• Konig R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyay S, Alamares J, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu B, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, Garcia-Sastre A, Young JAT, Palese P, Shaw ML, Chanda SK. Human Host Factors Required for Influenza Virus Replication. Nature. In Press.


• Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stelberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, Von Brunn A, Uhlmann M, Zeretzke C, Dong Y, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J. Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathogens. Sept 2009. [Pubmed] [PLoS Site]


• Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, Konig R, Bandyopadhyay S, Ideker T, Goff S, Krogan N, Frankel A, Young JAT, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathogens. [PLoS Site] [Pubmed]


• Wilmes G*, Bergkessel M*, Bandyopadhyay S, Chan A, Braberg H, Shales M, Collins SR, Whitworth BG, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. Cover Article: A Genetic Interaction Map of RNA Processing Factors Reveals Links Between Sem1/Dss1-Containing Complexes and mRNA Export and Splicing. Molecular Cell., Featured Article, December 2008. [Pubmed] [Molecular Cell] [Cover Image] *Equal Contribution


• 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 in Fission Yeast. Science, October 2008. [Pubmed] [Science]


• Konig 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] [Pubmed]


• 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 Image].


• 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]

• 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.

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