April 2018: Presented “Optimal Search Schemes for Approximate String Matching using Bidirectional FM-Index” at RECOMB-Seq 2018 in Paris
August 2018: “A mixed integer programming based algorithm for reliability analysis of structured linear systems,” by Vijayaraghavan, V., Kianfar, K., Ding, Y., and Parsaei, H, accepted and presented in IEEE CASE 2018, Munich, Germany

Research

Bioinformatics

  • NGS Data Analysis/Optimization Algorithms and Software

    • Optimal search schemes in approximate alignment of sequencing reads using bidirectional FM index

    • Map2Peak: From unmapped reads to ChIP-Seq peaks in half the time

Mixed Integer Programming

  • Theory and Computation of Cutting Planes

  • Capacity Planning in Complex Networks

Combinatorial Optimization in Complex Systems

  • Algorithms for reliability Analysis in large-scale systems

  • Algorithms for optimal coverage in service systems

Research

Bioinformatics

  • NGS Data Analysis/Optimization Algorithms and Software

    • Optimal search schemes in approximate alignment of sequencing reads using bidirectional FM index

    • Map2Peak: From unmapped reads to ChIP-Seq peaks in half the time

Mixed Integer Programming

  • Theory and Computation of Cutting Planes

  • Capacity Planning in Complex Networks

Combinatorial Optimization in Complex Systems

  • Algorithms for reliability Analysis in large-scale systems

  • Algorithms for optimal coverage in service systems

  • NGS Data Analysis/Optimization Algorithms and Software

    • Optimal search schemes in approximate alignment of sequencing reads using bidirectional FM index

    • Map2Peak: From unmapped reads to ChIP-Seq peaks in half the time

  • Theory and Computation of Cutting Planes

  • Capacity Planning in Complex Networks

  • Algorithms for reliability Analysis in large-scale systems

  • Algorithms for optimal coverage in service systems

Software

Map2Peak is an ultrafast peak calling bioinformatics tool which combines the process of read alignment and peak calling. Map2Peak focuses only on those genomic regions which are likely to contain Transcription Factor Binding Sites (TFBS). This software is developed by the Ph.D. student Krishna Reddy Gujjula. Please click on the above image to learn about the work.

This software is under development in collaboration with Dr. Knut Reinert’s Lab at FU Berlin.

Prinicpal Investigator

Ph.D. Students

Alumni

Publications

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Presentations

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Teaching

ISEN 622 (Linear Programming)

Development of the mathematics and algorithms associated with linear programming; convex sets and cones, polyhedral sets, duality theory, sensitivity analysis, simplex, revised simplex and dual simplex methods; also covered are bounded variables, column generation, decomposition, integer programming; computer assignment.

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ISEN 638 (Polyhedral Theory and Valid Inequalities)

Advanced knowledge of polyhedral theory and valid inequalities for (mixed) integer programming; introduction to fundamental concepts in polyhedral theory and several approaches to generation of valid inequalities; includes state-of-the-art advancements and current avenues of research.

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ISEN 668 (Integer Programming)

Formulation principles and general approaches for solving integer (and mixed, integer linear) programs including preprocessing, cutting plane methods, branch and bound, branch and cut, branch and price, and Lagrange relaxation; classical problem structures with special-purpose solution algorithms; fundamental theory of polyhedra, methods to generate valid inequalities and computational complexity.

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ISEN 370/315 (Production Systems Engineering)

Principles, models, and techniques for planning and analysis of production and distribution systems; application of linear, integer, and nonlinear optimization models and solution methods for aggregate planning, supply chain planning, push (MRP) and pull (JIT) material flow management, inventory control under deterministic and stochastic demands, operations scheduling, and production scheduling.

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ISEN 420/320 (Operations Research I)

Development and application of fundamental deterministic optimization models and solution methods; focus on quantitative modeling and formulation of linear, integer, and network flow problems; use of computer optimization software to model and solve real-life problems.

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ISEN 440/489 (Systems Thinking)

Systems thinking process, systems of systems and the fundamental considerations associated with the engineering of large-scale systems, or systems engineering including systems modeling, design and the system development process.

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ISEN 411 (Engineering Management Techniques)

Techniques relating to managing engineering activities; engineer's transition into management; engineering managerial functions; motivation of individual and group behavior; productivity assessment/improvement; managing the quality function and communications.

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Awards and Honors

  • Who is Who in America, 2011

  • IIE Pritsker Doctoral Dissertation Award, First Place , 2008, For dissertation: ``Generalized Mixed Integer Rounding Valid Inequalities''

  • INFORMS George Nicholson Paper Award, Honorable Mention (one of 6 finalists) , 2006

  • Phi Kappa Phi Honor Society, Member, since 2005

  • Alpha Pi Mu (Industrial Engineering Honor Society), Member, since 2006

Student’s Awards and Honors

  • Manish Bansal, Assistant Professor at Virginia Tech, 2016

  • Krishna Reddy Gujjula, TAMU College of Engineering Graduate Teaching Fellow, 2017

  • Manish Bansal, Invited Speaker for 2015 Mixed Integer Programming (MIP) Workshop, Booth School of Business, University of Chicago, IL, 2015

  • Manish Bansal, Second Prize in INFORMS 2013 Interactive Session Competition, INFORMS Annual Meeting, Minneapolis, MN, 2013

  • Manish Bansal, First Poster Prize in MIP 2013 Workshop, University of Wisconsin, Madison, WI, 2013

  • Manish Bansal, Selected and Received Travel Grant for Poster Presentation, MIP 2013 Workshop, University of Wisconsin, Madison, WI, 2013

  • Manish Bansal, Nominated for INFORMS Future Academician Colloquium, 2013

  • Sujeevraja Sanjeevi, Nominated for INFORMS Future Academician Colloquium ,2012

  • Sujeevraja Sanjeevi, Selected and Received Travel Grant for Poster Presentation , MIP 2012 Workshop, UC-Davis, Davis, CA, Jul. 2012

  • Sujeevraja Sanjeevi, Selected and Received Travel Grant for Poster Presentation , MIP 2010 Workshop, Atlanta, GA, Jul. 2010

  • Sujeevraja Sanjeevi, Second Place in Student Research Week Competition at Texas A&M, Mar. 2012

  • Manish Bansal, Merit Scholarship, ISEN Department, Texas A&M University (2008 and 2009)

  • Sujeevraja Sanjeevi, Merit Scholarship, ISEN Department, Texas A&M University (2007 and 2008)

Contact

Mailing Address: TAMU 3131, College Station, TX 77843-3131
Phone: 979-458-2362