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Research Interests:

Computational Biology (Algorithms for: geny, Protein Folding, RNA Folding, RNA Inverse Folding, Population Genetics, Kinship Analysis), Sensitivity Analysis, Theory (Approximation Algorithms and Computational Complexity ), Machine Learning and Data Mining.I do not keep works in progress on this website.

Any papers will be put here after getting accepted. If you are interested in collaborating or have a wild population you wish to analyze for sibling relationships please email me on firstname @ firstname nospace lastname dot com

Papers:

2012:

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

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 to appear in 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 " to appear in BMC Genomics.

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 " to appear in Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS) .

2010:

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)

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.

2009:

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) .

2008:

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.

2007:

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:

"Half-Sibs Reconstruction: A Theoretical Analysis", at DIMACS Workshop on Human Population Genomics

"Combinatorial Problems in Sibling Reconstruction", at Midwest Theory Day, Spring 2009, held at University of Wisconsin-Milwaukee..

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

"Reconstructing Sibling Relationships from Genetic Data", at INFORMS ICS Conference 2009 held at Charleston, SC.

"Qualitative methods for Sibling Reconstruction from genotyping data" at Midwest Theory Day, December 2008 held at Northwestern University, Evanston, IL.

"Reconstructing Sibling Relationships from Genetic Data", at Illinois Institute of Technology, Chicago, IL.

Poster Presentations:

"Reconstructing parents from genotyping data in wild populations", at 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB) 2009.

"Error Tolerant Sibship Reconstruction", at Intelligent Systems in Molecular Biology (ISMB) 2008.

"Error Tolerant Sibship Reconstruction in Wild Populations", at 4-th International Symposium on Bioinformatics Research and Applications (ISBRA) 2008.

"Reconstructing Sibling Relationships in Wild Populations", at First Midwest Symposium on Computational Biology and Bioinformatics (MSCBB) held at Northwestern University, October 2007.

" A combinatorial approach to kinship analysis using microsatellite data", at Eleventh Annual International Conference of Research in Computational Molecular Biology (RECOMB), April 2007.


Older Stuff:

Masters Thesis "Detecting Bad Code Smells for Refactoring by using historical data of Source Control System", National University of Computer and Emerging Sciences (NUCES), Lahore, 2005.

Undergraduate Final Year Project Report  "Urdu Computational Lexicon", 2003

F. Ahmad, U. Aziz, S. Sheikh, W. Ahmad, and F. Mahmood. "Urdu Computational Lexicon" Proceedings of IEEE INMIC Conf., Dec 2002

S. Sheikh. "A Study of Aspirated Continuants in Urdu" In Akhbar-e-Urdu (Newspaper of Urdu), 2002. 


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