Thank you for visiting my web page. I am an assistant professor at Institute of Advanced Research (IAR), Gandhinagar, India. On this web page, you can find more information about my research interests, publications, and software.

My doctoral research focused on understanding the complex relationships of the symbiotic and pathogenic species of Enterococci in human gut microbiota through comparative genomics and bioinformatics analyses. In my postdoctoral tenure, I tried to understand the nature and mechanisms of chemicals produced by human microbiome in different pathophysiological conditions.

I am interested in understanding the role of microbiome in human and environmental homeostasis using systems-level bioinformatics approaches with various next-generation sequencing data analysis methods and developing novel computational algorithms. .

Curriculum Vitae

Professional Experiences:

Academic Qualifications:

2018−2021 Postdoctoral Research Fellow, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.

2012−2018 Doctor of Philosophy (Ph.D.), Academy of Scientific and Innovative Research (AcSIR), India. Supervisor: Dr. Chitra Dutta [Chief scientist (Retired), Structural Biology & Bioinformatics, CSIR-IICB]. Co-Supervisor: Dr. Snehasikta Swarnakar [Senior Principal Scientist & Head of the Department, Infectious Diseases and Immunology, CSIR-IICB]. Title of the Ph.D. thesis: In-Silico Analysis of Enterococcal Genomes from the Human Microbiota.

2009−2011 Master of Technology (M.Tech) in Bioinformatics. West Bengal University of Technology (WBUT), Kolkata, West Bengal, India. Thesis Supervisor: Dr. Chitra Dutta [Chief scientist (Retired), Structural Biology & Bioinformatics, CSIR-IICB]. Title of the M.Tech thesis: Comparative Genome and Proteome Analysis of Streptococci in Human Microbiome.

2007−2009 Bachelor of Education (B.Ed) with specialization in teaching Life Sciences. Vidyasagar University, Midnapore, West Bengal, India.

2005−2007 Master of Science (M.Sc) in Zoology with specialization in Genetics. Vidyasagar University, Midnapore, West Bengal, India.

2002−2005 Bachelor of Science [B.Sc (H)] in Zoology, University of Burdwan, Burdwan, West Bengal, India. Other subjects – Chemistry, Botany.

Publications:

International Journals:

1. Bakshi, U., Gupta, V.K., Lee, A.R., Davis, J.M., Yong-Su, J., Freeman, M.F. and Sung, J., 2021. TaxiBGC: a Taxonomy-guided Approach for the Identification of Experimentally Verified Microbial Biosynthetic Gene Clusters in Shotgun Metagenomic Data. [Preprint: Link]

2. Gupta, V. K., Cunningham, K. Y., Hur, B., Bakshi, U., Huang, H., Warrington, K. J., Taneja, V., Myasoedova, E., Davis, J. M., and Sung, J., 2021. Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis. Genome medicine, 13(1), 149. [Download PDF] [PMID: 34517888, DOI: https://doi.org/10.1186/s13073-021-00957-0] [Media Coverage: Link]

3. Gupta, V.K., Kim, M., Bakshi, U., Cunningham, K.Y., Davis, J.M., Lazaridis, K.N., Nelson, H., Chia, N. and Sung, J., 2020. A predictive index for health status using species-level gut microbiome profiling. Nature Communications, 11(1):4635.[Download PDF] [PMID: 32934239, DOI: 10.1038/s41467-020-18476-8] [Media Coverage: Link1, Link2]

4. Roy, C., Rameez, M.J., Haldar, P.K., Peketi, A., Mondal, N., Bakshi, U., Mapder, T., Pyne, P., Fernandes, S., Bhattacharya, S. and Roy, R., 2020. Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau. Scientific reports, 10(1), pp.1-22. [Download_PDF] [PMID: 32246033, DOI: https://doi.org/10.1038/s41598-020-62797-z]

5. Roy, C., Bakshi, U., Rameez, M.J., Mandal, S., Haldar, P.K., Pyne, P. and Ghosh, W., 2019. Phylogenomics of an uncultivated, aerobic and thermophilic, photoheterotrophic member of Chlorobia sheds light into the evolution of the phylum Chlorobi. Computational biology and chemistry, 80, pp.206-216. [Download_PDF] [PMID: 30981103, DOI: https://doi.org/10.1016/j.compbiolchem.2019.04.001]

6. Bhattacharyya, C., Bakshi, U., Mallick, I., Mukherji, S., Bera, B. and Ghosh, A., 2017. Genome-guided insights into the plant growth promotion capabilities of the physiologically versatile Bacillus aryabhattai strain AB211. Frontiers in microbiology, 8, p.411. [Download_PDF] [PMID: 28377746, DOI: https://doi.org/10.3389/fmicb.2017.00411]

7. Bakshi, U., Sarkar, M., Paul, S. and Dutta, C., 2016. Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach–Identification of pathogen–specific and habitat-specific genes. Scientific reports, 6, p.38648. [Download_PDF] [PMID: 27924951, DOI: https://doi.org/10.1038/srep38648]

8. Chowdhury, A.R. and Bakshi, U., 2014. Pathophysiological responses from human gut microbiome. World Journal of Translational Medicine, 3(3), pp.133-140. [Download_PDF] [DOI: http://dx.doi.org/10.5528/wjtm.v3.i3.133]

International Conferences:

  1. Bakshi, U. and Sung, J., "TaxiBGC: a taxonomy-guided approach for the identification of microbial biosynthetic gene clusters in shotgun metagenomic data", International Human Microbiome Consortium (IHMC), Barcelona, Spain (2021).

  2. Bakshi, U., Gupta, V. and Sung, J., "Exploring the Diversity of Secondary Metabolite Production Potential in Human Microbiome Communities Using a Species-Resolved Biosynthetic Gene Cluster Detection Approach", Microbiome (Cold Spring Harbor Laboratory), New York, USA (2020).

  3. Bakshi, U., Sung, J., "Microbiome derived metabolites in health and disease", Balfour Surgery Research Symposium (Mayo Clinic), Rochester, MN, USA (2019).

  4. Bakshi, U., Sung, J., "Exploring the landscape of specialized metabolite production potential in human gut microbiomes across health and disease", Microbiome (Cold Spring Harbor Laboratory), New York, USA (2019).

  5. Bakshi, U., ‘Microbiome: Chemical Mechanisms and Biological Consequences (Keystone Symposia)’ Montreal, Québec, Canada (2019).

  6. Bakshi, U., Sarkar, M. and Dutta, C., "Genome-Based Understanding of Antibiotic Resistance in Enterococci", International Conference on Informatics and Integrative Biology, Kolkata, India (2014).

National Conferences:

  1. Bakshi, U., ‘Basics of Statistics and Databases in Bioinformatics’, Department of Bioinformatics (BIF-DBT), West Bengal University of Technology, Kolkata, India (2011).

  2. Bakshi, U., ‘Computational Biology for Experimentalists’, Department of Bioinformatics (BIF-DBT), West Bengal University of Technology, Kolkata, India (2010).

  3. Bakshi, U., ‘Bioinformatics in Genomics and Proteomics’, Indian Institute of Technology Kharagpur (IIT-KGP), Kharagpur, India (2009).

Software and Pipelines:

  1. Protein Disorder Prediction and Characterization (DisPC)- A large scale protein disorder prediction and analysis tool which is a meta-predictor in one hand and also performs a proteome wide analysis of function, binding region analysis and evolutionary conservation studies of the intrinsically disordered proteins (IDPs). DisPC is tested in several bacterial and fungal genomes for detailed genome wide analysis of IDPs. This pipeline can be used for large scale identification and characterization of IDPs in different domains of life. (Software: Link) [Publication (PMID): 27924951]

  2. Taxonomy-guided Identification of Biosynthetic Gene Clusters (TaxiBGC) - A Species-Resolved Biosynthetic Gene Cluster Detection Algorithm for Exploring the Diversity of Secondary Metabolite Production Potential in Human Microbiome Communities (Software: Link) [Preprint: Link].