Research Assistant Professor
Phone: (206) 221-6690
Office Location: Health Sciences J-263
Campus Box: 357735
Dr. Sujay Chattopadhyay holds an M.Tech. in biotechnology from Indian Institute of Technology, Kharagpur, and Ph.D. in computational biology from Indian Association for the Cultivation of Science, Kolkata.
His research focuses on understanding diverse evolutionary mechanisms in microbes, with an emphasis on the evolution of microbial virulence. One of his current projects involving Salmonella and E. coli genomes aims to assess (patho-)adaptive pressures in the accumulation of premature stop-codons and frameshift mutations leading to gene truncation in microbial pathogens. Another ongoing project is to detect mutational adaptive footprints in the evolution of Helicobacter pylori using his newly developed software package TimeZone. His research plans also include a novel computational approach to decode adaptive mutations in non-coding regions, and to study co-evolution of genes and regulatory regions across the genome of a given microbial species.
Visit this link for a complete list of publications
S. Chattopadhyay, S. Paul, D. E. Dykhuizen, E. V. Sokurenko. 2013. Tracking recent adaptive evolution in microbial species using TimeZone. Nature Protocols, In Press.
S. Paul, E. Linardopoulou, M. Billig, V. Tchesnokova, L. Price, J. Johnson, S. Chattopadhyay, E. V. Sokurenko. 2013. Role of homologous recombination in adaptive diversification of extra-intestinal Escherichia coli. Journal of Bacteriology, 195: 231-242.
S. Chattopadhyay, S. Paul, D. I. Kisiela, E. Linardopoulou, E. V. Sokurenko. 2012. Convergent molecular evolution of genomic cores in Salmonella enterica and Escherichia coli. Journal of Bacteriology, 194: 5002-5011.
D. I. Kisiela, S. Chattopadhyay, S. J. Libby, V. Tchesnokova, J. J. Kramer, E. Wheeler, R. I. Mackie, S. Clegg, E. V. Sokurenko. 2012. Convergent evolution of invasive serovars of Salmonella enterica via point mutations in the type 1 fimbrial adhesion FimH. PLoS Pathogens, 8: e1002733.
S. Chattopadhyay, V. Tchesnokova, A. McVeigh, D. I. Kisiela, K. Dori, A. Navarro, E. V. Sokurenko, S. J. Savarino. 2012. Adaptive evolution of class 5 fimbrial genes in enterotoxigenic Escherichia coli and its functional consequences. Journal of Biological Chemistry, 287: 6150-6158.
S. Chattopadhyay, S. J. Weissman, V. N. Minin, T. A. Russo, D. E. Dykhuizen, E. V. Sokurenko. 2009. High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection. Proceedings of the National Academy of Sciences USA, 106: 12412-12417.
S. Chattopadhyay, R. Paranjpye, D. E. Dykhuizen, E. V. Sokurenko, M. Strom. 2009. Comparative evolutionary analysis of the major structural subunit of Vibrio vulnificus type IV pili. Molecular Biology and Evolution, 26: 2185-2196.
S. Chattopadhyay, D. E. Dykhuizen and E. V. Sokurenko. 2007. ZPS: visualization of recent adaptive evolution of proteins. BMC Bioinformatics, 8: 187.
S. Chattopadhyay, M. Feldgarden, S. J. Weissman, D. E. Dykhuizen, G. van Belle and E. V. Sokurenko. 2007. Haplotype diversity in 'source-sink' dynamics of Escherichia coli urovirulence. Journal of Molecular Evolution, 64: 204-214.
E. V. Sokurenko, M. Feldgarden, E. Trintchina, S. J. Weissman, S. Avagyan, S. Chattopadhyay, J. R. Johnson and D. E. Dykhuizen. 2004. Selection footprint in the FimH adhesin shows pathoadaptive niche differentiation in Escherichia coli. Molecular Biology and Evolution 21: 1373-1383.