Dr. Tulika Prakash Srivastava

Dr.
Phone : 01905 -237922
E-mail : tulika[at]iitmandi[dot]ac[dot]in
Address : School of Basic Sciences

Indian Institute of Technology Mandi ,

near Bus Stand, Mandi - 175001

Himachal Pradesh

India

Research Interests:

  • Metagenomic sequencing and analysis of highthroughput sequence data obtained from different environments, including human body sites, soil, sediment, etc.
  • Complete genome sequencing and analysis of novel bacteria inhabiting different environments.
  • Development of computational tools and algorithms for metagenomic and genomic data analysis.
  • Development of novel algorithms for functional prediction of unknown/hypothetical proteins.
  • Human genome analysis and comparative genomics.

Educational


  • Ph.D. (in Bioinformatics): 2000 - 2005 under the supervision of Prof. Samir K Brahmachari at the Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi, India, registered at the University of Delhi, India Thesis Title: Comparative Genomics and In Silico Functional Analysis of Prokaryotic Genomes
  • M.Sc. 2yr (Chemistry): 1998 - 2000, Indian Institute of Technology (IIT), Kanpur, India
  • B.Sc. (H) (Chemistry: 1995 - 1998, Miranda House, University of Delhi, Delhi-110007, India.

Experience

    Positions HeldPeriodLaboratory
    Research ScientistOct 2010 - July 2012Laboratory for MetaSystems Research, Computational Biology Research Core, Quantitative Biology Center (QBiC), RIKEN, Yokohama,Japan.
    Postdoctoral ResearcherApr 2008 - Sept 2010MetaSystems Research Team, Advanced Science Institute, RIKEN, Yokohama, Japan
    Postdoctoral ResearcherApr 2006 - Mar 2008Genome Annotation and Comparative Analysis Team, Computational and Experimental Systems Biology Group, Genomic Sciences Center, RIKEN, Yokohama, Japan
    Senior Research Fellow2003 - Mar 2006G N Ramachandran Knowledge Center, Institute of Genomics and Integrative Biology, CSIR, Delhi, India

Honors and Awards

  • Received Ramalingaswamy Fellowship 2012 from Department of Biotechnology DBT) for five years.
  • Received CSHL Young Scientist Award to attend CSHL Genome Informatics Meeting 2006 held in Hinxton, UK.
  • Received HUGO Student Award to attend Human Genome Meeting 2005 held in Kyoto, Japan.
  • First prize for poster presentation entitled "Comprehensive Peptide Signature Database (CoPS)" in the Annual Symposium in Biomedical Sciences, University of Delhi, April 2003.

Publications

  1. Functional assignment of metagenomic data: challenges and applications. Prakash T, Taylor TD. Briefings in Bioinformatics (Epub ahead of print):1-17. (July 6, 2012).
    (This resource is a thorough review of methods used for metagenomic functional analysis, the challenges in the field with recommendations for possible solutions, and the various applications of the field)
  2. Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin." Sharma VK, Kumar N, Prakash T, Taylor TD. PLoS ONE 7(3):e34030. (April 4, 2012)
  3. Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of Th17 cell differentiation. Prakash T, Oshima K, Morita H, Fukuda S, Imaoka A, Kumar N, Sharma VK, Takahashi M, Saitou N, Taylor TD, Ohno H, Umesaki Y, Hattori M. Cell Host & Microbe 10(3):273-284.
  4. (September 15, 2011) (Cover Page Article)
    (This is the first report of the complete genome sequence of novel and yet unculturable microbe SFB, which is known to play an important role in regulating intestinal immunity. The study also helped in proposing the possible mechanism of its action.)
  5. Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes. Prakash T, Sharma VK, Adati N, Ozawa R, Kumar N, Nishida Y, Fujikake T, Takeda T, Taylor TD. PLoS One 2010 5(10), e13284.
    (First report on thorough identification and characterization of a novel type of gene found in eukaryotic genomes. The study resulted in the curation of the first comprehensive web resource of CGs from human genome and in proposing the various roles they can play.)
  6. MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets." Sharma VK, Kumar N, Prakash T, Taylor TD. Nucleic Acids Research 38(Database):D468-D472. (November 11, 2009)
  7. Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut. Hongoh Y*, Sharma VK*, Prakash T, Noda S, Toh H, Taylor TD, Kudo T, Sakaki Y, Toyoda A, Hattori M, Ohkuma M. Science 2008 322(5904):1108-1109.
  8. Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Hongoh Y*, Sharma VK*,Prakash T, Noda S, Taylor TD, Kudo T, Sakaki T, Toyoda A, Hattori M, Ohkuma M. Proc Natl Acad Sci USA 2008 105(14):5555-5560.
  9. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M. DNA Research, 2007, 14(4), 169-181.
  10. Structural assessment of glycyl mutations in invariantly conserved motifs. Prakash T, Sandhu KS, Singh NK, Bhasin Y, Ramakrishnan C, Brahmachari SK. Proteins: Structure, Function and Bioinformatics, 2007, 69(3), 617-632.
  11. Conformational Analysis of Invariant Peptide Sequences in Bacterial Genomes. Prakash T, Ramakrishnan C, Dash D, Brahmachari SK. J. Mol. Biol. 2005, 345, 937-955.
  12. CoPS: comprehensive peptide signature database. Prakash T, Khandelwal M, Dasgupta D, Dash D, Brahmachari SK. Bioinformatics, 2004, 20(16), 2886-2888.
  13. In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins. Bakshi R, Prakash T, Dash D, Brahmachari V. Biochem Biophys Res Commun. 2004, 320(1), 197-204.
  14. Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus. Sharma R, Maheshwari JK, Prakash T, Dash D, Brahmachari SK. Bioinformatics, 2004, 20(7), 1074-1080.

Software Copyrights

  • MetaBin: Fast and accurate taxonomic assignment of metagenomic sequences based on coding regions and sequence homology, Copyright, 2010.
  • ConjoinG: Database of Conjoined Genes, Copyright, 2009.
  • MetaBioME: Comprehensive Metagenomic Biomining Engine, Copyright, 2008.
  • CoPS: Comprehensive Peptide Signature Database, Copyright, 2003.

Research Funding/Grants Received

    Mitsubishi Foundation Grant of 5 million yen for the year 2007-2008 in collaboration with Dr. Todd D. Taylor for the project titled: Identification and mechanistic characterization of two novel classes of genes: co-transcribed genes and "gene desert" genes.

Conferences and Symposia

ORAL PRESENTATIONS DELIVERED

  • 14th Human Genome Meeting 2010. Montpellier, France, May 18-21, 2010. Title: "Chromosomal conformation patterns govern the formation of conjoined genes in eukaryotic genomes."
  • The 12th International Symposium on Microbial Ecology, ISME12. Cairns, Australia. Aug 17-22, 2008. Title: "Novel approach for the annotation of unannotated proteins in metagenomic datasets."
  • Indo-Brazil-South Africa (IBSA) Trilateral Workshop on "Functional Genomics, Life Science, GM Food and Agriculture" organized by DST and IGIB (CSIR) in July 2005, held at the Institute of Genomics and Integrative Biology.
  • Human Genome Meeting 2005 organized by the Human Genome Organization in April 2005, held at Kyoto, Japan, title: Conservation of invariant peptides in split genes.
  • International Conference on Mathematical Biology 2004 at Indian Institute of Technology, Kanpur, India, title: Identification and functional analysis of invariant peptide signatures in prokaryotes using comparative genomics.
  • Genome Informatics meet 2000 held at the Institute of Genomics and Integrative Biology, Delhi, India

POSTER PRESENTATIONS, SYMPOSIUMS AND WORKSHOPS ATTENDED

  • "Complete genome sequence of a rat strain of unculturable Segmented Filamentous Bacteria, a potent inducer of mucosal IgA." Tulika Prakash, Kenshiro Oshima, Hidetoshi Morita, Shinji Fukuda, Hiroshi Ohno, Naveen Kumar, Vineet K. Sharma, Todd D. Taylor, Akemi Imaoka, Yoshinori Umesaki, Masahira Hattori. International Human Microbiome Congress 2012, Paris, France, March 19 - 21 2012.
  • "Complete genome sequence of a rat strain of unculturable Segmented Filamentous Bacteria, a potent inducer of mucosal IgA." Tulika Prakash, Kenshiro Oshima, Hidetoshi Morita, Shinji Fukuda, Hiroshi Ohno, Naveen Kumar, Vineet K. Sharma, Todd D. Taylor, Akemi Imaoka, Yoshinori Umesaki, Masahira Hattori. International Human Microbiome Congress 2011, Vancouver, Canada, March 9 - 11 2011.
  • "Comparative Genome Analysis of Two Biotypes Of Vibrio vulnificus." Tulika Prakash, Keh-Ming Wu, Tsai-Lien Liao, Vineet K. Sharma, Carmen Amaro, Lien-I Ho, Todd D. Taylor, Shih-Feng Tsai. ISME13, 2010, Seattle, USA. Aug 22-27, 2010.
  • "Novel approach for the annotation of unannotated proteins in Metagenomic datasets." Tulika Prakash, Vineet K. Sharma, Naveen Kumar, Todd D. Taylor. Joint Computational Science Workshop 2009. Yokohama, Japan. July 9-10, 2009.
  • "Novartis Biotechnology Leadership Camp 2009." Novartis BioCamp 2009.Tokyo, Japan. June 24-26, 2009.
  • "Novel approach for the annotation of unannotated proteins in Metagenomic datasets." Tulika Prakash, Vineet K. Sharma, Naveen Kumar, Todd D. Taylor. The 8th International Workshop on Advanced Genomics, Expansion of Genome Science. Tokyo, Japan, June 16-18, 2009.
  • "Co-transcription of genes into single transcripts: Another regulatory mechanism for gene expression in vertebrates." Tulika P. Srivastava, Todd D. Taylor, Vineet K. Sharma, Yuichiro Nishida, Takayoshi Fujikake, Tadayuki Takeda, Ritsuko Ozawa, Maki Mushiake, Reina Okumura. HUGO's 13th Human Genome Meeting, HGM2008.Hyderabad, India. Sep 27-30, 2008.
  • "Co-transcription of genes into single transcripts-Another regulatory mechanism for gene expression in vertebrates." Tulika P. Srivastava, Todd D. Taylor, Vineet K. Sharma, Yuichiro Nishida, Takayoshi Fujikake, Tadayuki Takeda, Ritsuko Ozawa, Maki Mushiake, Reina Okumura, Yoshiyuki Sakaki. The Biology of Genomes. Cold Spring Harbor Laboratory, NY, USA. May 8-12, 2007.
  • Transcription-Mediated Chimerisms: New Genes Or Artifacts Of Transcription? Tulika P. Srivastava, Todd D. Taylor, Vineet K. Sharma, Yuichiro Nishida, Takayoshi Fujikake, Tadayuki Takeda, Maki Mushiake, Reina Okumura, Yoshiyuki Sakaki. Sixth Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics 2006. Wellcome Trust Genome Campus, Hinxton, UK. September 2006.
  • Conservation of invariant peptides in split genes. Tulika Prakash, Debasis Dash, Samir K. Brahmachari. Human Genome Meeting (HGM-2005), 2005, Kyoto, Japan.
  • Conformational analysis of invariant peptide sequences: their role as folding nucleus. Tulika Prakash, C. Ramakrishnan, Debasis Dash, Samir K. Brahmachari. BIOTECH-2004, Delhi, India.
  • Identification and functional analysis of invariant peptide signatures in prokaryotes using comparative genomics. Tulika Prakash, Debasis Dash, Shipra Sharma, Mamta Khandelwal, Mitali Mukerji, Samir K. Brahmachari. International Conference on Mathematical Biology 2004 at Indian Institute of Technology, Kanpur, India.
  • CoPS: comprehensive peptide signature database. Tulika Prakash, Mamta Khandelwal, Dipayan Dasgupta, Debasis Dash and Samir K. Brahmachari. International FAOBMB Science Congress, 2003 Indian Institute of Science, Bangalore, India.
  • Comprehensive Peptide Signature Database (CoPS). Tulika Prakash, Debasis Dash, Samir K. Brahmachari. Annual symposium at Dr. B.R. Ambedkar Center for Biomedical Research, Delhi, India in April 2003.
  • PLHOSTFA: A novel tool for identification of Functional Signatures. Debasis Dash, Tulika Prakash, Rohit Ghai, Samir K. Brahmachari. International symposium on Crystallography and Bioinformatics in Structural Biology 2001 Indian Institute of Science, Bangalore, India.

Other Activities

MEMBERSHIP OF PROFESSIONAL SOCIETIES /CONSORTIA

  • Member of Human Metagenome Consortium Japan (HMGJ), Jun 2008 - present
  • Member of International Society of Microbial Ecology, Jan 2009 - present
  • Member of Human Genome Organization (HUGO), April 2008 - present
  • Member of Genomics Standards Consortium, Mar 2008 - present

TEACHING EXPERIENCE

  • 2002 September - 2003 March, Faculty, PG-Diploma course in Bioinformatics at the Informatics Institute organized in collaboration with CSIR.
  • Contributed to the development of course and curriculum for bioinformatics (Functional annotation: Sequence, patterns and profiles and structural similarity methods, tools and approaches) for PG-Diploma course in Bioinformatics at the Informatics Institute organized in collaboration with CSIR, India.
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