CSIR - Centre for Cellular & Molecular Biology
Council of Scientific and Industrial Research
Ministry of Science & Technology, Govt. of India
Scientist
Email: tej@ccmb.res.in
Phone: 2862
DNA present within cells, collectively known as the genome, is the instruction manual read by the cellular machinery to live and function. My lab is interested in understanding how the variation in genomes of Indians predisposes them to disparities in health and disease. We study this at two levels.
First, we identify genetic variation of individuals using cutting-edge high throughput sequencing technologies. As part of large nation-wide population genomics programs, we map the natural variation in healthy genomes. In particular, our interests lie in two classes of variations known as structural variations and tandem repeats.
We also study how the same DNA sequence can give rise to different phenotypes, as observed in various cell types of a single organism. Despite having an identical genome, cells can be regulated differently via epigenetic mechanisms that result in cell specific gene expression patterns. Using single cell genomic technologies, we analyze the gene expression and epigenetic profiles of various cells to understand cell heterogeneity.
Finally, we develop new computational methods that enable faster and better analysis of complex biological data, as well as more interactive and intuitive data visualization.
Selected Publications
Pathak AK, Mishra GP, Uppili B, Walia S, Fatihi S, Abbas T, Banu S, Ghosh A, Kanampalliwar A, Jha A, Fatma S, Aggarwal S, Dhar MS, Marwal R, Radhakrishnan VS, Ponnusamy K, Kabra S, Rakshit P, Bhoyar RC, Jain A, Divakar MK, Imran M, Faruq M, Sowpati DT, Thukral L, Raghav SK, Mukerji M. Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes. Nucleic Acids Res. 2022 Feb 22;50(3):1551-1561. doi: 10.1093/nar/gkab1297.
Kumar V J, Banu S, Sasikala M, Parsa KVL, Sowpati DT, Yadav R, Tallapaka KB, Siva AB, Vishnubhotla R, Rao GV, Reddy DN. Effectiveness of REGEN-COV antibody cocktail against the B.1.617.2 (delta) variant of SARS-CoV-2: A cohort study. J Intern Med. 2022 Mar;291(3):380-383. Doi: 10.1111/joim.13408. Epub 2021 Nov 1.
Singh NK, Srivastava S, Zaveri L, Bingi TC, Mesipogu R, Kumar V S, Gaur N, Hajirnis N, Machha P, Shambhavi S, Khan S, Soujanya M, Nagabandi T, Mishra RK, Tallapaka KB, Sowpati DT†. Host transcriptional response to SARS-CoV-2 infection in COVID-19 patients. Clin Transl Med. 2021 Sep;11(9):e534. doi: 10.1002/ctm2.534.
Kulkarni O, Narreddy S, Zaveri L, Kalal IG, Tallapaka KB, Sowpati DT†. Evidence of SARS-CoV-2 reinfection without mutations in Spike protein. Clin Infect Dis. 2021 Feb 16:ciab136. doi: 10.1093/cid/ciab136. Online ahead of print.
Banu S, Jolly B, Mukherjee P, Singh P, Khan S, Zaveri L, Shambhavi S, Gaur N, Reddy S, Kaveri K, Srinivasan S, Gopal DR, Siva AB, Thangaraj K, Tallapaka KB, Mishra RK, Scaria V, Sowpati DT†. A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates. Open Forum Infect Dis. 2020 Sep 18;7(11):ofaa434. doi: 10.1093/ofid/ofaa434. eCollection 2020 Nov.
Saha P, Sowpati DT, Soujanya M, Srivastava I, Mishra RK. Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes. Epigenetics Chromatin. 2020 Oct 7;13(1):41. doi: 10.1186/s13072-020-00358-4.
Avvaru AK, Sharma D, Verma A, Mishra RK, Sowpati DT†. MSDB: a comprehensive, annotated database of microsatellites. Nucleic Acids Res. 2020 Jan 8;48(D1):D155-D159. doi: 10.1093/nar/gkz886.
Education & Experience
P.G: | Zoology ; Sri Venkateswara University, Tirupati ; 2002 |
Ph.D: | University of Hyderabad/Centre for DNA Fingerprinting and Diagnostics, Hyderabad ; Biochemistry ; 2012 |
Post.Doc: | Research Associate ; Indian Institute of Technology, Delhi ; 2012 - 2013 Research Associate, CSIR-CCMB ; 2013 - 2014 ; Project Scientist ; CSIR-CCMB ; 2014 - 2019 |
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Title | Journal | Year |
---|---|---|
The unique N-terminal region of Mycobacterium tuberculosis Sigma Factor A (σA) plays a dominant role in the essential function of this protein | J Biol Chem | 2023 |
A cross-sectional study on the nasopharyngeal microbiota of individuals with SARS-CoV-2 infection across three COVID-19 waves in India | Front Microbiol | 2023 |
Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes | Nucleic Acids Res | 2022 |
SARS-CoV-2 seroprevalence in the city of Hyderabad, India in early 2021 | IJID Reg. | 2022 |
Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers. | Sci Rep | 2022 |
SARS-CoV-2 Variant Delta Potently Suppresses Innate Immune Response and Evades Interferon-Activated Antiviral Responses in Human Colon Epithelial Cells | Microbiol Spectr | 2022 |
Clinical outcomes in individuals hospitalized with SARS-CoV-2 Delta variant (B.1.617.2) who had been vaccinated with Covishield (ChAdOx1) and Covaxin (BBV-152) | IJID Reg. | 2022 |
Structural and developmental dynamics of Matrix associated regions in Drosophila melanogaster genome | BMC Genomics | 2022 |
Tissue- specific transcriptome recovery on withdrawal from chronic alcohol exposure in zebrafish. | Alcohol. 2021 Mar;91:29-38. doi: 10.1016/j.alcohol.2020.10.001. Epub 2020 Oct 8. PMID: 33038458. | 2021 |
C3G Regulates STAT3, ERK, Adhesion Signaling, and Is Essential for Differentiation of Embryonic Stem Cells. | Stem Cell Rev Rep. 2021 Aug;17(4):1465-1477. doi: 10.1007/s12015-021-10136-8. Epub 2021 Feb 23. PMID: 33624208; PMCID: P | 2021 |
SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants. | J Biosci. 2021;46(1):22. doi: 10.1007/s12038-021-00145-7. PMID: 33737495; PMCID: PMC7895735. | 2021 |
SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. | Nature. 2021 Sep 6. doi: 10.1038/s41586-021-03944-y. Epub ahead of print. PMID: 34488225. | 2021 |
Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Reinfection Without Mutations in the Spike Protein. | Clin Infect Dis. 2021 Sep 7;73(5):e1239-e1241. doi: 10.1093/cid/ciab136. PMID: 34492695; PMCID: PMC7929054. | 2021 |
Host transcriptional response to SARS-CoV-2 infection in COVID-19 patients. | Clin Transl Med. 2021 Sep;11(9):e534. doi: 10.1002/ctm2.534. PMID: 34586723; PMCID: PMC8453261. | 2021 |
Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. | Science. 2021 Oct 14:eabj9932. doi: 10.1126/science.abj9932. Epub ahead of print. PMID: 34648303. | 2021 |
Effectiveness of REGEN-COV antibody cocktail against the B.1.617.2 (delta) variant of SARS-CoV-2: A cohort study. | J Intern Med. 2021 Nov 1. doi: 10.1111/joim.13408. Epub ahead of print. PMID: 34719811. | 2021 |
Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes. | Epigenetics Chromatin. 2020 Oct 7;13(1):41. doi: 10.1186/s13072-020-00358-4. PMID: 33028366; PMCID: PMC7541242. | 2020 |
Transcriptomic dataset of zebrafish tissues following chronic alcohol exposure and withdrawal. | Data Brief. 2020 Oct 21;33:106442. doi: 10.1016/j.dib.2020.106442. PMID: 33163595; PMCID: PMC7607250. | 2020 |
A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates. | Open Forum Infect Dis. 2020 Sep 18;7(11):ofaa434. doi: 10.1093/ofid/ofaa434. PMID: 33200080; PMCID: PMC7543508. | 2020 |
Long-Read Genome Sequencing and Assembly of Leptopilina boulardi: A Specialist Drosophila Parasitoid. | G3 (Bethesda). 2020 May 4;10(5):1485-1494. doi: 10.1534/g3.120.401151. PMID: 32217632 | 2020 |
MSDB: a comprehensive, annotated database of microsatellites. | Nucleic Acids Res. 2020 Jan 8;48(D1):D155-D159. doi: 10.1093/nar/gkz886. PMID: 31599331 | 2020 |
Epigenomic and genomic landscape of Drosophila melanogaster heterochromatic genes. | Genomics. 2019 Mar;111(2):177-185. doi:10.1016/j.ygeno.2018.02.001. Epub 2018 Feb 10. PMID: 29432976. | 2019 |
The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene. | Epigenomics. 2019 Feb;11(3):251-266. doi: 10.2217/epi-2018-0060. Epub 2019 Jan 23. PMID: 30672333. | 2019 |
Patterns of microsatellite distribution across eukaryotic genomes. | BMC Genomics. 2019 Feb 22;20(1):153. doi: 10.1186/s12864-019-5516-5. PMID: 30795733; | 2019 |
PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences. | Bioinformatics. 2018 Mar 15;34(6):943-948. doi: 10.1093/bioinformatics/btx721. PMID: 29121165. | 2018 |
MSDB: A Comprehensive Database of Simple Sequence Repeats. | Genome Biol Evol. 2017 Jun 1;9(6):1797-1802. doi: 10.1093/gbe/evx132. PMID: 28854643; | 2017 |
C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search. | BMC Bioinformatics. 2017 Sep 13;18(Suppl 10):392. doi:10.1186/s12859-017-1786-6. PMID: 28929968 | 2017 |
Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection. | Sci Rep. 2016 Apr 26;6:25006. doi: 10.1038/srep25006. PMID: 27112593 | 2016 |
Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights. | PLoS One. 2016 Nov 28;11(11):e0166854. doi: 10.1371/journal.pone.0166854. PMID: 27893794 | 2016 |
Human mesenchymal stem cells: New sojourn of bacterial pathogens. | Int J Med Microbiol. 2015 May;305(3):322-6. doi: 10.1016/j.ijmm.2015.01.001. Epub 2015 Jan 13. PMID: 25648374. | 2015 |
Expansion of the polycomb system and evolution of complexity. | Mech Dev. 2015 Nov;138 Pt 2:97-112. doi: 10.1016/j.mod.2015.07.013. Epub 2015 Aug 7. PMID: 26259680. | 2015 |
Gene cooption in mycobacteria and search for virulence attributes: comparative proteomic analyses of Mycobacterium tuberculosis, Mycobacterium indicus pranii and other mycobacteria. | Int J Med Microbiol. 2014 Jul;304(5-6):742-8. doi: 10.1016/j.ijmm.2014.05.006. Epub 2014 May 29. PMID: 24951307. | 2014 |
A ChIP- on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes. | Genom Data. 2014 May 10;2:78-81. doi: 10.1016/j.gdata.2014.05.001. PMID: 26484075 | 2014 |
An intronic DNA sequence within the mouse Neuronatin gene exhibits biochemical characteristics of an ICR and acts as a transcriptional activator in Drosophila. | Mech Dev. 2008 Nov-Dec;125(11-12):963-73. doi: 10.1016/j.mod.2008.08.002. Epub 2008 Aug 28. PMID: 18789387. | 2008 |
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