DasGupta's Lab for Discrete Algorithmic Problems in Biology

This lab investigates designing efficient algorithms, using techniques from combinatorial optimization and machine learning, for computationally challenging problems in several areas in computer science and bioinformatics, such as sequencing problems, structure comparison problems and problems related to biological networks in systems biology. Some representative research publications by (former/current) students supported by this lab are as follows (students supported are shown in bold red):

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, Volume 24, Number 2, pp. 293-295, January 2008 (doi: 10.1093/bioinformatics/btm571 ).
Joe Dundas , T.A. Binkowski, Bhaskar DasGupta and Jie Liang, Topology Independent Protein Structural Alignment, BMC Bioinformatics, 8:388, 2007.
Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, , Eduardo Sontag, Alexander Zelikovsky and Kelly Westbrooks, A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence, 7th Workshop on Algorithms in Bioinformatics (WABI), R. Giancarlo and S. Hannenhalli (Eds.), LNBI 4645, © Springer-Verlag Berlin Heidelberg, pp. 407-419, September 2007.
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,
Réka Albert, Bhaskar DasGupta, Riccardo Dondi, Sema Kachalo, Eduardo Sontag, Alexander Zelikovsky and Kelly Westbrooks, A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence, Journal of Computational Biology , Volume 14, Number 7, pp. 927-949, 2007.
Bhaskar DasGupta, German Andres Enciso, Eduardo Sontag and Yi Zhang , Algorithmic and Complexity Results for Decompositions of Biological Networks into Monotone Subsystems, Biosystems, Volume 90, Issue 1, pp. 161-178, July-August 2007.
Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert Sloan, György Turàn and Yi Zhang , The Inverse Protein Folding Problem on 2D and 3D Lattices, Discrete Applied Mathematics (special issue on computational molecular biology series edited by Sorin Istrail, Pavel Pevzner and Ron Shamir), Vol. 155, Issues 6-7, pp. 719-732, 2007.
Bhaskar Dasgupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani, Inapproximability Results for the Lateral Gene Transfer Problem , Journal of Combinatorial Optimization, Vol. 11, No. 4, pp. 387-405, June 2006.
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 (WEA), LNCS 4007, pp. 253-264, © Springer-Verlag, 2006.
Bhaskar DasGupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani, Inapproximability Results for the Lateral Gene Transfer Problem, 9^th Italian Conference on Theoretical Computer Science (ICTCS'05), M. Coppo et al. (Eds.), LNCS 3701, © Springer-Verlag, pp. 182-195, 2005.
Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert Sloan, György Turàn and Yi Zhang , The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices, 15^th Annual Combinatorial Pattern Matching Symposium (CPM), LNCS 3109, C. S. Sahinalp, S. Muthukrishnan and U. Dogrusoz (editors), pp. 244-253, July 2004.
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Former MS student Ms. Sarita Lella is thankfully acknowledged for help in implementational works in the following paper:

Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao and Michael Snyder, Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search, Journal of Computational Biology, Vol. 11, No. 4, pp. 766-785, July 2004.

Please check the publications page of DasGupta for a more complete and up-to-date list of publications that has been produced by this lab.

Please check the software webpage for developed softwares.

Current MS/PhD students:

Kedsuda Apichonbancha, Computer Science
Renee McElhaney, Bioengineering

Our research has been supported by several NSF grants such as:

NSF DBI-0543365 7/1/2006--6/30/2009 (co-PI, subcontract from University of Connecticut)
NSF IIS-0612044 7/1/2006--6/30/2009 (co-PI)
NSF (career) IIS-0346973 4/15/2004--3/31/2009 (PI)
NSF CCR-0208749 9/1/2002--12/31/2005 (PI)
NSF CCR-0206795 8/15/2002--7/31/2005 (PI)
NSF CCR-9800086/CCR-0296041/CCR-0220502 8/15/1998--7/31/2004 (PI)