Sourav Bandyopadhyay sourav@bioeng.ucsd.edu
Projects: -Detection of functional orthologs by comparing protein networks -Analysis/comaprison Of herpesviral interaction networks -Analysis of human protein kinase interaction networks by comparison to yeast
! Intro/Background * My research currently is pretty diverse as I look for a topic to really focus on. Mainly ive been interested in the analysis of protein interaction networks and methods for finding conservation.
! Detection of functional orthologs by comparing protein networks * Reversing the logic of pathblast (looking for conserved paths among orthologs) we hypothesized that by looking at paralogs (cases in which duplication makes it ambiguous as to which is the functional ortholog) we could determine which of the duplicated genes was acting in the same way as its common ancestor.
* Systematic identification of functional orthologs by protein network comparison !bandyopadhyay_GR2006.pdf bandyopadhyay_GR2006.pdf
! Analysis/comparison Of herpesviral interaction networks * Using yeast two hybrid networks for 5 herpesvirus we are interested in determining both pairwise conserved network structures as well as a pan-virus netowork with the hopes of elucidating the conserved mechanisms of action among them. * Herpesviral protein networks and their interaction with the human proteome. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16339411&query_hl=11&itool=pubmed_docsum
! Analysis of human protein kinase interaction networks by comparison to yeast * By comparing an experimental Y2H network in Human to known Y2H data in yeast as well as kinase-substrate interactions in yeast we would like to determine conserved kinase cascades as well as novel kinase-sustrate phosphorylations based on conservation with yeast. * Global analysis of protein phosphorylation in yeast. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16319894&query_hl=9&itool=pubmed_docsum
! Future Directions * In Silico approaches to validation of methods for finding conserved network structures/active modules. * HIV transcriptional/metabolic profiling network analysis
! Presentations * Lab Retreat Presentation /cellar/[Journal Club]/LabRetreat2006/Bandyopadhyay_NewApproaches.ppt
! Sources * http://bioinf.ucsd.edu/~sbandyop/ * Discovering regulated networks during HIV-1 latency and reactivation !bandyopadhyay_PSB2006.pdf bandyopadhyay_PSB2006.pdf