Sourav Bandyopadhyay
University of California, San Diego
Graduate Program in Bioinformatics
Powell Focht Bioengineering Hall, Room 210, Mail Code 0419
9500 Gilman Drive
La Jolla, CA 92093-0419
sourav_at_bioeng.ucsd.edu
blogging the biotechnology revolution
systems biology paper watch
#Research Interests:
I am in the Bioinformatics PhD program at UCSD in the Ideker Lab. Generally, my interests are in comparative genomics and systems biology. Lately I have been focusing on the generation and utilization of high throughput protein-protein interaction data.
Before coming to UCSD I was at the NIH in the NIA in the Laboratory of Neurogenetics and also at EraGen Biosciences. At the Laboratory of Neurogenetics, NIH I worked on studying the function and evolution of genes implicated in neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. I also developed software to facilitate the warehousing and mining of human genetic variation data. This latter project has led to the development of an open software suite called GERON (GEnetics Research ONline). At EraGen Biosciences I developed software to optimize probe and primer selection for various SNP based assays. I did my undergradute studies at the University of Wisconsin - Madison in Computer Science and Molecular Biology.
#Publications:
- Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park H, Hayles J, Hoe K, Kim D, Ideker T, Grewal SI, Weissman JS, Krogan NJ. Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map (E-MAP) in Fission Yeast. Science, October 2008 [Science Express]
- König R, Zhou Y, Elleder D, Diamond TL, Bonamy GMC, Irelan JT, Chiang C, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, Bandyopadhyay S, Ideker T, Orth AP, Miraglia LJ, Bushman FD, Young JA, Chanda SK. Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication. Cell , Oct 2008.[Cell]
- Bandyopadhyay S, Kelley RM, Krogan NJ, Ideker T. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Computational Biology, April 2008.[PLOS site] [Supplementary Site]
- Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Featured Review. Nature Reviews Genetics Sept 2007. [Pubmed] [Nature Site]
- Bandyopadhyay S, Sharan R, Ideker T. Cover Article: Systematic identification of functional orthologs by protein network comparison. Genome Research. March 2006. [GR Site] [Pubmed] [Supplementary Site] [Cover].
- Bandyopadhyay S, Kelley RM, Ideker T. Discovering regulated networks during HIV-1 latency and reactivation. Pac. Symp. Biocomp. Jan 2006. [Pubmed] [PSB Site]
- Canet-Aviles RM, Wilson MA, Miller DW, Ahmad R, McLendon C, Bandyopadhyay S, Baptista MJ, Ringe D, Petsko GA, Cookson MR. The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9103-8. [Pubmed]
- Bandyopadhyay S, Cookson MR. Evolutionary and functional relationships within the DJ1 superfamily. BMC Evol Biol. 2004 Feb 19;4(1):6. [Pubmed]
#Previous
#Talks:
- Pacific Symposium on Biocomputing, 2006. Discovering regulated networks during HIV-1 latency and reactivation. Paper selected for oral presentation. [Slides] [Session overview]
- CSHL/Wellcome Trust: Interactome Networks, 2006. Conserved Network Analysis of the Human MAPK Interactome. [Meeting Overview]
- Meeting of the American Society for Cell Biology (ASCB), 2007. Searching for signaling in high-throughput data. Session: Making 'omics useful to cell biologists.
- Yeast Genetics and Molecular Biology Meeting, 2008. Integrating physical and genetic maps: Functional maps of protein complexes from quantitative genetic interaction data. Platform presentation.
#Links:
Labs:
Laboratory for Integrative Network Biology - Ideker Lab
Winzeler lab at The Scripps Research Institute
Phil Bourne - Structural Biology
The Laboratory of Neurogenetics at the NIH.
Mark Craven - My Undergraduate Research Advisor.
Projects:
BioinfBlog- A Systems Biology and Bioinformatics Blog. Support scientific blogging!
The GERON project: Data warehouse for human genetic and clinical phenotype and sample data.
Cytoscape network visualization tool
Schools:
UCSD Bioinformatics Graduate Program
University of Wisconsin-Madison Computer Science
University of Wisconsin-Madison Molecular Biology
Conferences:
ISMB - International Conference on Intelligent Systems for Molecular Biology (Brazil 2006)
RECOMB - International Conference on Research in Computational Molecular Biology (Venice 2006)
PSB - Pacific Symposium on Biocomputing (Maui)
Interactome Networks (UK)
More at the ISCB events page
Companies:
Eragen Biosciences - Where I interned and worked for a while.
Computing Resources:
Granite - NCBR Rocks Grid
Teragrid - SDSC
#Personal:
- Soccer - Ive played ever since I can remember and all through high-school. Lately ive been playing up to three times a week in various scheduled pick up games. You can join our webgroup at Zanby Groups
- Mountain Biking - Ive been doing this since undergrad around Madison, WI with my roomate John. I ride a Gary Fisher Supercaliber hardtail and a Specialized P3 (which got stolen :( ). There are some great trails in Socal!
- Backpacking - In 2005 we took a great trip to Inyo NP and spent 4 days in the wilderness. 2006 was Sequoia/King's Canyon NP. Where will it be next year?
- Surfing - Living in San Diego you just have to, great surf year 'round. I have a 8 foot longboard that I use mostly to fall on my head.
- Climbing - Theres some good climbing in Southern California and Joshua Tree is not far away. Here are some routes for mission gorge in San Diego.
- Photography - Just got a FujiFinePix 5200 to play around with. For the latest pictures take a look at my Flickr Album
- Cheif Technology Evangelist at the Ideker lab - yes I have to have the latest and greatest. Including roomba hacking!
