Structural Biology & Bio-Informatics Division

Dr. Sandip Paul

Ramanujan Fellow

Ph.D (2011) Jadavpur University, Kolkata, INDIA.
Senior Fellow (2011-2016) Department of Microbiology, University of Washington, Seattle, USA



Current Research Interest

The human body is home to numerous microorganisms, including bacteria, archaea, viruses, and fungi, collectively known as human microbiome. The advances in the genomic technologies like high-throughput DNA sequencing and metagenomic studies revealed the highly diverse nature of the microbial communities and their crucial role in human health and in disease.
At present the primary research focus of the lab is to analyse the human microbiome data between diverse microbial communities for understanding human health and diseases that are associated with the microbiota in India. The specific research themes are:

  1. Analysis of community structure at different taxonomic levels across healthy and disease state.
  2. Systematic analysis (simulations, mathematical models) of community interaction across the microbiota.
  3. Exploring the various clinical-state associated metabolic interactions in comparison to their respective healthy state.
  4. Examine the effect of pathogens in microbial community.

Positions are open for prospective candidates who have a good balance of in-depth knowledge in microbial evolution (theories and applications) and computer programming. Candidates should have their own fellowship. Knowledge of next generation sequence analyses would be considered as a plus.


List of Selected Publications

  1. Paul S., Sokurenko E. V., Chattopadhyay S. (2016) Corrected Genome Annotations Reveal Gene Loss and Antibiotic Resistance as Drivers in the Fitness Evolution of Salmonella Typhimurium. J Bacteriol, [Epub ahead of print].
  2. Johnson T., Aziz M., Liu C., Sokurenko E., Kisiela D., Paul S., Andersen P., Johnson J., Price L. (2016) Complete genome sequence of a CTX-M-15-producing Escherichia coli strain from the H30Rx subclone of sequence type 131 (ST131) from a patient with recurrent urinary tract infections, closely related to a lethal urosepsis isolate from the patient's sister. Genome Announc, 12(4):3.
  3. Paul S., Minnick M. F., Chattopadhyay S. (2016) Mutation-Driven Divergence and Convergence Indicate Adaptive Evolution of the Intracellular Human-Restricted Pathogen, Bartonella bacilliformis. PLoS Negl Trop Dis, 10(5):e0004712.
  4. Paul S., Bhardwaj A., Bag S. K., Sokurenko E. V., Chattopadhyay S. (2015) PanCoreGen - profiling, detecting, annotating protein-coding genes in microbial genomes. Genomics, 106(6):367-372.
  5. Lasaro M., Liu Z., Bishar R., Kelly K., Chattopadhyay S., Paul S., Sokurenko E., Zhu J., Goulian M. (2014) An E. coli isolate for studying colonization of the mouse intestine and its application to two-component signaling knockouts. J Bacteriol, 196(9):1723-1732.
  6. Chattopadhyay S., Paul S., Dykhuizen D. E., Sokurenko E. V. (2013) Tracking recent adaptive evolution in microbial species using TimeZone. Nature Protocols, 8(4):652-665.
  7. Kisiela D. I., Chattopadhyay S., Tchesnokova V., Paul S., Weissman S. J., Medenica I., Clegg S., Sokuernko E. V. (2013) Evolutionary analysis points to divergent physiological roles of type 1 fimbriae in Salmonella and E. coli. mBio, 4(2):e00625-12.
  8. Paul S., Million-Weaver S., Chattopadhyay S., Sokurenko E. V., Merrikh H. (2013) Replication-transcription conflicts increase the rate of evolution in specific genes. Nature, 495:512-515.
  9. Chattopadhyay S., Taub F., Paul S., Weissman S.J., Sokurenko E. V. (2013) Microbial variome database: point mutations, adaptive or not, in bacterial core genomes. Mol Biol Evol, 30(6):1465-1470.
  10. Paul S., Linardopoulou E., Billig M., Tchesnokova V., Price L., Johnson J., Chattopadhyay S., Sokurenko E. V. (2013) Role of homologous recombination in adaptive diversification of extra-intestinal Escherichia coli. J Bacteriol, 195(2):231-242.
  11. Chattopadhyay S., Paul S., Kisiela D. I., Linardopoulou E., Sokurenko E. V. (2012) Convergent molecular evolution of genomic cores in Salmonella enterica and Escherichia coli. J Bacteriol, 194(18):5002-5011.
  12. Dutta C., Paul S. (2012) Microbial Lifestyle and Genome Signatures. Current Genomics, 13(2):153-162.
  13. Dutta A., Paul S., Dutta C. (2010) GC-rich intra-operonic spacers in prokaryotes: possible relation to gene order conservation. FEBS Lett, 584(22):4633-4638.
  14. Paul S., Dutta A., Bag S.K., Das S., Dutta C.  (2010) Distinct, Ecotype-specific Genome & Proteome Signatures in the Marine Cyanobacteria Prochlorococcus. BMC Genomics, 11(1):103.
  15. Paul S., Bag S.K., Das S., Harvill E.T., Dutta C. (2008) Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biology, 9(4):R70.
  16. Bag S. K., Paul S., Ghosh S., Dutta, C. (2007) Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human–Mouse Orthologs of Two Compositional Extrema. DNA Res, 14(4):141-154.
  17. Das S., Paul S., Bag S., Dutta, C. (2006) Analysis of Nanoarchaem equitans genome and proteome composition:  indications for hyperthermophilic and parasitic adaptation. BMC Genomics, 7(1):186.
  18. Das S., Paul S., Dutta C. (2006) Evolutionary constraints on codon and amino acid usage in two different strains of human pathogenic actinobacteria Tropheryma whipplei. J. Mol. Evol, 62(5):645-658.
    Das S., Paul S., Dutta C. (2006) Synonymous codon usage in adenoviruses: influence of mutation, selection and protein hydropathy. Virus Res, 117(2):227-236.
  19. Das, S., Pan, A., Paul, S., Dutta, C. (2005) Comparative Analyses of Codon and Amino Acid Usage in Symbiotic Island and Core Genome in Nitrogen-Fixing Symbiotic Bacterium Bradyrhizobium japonicum. J Biomol Struct Dyn, 23(2):221-232.
  20. Das S.,  Paul S., Chatterjee S., Dutta C. (2005) Codon  and amino acid usage in two major   human pathogens of genus Bartonella –optimization between replication-transcriptional selection, translational control and cost minimization. DNA Res, 12(2):91-102.
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Updated on 16 th Nov, 2016

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