyploidy Events In Plants", Journal of Computational Biology 2009, 16(8): 1071­1083. a [11] M. S. Bansal and D. Fern´ndez-Baca, "Computing Distances Between Partial Rankings", Information Processing Letters 2009, 109(4): 238­241. [12] M. S. Bansal and O. Eulenstein, "An (n2 / log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem", IEEE/ACM Transactions on Computational Biology and Bioinformatics 2008, 5(4): 514­ 524. [13] A. Wehe, M. S. Bansal, J. G. Burleigh, and O. Eulenstein, "DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony", Bioinformatics 2008, 24(13): 1540­1541. a [14] D. Chen, J. G. Burleigh, M. S. Bansal, and D. Fern´ndez-Baca, "PhyloFinder: An Intelligent Search Engine for Phylogenetic Tree Databases", BMC Evolutionary Biology 2008, 8:90.

Refereed Conference Publications

[15] M. S. Bansal, E. J. Alm, and M. Kellis, "Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss". Seventeenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013), LNCS 7821 : 1­13. [16] M. S. Bansal, E. J. Alm, and M. Kellis, "Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss". Twentieth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2012); Bioinformatics 2012, 28: i283­i291. [17] M. S. Bansal, J. P. Gogarten, and R. Shamir, "Detecting Highways of Horizontal Gene Transfer". Eighth Annual RECOMB Comparative Genomics Workshop (RECOMB-CG 2010), LNCS 6398 : 109­120. [18] H. Narayanappa, M. S. Bansal, and H. Rajan, "Property-Aware Program Sampling", Ninth ACM SIGPLAN-SIGSOFT Workshop on Program Analysis for Software Tools and Engineering (PASTE 2010): 45­52. [19] J. G. Burleigh, M. S. Bansal, O. Eulenstein, and T. J. Vision, "Inferring Species Trees From Gene Duplication Episodes". First ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2010): 198­203. [20] M. S. Bansal, J. G. Burleigh, and O. Eulenstein, "Efficient genome-scale phylogenetic analysis under the duplication-Loss and deep coalescence cost models", Eighth Asia-Pacific Bioinformatics Conference (APBC 2010); BMC Bioinformatics 2010, 11(Suppl 1): S42. [21] M. S. Bansal, W. Chang, O. Eulenstein, and D. Fern´ndez-Baca, "Generalized Binary Tanglegrams: a Algorithms and Applications". First International Conference on Bioinformatics and Computational Biology (BICoB 2009), LNCS 5462 : 114­125. This paper won the Best Paper Award.

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[22] M. S. Bansal and O. Eulenstein, "The Multiple Gene Duplication Problem Revisited", Sixteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008); Bioinformatics 2008, 24(13): i132­i138. [23] M. S. Bansal and O. Eulenstein, "The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches", Fourth International Symposium on Bioinformatics Research and Applications (ISBRA 2008), LNCS 4983 : 14­25. [24] J. G. Burleigh, M. S. Bansal, A. Wehe, and O. Eulenstein, "Locating Multiple Gene Duplications Through Reconciled Trees", Twelfth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008), LNCS 4955 : 273­284. a [25] M. S. Bansal, J. Dong, and D. Fern´ndez-Baca, "Comparing and Aggregating Partially Resolved Trees", Eighth Latin American Theoretical Informatics Symposium (LATIN 2008), LNCS 4957 : 72­83. [26] M. S. Bansal and O. Eulenstein, "An (n2 / log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem", Seventh Workshop on Algorithms in Bioinformatics (WABI 2007), LNCS 4645 : 124­135. [27] M. S. Bansal, J. G. Burleigh, O. Eulenstein, and A. Wehe, "Heuristics for the Gene-Duplication Problem: A (n) Speed-Up for the Local Search", Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), LNCS 4453 : 238­252.

Manuscripts Under Review

[28] M. S. Bansal and O. Eulenstein, "Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony". [29] M. S. Bansal, Y. Wu, E. J. Alm, and M. Kellis, "Reliable and Accurate Gene Tree Reconstruction for Deciphering Microbial Evolution".

Software Packages

I have written or co-written several powerful software packages for phylogenetic and evolutionary analyses, many of which are actively used by the research community. Six of these are listed below: · RANGER-DTL: (http://compbio.mit.edu/ranger-dtl/) Short for Rapid ANalysis of Gene family Evolution using Reconciliation-DTL, this is a software package for inferring gene family evolution by speciation, gene duplication, horizontal gene transfer, and gene loss. RANGER-DTL implements the efficient algorithms presented in ref. [16] and makes it possible to perform rigorous evolutionary analyses of even large gene families with thousands of taxa. · RF-Supertrees: (http://genome.cs.iastate.edu/CBL/RFsupertrees/) This is a fast and accurate supertree program for rooted phylogenetic trees. RF-supertrees implements efficient search algorithms described in ref. [8] and constructs a supertree that minimizes the total Robinson-Foulds distance between the supertree and the input trees. · DupTree: (http://genome.cs.iastate.edu/CBL/DupTree/) This is a tool box for constructing species phylogenies from genome-scale multi-locus data using gene tree parsimony. DupTree implements the fast local search algorithm from ref. [27] and was programmed jointly with fellow graduate student Andr´ Wehe. e · DupLoss and DeepC: (http://genome.cs.iastate.edu/CBL/iGTP/) These programs extend on the program DupTree and make it possible to construct species phylogenies, from genome-scale multi-locus data, under the duplication-loss and deep coalescence cost models respectively. They implement the local search algorithms described in ref. [18] and are available as part of the iGTP [7] package. · HiDe: (http://acgt.cs.tau.ac.il/hide/) Short for Highway Detection, HiDe is a software package for inferring highways of horizontal gene transfer (representing large-scale horizontal transfer of genes) in

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the evolutionary history of a set of species. HiDe implements the highway detection method described in ref. [1] and was programmed by undergraduate summer student Guy Banay under my supervision.

Selected Recent Awards and Honors

Best Paper Award at the International Conference on Bioinformatics and Computational Biology (BICoB) 2009. Awarded the Dr. Robert Stewart Early Research Recognition Award by the Department of Computer Science at Iowa State University, for the academic year 2007­2008. It is awarded competitively to one graduate student each academic year. Awarded the Edmond J. Safra Postdoctoral Fellowship at Tel Aviv University for the academic years 2009­2010 and 2010­2011. Multiple Travel Awards for attending leading scientific conferences including RECOMB 2007 ($700), ISMB 2008 ($600), RECOMB-CG 2010 ($450), ISMB 2012 ($900).

Talks at Conferences and Workshops

1. "Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss"; International Conference on Research in Computational Molecular Biology (RECOMB), April 2013, Beijing, China. 2. "Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss"; International Conference on Intelligent Systems for Molecular Biology (ISMB), July 2012, Long Beach, USA. 3. "Reconciliation revisited: Towards more accurate inference of gene family evolution"; Mathematical and Computational Evolutionary Biology (MCEB), June 2012, Montpellier, France. 4. "Reconstructing gene family evolution by speciation, duplication, horizontal transfer & loss"; Boston Evolutionary Genomics Supergroup Meeting, August 2011, Cambridge, USA. 5. "Detecting Highways of Horizontal Gene Transfer"; RECOMB Comparative Genomics Workshop (RECOMB-CG), October 2010, Ottawa, Canada. 6. "Detecting Highways of Horizontal Gene Transfer"; Bertinoro Computational Biology Meeting, May 2010, Bertinoro, Italy. 7. "Detecting Highways of Horizontal Gene Transfer"; Stringology Research Workshop, May 2010, TelAviv, Israel. 8. "Genome-Scale Phylogenetic Analyses using Gene Tree Parsimony"; Asia-Pacific Bioinformatics Conference (APBC), January 2010, Bangalore, India. 9. "Generalized Binary Tanglegrams"; International Conference on Bioinformatics and Computational Biology (BICoB), April 2009, New Orleans, USA. 10. "The multiple gene duplication problem revisited"; International Conference on Intelligent Systems for Molecular Biology (ISMB), July 2008, Toronto, Canada. 11. "The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches"; International Symposium on Bioinformatics Research and Applications (ISBRA), May 2008, Atlanta, USA. 12. "Heuristics for the Gene-Duplication Problem: A (n) Speed-up of the Local Search"; International Conference on Research in Computational Molecular Biology (RECOMB), April 2007, San Francisco, USA.

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Invited Talks

1. "Accurate gene tree reconstruction using TreeFix and TreeFix-DTL"; Symposium and Workshop on New Methods for Phylogenomics and Metagenomics, University of Texas, Austin, USA. February 2013. 2. "Reconciliation revisited: Towards faster and more accurate inference of gene family evolution by duplication, transfer, and loss"; Computational and Statistical Phylogenomics Meeting, Vigo, Spain. September 2012. 3. "Systematic Detection of Large-Scale Horizontal Gene Transfer Events on the Tree of Life"; Computer Science Colloquium, Iowa State University, Ames, USA. April 2011. 4. "Inferring Species Trees and Large-Scale Horizontal Gene Transfer from Discordant Gene Trees"; Computational Biology Group and Laboratory for Microbiology, Massachusetts Institute of Technology, Cambridge, USA. October 2010. 5. "Inferring Species Trees and Large-Scale Horizontal Gene Transfer from Discordant Gene Trees"; Evolutionary Genomics Research Group, NCBI, National Institutes of Health, Bethesda, USA. July 2010. 6. "The Gene-Duplication Problem"; Computational Genomics Research Group, Tel Aviv University, Tel Aviv, Israel. February 2009.

Teaching Experience

Teaching Assistant: Department of Computer Science, Iowa State University, USA. As a TA, I assisted several faculty members in teaching their courses. Typical TA duties included conducting lab sessions and recitations, grading student homework and exams, and, in general, helping students understand the course material. I have been a TA for the following courses: 1. Spring 2008 : Computational Geometry. (Graduate level course; 10 hours/week) 2. Fall 2006 : Design and Analysis of Algorithms. (Graduate level course; 20 hours/week) 3. Fall 2005 : Introduction to Data Structures. (20 hours/week) 4. Summer 2005 : Introduction to Object Oriented Programming. (20 hours/week) 5. Spring 2005 : Introduction to Data Structures. (20 hours/week) 6. Fall 2004 : Introduction to Object Oriented Programming. (20 hours/week) Guest Lecturer: I enjoy teaching and have had the opportunity to teach several classes at ISU and MIT as a guest lecturer. 1. Fall 2012 : Computational Biology: Genomes, Networks, Evolution. (One lecture) Instructor: Prof. Manolis Kellis; Undergraduate/Graduate level course at MIT 2. Fall 2011 : Computational Biology: Genomes, Networks, Evolution. (One lecture) Instructor: Prof. Manolis Kellis; Undergraduate/Graduate level course at MIT 3. Fall 2008 : Design and analysis of Algorithms. (Two lectures) Instructor: Prof. David Fern´ndez-Baca; Graduate level course at ISU a 4. Spring 2008 : Computational Geometry. (Three lectures) Instructor: Prof. David Fern´ndez-Baca; Graduate level course at ISU a 5. Fall 2007 : Algorithms for Phylogenetic Problems. (One lecture) Instructor: Prof. Oliver Eulenstein; Graduate level course at ISU 6. Fall 2007 : Design and Analysis of Algorithms. (Two lectures) Instructor: Prof. David Fern´ndez-Baca; Undergraduate level course at ISU a

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Student Mentoring

· Provided research mentoring to several junior graduate students at ISU and MIT. · Directly supervised and mentored an undergraduate summer student during my postdoc at TAU, resulting in two peer-reviewed publications (refs. [1] and [3]) with the student. · Served as course project mentor for several groups in Manolis Kellis' computational biology course at MIT during the years 2011 and 2012.

Employment History

Postdoctoral Associate: January 2011 ­ Present ; Computational Biology Research Group, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, USA. Mentors: Prof. Manolis Kellis and Prof. Eric J. Alm. Postdoctoral Fellow: July 2009 ­ December 2010 ; Algorithms for Computational Genomics Group, The Blavatnik School of Computer Science, Tel Aviv University, Israel. Mentor : Prof. Ron Shamir. Visiting Graduate Student: Summer 2007 ; Prof. Michael Sanderson's Lab, Department of Ecology and Evolutionary Biology, University of Arizona, USA. Research/Teaching Assistant: Fall 2004 ­ Summer 2009 ; Department of Computer Science, Iowa State University, USA.

Professional Service

Conference program committees: · International Conference on Bioinformatics and Computational Biology (BICoB) 2012. · International Workshop on Data Mining in Bioinformatics (BIOKDD) 2012. · ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB) 2012. · International Conference on Bioinformatics and Computational Biology (BICoB) 2013. · International Conference on Intelligent Systems for Molecular Biology (ISMB) 2013. Journal reviewer for: · IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) · Journal of Computational Biology (JCB) · Information Processing Letters (IPL) · Bioinformatics · BMC Bioinformatics · Molecular Phylogenetics and Evolution (MPE) Conference reviewer for: · International Conference on Research in Computational Molecular Biology (RECOMB) · ACM-SIAM Symposium on Discrete Algorithms (SODA) · Pacific Symposium on Biocomputing (PSB) · Combinatorial Pattern Matching (CPM) · Latin American Theoretical Informatics (LATIN) · International Symposium on Bioinformatics research and Applications (ISBRA) 6

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