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

2018

Kianfar, Kiavash; Pockrandt, Christopher; Torkamandi, Bahman; Luo, Haochen; Reinert, Knut

Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index Journal Article

In review, 2018.

Abstract | Links | BibTeX

2017

Bansal, Manish; Kianfar, Kiavash

Facets for continuous multi-mixing set with general coefficients and bounded integer variables Journal Article

Discrete Optimization, 26 , pp. 1-25, 2017.

Abstract | Links | BibTeX

Bansal, Manish; Kianfar, Kiavash

Planar Maximum Coverage Location Problem with Partial Coverage and Rectangular Demand and Service Zones Journal Article

INFORMS Journal on Computing, 29 , pp. 152-169, 2017.

Abstract | Links | BibTeX

2016

Sanjeevi, Sujeevraja; Masihabadi, Sina; Kianfar, Kiavash

Using cuts for mixed integer knapsack sets to generate cuts for mixed integer polyhedral conic sets Journal Article

Mathematical Programming, 159 , pp. 571-583, 2016, ISSN: 0025-5610.

Abstract | Links | BibTeX

2015

Bansal, Manish; Kianfar, Kiavash

n-Step cycle inequalities: facets for continuous multi-mixing set and strong cuts for multi-module capacitated lot-sizing problem Journal Article

Mathematical Programming, 154 , pp. 113-144, 2015, ISSN: 0025-5610.

Abstract | Links | BibTeX

2014

Bansal, Manish; Kianfar, Kiavash

n-Step Cycle Inequalities: Facets for Continuous n-Mixing Set and Strong Cuts for Multi-Module Capacitated Lot-Sizing Problem Conference

Integer Programming and Combinatorial Optimization, 8494 , Springer, Cham, 2014, ISBN: 978-3-319-07556-3.

Abstract | Links | BibTeX

2013

Bansal, Manish; Kianfar, Kiavash; Ding, Yu; Moreno-Centeno, Erick

Hybridization of Bound-and-Decompose and Mixed Integer Feasibility Checking to Measure Redundancy in Structured Linear Systems Journal Article

IEEE Transactions on Automation Science and Engineering , 10 , pp. 1151-1157, 2013, ISSN: 1558-3783.

Abstract | Links | BibTeX

2012

Sanjeevi, Sujeevraja; Kianfar, Kiavash

Mixed n-step MIR inequalities: Facets for the n-mixing set Journal Article

Discrete Optimization, 9 , pp. 216-235, 2012.

Abstract | Links | BibTeX

Kianfar, Kiavash

On n-step MIR and partition inequalities for integer knapsack and single-node capacitated flow sets Journal Article

Discrete Applied Mathematics, 160 , pp. 1567-1582, 2012.

Abstract | Links | BibTeX

Alvarado, Michelle M; Ntaimo, Lewis; Banerjee, Amarnath; Kianfar, Kiavash

Reducing pediatric medication errors: A survey and taxonomy Journal Article

IIE Transactions on Healthcare Systems Engineering, 2 , pp. 142-155, 2012.

Abstract | Links | BibTeX

Atamtürk, Alper; Kianfar, Kiavash

n-step mingling inequalities: new facets for the mixed-integer knapsack set Journal Article

Mathematical Programming, 132 , pp. 79-98, 2012, ISSN: 0025-5610.

Abstract | Links | BibTeX

Farzaneh, Mohamadreza; Memisoglu, Gokhan; Kianfar, Kiavash

Optimal Deployment of Emission Reduction Technologies for Large Fleets Journal Article

Transportation Research Record, 2287 , pp. 18-26, 2012, ISSN: 0361-1981.

Abstract | Links | BibTeX

2011

Fathi, Yahya; Kianfar, Kiavash

An efficient model for the crosscut optimisation problem in a wood processing mill Journal Article

International Journal of Production Research, 50 , pp. 485-497, 2011.

Abstract | Links | BibTeX

Kianfar, Kiavash

Branch-and-Bound Algorithms Journal Article

Wiley Encyclopedia of Operations Research and Management Science, 2011.

Abstract | Links | BibTeX

2010

Kianfar, Kiavash; Fathi, Yahya

Generating facets for finite master cyclic group polyhedra using n-step mixed integer rounding functions Journal Article

European Journal of Operational Research, 207 , pp. 105-109, 2010.

Abstract | Links | BibTeX

Kianfar, Kiavash; Pourhabib, Arash; Ding, Yu

An Integer Programming Approach for Analyzing the Measurement Redundancy in Structured Linear Systems Journal Article

IEEE Transactions on Automation Science and Engineering , 8 , pp. 447-450, 2010, ISSN: 1545-5955.

Abstract | Links | BibTeX

Sanjeevi, Sujeevraja; Kianfar, Kiavash

A polyhedral study of triplet formulation for single row facility layout problem Journal Article

Discrete Applied Mathematics, 158 , pp. 1861-1867, 2010.

Abstract | Links | BibTeX

2009

Kianfar, Kiavash; Fathi, Yahya

Generalized mixed integer rounding inequalities: facets for infinite group polyhedra Journal Article

Mathematical Programming, 120 , pp. 313-346, 2009, ISSN: 0025-5610.

Abstract | Links | BibTeX

Presentations

2017

Luo, Haochen; Kianfar, Kiavash

n-step cut-set inequalities for multi-module capacitated network design problems Presentation

INFORMS Annual Meeting, Houston, 01.10.2017.

BibTeX

Vijayaraghavan, Vishnu; Kianfar, Kiavash; Ding, Yu; Parsaei, Hamed

A decomposition algorithm to measure redundancy in structured linear systems Presentation

INFORMS Annual Meeting, Houston, TX, 01.10.2017.

BibTeX

Vijayaraghavan, Vishnu; Kianfar, Kiavash; Schaefer, Andrew

A regularized cutting plane algorithm for inverse mixed integer programming problems Presentation

INFORMS Annual Meeting, Houston, TX, 01.10.2017.

BibTeX

Bansal, Manish; Kianfar, Kiavash

Maximum-Demand Rectangular Location Problem Presentation

INFORMS Computing Society Conference, Austin, TX, 01.01.2017.

BibTeX

2016

Luo, Haochen; Kianfar, Kiavash

Polyhedral study of a generalization of the continuous mixing set Presentation

INFORMS Annual Meeting, Nashville, TN, 01.11.2016.

BibTeX

Vijayaraghavan, Vishnu; Kianfar, Kiavash; Ding, Yu; Parsaei, Hamed

Measuring degree of redundancy in linear systems by combining l1 minimization and integer programming Presentation

INFORMS Annual Meeting, Nashville, TN, 01.11.2016.

BibTeX

Vijayaraghavan, Vishnu; Kianfar, Kiavash; Schaefer, Andrew

An improved algorithm to solve inverse integer programming Presentation

INFORMS Annual Meeting, Nashville, TN, 01.11.2016.

BibTeX

Kianfar, Kiavash

Mathematical Optimization and Data Analysis Lab Presentation

Texas Optimization Day, College Station, TX, 01.04.2016.

BibTeX

2015

Bansal, Manish; Kianfar, Kiavash

Facets for continuous multi-mixing set with general coefficients and bounded integer variables Presentation

INFORMS Annual Meeting, Philadelphia, PA, 01.11.2015.

BibTeX

Bansal, Manish; Kianfar, Kiavash

Maximum-Demand Rectangular Location Problem Presentation

INFORMS Computing Society Conference, Richmond, VA, 01.01.2015.

BibTeX

2014

Bansal, Manish; Kianfar, Kiavash

Continuous n-mixing: a unified framework for lot-sizing, facility location and network design problems Presentation

INFORMS Annual Meeting, San Francisco, CA, 01.11.2014.

BibTeX

Bansal, Manish; Kianfar, Kiavash

n-step cycle inequalities: facets for continuous n-mixing set and strong cuts for multi-module capacitated lot-sizing problem Presentation

17th International Conference of Integer Programming and Combinatorial Optimization, Bonn, Germany, 01.06.2014.

BibTeX

Bansal, Manish; Kianfar, Kiavash

Valid inequalities for multi-module capacitated lot-sizing, facility location, and network design problems Presentation

INFORMS Optimization Society Conference, Rice University, Houston, TX, 01.03.2014.

BibTeX

2013

Bansal, Manish; Kianfar, Kiavash

Facet-defining valid inequalities for constant-batch and multi-module capacitated lot-sizing problem Presentation

INFORMS Annual Meeting, Minneapolis, MN, 01.10.2013.

BibTeX

Bansal, Manish; Kianfar, Kiavash

Generalizations of Continuous Mixing Set: Extended Formulations and Facets Presentation

INFORMS Annual Meeting, Minneapolis, MN, 01.10.2013.

BibTeX

2012

Bansal, Manish; Kianfar, Kiavash

Cuts for linear MIPs using n-step conic MIR Presentation

INFORMS Annual Meeting, Phoenix, AZ, 01.11.2012.

BibTeX

Bansal, Manish; Kianfar, Kiavash

Valid inequalities for some generalizations of the continuous mixing set Presentation

INFORMS Annual Meeting, Phoenix, AZ, 01.10.2012.

BibTeX

Masihabadi, Sina; Sanjeevi, Sujeevraja; Kianfar, Kiavash

n-step Conic MIR and Mixed n-step MIR Presentation

MIP 2012 Workshop, University of California at Davis, 01.07.2012.

BibTeX

2011

Kianfar, Kiavash

Facets for Single-node Capacitated Flow Set Using n-step MIR Presentation

INFORMS Annual Meeting, Charlotte, NC, 01.11.2011.

BibTeX

Masihabadi, Sina; Sanjeevi, Sujeevraja; Kianfar, Kiavash

n-step Conic Mixed Integer Rounding Cuts Presentation

INFORMS Annual Meeting, Charlotte, NC, 01.11.2011.

BibTeX

Sanjeevi, Sujeevraja; Kianfar, Kiavash

Mixing n-step MIR Inequalities Presentation

INFORMS Annual Meeting, Charlotte, NC, 01.11.2011.

BibTeX

Bansal, Manish; Kianfar, Kiavash

Maximum Reward Rectangular Location Problem Presentation

INFORMS Annual Meeting, Charlotte, NC, 01.11.2011.

BibTeX

2010

Kianfar, Kiavash

On n-step MIR and Partition Inequalities for Integer Knapsack and Capacitated Flow Sets Presentation

INFORMS Annual Meeting, Austin, TX, 01.11.2010.

BibTeX

Sanjeevi, Sujeevraja; Kianfar, Kiavash

A Polyhedral Study of Triplet Formulation for Single Row Facility Layout Problem Presentation

INFORMS Annual Meeting, Austin, TX, 01.11.2010.

BibTeX

Bansal, Manish; Kianfar, Kiavash

An Exact Algorithm for Covering Rectangular Requests with Multiple Rectangular Target Presentation

INFORMS Annual Meeting, Austin, TX, 01.11.2010.

BibTeX

Kianfar, Kiavash; Pourhabib, Arash; Ding, Yu

Integer Programming Approach for Analyzing the Measurement Redundancy in Structured Linear Systems Presentation

INFORMS Annual Meeting, Austin, TX, 01.11.2010.

BibTeX

McGaha, Michelle; Ntaimo, Lewis; Banerjee, Amarnath; Kianfar, Kiavash

Reducing Medication Errors in Pediatrics Presentation

INFORMS Annual Meeting, Austin, TX, 01.11.2010.

BibTeX

Farzaneh, Mohamadreza; Memisoglu, Gokhan; Kianfar, Kiavash

Optimal Deployment of Emissions Reduction Technologies for Large Fleets Presentation

INFORMS Annual Meeting, Austin, TX, 01.11.2010.

BibTeX

Bansal, Manish; Kianfar, Kiavash

An Exact Algorithm for Coverage Problem with a Single Rectangle Presentation

IIE Annual Meeting, Cancun, Mexico, 01.06.2010.

BibTeX

2009

Atamtürk, Alper; Kianfar, Kiavash

n-step Mingling Inequalities and Their Facet-defining Properties Presentation

INFORMS Annual Meeting, San Diego, CA, 01.10.2009.

BibTeX

Atamtürk, Alper; Kianfar, Kiavash

n-step Mingling Inequalities: Facets for the Mixed Integer Knapsack Set Presentation

ISMP (International Symposium on Mathematical Programming), Chicago, 01.08.2009.

BibTeX

Atamtürk, Alper; Kianfar, Kiavash

n-step Mingling Inequalities: Facets for the Mixed Integer Knapsack Set Presentation

MIP 2009 Workshop, University of California, Berkeley, 01.06.2009.

BibTeX

2008

Atamtürk, Alper; Kianfar, Kiavash

n-step Mingling Inequalities Presentation

INFORMS Annual Meeting, Washington, DC, 01.10.2008.

BibTeX

Kianfar, Kiavash

On MIR and Facets of Group Problems Presentation

INFORMS Southwest Regional Conference, College Station, TX, 01.04.2008.

BibTeX

2007

Kianfar, Kiavash

n-step MIR functions: Facets for Finite and Infinite Group Problems Presentation

INFORMS Annual Meeting, Seattle, WA, 01.11.2007.

BibTeX

2006

Kianfar, Kiavash

Generalized MIR Inequalities Presentation

INFORMS Annual Meeting, Pittsburgh, PA, 01.11.2006.

BibTeX

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