Software links
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FIN-STAB: an interactive software for shock simulator for financial networks
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DNA-BAR -- Distinguisher Selection for Robust DNA Barcoding
(developed in collaboration with Prof. Ion Mandoiu and his group from University of Connecticut)
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Link to the software webpage
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Related papers explaining key concepts:
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Piotr Berman, Bhaskar DasGupta and Ming-Yang Kao,
Tight Approximability Results for Test Set Problems in Bioinformatics,
Journal of Computer & System Sciences,
71 (2), 145-162, 2005.
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Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and
Alex Shvartsman,
Highly Scalable Algorithms for Robust String Barcoding,
International Journal of Bioinformatics Research & Applications,
1 (2), 145-161, 2005.
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Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and
Alex Shvartsman,
DNA-BAR: Distinguisher Selection for DNA Barcoding,
Bioinformatics,
21 (16), 3424-2426, 2005.
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Bhaskar DasGupta, Kishori Konwar, Ion Mandoiu and
Alex Shvartsman,
Highly Scalable Algorithms for Robust String Barcoding,
2005 International Workshop on Bioinformatics Research and
Applications
,
LNCS 3515,
Vaidy S. Sunderam, Geert Dick van Albada, Peter M. A. Sloot, et al. (editors),
Springer Verlag,
1020-1028, 2005.
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Software for decomposing a biological network into monotone subsystems
(developed in collaboration with Prof. Eduardo Sontag and his group from Rutgers University)
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Related papers explaining key concepts:
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Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang,
Algorithmic and Complexity Results for Decompositions
of Biological Networks into Monotone Subsystems
,
5th International Workshop Experimental Algorithms,
LNCS 4007, 253-264, Springer-Verlag, 2006.
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Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang,
Algorithmic and Complexity Results for Decompositions
of Biological Networks into Monotone Subsystems,
Biosystems,
90 (1), 161-178, 2007
NET-SYNTHESIS: Software for synthesis of a biological signal trasduction network
from indirect experimental evidences
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Link to the software webpage
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Related papers explaining key concepts:
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Réka Albert, Bhaskar DasGupta and Eduardo Sontag, Inference of signal transduction networks from double causal evidence , Methods in Molecular Biology: Topics in Computational Biology, D. Fenyo (ed.), 673, Chapter 16, © Springer Science+Business Media, LLC, 2010.
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Réka Albert, Bhaskar DasGupta, Riccardo Dondi and Eduardo Sontag,
Inferring (Biological) Signal Transduction Networks via Transitive Reductions of
Directed Graphs,
Algorithmica.
51 (2), 129-159, 2008.
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Sema Kachalo, Ranran Zhang, Eduardo Sontag, Réka Albert and
Bhaskar DasGupta,
NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction networks
,
Bioinformatics, 24 (2), 293-295, 2008
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Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Eduardo Sontag, Alexander
Zelikovsky and Kelly Westbrook,
A Novel Method for
Signal Transduction Network Inference from Indirect Experimental Evidence,
Journal of Computational Biology
,
14 (7), 927-949, 2007
(extended abstract in
7th Workshop on Algorithms in Bioinformatics,
R. Giancarlo and S. Hannenhalli (Eds.), LNBI 4645,
Springer-Verlag, 407-419, 2007).
CPalign: Software and web server for topology independent protein structural alignment
(developed by Prof. Jie Liang and his group at UIC in collaboration)
Related papers explaining key concepts:
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Bhaskar DasGupta, Joseph Dundas and Jie Liang, Algorithmic Methodologies for Discovery of Non-sequential Protein Structure Similarities, to appear in Algorithmic and AI Methods for Protein Bioinformatics, Y. Pan, J. Wang and M. Li (editors), Wiley book series on Bioinformatics, Wiley, 2013.
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Joe Dundas, T.A. Binkowski, Bhaskar DasGupta and Jie Liang,
Topology Independent Protein Structural Alignment,
BMC Bioinformatics, 8:388, 2007.
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Joe Dundas, T.A. Binkowski, Bhaskar DasGupta and Jie Liang
Topology Independent Protein Structural Alignment,
7th Workshop on Algorithms in Bioinformatics (WABI),
R. Giancarlo and S. Hannenhalli (Eds.),
LNBI 4645,
©
Springer-Verlag Berlin Heidelberg,
171-182, 2007.
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T. Andrew Binkowski, Bhaskar DasGupta and Jie Liang,
Order independent structural alignment of
circularly permutated proteins,
26th Annual International Conference IEEE Engineering in Medicine and
Biology Society,
2781-2784, 2004.
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Software for causal network inference via set-covering method
(developed in collaboration with Joe Dundas at UIC Bioengineering department)
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KINALYZER: A Computer Program for Reconstructing Sibling Groups
(developed in collaboration with Prof. Tanya Berger-Wolf and Prof. Mary Ahsley's group at UIC and
Prof. Wanpracha Chaovalitwongse's group at Rutgers)
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Link to the software webpage
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Related papers explaining key concepts:
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Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A. Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse, Chun-An Chou and Bhaskar DasGupta, Combinatorial Reconstruction of Half-sibling Groups from Microsatellite Data, Journal of Bioinformatics and Computational Biology, 8(2), 337-356, 2010.
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Mary Ashley, Tanya Y. Berger-Wolf, Piotr Berman, Wanpracha Chaovalitwongse, Bhaskar DasGupta and Ming-Yang Kao,
On Approximating Four Covering/Packing Problems,
Journal of Computer and System Sciences,
75 (5), 287-302, 2009.
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Mary V. Ashley, Tanya Y. Berger-Wolf, Wanpracha Chaovalitwongse,
Bhaskar DasGupta, Ashfaq Khokhar and Saad Sheikh,
On Approximating An Implicit Cover Problem in Wild Population Study, Discrete Mathematics, Algorithms and Applications, 2 (1), 21-31, 2010
(conference version in
5th International Conference on Algorithmic Aspects in Information and Management, A. Goldberg and Y. Zhou (Eds.), LNCS 5564, 43-54, ©Springer-Verlag Berlin Heidelberg, 2009).
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Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse and Bhaskar DasGupta, Combinatorial Reconstruction of Half-Sibling Groups, Computational Systems Bioinformatics (proceedings of the CSB 2009 conference), 8, P. Markstein and Y. Xu (editors), © Life Sciences Society, 59-67, 2009.
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Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse, Bhaskar DasGupta,
Priya Govindan, Saad Sheikh and Tanya Y. Berger-Wolf,
KINALYZER, A Computer Program for Reconstructing Sibling Groups,
Molecular Ecology Resources, 9 (4), 1127-1131, 2009.
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Wanpracha Chaovalitwongse, Chun-An Chou, Tanya Berger-Wolf, Bhaskar DasGupta,
Saad Sheikh, Mary Ashley and Isabel Caballero,
New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers,
INFORMS Journal of Computing, 22 (2), 180-194, 2010.
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Mary. Ashley, Tanya Y. Berger-Wolf, Isabel Caballero, Wanpracha Chaovalitwongse,
Chun-An Chou, Bhaskar DasGupta and Saad Sheikh,
Full Sibling Reconstructions in Wild Populations From Microsatellite Genetic Markers,
in Computational Biology: New Research, A. S. Russe (editor), Nova Science Publishers, 231-258, 2009.
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Saad I. Sheikh, Tanya Y. Berger-Wolf, Mary V. Ashley,
Isabel C. Caballero, Wanpracha Chaovalitwongse and Bhaskar DasGupta,
Error Tolerant Sibship Reconstruction in Wild Populations,
Computational Systems Bioinformatics
(7th Annual International Conference on Computational Systems Bioinformatics, 26-29 August 2008),
Peter Markstein and Ying Xu (editors), 273-284, World Scientific Publishers, 2008.
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Saad I. Sheikh, Tanya Y. Berger-Wolf, Ashfaq A. Khokhar and Bhaskar DasGupta,
Consensus Methods for Reconstruction of Sibling Relationships from Genetic Data,
4th Multidisciplinary Workshop on Advances in Preference Handling,
Chicago, IL, 2008.
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Tanya Y. Berger-Wolf, Saad Sheikh, Bhaskar DasGupta, Mary Ashley,
Isabel Caballero and Wanpracha Chaovalitwongse,
Reconstructing Sibling Relationships in Wild Populations,
Bioinformatics, 23 (13),
i49-i56, 2007 (special issue for
15th Annual Conference on
Intelligent Systems in Molecular Biology,
,
2007).
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Wanpracha Chaovalitwongse, Tanya Y. Berger-Wolf, Bhaskar DasGupta,
and Mary Ashley,
Set Covering Approach for Reconstruction of Sibling Relationships,
Optimization Methods and Software,
22 (1), 11-24, 2007.
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Tanya Y. Berger-Wolf, Bhaskar DasGupta, Wanpracha Chaovalitwongse and Mary
Ashley,
Combinatorial Reconstructions of Sibling Relationships,
6th International Symposium on Computational Biology and Genome
Informatics,
Salt Lake City, Utah,
1252-1255,
2005.