Structural Biology & Bio-Informatics Division

Dr. Sucheta Tripathy

Principal Scientist, Ramalingaswamy Fellow, Associate Professor (AcSIR)

Education:
Ph.D Plant Molecular Biology 1998 (Center For Plant Molecular Biology, Hyderabad)
Training in Software Technology for PGDST at NCST(Now cDAC, dept. of science and Technology), Mumbai,2000
Bioinformatics Training, DSQ Biotech, Chennai, India, 2000

Professional Preparation:
Lecturer at Ratnam College, Mumbai University (1998-2000)
Scientist (Bioinformatics division) at DSQ biotech limited (2000-2001)
Scientist and Head Bioinformatics division at Avesthagengrain Pvt. Ltd.(2001-2002)
Senior scientist and Bioinformatics Team lead at Virginia Bioinformatics Institute at Virginia tech (2002-2012)

Contact - tsucheta@iicb.res.in / tsucheta@gmail.com

 

Additional Info:

https://sites.google.com/site/suchetalab/
https://twitter.com/tsucheta

 

Current Research Interest

My lab is currently interested in the following research areas:

  1. Can we predict transcript expression of a given cell line under a given condition by using existing data such as transcription factor binding sites, CAGE tag data, epigenetic data and physical structure of DNA?
  2. How to exploit the non-ribosomal protein synthetic pathway for over production of bio-active and bio-energy compounds from photosynethic prokaryotes using nextgen genomics.
  3. Nextgen genomics data dissemination and portrayal using efficient data structures and schemas.
  4. Development of novel algorithms and softwares for genome and transcriptome assembly and annotation.

We will try to answer these questions using computational means. My lab will focus on three overlapping areas:

    1. Nextgen genomics and transcriptomics;
    2. Computational and Systems Biology;
    3. Algorithm and resource development.

    1. Nextgen sequencing methods have brought about a paradigm shift in our understanding of several life forms. With reduced cost and increased speed, this method has become the choicest tool for every biologist. RNAseq technology has entailed users with the power to profile transcriptomes quickly and reproducibly.  I wish to answer biological questions by using the power of nextgen sequencing methods. The role of such methods has already been documented in gene expression profiling, gene regulation, gene structure and function prediction, marker development and quick identification of rare transcripts. This relatively simplistic method can have diverse applications from complicated genetic diseases in humans to finding rare transcripts in biomass production in blue green algae. IICB currently boasts of several nextgen sequencers attached with compute clusters for data analysis. All the nextgen sequencing proposals will be collaborative initiatives, where computational and sequencing part will be taken care of by my group. My lab has basic infrastructure for isolation and maintenance of microbe cultures.
    2. Computational Biology has recently emerged as an area that amalgamates pure biology, mathematics, statistics and computer science. The avalanche of information generated by day to day research undertaking can’t be handled by humans anymore. In order to make some sense out of the data, it is imperative to process them with the help of computers. My group stays solidly focused on development of pipelines, databases, tera data visualization and data analysis protocols using the existing methods. The data that we will handle ranges from RNAseq data, genomics data, human microarray data, human cancer data, freshly generated human genetics data, microbial disease data. We have created genome portals that undergo constant up gradation and building intelligence into it. Our group will focus on building an entire bioinformatics resource built around our genome portal for wider community usage.
    3. Bioinformatics and algorithm development still remains a big bottleneck in processing the huge amounts of biological data. One of my thrust areas is on development of algorithms for genomics and proteomics. Although many algorithms are already developed in gene prediction, sequence assembly, annotations, differential gene expression analysis, yet lot needs to be done in this effort. Each organism comes with specific challenges that act as severe impediments in the analysis protocol. My group in collaboration with statisticians and mathematicians would like to build new softwares and algorithms that will be used to fulfill my other aims.

These three programs are synergistic to each other and will work towards collective goals as mentioned above. Our lab will mainly focus on developing hypothesis, but our collaborators will take this to the next level, that is lab testing, proof of hypothesis and commercialization

Names of the group members including regular staff with designation and research fellows

Who will fit into the lab?

If you get excited with new ideas and exude enthusiasm about new problems, you will fit into this lab. You may not be already packaged with great programming skills, but when you go out of the lab you are expected to have learnt and mastered programming as well as mathematics and statistics. You should be willing to learn new things quickly and should be able to generate new ideas. If all these describe you and you have a CSIR/UGC fellowship please write to me directly at tsucheta@iicb.res.in or tsucheta@gmail.com for more information.

List of important Publications

  1. Mathu Malar C, Deeksha Singh, Diya Sen , Sushma Bhan, Subhadeep Das, Akash Gupta, Siba Prasad Adhikary and Sucheta Tripathy. .Draft Genome Sequence of Terrestrial hydrophobic Cyanobacterium Tolypothrix Boutellei VB521301 [Genome Announcement, 2015, In press]. JIF: awaited
  2. Diya Sen, Mathu Malar C., Deeksha Singh, Neha Sanghi, Arpita Ghorai, Gyan Prakash Mishra, Madhavi Madduluri, Siba Prasad Adhikary and Sucheta Tripathy. Draft genome sequence of the terrestrial cyanobacterium Scytonema millei VB511283 isolated from Eastern India. [Genome Announcement, 2015, In Press]. JIF: awaited
  3. A Tale of Effectors; Their Secretory Mechanisms and Computational Discovery in Pathogenic, Non-Pathogenic and Commensal Microbes.S Bhowmick, S Tripathy - Mol Biol, 2014.
  4. Bhowmick S, Malar M, Das A, Kumar Thakur B, Saha P, Das S, Rashmi HM, Batish VK, Grover S, Tripathy S. Draft Genome Sequence of Lactobacillus casei Lbs2.Genome Announc. 2014 Dec 24;2(6). pii: e01326-14. doi: 10.1128/genomeA.01326-14.PubMed PMID: 25540344; PubMed Central PMCID: PMC4276822.

Book Chapter:

  1. Tripathy, S., Deeksha Singh, Mathu Malar C. and Abhishek Das. Dissecting Transcriptomes of Cyanobacteria for novel metabolite production. Willey Interscience [In Press]

Publications prior to joining IICB:

  1. Jiang RH, de Bruijn I, Haas BJ, Belmonte R, Löbach L, Christie J, van denAckerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E,Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJ, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JH, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P. Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. PLoS Genet. 2013 Jun;9(6):e1003272. doi: 10.1371/journal.pgen.1003272. Epub 2013 Jun 13. PubMed PMID: 23785293; PubMed Central PMCID: PMC3681718. [JIF: 8.167]
  2. Tripathy,S*., Tejal Deo, Brett M Tyler (2012)  Oomycete transcriptomics database: A resource for oomycete transcriptomes.   BMC Genomics.[JIF: 4.2][Highly accessed]
  3. Tripathy, S*., Rays H Y Jiang (2012)  Massively parallel sequencing technology in pathogenic microbes.   Methods Mol Biol 835: 271-294. [JIF: 13.9]
  4. Qunqing Wang1, Changzhi Han1, Adriana Ferreira2, Wenwu Ye1, Tripathy, S.,2, Shiv Kale2, Biao Gu2,3, Xiaoli Wang1, Xiaoli Yu1, Tiuli Liu1, Yao Yao1, Xinle Wang1, Zhengguang Zhang1, Baoping Cheng1, Suomeng Dong1, Weixing Shan3, Xiaobo Zheng1, Daolong Dou1,2, Brett M. Tyler2,4 and Yuanchao Wang1,4   Transcriptional programming and functional interactions within the Phytophthora sojae RXLR effector repertoire. Plant Cell 2011 23:2064-2086l (Featured in cover of Plant Cell, August 2011). [JIF: 10.68]
  5. Laura Baxter, Tripathy, S., et al., [Joint First Author]  Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science 10 December 2010: 1549-1551.Featured in science cover  [JIF: 31.364]
  6. C. André Lévesque, Henk Brouwer, Liliana Cano, John P. Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P. Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W. Beakes, Jeffrey L. Boore, Dana Busam, Bernard Dumas, Steve Ferriera,Susan I. Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays H.Y. Jiang, Justin Johnson, Theerapong Krajaejun,Haining Lin, Harold J.G. Meijer, Barry Moore, Paul Morris, Vipaporn Phuntmart, Daniela Puiu,Jyoti Shetty, Jason E. Stajich, Tripathy, S.,, Stephan Wawra, Pieter van West, Brett R.Whitty, Pedro M. Coutinho, Bernard Henrissat, Frank Martin, Paul D. Thomas, Brett M. Tyler,Ronald P. De Vries, Sophien Kamoun, Mark Yandell, Ned Tisserat, and C. Robin Buell(2010). Genome sequence of the necrotrophic plant pathogen, Pythium ultimum,reveals original pathogenicity mechanisms and effector repertoire. Genome Biology 2010 Jul 13;11(7):R73. [Epub ahead of print] PubMed PMID: 20626842. [JIF: 6.89]
  7. Wang, H., L. Waller, Tripathy, S.,, S.K. St. Martin, L. Zhou, K. Krampis, D.M. Tucker, Y. Mao, I. Hoeschele, M.A. Saghai Maroof, B.M. Tyler, and A.E. Dorrance. 2010. Analysis of Genes   Underlying Soybean QTL Conferring Partial Resistance to Phytophthora sojae. The Plant Genome 3: 23-40. . [JIF : 4.659]
  8. M. A. Saghai Maroof, Dominic M. Tucker, Jeffrey A. Skoneczka, Brian C. Bowman, Tripathy, S.,, and Sue A. Tolin. 2010. Fine Mapping and Candidate Gene Discovery of the Soybean Mosaic Virus Resistance Gene, Rsv4Plant Gen. July 2010 3:14-22; doi:10.3835 The Plant Genome. 2009.07.0020 . [JIF: 4.659]
  9. Lecong Zhou, Santiago X. Mideros, Lei Bao, Regina Hanlon, Felipe Arredondo, Tripathy, S.,, Konstantinos Krampis, Adam Jerauld, Clive Evans, Steven K. St. Martin, Saghai M.A. Maroof, Ina Hoeschele, Anne E. Dorrance and Brett M. Tyler.(2008) Infection and Genotype Remodel the Entire Soybean Transcriptome. BMC Genomics. 2009 Jan 26;10(1):49 Highly accessed. [JIF : 4.21]
  10. Jiang RH, Tripathy S, Govers F, Tyler BM.(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. 2008 Mar 25;105(12):4874-9. Epub 2008 Mar 14. . [JIF : 9.771]
  11. Trudy Torto-Alalibo1, Tripathy, S.,et. al. The Phytophthora sojae EST Dataset: A Resource for Gene Discovery Specific to Different Morphological and Infection Stages in P. sojae. Molecular Plant Microbial Interaction.2007. 20:781-793. . [JIF : 4.4]
  12. Brett M. Tyler,1, Tripathy, S.,,1 Xuemin Zhang,1et. al. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis Genome sequences of the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum reveal a photosynthetic past and recent massive expansion and diversification of potential pathogenicity gene families. Science. 303: 1261-1265,2006. [JIF : 31.364]
  13. Tripathy S*, Tyler BM (2006).  The repertoire of transfer RNA genes is tuned to codon usage bias in the genomes Phytophthora sojae and Phytophthora ramorum. Mol. plant-Microbe Interact. 19(12):1329-1336 [JIF:  4.4]
  14. Tripathy, S.,, V. N. Pandey, B. Fang, F. Salas, B. M. Tyler; VMD a community annotation database for oomycetes and microbial genomes. Nucleic Acids Res. 34. D379-D381, 2006. Featured in Science Netwatch. [JIF: 8.808]
  15. Zhang X, Scheuring C, Tripathy S et al.,(2006) An integrated BAC and genome sequence physical map of Phytophthora sojae. Mol. Plant-Microbe Interact. 19(12): 1302-1310. [JIF: 4.4]
  16. Tyler, Brett; Tripathy, S., Grunwald, Nik; Lamour, Kurt; Ivors, Kelly; Garbelotto, Matteo; Rokhsar, Daniel; Putnam, Nik; Grigoriev, Igor; Boore, Jeffrey  2006.  Genome sequence of Phytophthora ramorum: implications for management.   In: Frankel, Susan J.; Shea, Patrick J.; and Haverty, Michael I., tech. coords. Proceedings of the sudden oak death second science symposium: the state of our knowledge. Gen. Tech. Rep. PSW-GTR-196. Albany, CA: Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture: 157-158. [JIF : undetermined]
  17. Tripathy, S*.,, G.M.Reddy; In Vitro Callus Induction and Plantlet Regeneration from Indian Cotton Cultivars, Plant Cell Biotechnology and Molecular Biology. An International Journal on Biotechnological Research, 3&4:137-142, 2002, [JIF : undetermined]
  18. Tripathy, S*.,, G.M.Reddy; A study on the influence of genotype, medium and additives on the induction of multiple shoots in Indian cotton cultivars; Asian Journal of Microbiology, Biotechnology & Environmental Sciences, 4:515-519, 2002. [JIF : undetermined]

Book chapters

  1. Tripathy, S.* (2011)  Cancer and Diet   In: Herbal perspectives Edited by:T. Parimelazhagan, S. Manian and M. Pugalenthi, Satish Serial. 486 isbn:8189304917
  2. Brett M. Tyler4, Rays H.Y. Jiang, Lecong Zhou, Tripathy, S.,, Daolong Dou, Trudy Torto-Alalibo, Hua Li, Yongcai Mao, Bing Liu, Miguel Vega-Sanchez, Santiago X. Mideros, Regina Hanlon, Brian M. Smith, Konstantinos Krampis, Keying Ye, Steven St. Martin, Anne E. Dorrance, Ina Hoeschele and M.A. Saghai Maroof(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)

[* - corresponding author]

 

 
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