Saad Sheikh

Postdoctoral Researcher

Computer & Information Science & Engineering

University of Florida

Email : lastname at cise dot ufl dot edu
I am currently working with Sanjay Ranka, Tamer Kahveci and Gordon Burleigh as a postdoc on various problems in inferring phylogenies.

Previously I was a postdoc at the INRIA-AMIB Project at Ecole Polytechnique first on a CNRS postdoc, and then on an INRIA postdoc. Before that, my PhD was supervised by Tanya Berger-Wolf and Ashfaq Khokhar at UIC.

I recently organized the 1st International Workshop on Robustness and Stability of Biological Systems and Computational Solutions, held in conjunction with ACM BCB this year. I also chaired the PhD Student Forum.

For fun, my Erdos number is at most 4: Erdos <-> Aviezri Fraenkel <-> Edward M Reingold <-> Tanya Berger-Wolf <-> Me.

OR

Me <-> R. Backofen <-> B.Berger <-> D. J. Kleitman <-> P. Erdos.

It seems Microsoft Academic Search would like to credit me with a lot more than I have actually done... Thank you for this. On Google Scholar I created a profile and can manage it.

I helped organize or served in the PC of:

ACM CIKM 2012, ACM BCB 2012, BIOKDD 2012, BiCoB 2012, ICOSST 2011, LIX Bioinformatics Colloquium 2010.

I have served as reviewer for:

Workshop on Algorithms in Bioinformatics (WABI), International Computing and Combinatorics Conference (COCOON), Tools and Algorithms for the Construction and Analysis of Systems (TACAS), Journal of Combinatorial Optimization, Advances in Bioinformatics.

Software

Merging Phylogenetic Trees while optimizing quality

Stability of Phylogenetic Trees

KINALYZER: Sibling Reconstruction from Microsatellite Markers

BBP: Folding of Transmembrane Beta Barrel Proteins

Nested Web Logo

List of papers:

2012:

  • Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty and Peter Clote. Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches, PLoS ONE and RECOMB 2013.

  • Saad Sheikh, Tamer Kahveci, Sanjay Ranka and Gordon Burleigh. Stability Analysis of Phylogenetic Trees, Bioinformatics.

  • Daehan Won, Chun-An Chou, W. Art Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar Dasgupta, Ashfaq A. Khokhar, Mary V. Ashley, Jason Palagi, Marco Maggioni, and S. Sheikh. An integrated optimization framework for inferring two-generation kinships and parental genotypes from microsatellite samples, Proceedings of ACM BCB 2012.

  • S. I. Sheikh, R. Backofen and Y. Ponty. Impact Of The Energy Model On The Complexity Of RNA Folding With Pseudoknots, Proceedings of CPM 2012.

  • S. I. Sheikh, V. D. T. Tran, P. Chassignet, and J. M. Steyaert. Knowledge-based Consensus Methods for Secondary Structure Prediction of Transmembrane Beta-barrel Proteins, Proceedings of BiCoB 2012 .

  • V. D. T. Tran, P. Chassignet, S. I. Sheikh, and J. M. Steyaert. A graph-theoretic approach for classification and structure prediction of transmembrane beta-barrel proteins. BMC Genomics 13(Suppl 2):S5, 2012.

    Upto 2011:

  • V. D. T. Tran, P. Chassignet, S. I. Sheikh, and J. M. Steyaert. Energy-based Classification and Structure Prediction of Transmembrane Beta-Barrel Proteins. Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS 2011).

  • J. V. Schmidt, C. Chen, S. I. Sheikh, M. G. Meekan, B. M. Norman, and S. Juong. Paternity analysis in a litter of whale shark embryos Endangered Species Research 12(2), 2010

  • S. I. Sheikh, A. A. Khokhar and T. Y. Berger-Wolf. Efficient and scalable parallel reconstruction of sibling relationships from genetic data in wild- populations Proceedings of Tenth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2010) held with IPDPS.

  • M. V. Ashley, T. Y. Berger-Wolf, W. Chaovalitwongse, B. DasGupta, A. Khokhar and S. Sheikh. On Approximating An Implicit Cover Problem in Wild Population Study Discrete Mathematics, Algorithms and Applications.

  • S. I. Sheikh, T. Y. Berger-Wolf, A. Khokhar, I. C. Caballero, C.A. Chou M. V. Ashley, W. Chaovalitwongse and B. DasGupta. Combinatorial Reconstruction of Half-Sibling Groups Special Issue of Journal of Bioinformatics and Computational Biology, April 2010.

  • S. I. Sheikh, T. Y. Berger-Wolf, A. Khokhar, I. C. Caballero, M. V. Ashley, W. Chaovalitwongse and B. DasGupta Combinatorial Reconstruction of Half-Sibling Groups Proceedings of 8th Annual International Conference on Computational Systems Biology (CSB 2009) (Acceptance Rate: 23 % ) .

  • M. V. Ashley, T. Y. Berger-Wolf, W. Chaovalitwongse, B. DasGupta, S. Sheikh. On Approximating An Implicit Cover Problem in Biology Proceedings of 5th International Conference on Algorithmic Aspects in Information and Management 2009 (to appear) .

  • W. Chaovalitwongse, C-A Chou, T. Y. Berger-Wolf, B. DasGupta, S. Sheikh, M. V. Ashley, I. C. Caballero. New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers INFORMS Journal of Computing .

  • M. Ashley, T. Berger-Wolf, I. Caballero, W. Chaovalitwongse, B. DasGupta and P. Govindan, S. Sheikh. Full Sibling Reconstructions in Wild Populations From Microsatellite Genetic Markers accepted for the Computational Biology: New Research, Nova Science Publishers. (Book Chapter) .

  • M. V. Ashley, I. C. Caballero, W. Chaovalitwongse, Bhaskar DasGupta, Priya Govindan, S. Sheikh and Tanya Y. Berger-Wolf KINALYZER, A Computer Program for Reconstructing Sibling Groups Molecular Ecology Resources 9(4) .

  • S. I. Sheikh, T. Y. Berger-Wolf, M. V. Ashley, I. C. Caballero, W. Chaovalitwongse and B. DasGupta Error-Tolerant Sibship Reconstruction for Wild Populations 7th Annual International Conference on Computational Systems Biology (CSB 2008) (Acceptance Rate: 22 % ) .

  • S. I. Sheikh, T. Y. Berger-Wolf, A. A. Khokhar and B. DasGupta Consensus Methods for Reconstruction of Sibling Relationships from Genetic Data Proceedings of the 4th Multidisciplinary Workshop on Advances in Preference Handling at AAAI 08.

  • T. Y. Berger-Wolf, S. I. Sheikh, B. DasGupta, M. Ashley, W. Chaovalitwongse and S. P. Lahari. Reconstructing Sibling Relationships in Wild Populations Procedings of 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) 2007 (Acceptance Rate 15%) and Bioinformatics, 23(13).

  • S. Sheikh, T. Y. Berger-Wolf, W. Chaovalitwongse, B. DasGupta, and M. Ashley. Reconstructing Sibling Relationships from Microsatellite Data European Conf. on Computational Biology (ECCB), Jan 2007. (Short Paper)

    Talks:

    2011

    Feb From Sibling Reconstruction to Protein Folding and Beyond, University of Central Florida, Orlando, FL.

    Feb From Sibling Reconstruction to Protein Folding and Beyond, University of Florida, Gainesville, FL.

    Feb From Sibling Reconstruction to Protein Folding and Beyond, Florida International University, Miami, FL.

    Jan Consensus and Energy-based Structure Prediction of Transmembrane Beta-Barrel Proteins, LRI, Universite Paris-Sud, Orsay, France.

    2010

    July Efficient and scalable parallel reconstruction of sibling relationships from genetic data in wild-populations, Boston College, Boston, MA.

    July Efficient and scalable parallel reconstruction of sibling relationships from genetic data in wild-populations, Boston University, Boston, MA.

    2009

    Oct Reconstruction of Parental Genotype from Microsatellite Data, INFORMS 2009 Annual Meeting, San Diego, CA.

    Apr Half-Sibling Reconstruction A Theoretical Analysis, DIMACS Workshop on Algorithmics in Human Population-Genomics, DIMACS, Rutgers University

    Apr Combinatorial problems in Kinship Analysis, Midwest Theory Day, University of Wisconsin at Milwaukee

    Jan Reconstructing Sibling Relationships from Genetic Data, University of Illinois at Urbana- Champaign

    Jan Reconstructing Sibling Relationships from Genetic Data, INFORMS ICS conference 2009, Charleston, SC

    2008

    Dec Qualitative methods for Sibling Reconstruction from genotyping data, Midwest Theory Day, Northwestern University

    Nov Reconstructing Sibling Relationships from Genetic Data, Illinois Institute of Technology

    Last updated: Dec 2012