Sucheta Tripathy , Ph.D.

Principal Scientist
Structural Biology & Bioinformatics
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Research Focus

Computational Genomics and Bio-engineering. We use this for metabolite and energy compound production.

Research Interest

Indigenous microbes have remarkable properties generating plethora of metabolic and energy compounds. India is megadiverse nation and most of our microbes are un-explored. Our primary interest is to dissect the genomes of indigenous microbes namely Cyanobacteria and fungi and understand their genomics using second and third generation sequencing technologies. We use rapid RNAseq technology to understand the transcriptional changes occurring in microbes under various stress conditions leading to production of bio-metabolites as well as bioactive compounds. We use this information and validate this by using several cutting edge methods. Our goal is to engineer these genes for commercial production of bio-metabolites and active compounds.  Our lab has so far analyzed and submitted to Genbank close to 60 genomes and transcriptomes. Out of which more than 50% are sequenced and analyzed in-house. We also carry out sequencing using oxford nanopore in our lab.

We also undertake big data analysis for the data generated by us as well as for our collaborators using our own inhouse software as well as using open source publicly available softwares. While analyzing the genomes we have created several useful resources that is widely used all over the world (e.g; http;//eumicrobedb.org; http://bgagenomics.iicb.res.in/ and Genome Annotator Lite (GAL: https://hub.docker.com/r/cglabiicb/gal/). In addition, we have created and released several useful R statistical packages widely used for feature selections, and clustering big data

Credentials

Ph.D in Plant Molecular Biology from CPMB, Hyderabad

 

Sl. No Institution/Organization Position Duration
1. Indian Institute Of Chemical Biology, Kolkata, India Principal Scientist and Ramalingaswamy fellow 2012 Oct -
2. Virginia Bioinformatics Institute, Virginia Tech, USA Senior Research Scienist 2002 Sept - 2012 July
3. Avesthagengraine Pvt. limited, Bangalore, India Head Bioinformatics division 2001 Nov - 2002 July
4. DSQ Biotech limited, Chennai, India Scientist 2000 Aug - 2001 oct
5. Mumbai University, Mumbai, India Lecturer 1997 June - 2000 July
 

Honours & Awards

Sl. No Name of award Awarding agency Year
1. Full Travel award to attend open school grid computing workshop NSF 2015
2. Invited Chair of OMGN, Asilomar, USA Oomycetes Molecular Genetics Network 2013
3. Ramalingaswamy re-entry Fellowship DBT 2012-2017
4. Invited Chair OMGN, with full travel support, Nanjing, China Oomycetes Molecular Genetics Network 2012
5. OMGN Travel Award, Asilomar, CA, USA Oomycetes Molecular Genetics Network 2011
6. Annotation Jamboree of Pythium ultimum, MSU, Michigan, USA Michigan State University, USA 2009
7. OMGN Travel award to Scotland Oomycetes Molecular Genetics Network 2008
8. Travel award to attend optimal control theory University of Tenesse, USA. 2003, Septmeber
9. Travel award to attend optimal control theory University of Tenesse, USA. 2003, July
10. CSIR (SRF) CSIR 1995
11. CSIR (JRF- NET) CSIR 1993

 

Grant Supports

 

Funding Agency Years Active Role Present status Funded Value(in lakhs)
DBT 2017-2020 PI Active 83.72
DBT 2016-2019 PI Active 55
ICAR 2014-2017 PI Completed 32
DBT(Ramaligaswamy) 2012-2017 PI Completed 32
CSIR (genesis) 2012-2014 co-PI Completed 7
DST 2017-2020 co-PI Active 30

Patents & Publications

Publications from CSIR-IICB

 

2019

  1. Banerjee, N., Das, S., Tripathy, S. et al. MicroRNAs play an important role in contributing to arsenic susceptibility in the chronically exposed individuals of West Bengal, India Environ Sci Pollut Res (2019). https://doi.org/10.1007/s11356-019-05980-8
  2. Malar C M, Yuzon JD, Panda A, Kasuga T, Tripathy S*. Updated assembly resource of Phytophthora ramorum Pr102 isolate incorporating long reads from PacBio sequencing. Mol Plant Microbe Interact. 2019 Jul 15. doi: 10.1094/MPMI-05-19-0147-A. [Epub ahead of print] PubMed PMID: 31306082.
  3. Panda A, Chaudhari NM, Mukherjee M, Ghosh S, Sarangi AN, Mathu Malar C, KantS, Sen D, Das A, Das S, Singh D, Prusty A, Tripathy S*. Genome/transcriptome collection of plethora of economically important, previously unexplored organisms from India and abroad. Data Brief. 2019 Jun 5;25:104099. doi: 10.1016/j.dib.2019.104099. eCollection 2019 Aug. PubMed PMID: 31294057; PubMed Central PMCID: PMC6595405.
  4. Panda A, Chaudhari NM, Tripathy S*. Genome Annotator Light (GAL): A Docker-based package for genome analysis and visualization. Genomics. 2019  Mar 26. pii: S0888-7543(18)30700-6. doi: 10.1016/j.ygeno.2019.03.012. PubMed PMID: 30926570.[IF: 3.327]
  5. Malar C M, Yuzon JD, Das S, Das A, Panda A, Ghosh S, Tyler BM, Kasuga T, Tripathy S*. Haplotype-phased genome assembly of virulent Phythophthora ramorum isolate ND886 facilitated by long-read sequencing reveals effector polymorphisms  and copy number variation. Mol Plant Microbe Interact. 2019 Feb 22. doi: 10.1094/MPMI-08-18-0222-R. PubMed PMID: 30794480. [IF: 4.275]
  6. Sen D, Paul K, Saha C, Mukherjee G, Nag M, Ghosh S, Das A, Seal A, Tripathy S*. A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1-a comparative genomics viewpoint. DNA Res. 2019 Jan 7. doi: 10.1093/dnares/dsy044. PubMed PMID: 30615101. [IF: 5.24

 

2018

  1. P Nasker, M Mukherjee, S Kant, S Tripathy, A Sinha, M Das. Fluorine substituted nano hydroxyapatite: Synthesis, bio-activity and antibacterial response study. Ceramics International 44 (17), 22008-22013. [IF: 3.057].
  2. Vetukuri RR, Tripathy S*#, Malar C M#, Panda A, Kushwaha SK, Chawade A, Andreasson E, Grenville-Briggs LJ, Whisson SC. Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora. Genome Biol Evol. 2018 Sep 1;10(9):2432-2442.doi: 10.1093/gbe/evy162. PubMed PMID: 30060094; PubMed Central PMCID: PMC6152947. [#Joint first author] [IF: 3.94].
  3. Sinha, R., M. M. C, Raghwan, S. Das, S. Das, M. Shadab, R. Chowdhury, S. Tripathy* and N. Ali* (2018). “Genome Plasticity in Cultured Leishmania donovani: Comparison of Early and Late Passages.” Frontiers in Microbiology 9(1279). [IF:4.07]
  4. Sheikh, L., S. Sinha, Y. N. Singhababu, V. Verma, S. Tripathy and S. Nayar (2018). “Traversing the profile of biomimetically nanoengineered iron substituted hydroxyapatite: synthesis, characterization, property evaluation, and drug release modeling.” RSC Advances 8(35): 19389-19401. [IF: 3.7]
  5. Elliott M, Yuzon J, C MM, Tripathy S, Bui M, Chastagner GA, Coats K, Rizzo DM, Garbelotto M, Kasuga T. Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts. BMC Genomics. 2018 May 2;19(1):320. doi: 10.1186/s12864-018-4709-7. PubMed PMID: 29720102; PubMed Central PMCID: PMC5932867 [IF: 3.729]
  6. Dey T, Saville A, Myers K, Tewari S, Cooke DEL, Tripathy S, Fry WE, Ristaino JB, Guha Roy S. Large sub-clonal variation in Phytophthora infestans from recent severe late blight epidemics in India. Sci Rep. 2018 Mar 13;8(1):4429. doi: 10.1038/s41598-018-22192-1. [IF: 4.2]
  7. Panda A, Sen D, Ghosh A, Gupta A, C MM, Prakash Mishra G, Singh D, Ye W, Tyler BM, Tripathy S*. EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes. Mol Plant Pathol. 2018 Jan;19(1):227-237. doi: 10.1111/mpp.12505. Epub 2017 Jan 3. [IF: 4.7]

 

2017

  1. Majumder R, Sheikh L, Naskar A, Vineeta, Mukherjee M, Tripathy S*. Depletion of Cr(VI) from aqueous solution by heat dried biomass of a newly isolated fungus Arthrinium malaysianum: A mechanistic approach. Sci Rep. 2017 Sep 12;7(1):11254. doi: 10.1038/s41598-017-10160-0.[IF: 4.2]

 

2016

  1.  Mukherjee S, Chandrababunaidu MM, Panda A, Khowala S, Tripathy S*. Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. Front Microbiol. 2016 May 13;7:596. doi: 10.3389/fmicb.2016.00596. eCollection 2016. [IF: 4.07]
  2. Mohan A, Singh RS, Kumari M, Garg D, Upadhyay A, Ecelbarger CM, Tripathy S, Tiwari S. Urinary Exosomal microRNA-451-5p Is a Potential Early Biomarker of Diabetic Nephropathy in Rats. PLoS One. 2016 Apr 21;11(4):e0154055. doi: 10.1371/journal.pone.0154055. eCollection 2016. [IF: 2.3]
  3. Sheikh L, Tripathy S, Nayar S, 2016. Biomimetic matrix mediated room temperature synthesis and characterization of nano-hydroxyapatite towards targeted drug delivery. RSC Advances 6, 62556-71 [IF: 3.3]

 

2015

  1. Mathu Malar Chandrababunaidu, Deeksha Singh, Diya Sen, Sushma Bhan, Subhadeep Das, Akash Gupta, Siba Prasad Adhikary, Sucheta Tripathy* (2015) Draft Genome Sequence of Tolypothrix boutellei Strain VB521301. Genome announcements 3:    02. [IF: 1.44]
  2. Diya Sen, Mathu Malar Chandrababunaidu, Deeksha Singh, Neha Sanghi, Arpita Ghorai, Gyan Prakash Mishra, Madhavi Madduluri,Siba Prasad Adhikary, Sucheta Tripathy* (2015) Draft Genome Sequence of the Terrestrial Cyanobacterium Scytonema millei VB511283, Isolated from Eastern India. Genome announcements 3:    03. [IF: 1.44]
  3. Sourav Bhattacharyya, Mathu Malar Chandrababunaidu, Deeya Sen, Arijit Panda, Arpita Ghorai, Sushma Bhan, Neha Sanghi, Sucheta Tripathy* (2015) Draft Genome Sequence of Exopolysaccharide-Producing Cyanobacterium Aphanocapsa montana BDHKU 210001. Genome announcements 3:    03. [IF: 1.44]
  4. Deeksha Singh, Mathu Malar Chandrababunaidu, Arijit Panda, Diya Sen, Sourav Bhattacharyya, Siba Prasad Adhikary, Sucheta Tripathy* (2015) Draft Genome Sequence of Cyanobacterium Hassallia byssoidea Strain VB512170, Isolated from Monuments in India. Genome announcements 3:    03. [IF: 1.44]
  5. Mathu Malar Chandrababunaidu, Diya Sen, Sucheta Tripathy* (2015) Draft Genome Sequence of Filamentous Marine Cyanobacterium Lyngbya confervoides Strain BDU141951. Genome announcements 3:    03. [IF: 1.44]
  6. Subhadeep Das, Deeksha Singh, Madhavi Madduluri, Mathu Malar Chandrababunaidu, Akash Gupta, Siba Prasad Adhikary, Sucheta Tripathy* (2015) Draft Genome Sequence of Bioactive-Compound-Producing Cyanobacterium Tolypothrix campylonemoides Strain VB511288. Genome announcements 3:    04. [IF: 1.44]
  7. Abhishek Das, Arijit Panda, Deeksha Singh, Mathu Malar Chandrababunaidu, Gyan Prakash Mishra, Sushma Bhan, Siba Prasad Adhikary, Sucheta Tripathy* (2015) Deciphering the Genome Sequences of the Hydrophobic Cyanobacterium Scytonema tolypothrichoides VB-61278. Genome announcements 3:    04. [IF: 1.44]

 

2014

  1.  Bhowmick S, Malar M, Das A, Kumar Thakur B, Saha P, Das S, Rashmi HM, Batish VK, Grover S, Tripathy S*. Genome Announc. 2014 Dec 24;2(6). pii: e01326-14. doi: 10.1128/genomeA.01326-14. [IF: 1.44]
  2. A Tale of Effectors; Their Secretory Mechanisms and Computational Discovery in Pathogenic, Non-Pathogenic and Commensal Microbes. S Bhowmick, S Tripathy*Mol Biol, 2014.

 

Publication from the Virginia Tech, USA.

2013

  1. Rays H Y Jiang et al.,, Sucheta Tripathy, et al., (2013)  Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica.   PLoS genetics 9: 6. Jun [IF: 7.528]

 

2012

  1. Sucheta Tripathy*, Tejal Deo, Brett M Tyler (2012) Oomycete transcriptomics database: A resource for oomycete transcriptomes.   BMC Genomics. [IF: 3.867]
  2. Sucheta Tripathy*, Rays H Y Jiang (2012) Massively parallel sequencing technology in pathogenic microbes.   Methods Mol Biol 835: 271-294. [IF: 2.2]

 

2011

  1. Qunqing Wang, et al., Sucheta Tripathy, et al.(2011) Transcriptional programming and functional interactions within the Phytophthora sojae RXLR effector repertoire.   Plant Cell 23: 6. 2064-2086 Jun. [IF: 10.5]

 

2010

  1. M A Saghai Maroof, Dominic M Tucker, Jeffrey A Skoneczka, Brian C Bowman, Sucheta Tripathy, Sue A Tolin (2010)  Fine Mapping and Candidate Gene Discovery of the Soybean Mosaic Virus Resistance Gene, Rsv4   The Plant Genome 3: 14-22. [IF: 3.933]
  2. C André Lévesque, et al. Sucheta Tripathy, et al. (2010) Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire.   Genome Biol 11: 7. 07. [IF: 11.313]
  3. Laura Baxter+, Sucheta Tripathy+, et. al. (2010) Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.   Science 330: 6010. 1549-1551 Dec [+joint first author]. [IF: 34.661]
  4. H Wang, L Waller, S Tripathy, S K St Martin, L Zhou, K Krampis, D M Tucker, Y Mao, I Hoeschele, M A Saghai Maroof, B M Tyler, A E Dorrance (2010) Analysis of Genes Underlying Soybean QTL Conferring Partial Resistance to Phytophthora sojae.   The Plant Genome 3: 23-40 [IF: 3.933]

 

2009

  1.  Lecong Zhou, Santiago X Mideros, Lei Bao, Regina Hanlon, Felipe D Arredondo, Sucheta Tripathy, Konstantinos Krampis, Adam Jerauld, Clive Evans, Steven K St Martin, M A Saghai Maroof, Ina Hoeschele, Anne E Dorrance, Brett M Tyler (2009) Infection and genotype remodel the entire soybean transcriptome. BMC Genomics 10:  01.  [IF: 3.867]

 

2008

  1. Rays H Y Jiang, Sucheta Tripathy, Francine Govers, Brett M Tyler (2008) RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members. Proc Natl Acad Sci U S A 105:    4874-4879 Mar. [IF: 9.423]

 

2007

  1. Trudy A Torto-Alalibo, Sucheta Tripathy, Brian M Smith, Felipe D Arredondo, Lecong Zhou, Hua Li, Marcus C Chibucos, Dinah Qutob, Mark Gijzen, Chunhong Mao, Bruno W S Sobral, Mark E Waugh, Thomas K Mitchell, Ralph A Dean, Brett M Tyler (2007)  Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection. Mol Plant Microbe Interact 20:    781-793 Jul. [IF: 4.332]

 

2006

  1. Sucheta Tripathy, Varun N Pandey, Bing Fang, Fidel Salas, Brett M Tyler (2006) VMD: a community annotation database for oomycetes and microbial genomes. Nucleic Acids Res 34:  Database issue.  D379-D381 Jan. Featured in Science. [IF: 9.122]
  2. Brett M Tyler, Sucheta Tripathy, Xuemin Zhang, Paramvir Dehal, Rays H Y Jiang, Andrea Aerts, Felipe D Arredondo, Laura Baxter, Douda Bensasson, Jim L Beynon, et al.,(2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313:    1261-1266 Sep. [IF: 34.661]
  3. Xuemin Zhang, Chantel Scheuring, Sucheta Tripathy, Zhanyou Xu, Chengcang Wu, Angela Ko, S Ken Tian, Felipe Arredondo, Mi-Kyung Lee, Felipe A Santos, et. al., (2006) An integrated BAC and genome sequence physical map of Phytophthora sojae. Mol Plant Microbe Interact 19:    1302-1310 Dec.  [IF: 4.332]
  4. Sucheta Tripathy*, Brett M Tyler (2006) The repertoire of transfer RNA genes is tuned to codon usage bias in the genomes of Phytophthora sojae and Phytophthora ramorum. Mol Plant Microbe Interact 19:    1322-1328 Dec. [IF: 4.332]

 

2002

  1. Sucheta Tripathy, G M Reddy (2002) In Vitro callus induction and plantlet regeneration from Indian cotton cultivars Plant Cell Biotechnology and Molecular Biology 3:  3&4.  137-142.
  2. Sucheta Tripathy, G M Reddy (2002)  A Study on the influence of genotype, medium and additives on the induction of multiple shoots in Indian cotton cultivars Asian Jr. of Microbiol Biotech. Env. Sc. 4:  4.  515-519.

 

 Book chapters

  1. Verma S, Tripathy S., Raychaudhuri S, Swarnakar S. Chapter: Insights into Metalloproteinases Regulation in Gastrointestinal Cancers: Epigenetic Influences in the Book: Gastrointestinal Cancers: Prevention, Detection and Treatment. Editor, A Tyagi. Nova Publication (2016) (in press)
  2. Dissecting Transcriptomes of Cyanobacteria for novel metabolite production . Sucheta Tripathy*, Deeksha Singh, Mathumalar C, Abhishek Das.Genomics, Proteomics and Metabolomics in nutraceuticals and functional foods, edited by Bagchi for John Wiley & Sons
  3. Sucheta Tripathy (2011)  cancer and Diet In: Herbal Perspective: Present and Future 468 Vedam Books isbn:8189304917.
  4. Brett M Tyler, Rays H Y Jiang, Lecong Zhou, Sucheta Tripathy, Daolong Dou, Trudy Torto-Alalibo, Hua Li, Yongcai Mao, Bing Liu, et al  (2008)  Functional Genomics and Bioinformatics of the Phytophthora sojae Soybean Interaction.ISSN:1568-1009,ISBN:978-0-387-76722-2 (Print) 978-0-387-76723-9 (Online) In: Genomics of Disease  Edited by:J.P. Gustafson, J.Taylor, G. Stacey.   67-78 isbn:978-0-387-76723-9.

* Author for correspondence

 

 

Products

  •  Genome Annotator Lite -> https://hub.docker.com/r/cglabiicb/gal/: A software package to analyze and visualize the genome in a database

  •  www.eumicrobedb.org -> A complete resource for oomycetes genomes

  •  http://bgagenomics.iicb.res.in -> A comprehensive resource for all completely sequenced Cyanobacterial genomes.

  •  OmicsPCA -> Quantitative integration and analysis of multiple omics assays from heterogeneous samples 
    (https://bioconductor.org/packages/release/bioc/html/OMICsPCA.html)

  • SigFeature -> Significant feature selection using SVM-RFE & t-statistic 
    (https://www.bioconductor.org/packages/devel/bioc/html/sigFeature.html)