Vineet K. Sharma



Introduction

At present, I am working as an Assistant Professor at Indian Institutes of Science Education and Research (IISER) Bhopal, India, and as a Visiting Scientist in the Laboratory for MetaSystems Research at the RIKEN Quantitative Biology Center in Yokohama, Japan.

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

Current Research Interests

  • Metagenomic analysis
  • Development of computational tools for metagenomic data analysis
  • Genomic analysis of uncultivable bacteria present in human gut and other novel bacteria
  • Development of iMetaSys pipeline for automated annotation and analysis of metagenomic data
  • MetaBioME: Software for exploring commercially useful enzymes (CUEs) in metagenomic datasets
  • Identification of conjoined genes in human and other genomes
  • TseTse fly cDNA annotation and analysis

Contact Information

Assistant Professor
Department of Biological Sciences
Indian Institute of Science Education and Research (IISER) Bhopal
ITI (Gas Rahat) Building, Govindpura
Bhopal (MP), India
E-mail: vineetks(at)iiserbhopal.ac.in

OR

Visiting Scientist
Laboratory for Integrated Bioinformatics
RIKEN Center for Integrative Medical Sciences
1-7-22 Suehiro-cho, Tsurumi-ku
Yokohama, Kanagawa 230-0045 Japan
E-mail: vineetks@gsc.riken.jp

Software and Databases

MetaBioME : Comprehensive Metagenomic Biomining Engine

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

EXPOLDB Expression Linked Polymorphism Database

  • During my PhD, in IGIB, our team developed this database. EXPOLDB is a resource for investigating the natural variations in gene expression in humans and aims to provide insights into gene regulation by linking gene expression data from microarray experiments with the distribution of cis modulators of transcription. It is the first systematic effort to collect gene expression data from microarrays and link them with the distribution of (TG/CA)n repeats. The EXPOLDB profile of genes is also linked by GeneCards.

ArrayD

  • During my PhD, in IGIB, our team developed this software which is a general purpose software for microarray design. ArrayD is a software for standard cartesian robots. The software aids users in preparing a judicious and elegant design and is universally applicable.

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
  • "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 Arcobacter butzleri ED-1 and Arcobacter sp. strain L, both isolated from a microbial fuel cell." Toh H, Sharma VK, Oshima K, Kondo S, Hattori M, Ward FB, Free A, Taylor TD. J Bacteriol 193(22):6411-6412. (November, 2011) PMID 22038970
  • "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 (* These authors contributed equally to this work). 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
  • "Abundance of dinucleotide repeats and gene expression are inversely correlated: a role for gene function in addition to intron length." Sharma VK, Kumar N, Brahmachari SK, Ramachandran S. Physiological Genomics 31(1):96-103. (June, 2007) PMID 17550993
  • "Expoldb: EXpression linked POLymorphism DataBase with inbuilt tools for analysis of expression and simple repeats." Sharma VK, Sharma A, Kumar N, Khandelwal M, Mandapati KK, Horn-Saban S, Strichman-Almashanu L, Lancet D, Brahmachari SK, Ramachandran S. BMC Genomics 7:258-265. (October, 2006) PMID 17038195
  • "(TG/CA)n repeats in human gene families: abundance and selective patterns of distribution." Sharma VK, Brahmachari SK, Ramachandran S. BMC Genomics 6(1):83-94. (June, 2005) PMID 15935094
  • "Assessing natural variations in gene expression in humans by comparing with monozygotic twins using microarrays." Sharma A, Sharma VK, Horn-Saban S, Lancet D, Ramachandran S, Brahmachari SK. Physiol Genomics 21(1):117-123. (March 21, 2005) PMID 15644424
  • "ArrayD: A general purpose software for microarray design." Sharma A, Srivastava GP, Sharma VK, Ramachandran S. BMC Bioinformatics 5(142 doi:10.1186/1471-2105-5-142):1-6. (October 2, 2004) PMID 15461789
  • "(TG/CA)n repeats in human housekeeping genes." Sharma VK, B-Rao C, Sharma A, Brahmachari SK, Ramachandran S. Journal of Biomolecular Structure and Dynamics 21(2):303-310. (October, 2003) PMID 12956614

Book Chapters

  • "(TG/CA)n repeats in human genome: Insilico analysis of the distribution and functional role of these repeats as cis modulators of transcription" in Mathematical Biology. Sharma VK, Sharma A, Brahmachari SK, Ramachandran S (2005). Ed: . Pub: Anamaya Publishers, India. Page(s): . ISBN

International Conferences

  • "MetaBin: a program for fast, accurate and highly sensitive taxonomic assignments of metagenomic sequences." International Human Microbiome Congress". Hyatt Regency, Vancouver, Canada. March 9-11 2011. (Poster)
  • "iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench." International Symposium on Microbial Ecology "Stewards of a changing planet". Seattle, USA. August 22-27 2010. (Poster)
  • "Comparative analysis of (TG/CA)n repeats in the human and chimpanzee genomes." Human Genome Meeting HGM 2010 "Next Generation Genomics and Medicine". Montpellier, France. May 18-21 2010. (Poster)
  • "iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench." 1st MetaHIT Conference on Human Metagenomics. Shenzhen, China. March 1-3 2010. (Talk)
  • "iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench." 3rd Congress of European Microbiologists (FEMS 2009) "Microbes and Man - interdependence and future challenges". Gothenberg, Sweden. June 28–July 2, 2009. (Poster)
  • "iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench." 8th International Workshop on Advanced Genomics. Tokyo, Japan. June 16-18, 2009. (Poster)
  • "MetaBioME: Comprehensive Metagenomic BioMining Engine to Search Novel Biocatalysts in Metagenomic Datasets." HUGO's 13th Human Genome Meeting, HGM2008. Hyderabad, India. Sep 27-30, 2008. (Poster)
  • "MetaBioME: A Powerful Magnet for Finding Bioicatalyst Needles in Metagenomic Haystacks." The 12th International Symposium on Microbial Ecology (ISME12). Cairns, Australia. August 17-22, 2008. (Talk)
  • "Metagenomics to MetaBiotechnology: Potentials and limitations." The Sixth Asia-Pacific Bioinformatics Conference, APBC2008. Kyoto, Japan. January 14-17, 2008. (Poster)
  • ""Complete genome of an uncultured bacterial symbiont in the termite gut"." The 7th International Workshop on Advanced Genomics. Tokyo, Japan. November 27-28, 2007. (Participation/Poster by team - Best Poster- Runner's up prize)
  • "TseTse cDNA annotation." "Training Course and Workshop on Annotation and Bioinformatics Analysis of Glossina (Tsetse Fly) cDNAs" IGGI Transcriptome workshop. South African National Bioinformatics Institutes (SANBI), University of the Western Cape, Cape Town, South Africa. November 12-17, 2007. (Participant)
  • ""Tardigrades: Model organisms to study cryptobiosis"." The Biology of Genomes, Cold Spring Harbor Laboratory/Wellcome Trust conference. Cold Spring Harbor Laboratory, NY, USA. May 8-12, 2007. (Poster)
  • "Participant." Sixth Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics. Wellcome Trust Conference Centre in Hinxton, UK. September, 2006. (Participant)
  • "Novartis International Biotechnology Leadership Camp 2007." Novartis BIOCAMP 2007. Academy Hills, Roppongi, Tokyo, Japan. October 6-8, 2007. (BIOCAMP- Received award for "Outstanding Performance")
  • "Analysis and understanding of repetitive sequence in the genome." Human Genome Meeting. Kyoto, Japan. April 18-21, 2005. (talk/poster - Received HUGO Student Award)
  • "(TG/CA)n repeats in human genome: Insilico analysis of the distribution and functional role of these repeats as cis modulators of transcription." International Conference on Mathematical Biology. Indian Institute of Technology, Kanpur, India. 2004. (talk)
  • "(TG/CA)n repeats in human genome: Selective abundance and role in transcriptional modulation." BIOTECH-2004, Challenges and Opportunities. New Delhi, India. October, 2004. (poster)
  • "(TG/CA)n repeats in human genome." Annual Symposium. Dr. B.R. Ambedkar Center for Biomedical Research, Delhi, India. 2003. (poster - Received Best Poster - First Prize)
  • "Role of (TG/CA)n repeats as cis-modulators of transcription." International FAOBMB Science Congress. Bangalore, India. 2003. (poster)
  • "(TG/CA)n repeats in human housekeeping genes." National Symposium on Emerging Trends in Biomedical Sciences. Bundelkhand University, Jhansi, India. 2002. (talk)
  • "SNPs in human genome." Genome Informatics. Institute of Genomics and Integrative Biology, Delhi, India. 2000. (talk)
  • International Symposium on Structural Biology and Bioinformatics. Indian Institute of Sciences, Bangalore, India. 2001. (participant)