Tulika P. Srivastava

Introduction

I was working as a Research Scientist in the Laboratory for MetaSystems Research, Computational Biology Research Core at RIKEN Center for Computational and Quantitative Life Science in Yokohama, Japan. I joined RIKEN as a postdoctoral researcher in April 2006. I completed my PhD in Bioinformatics from the Institute of Genomics and Integrative Biology, CSIR, Delhi, India.

Contact Information

E-mail: tulikaps@gsc.riken.jp

Current Research Interests

Bioinformatics, Metagenomics, Systems Biology, and Genomics

  • Identification and analysis of Segmented Filamentous Bacteria (SFB), a potent inducer of mucosal IgA, from human gut metagenomic data.
  • Annotation and comparative analysis of a novel strain of Vibrio vulnificus genome.
  • Development of a novel approach for the annotation of unannotated proteins in metagenomic datasets.
  • Annotation and comparative analysis of in-house generated Metagenomics datasets, including human gut metagenome and microbial fuel cell metagenome.
  • Development of computational tools and resources for metagenomic data analysis including iMetaSys, MetaBioME , Metabin etc.
  • Identification and analysis of Conjoined Genes in eukaryotic genomes (ConjoinG ).
  • Discovery of conjoined genes in human stomach and kidney cancer using next-generation RNA sequencing.

Publications

  • "Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis." International Glossina Genome Initiative. Science 344(6182):380-386. (April 25, 2014) PMID 24763584
  • "Functional assignment of metagenomic data: challenges and applications." Prakash T, Taylor TD [1]. Briefings in Bioinformatics 13(E6):1-17. (July 6, 2012) PMID 22772835
  • "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) PMID 22496776
  • "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. (September 15, 2011) PMID 21925114
  • "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 5(10):1-9 e13284. (October 12, 2010) PMID 20967262
  • "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) PMID 19906710
  • "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 (* These authors contributed equally to this work). Science 322(5904):1108-1109. (November 14, 2008) PMID 19008447
  • "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 105(14):5555-5560. (April 8, 2008) PMID 18391199
  • "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 14(4):169-181. (August, 2007) PMID 17916580
  • "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 69(3):617-632. (Nov 15, 2007) PMID 17623846
  • "Conformational analysis of invariant peptide sequences in bacterial genomes." Prakash T, Ramakrishnan C, Dash D, Brahmachari SK. J Mol Biol 345(5):937-955. (February 4, 2005) PMID 15644196
  • "CoPS: Comprehensive Peptide Signature database." Prakash T, Khandelwal M, Dasgupta D, Dash D, Brahmachari SK. Bioinformatics 20(16):2886-2888. (November 1, 2004) PMID 15166019
  • "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 320(1):197-204. (July 16, 2004) PMID 15207721
  • "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 20(7):1074-1080. (May 1, 2004) PMID 14764577

Conferences and Meetings

  • "Novel approach for the annotation of unannotated proteins in Metagenomic datasets." Joint Computational Science Workshop 2009. Yokohama, Japan. July 9-10, 2009. (Poster)
  • "Novartis Biotechnology Leadership Camp 2009." Novartis BioCamp 2009. Tokyo, Japan. June 24-26, 2009. (Participant)
  • "Novel approach for the annotation of unannotated proteins in Metagenomic datasets." The 8th International Workshop on Advanced Genomics, Expansion of Genome Science. Tokyo, Japan. June 16-18, 2009. (Poster)
  • "Co-transcription of genes into single transcripts: Another regulatory mechanism for gene expression in vertebrates." HUGO's 13th Human Genome Meeting, HGM2008. Hyderabad, India. Sep 27-30, 2008. (Poster)
  • "Novel approach for the annotation of unannotated proteins in metagenomic datasets." The 12th International Symposium on Microbial Ecology, ISME12. Cairns, Australia. Aug 17-22, 2008. (Talk)
  • "Co-transcription of genes into single transcripts: Another regulatory mechanism for gene expression in vertebrates." The Biology of Genomes. Cold Spring Harbor Laboratory, NY, USA. May 8-12, 2007. (Poster)
  • "Transcription-mediated chimerisms: new genes or artifacts of transcription?." Sixth Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics 2006. Wellcome Trust Genome Campus, Hinxton, UK. September 2006. (Poster)
  • "Achilles' heels in prokaryotic genomes." Indo-Brazil-South Africa (IBSA) Trilateral Workshop on “Functional Genomics, Life Science, GM Food and Agriculture”. Institute of Genomics and Integrative Biology, Delhi, India (organized by DST and IGIB,CSIR). July 2005. (Talk)
  • "Conservation of invariant peptides in split genes." Human Genome Meeting 2005. Kyoto, Japan (organized by the Human Genome Organization). April 2005. (Talk & Poster - Received HUGO Student Award)
  • "Conformational analysis of invariant peptide sequences: their role as folding nucleus." BIOTECH-2004. Delhi, India. October 2004. (Poster)
  • "Identification and functional analysis of invariant peptide signatures in prokaryotes using comparative genomics." International Conference on Mathematical Biology 2004. Indian Institute of Technology, Kanpur, India. February 2004. (Talk & Poster)
  • "CoPS: comprehensive peptide signature database." International FAOBMB Science Congress, 2003. Indian Institute of Science, Bangalore, India. December 2003. (Poster)
  • "Comprehensive Peptide Signature Database (CoPS)." Annual symposium at Dr. B.R. Ambedkar Center for Biomedical Research. Dr. B.R. Ambedkar Center for Biomedical Research, Delhi, India. April 2003. (Poster - Received First Prize)
  • "PLHOSTFA: A novel tool for identification of functional signatures." International symposium on Crystallography and Bioinformatics in Structural Biology. Indian Institute of Science, Bangalore, India. November 2001. (Poster)
  • "Protein coding genes and conserved domains in the human genome." Genome Informatics meet 2000. Institute of Genomics and Integrative Biology, Delhi, India. October 2000. (Talk)

Software and Databases

ConjoinG is a database of 800 Conjoined Genes identified in the Human Genome. A Conjoined Gene (CG) is defined as a gene formed at the time of transcription by combining at least part of one exon from each of two or more distinct (parent) genes which lie on the same chromosome, in the same orientation, and translate independently into different proteins. In some cases, the transcripts formed by CGs are translated to form chimeric or completely novel proteins.

  • MetaBioME : Comprehensive Metagenomic Biomining Engine

MetaBioME is a database to explore commercially useful enzymes (CUEs) in metagenomic datasets.

  • PLHOSTFA: Peptide Library Based Homology Search Tool (Function Assigment)

PLHOSTFA is a web based software to do a genome-wise comparison of several thousand proteins of one genome with all the other proteins of various other genomes. This software is based on a novel peptide library approach in which octa-peptide libraries of selected organisms are compared and invariant peptides occurring in a minimum number of organisms (specified by the user) are returned. These invariant peptides were found to occur in functionally identical or related proteins and hence can be used as potential functional signatures.

  • CoPS:Comprehensive Peptide Signature Database

CoPS is a collection of 12076 invariant signature peptides which are extracted from 52 bacterial genomes with a minimum occurrence in 7 organisms using PLHOSTFA (Peptide Library based Homolgy Search Tool). These Functional Signatures are distributed over 2605 bacterial and 112 human hypothetical proteins and new unknown proteins could also be assigned functions based on these signatures using Protein Annotation.