Sandip Paul , Ph.D.

Ramanujan Fellow
Structural Biology & Bioinformatics
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Research Focus

Comparative metagenomics, microbial evolution, human microbiome

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:

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

Credentials

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

Honours & Awards

  • Present: Member, Indian National Young Academy of Science (INYAS)
  • 2016: Ramanujan Fellowship, SERB, Department of Science & Technology, India

Grants & Supports

Ramanujan Fellowship Grant

Patents & Publications

SELECTED PUBLICATIONS

  1. Chaudhari N. M., Gautam A., Gupta V. K., Dutta C., Paul S*; PanGFR-HM: a dynamic web resource for pan-genomic and functional profiling of human microbiome with comparative features. 2018 , Front. Microbiol. , 9 , 30349509 , 10.3389/fmicb.2018.02322
  2. Gupta V. K., Paul S., Dutta C.; Geography, ethnicity or subsistence-specific variations in human microbiome composition & diversity. 2017 , Front. Microbiol. , 8 , 28690602 , 10.3389/fmicb.2017.01162
  3. Kisiela D. I., Radey M., Paul S., Porter S., Polukhina K., Tchesnokova V., Shevchenko S., Chan D., Aziz M., Johnson T. J., Price L. B., Johnson J. R., Sokurenko E. V. ; Inactivation of transcriptional regulators during within-household evolution of Escherichia coli. 2017 , J Bacteriol , 199 , 28439032 , 10.1128/JB.00036-17
  4. Bakshi U., Sarkar M., Paul S., Dutta C.; Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach - Identification of pathogen-specific and habitat-specific genes. 2016 , Scientific Reports , 6 , 27924951 , 10.1038/srep38648
  5. Paul S., Sokurenko E. V., Chattopadhyay S.; Corrected Genome Annotations Reveal Gene Loss and Antibiotic Resistance as Drivers in the Fitness Evolution of Salmonella enteric Serovar Typhimurium. 2016 , J Bacteriol , 198 , 3152-3161 , 27621280 , 10.1128/JB.00545-16
  6. Paul S., , Minnick M. F., Chattopadhyay S.; Mutation-Driven Divergence and Convergence Indicate Adaptive Evolution of the Intracellular Human-Restricted Pathogen, Bartonella bacilliformis. 2016 , PLoS Negl Trop Dis , 10 , 27167125 , 10.1371/journal.pntd.0004712
  7. Paul S*., Bhardwaj A., Bag S. K., Sokurenko E. V., Chattopadhyay S.; PanCoreGen - profiling, detecting, annotating protein-coding genes in microbial genomes. 2015 , Genomics , 106 , 367-372 , 26456591 , 10.1016/j.ygeno.2015.10.001
  8. Goswami A., Roy Chowdhury A., Sarkar M., Saha S.K., Paul S., Dutta C.; Strand-biased gene distribution, purine asymmetry and environmental factors influence protein evolution in Bacillus. 2015 , FEBS Lett , 589 , 629-638 , 25639611 , 10.1016/j.febslet.2015.01.028
  9. Lasaro M., Liu Z., Bishar R., Kelly K., Chattopadhyay S., Paul S., Sokurenko E., Zhu J., Goulian M.; Escherichia coli isolate for studying colonization of the mouse intestine and its application to two-component signaling knockouts. 2014 , J Bacteriol , 196 , 1723-1732 , 24563035 , 10.1128/JB.01296-13
  10. Chattopadhyay S., Paul S., Dykhuizen D. E., Sokurenko E. V. ; Tracking recent adaptive evolution in microbial species using TimeZone. 2013 , Nature Protocols , 8 , 652-665 , 23471110 , 10.1038/nprot.2013.031
  11. Kisiela D. I., Chattopadhyay S., Tchesnokova V., Paul S., Weissman S. J., Medenica I., Clegg S., Sokuernko E. V.; Evolutionary analysis points to divergent physiological roles of type 1 fimbriae in Salmonella and E. Coli. 2013 , mBio , 4 , e00625-12 , 23462115 , 10.1128/mBio.00625-12
  12. Paul S., Million-Weaver S., Chattopadhyay S., Sokurenko E. V., Merrikh H.; Accelerated gene evolution through replication–transcription conflicts. 2013 , Nature , 495 , 512-515 , 23538833 , 10.1038/nature11989.
  13. Chattopadhyay S., Taub F., Paul S., Weissman S.J., Sokurenko E. V.; Microbial variome database: point mutations, adaptive or not, in bacterial core genomes. 2013 , Mol Biol Evol , 30 , 1465-1470 , 23493258 , 10.1093/molbev/mst048
  14. Paul S., Linardopoulou E., Billig M., Tchesnokova V., Price L., Johnson J., Chattopadhyay S., Sokurenko E. V.; Role of homologous recombination in adaptive diversification of extra-intestinal Escherichia coli. 2013 , J Bacteriol , 195 , 231-242 , 23123908 , 10.1128/JB.01524-12
  15. Chattopadhyay S., Paul S., Kisiela D. I., Linardopoulou E., Sokurenko E. V. ; Convergent molecular evolution of genomic cores in Salmonella enterica and Escherichia coli. 2012 , J Bacteriol , 194 , 5002-5011 , 22797756 , 10.1128/JB.00552-12
  16. Dutta C., Paul S. ; Microbial Lifestyle and Genome Signatures. 2012 , Current Genomics , 13 , 153-162 , 23024607 , 10.2174/138920212799860698
  17. Dutta A., Paul S., Dutta C. ; GC-rich intra-operonic spacers in prokaryotes: possible relation to gene order conservation. 2010 , FEBS Lett , 584 , 4633-4638 , 20971109 , 10.1016/j.febslet.2010.10.037
  18. Paul S., Dutta A., Bag S.K., Das S., Dutta C. ; Distinct, Ecotype-specific Genome & Proteome Signatures in the Marine Cyanobacteria Prochlorococcus. 2010 , BMC Genomics , 11 , 103 , 20146791 , 10.1186/1471-2164-11-103
  19. Paul S., Bag S.K., Das S., Harvill E.T., Dutta C.; Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. 2008 , Genome Biology , 9 , R70 , 18397532 , 10.1186/gb-2008-9-4-r70
  20. Bag S. K., Paul S., Ghosh S., Dutta, C.; Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human–Mouse Orthologs of Two Compositional Extrema. 2007 , DNA Res , 14 , 141-154 , 17895298 , 10.1093/dnares/dsm015
  21. Das S., Paul S., Bag S., Dutta, C. ; Analysis of Nanoarchaem equitans genome and proteome composition:  indications for hyperthermophilic and parasitic adaptation. 2006 , BMC Genomics , 7 , 186 , 16869956 , 10.1186/1471-2164-7-186
  22. Das S., Paul S., Dutta C.; Evolutionary constraints on codon and amino acid usage in two different strains of human pathogenic actinobacteria Tropheryma whipplei. 2006 , J. Mol. Evol , 62 , 645-658 , 16557339 , 10.1007/s00239-005-0164-6
  23. Das S., Paul S., Dutta C.; Synonymous codon usage in adenoviruses: influence of mutation, selection and protein hydropathy. 2006 , Virus Res , 117 , 227-236 , 16307819 , 10.1016/j.virusres.2005.10.007
  24. Das, S., Pan, A., Paul, S., Dutta, C.; Comparative Analyses of Codon and Amino Acid Usage in Symbiotic Island and Core Genome in Nitrogen-Fixing Symbiotic Bacterium Bradyrhizobium japonicum. 2005 , J Biomol Struct Dyn , 23 , 221-232 , 16060695 , 10.1080/07391102.2005.10507061
  25. Das S.,  Paul S., Chatterjee S., Dutta C.; Codon  and amino acid usage in two major   human pathogens of genus Bartonella – optimization between replication-transcriptional selection, translational control and cost minimization. 2005 , DNA Res , 12 , 91-102 , 16303741 , 10.1093/dnares/12.2.91

 

Products

PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features (http://www.bioinfo.iicb.res.in/pangfr-hm/)