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Personal Details

Designation : Associate Professor Department : Biological Sciences E-Mail : vineetks@iiserb.ac.in Phone : +91 755 269 1401, 669 1401 Fax : +91 755 669 2392



Awards and Fellowships


  • Awarded with Letter of appreciation by Dr. R. Noyori (Nobel Laureate), President, RIKEN, Japan during Annual Awarding Ceremony, 2008 for astonishing scientific achievement at RIKEN.
  • Awarded for Outstanding Performance at Novartis International Biotechnology Leadership Camp 2007, Tokyo, Japan.
  • Awarded HGM Student Award at the Human Genome Meeting, Kyoto, Japan, 2005.
  • Awarded Senior Research Fellowship from Council of Scientific and Industrial Research (CSIR), India (April 2003 to March 2006).
  • Selected for Lecturer-ship through the nationwide exam NET (National Eligibility Test) conducted by CSIR and UGC (University Grant Commission), 2000.
  • Received Catch them Young Scholarship during M.Sc on the basis of Merit under the CSIR-UGC fellowship model.

Academic Details


  • Ph.D. in Bioinformatics 2000-2005, from the Institute of Genomics and Integrative Biology (IGIB), CSIR and registered at Ambedkar Center for Biomedical Research, University of Delhi, India.
  • M.Sc. in Biomedical Sciences 1998-2000, Ist division, Among top ten students, Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
  • Masters in Intellectual Property Law (MIPL) 2011- pursuing, School of Law, Delhi and Queensland University, Australia
  • Management 1996-1998, Higher Diploma in Sales and Marketing Management (18 months) from National Institute of Sales, Delhi, India.
  • B.Sc (Honours) in Microbiology 1995-1998, Ist division, Among top ten students, University of Delhi, Delhi, India.

BS-MS Teaching and Laboratory


  • Genome Sequencing and Metagenomics, PhD Course, 2012
  • BS-MS First Year Laboratory, 2012

    Research


    • MetaBioSys lab at IISER Bhopal, primarily focus on Metagenomics, Bioinformatics and Systems Biology. Metagenomics has emerged as a culture independent approach to directly extract and sequence the microbes from their environment which cannot be cultured by conventional methods. We are carrying out interesting and challenging metagenomics projects at our lab.

    Current Research Interests


    • Metagenomic analysis of various environments such as human gut, soil, sediment etc.
    • Complete genome sequencing and analysis of novel bacteria.
    • Development of computational tools for metagenomic and genomic data analysis.
    • Metabiolic pathway reconstruction in newly sequenced genomes.
    • Human genome analysis.

    Past projects carried out at RIKEN, Japan and IGIB, Delhi


    • Genomics Analysis of Novel Organisms Prokaryotes (Termite Gut Bacteria): Genome Sequencing, Analysis and annotation of two bacterial genomes from Termite gut with the aim to identify novel enzymes significant for its survival or for bio-fuel production.

    Metagenomic analysis of human gut microbiome


    • Using fecal samples from 13 healthy individuals of various ages, including unweaned infants, to identify the genomic features common to all human gut microbiomes as well as those variable among them.

    Software/Web Server/Knowledge-base development


    • MetaBioME (Comprehensive Metagenomic BioMining Engine): Identify novel commercially useful enzymes (biocatalysts) employed in Industry, Medicine, Agriculture, Biotechnology, Environment, etc., from metagenomic datasets. MetaBin: Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin. EXPOLDB (Expression Linked Polymorphism Database): A useful resource to link gene expression data from human Gene Chip experiments with the distribution of (TG/CA)n and other repeats within genes. ArrayD: Software for designing cDNA microarrays.

    Human Genome Analysis


    • Genome wide analysis of repetitive sequences in human and other primate genomes. Identification and analysis of novel conjoined genes in human and other genomes. Assessing natural variation in humans by comparing with monozygotic twins using microarrays.

    Publications in International Journals


    • ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins. Gupta S, Madhu MK,Sharma AK, Sharma VK, 2016.   Journal of Translational Medicine  14(1):178. doi: 10.1186/s12967-016-0928-3.

    • Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Saxena R, Dhakan D, Mittal P, Waiker P, Chowdhury A, Ghatak A and Sharma VK. 2016.   Frontiers in Microbiology. (accepted)  

    • Prediction of Biofilm Inhibiting Peptides: An In Silico Approach. Gupta S, Sharma AK, Jaiswal SK, Sharma VK, 2016.   Frontiers in Microbiology  Jun 16;7:949. doi: 10.3389/fmicb.2016.00949

    • Metagenomic Insight into Human Microflora: Implications in Health and Disease. Saxena R, Sharma VK, 2016.   Medical and Health Genomics  Chapter 9, Page 107-117

    • Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins. Sharma AK, Kumar S, Kumar H, Dhakan DB, Sharma VK, 2016. 17(1):411. doi: 10.1186/s12864-016-2753-8.   BMC Genomics  .

    • Reconstruction of bacterial and viral genomes from multiple metagenomes. Gupta A, Kumar S, Prasoodanan PK, Harish K, and Sharma VK. 2016. 7:469. doi: 10.3389/fmicb.2016.00469.   Frontiers in Microbiology.  

    • Prediction of Anti-inflammatory proteins/peptides: an insilico approach. Gupta S, Sharma AK, Shastri V, Madhu MK,Sharma VK, 2016.   Journal of Translational Medicine  (Accepted)

    • Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences. Sharma AK, Gupta A, Kumar S, Dhakan DK, Sharma VK. 2015  Genomics . pii: S0888-7543(15)00054-3

    • 16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets. Chaudhary N*, Sharma AK*, Agarwal P, Gupta A, Sharma VK.2015  PLoS ONE . 10(2):e0116106.

    • Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from Rhizopheric region of Mangrove trees in Andaman Islands, India. Jaiswal SK, Saxena S, Mittal P, Gupta A, Sharma AK, Sharma VK, 2016.   Genome Announcements (Accepted)  

    • Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. International Glossina Genome Initiative 2014. Science Vol. 344 no. 6182 pp. 380-386.

    • MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data. Gupta A, Kapil R, Dhakan DK, Sharma VK. 2014. PLoS ONE . 9(4):e93907

    • Draft genome sequence of Lactobacillus plantarum Lp91, a promising Indian probiotic isolate of human gut origin. Grover S*, Sharma VK*, Mallappa R, Batish V. (*: equal authors and contributors) 2013.Genome Announcements. Volume 1 Issue 6 e00976-13.

    • Draft Genome Sequence of Tepidimonas taiwanensis Strain MB2, a Chemolithotrophic Thermophile Isolated from a Hot Spring in Central India. Dhakan D.B., Saxena, R., Chaudhary N., Sharma V.K. 2015. Genome Announc. . Accepted

    • Draft Genome Sequence of Gulbenkiania mobilis Strain MB1, a Sulfur Metabolising Thermophile Isolated from a Hot Spring in Central India. Saxena, R., Chaudhary N., Dhakan D.B., Sharma V.K. 2015. Genome Announc. . 2015 3(6): e01295-15

    • Using the taxon-specific genes for the taxonomic classification of bacterial genomes. Gupta A and Sharma VK. 2015. BMC Genomics . 16(1), 396.

    • Draft genome sequence of Lactobacillus fermentum Lf1, an Indian isolate of human gut origin. Grover S*, Sharma VK*, Mallappa R, Batish V. (*: equal authors and contributors) 2013. Genome Announcements. Volume 1 Issue 6 e00883-13.

    • MetaBin: Taxonomic binning of metagenomic sequences. Sharma VK, Taylor TD. 2013. Encyclopedia of Metagenomics, Springer Publications. Invited Review.

    • MetaBioME:Comprehensive metagenomic biomining engine. Sharma VK, Taylor TD. 2013.Encyclopedia of Metagenomics, Springer Publications. Invited Review.

    • Methane oxidation and methane driven redox process during sequential reduction of a flooded soil ecosystem. Mohanty SR, Kollah B, Sharma VK, Singh AB, Singh M, Rao AS. 2013. Annals of Microbiology. 10.1007/s13213-013-0633-x.

    • Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin. Sharma VK, Kumar N, Prakash T, Taylor TD. 2012. PLoS ONE. 7(4): e34030.

    • Complete Genome Sequences of Arcobacter butzleri ED-1 and Arcobacter sp.-L, Isolated from a Microbial Fuel Cell. Toh H, Sharma VK, Oshima K, Kondo S, Hattori M, Ward F, Free A, Taylor TD. 2011.Journal of Bacteriology Nov;193(22):6411-2.

    • 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, Kim SW, Takahashi M, Saitou N, Taylor TD, Ohno H, Umesaki Y, Hattori M. 2011. Cell Host Microbe (Cover page) 10(3):273-84.

    • MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. Sharma VK, Kumar N, Prakash T, Taylor TD, 2010. Nucleic Acids Research doi: 10.1093/nar/gkp1001.

    • Expression of Conjoined Genes: Another Mechanism for Genetic Regulation in Eukaryotes. Prakash T, Sharma VK, Adati N, Ozawa R, Kumar N, Nishida Y, Fujikake T, Mushiake M, Okumura R, Takeda T, Taylor TD. 2010. PLoS ONE 5(10):1-9 e13284. doi:10.1371/journal.pone.0013284.

    • Complete genome of the N2-fixing intracellular symbionts of a termite gut flagellate. Hongoh Y*, Sharma VK*, Prakash T, Noda S, Jun-Ichi, Inoue, Kudo T, Taylor TD, Sakaki Y, Toyoda A, Hattori M, Ohkuma M (*: equal authors and contributors), 2008. Science 322(5904):1108-1109.

      (Revealed the genome of an unculturable endosymbiotic bacteria coupling N2 fixation to cellulolysis within protist cells in termite gut; Widely covered by media, press and news : GenomeWeb (New York), New York Times, Japanese press (Nikkei-BTJ, RIKEN official press release, Yomiuri online).

    • 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 Y, Toyoda A, Hattori M, Ohkuma M. (*: equal authors and contributors), 2008, Proc Natl Acad Sci USA 105(14): 5555-60.

      (First genomic sequence of an unculturable bacterial endosymbiont from termite gut; applications in biofuel and biotechnology)

    • 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, 2007,Physiological Genomics 31: 96-103.

    • 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., 2007, DNA Res. 14(4):169-181.

    • 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, 2006, BMC Genomics 7:258-265.

    • (TG/CA)n repeats in human gene families: abundance and selective patterns of distribution. Sharma VK, Brahmachari SK, Ramachandran S, 2005, BMC Genomics 6(1):83-94.

    • 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, 2005,Physiol Genomics 21(1):117-123.

      (First report of variations in gene expression in human monozygotic twins: Faculty of 1000: evaluations for Sharma et al. Physiological Genomics Mar 21 21(1):117-23.)

    • ArrayD: A general purpose software for Microarray design. Sharma A, Srivastava GP, Sharma VK, Ramachandran S, 2004, BMC Bioinformatics 5:142-147.

    • (TG/CA)n repeats in human housekeeping genes. Sharma VK, B-Rao C, Sharma A, Brahmachari SK, Ramachandran S, 2003, J Bio Mol Str Dyn 21(2):303-310.

    Book Chapters


    • MetaBioME:Comprehensive metagenomic biomining engine. Sharma VK, Taylor TD. 2013.Encyclopedia of Metagenomics, Springer Publications. Invited Review.

    • MetaBin: Taxonomic binning of metagenomic sequences. Sharma VK, Taylor TD. 2013. Encyclopedia of Metagenomics, Springer Publications. Invited Review.

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

    CopyRights


    • Collective algorithms for repeat analysis, 2002, IGIB
    • EXPOLDB: Expression Linked Polymorphism Database, 2002, IGIB
    • ArrayD: A general purpose software for Microarray design, 2004, IGIB
    • MetaBioME: Comprehensive metagenomic biomining engine, 2008, RIKEN
    • SuperGene: Software for finding genes in metagenomic sequences, 2008, RIKEN
    • iMetaSys: Integrated Metagenomic Analysis Pipeline, 2008, RIKEN
    • ConjoinG: Database of Conjoined Genes, 2009, RIKEN
    • MetaBin: Software for phylogenetic binning of metagenomic sequences, 2010, RIKEN

    Selected Presentations


    • SNPs in human genome. Genome Informatics. Institute of Genomics and Integrative Biology, Delhi, India. 2000. (Talk)
    • (TG/CA)n repeats in human housekeeping genes. National Symposium on Emerging Trends in Biomedical Sciences. Bundelkhand University, Jhansi, India. 2002. (Talk)
    • Probing the functional role of (TG/CA)n repeats as cis-modulators of transcription. Annual Symposium. Dr. B.R. Ambedkar Center for Biomedical Research, Delhi, India. 2003. (Poster - Received Best Poster - First Prize)
    • (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)
    • Analysis and understanding of repetitive sequence in the genome. Human Genome Meeting. Kyoto, Japan. April 18-21, 2005. (Talk/Poster - Received HUGO Student Award)
    • Sixth Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics. Wellcome Trust Conference Centre, Hinxton, UK. September, 2006. (participant)
    • Tardigrades: Model organisms to study cryptobiosis. The Biology of Genomes. Cold Spring Harbor Laboratory, NY, USA. May 8-12, 2007. (Poster)
    • Novartis International Biotechnology Leadership Camp 2007. Novartis BIOCAMP 2007. Academy Hills, Roppongi, Tokyo, Japan. 6-8 October, 2007. (Participant- Received award for "Outstanding Performance")
    • 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. Nov 12-17, 2007. (Participant/Annotator)
    • Metagenomics to MetaBiotechnology: Potentials and limitations. The Sixth Asia-Pacific Bioinformatics Conference, APBC2008. Kyoto. 14-17 Jan, 2008. (Poster) Complete genome of an uncultured bacterial symbiont in the termite gut. The 7th International Workshop on Advanced Genomics. Tokyo. 27-28 Nov, 2007. (Participation/Poster
    • Bridging the gap between computational sciences and cellular/developmental biology, From Molecules to Cellular Scales. Centre for Developmental Biology, RIKEN, Kobe, May 24th, 2008. (Talk)
    • MetaBioME: A powerful magnet for finding biocatalyst needles in metagenomic haystacks. International Society for Microbial Ecology (ISME), 12th Symposia, Cairns, Australia, Aug, 2008. (Talk)
    • iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench, International Advanced Genomics Workshop, 2009, Tokyo, Japan. (Poster)
    • iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench, FEMS2009, June 28th - July 2nd, 2009, Sweden. (Poster)
    • Meeting the Computational Challenges of Metagenomics, Joint Computational Science Workshop 2009, July 9-10, 2009. RIKEN, Japan. (Talk)
    • iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench, 1st MetaHIT International Conference on Human Metagenomics, 1-3 March 2010, Shenzhen, China. (Talk)
    • Comparative analysis of (TG/CA)n repeats in the human and chimpanzee genomes, HGM 2010, Montpellier, 18th-22nd May, 2010, France. (Poster)
    • Systemic Understanding of our Microbial Planet: A Valiant Metagenomic Initiative, The 2010 GSC Tanabata Meeting, July 15th, 2010, Japan.
    • iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench, 13th International Symposium on Microbial Ecology ISME13, Aug 22-27, 2010, Seattle, USA. (Poster)
    • 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)

    Resources at MetaBioSys (Metagenomics, Bioinformatics and Systems Biology) Laboratory


    Metagenomics Laboratory


    • Well equipped laboratory with facilities for DNA isolation from environmental samples, sample preparation for sequencing, culturing of microbes and functional characterization.
    • Genetic Analyzer is available as institute's genomic facility for traditional DNA sequencing. Next-generation sequencer will be procured soon.

    Computational Laboratory


    • High-end Linux workstations are available for students
    • A 100 core cluster comprising of high-end workstations will support the computational analysis
    • A 2100 core IBM High Performance Computing cluster is under installation as common Institute's facility which will provide support for the computational work at our lab.

    People at MetaBioSys Lab @ IISER Bhopal


    • Dr. Abhijit Maji, Postdoctoral Fellow
    • Dr. Sudheer Gupta, Postdoctoral Fellow (now at AIIMS Bhopal)
    • Dr. Sanjiv Kumar, Postdoctoral Fellow (now at University of Connecticut Health Center, Connecticut, USA)

    Graduate Students


    • Darshan Kumar Dhakan, PhD Student
    • Ankit Gupta, PhD Student
    • Rituja Saxena, PhD Student
    • Ashok K. Sharma, PhD Student
    • Parul Mittal, PhD Student
    • Shubham Jaiswal, PhD Student

    Master's Students


    • Gopal Srivastava
    • Ankita Roy
    • Vibhuti Shastri
    • Dipesh Chowthe

    Past Project Students


    • Enosh Philips, MTech Thesis (6 months) Student, Thesis Title: Text Mining of NCBI PubMed Database Using a Bioinformatics Approach.
    • Ankit Gupta, BSMS student, IISER Bhopal
    • Vishnu Prasoodanan, BSMS student IISER Bhopal
    • Pratik Labhane, BSMS student, IISER Bhopal
    • Midhun Mohan, BSMS student, IISER Bhopal

    Software and Databases


    MetaBin: A software for Fast and accurate taxonomic assignments of metagenomic sequences using MetaB


    • Taxonomic assignment of sequence reads is a challenging task in metagenomic data analysis. We developed the MetaBin program and web server for better homology-based taxonomic assignments using an ORF-based approach. By implementing Blat as the faster alignment method in place of Blastx, the analysis time has been reduced by several fold. It is benchmarked using both simulated and real metagenomic datasets, and can be used for both single and paired-end sequence reads of varying lengths (>45 bp). To our knowledge, MetaBin is the only available program that can be used for the taxonomic binning of short reads (<100 bp) with high accuracy and high sensitivity using a homology-based approach. It provides several options including taxonomic analysis, construction of taxonomic trees, creation of a composition chart, functional analysis using COGs, and comparative analysis of multiple metagenomic datasets. MetaBin web server and a standalone version are available freely at http://metabin.riken.jp/.

    MetaBioME: a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs)


    • Microbial enzymes have tremendous applications as biocatalysts in several industries, biotechnology, agriculture and pharmaceutical products. However, only a few enzymes are currently employed in such applications due to limited genomic information of known microbes. The yet unculturable majority (98%) of microbes conceal enormous treasure of unknown biological functions and mechanisms locked in their unidentified genes, proteins and biochemical pathways. The upcoming metagenomic data from several projects could be of enormous use in life sciences, medicine, industry, biotechnology and human health. At RIKEN, we carried out the comprehensive mining of the 10 diverse publicly available metagenomic datasets to discover novel genes and proteins similar to the known biocatalysts. Using our strategy and the main results of our analysis we have developed a comprehensive Metagenomic BioMining Engine (MetaBioME: http://metasystems.riken.jp/metabiome/) platform which provides a unique opportunity to identify new proteins and enzymes in the metagenomic datasets.