Department of Biological Sciences
Indian Institute of Science Education and Research Bhopal


Personal Details


  • Name: Dr. Vineet K. Sharma
  • Designation: Associate Professor
  • Department: Biological Sciences
  • E-Mail: vineetks[AT]iiserb.ac.in
  • Phone: +91 755 269 1401, 669 1401


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.
Authors Title of Article Journal Year
Vineet Kumar Sharma
Kundan Kumar
Shubham Jaiswal
Gaurao Dhoke
Ashok Sharma
Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme JOURNAL OF CELLULAR BIOCHEMISTRY 2018
Pullikan Joby
Abhijit Maji
Darshan Dhakan
Tony Grace
Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders Microbial Ecology 2018
Ashok K. Sharma
Gopal Srivastava
ToxiM: A Toxicity Prediction Tool for Small Molecules Developed Using Machine Learning and Chemoinformatics Approaches Frontiers in Pharmacology 2017
Abhijit Maji
Richa Misra
Darshan Dhakan
Vineet K Sharma
Rup Lal
Yogendra Singh
Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers Environmental Microbiology 2017
vineet k sharma
sudheer gupta
ashok sharma
vibhuti shastri
midhun madhu
Prediction of Anti-inflammatory proteins/peptides: an insilico approach. Journal of Translational Medicine 2017
vineet k sharma
shubham jaiswal
rituja saxena
Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizopheric Region of Mangrove Trees in the Andaman Islands, India. Genome Announcements 2017
vineet k sharma
parul mittal
rituja saxena
Draft Genome Sequence of Anoxybacillus mongoliensis Strain MB4, a Sulfur-Utilizing Aerobic Thermophile Isolated from a Hot Spring in Tattapani, Central India. Genome Announcements 2017
Nikhil Chaudhary
Ankit Gupta
vineet k sharma
BioFuelDB: a database and prediction server of enzymes involved in biofuels production. Journal of Biomolecular Structure and Dynamics 2017
vineet k sharma
ashok sharma
nikhil chaudhary
Shubham jaiswal
.A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by human gut microbiota. Scientific Reports 2017
vineet k sharma
sudheer gupta
parul mittal
midhun k madhu
IL17eScan: a tool for the identification of peptides inducing IL-17 response. Frontiers in Immunology 2017
Sudheer Gupta
Midhun K. Madhu
Ashok K. Sharma
Vineet K. Sharma
ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins Journal of Translational Medicine 2016
Ashok K. Sharma
Sanjiv Kumar
Harish K.
Darshan Dhakan
Vineet K. Sharma
Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins BMC Genomics 2016
Ankit Gupta
Sanjiv Kumar
Vishnu P.K. Prasoodanan
Harish K.
Ashok K. Sharma
Vineet K. Sharma
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes Frontiers in Microbiology 2016
Darshan Dhakan
Rituja Saxena
Nikhil Chaudhary
Vineet K. Sharma
Draft Genome Sequence of Tepidimonas taiwanensis Strain MB2, a Chemolithotrophic Thermophile Isolated from a Hot Spring in Central India American Society of Microbiology All-Inclusive Package 2016
Rituja Saxena
Vineet K. Sharma
A Metagenomic Insight Into the Human Microbiome: Its Implications in Health and Disease Medical and Health Genomics 2016
Vineet K Sharma
Prediction of Biofilm Inhibiting Peptides: An In Silico Approach. Frontiers in Microbiology 2016
vineet k sharma
Sudheer Gupta
Ashok Sharma
Shubham jaiswal
Prediction of Biofilm Inhibiting Peptides: An In Silico Approach. Frontiers in Microbiology 2016
vineet k sharma
rituja saxena
darshan dhakan
parul mittal
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Frontiers in Microbiology 2016
Rituja Saxena
Nikhil Chaudhary
Darshan Dhakan
Vineet K. Sharma
Draft Genome Sequence of Gulbenkiania mobilis Strain MB1, a Sulfur-Metabolizing Thermophile Isolated from a Hot Spring in Central India Genome Announcements 2015
Ashok K. Sharma
Ankit Gupta
Sanjiv Kumar
Darshan Dhakan
Vineet K. Sharma
Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences Genomics 2015
Ankit Gupta
Vineet K. Sharma
Using the taxon-specific genes for the taxonomic classification of bacterial genomes BMC Genomics 2015
Nikhil Chaudhary
Ashok K. Sharma
Piyush Agarwal
Ankit Gupta
Vineet K. Sharma
16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets PLoS One 2015
Ankit Gupta
Rohan Kapil
Darshan Dhakan
Vineet K. Sharma
MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data PLoS One 2014
Vineet K. Sharma
Members of International Glossina Genome Initiative
Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis Science 2014
Santosh Ranjan Mohanty
Bharati Kollah
Vineet Kumar Sharma
Amar Bahadur Singh
Muneshwar Singh
A. Subba Rao
Methane oxidation and methane driven redox process during sequential reduction of a flooded soil ecosystem Annals of Microbiology 2013
Sunita Grover
Vineet K. Sharma
Rashmi H. Mallapa
Virender Batish
Draft Genome Sequence of Lactobacillus plantarum Strain Lp91, a Promising Indian Probiotic Isolate of Human Gut Origin Genome Announcements 2013
Sunita Grover
Vineet K. Sharma
Rashmi H. Mallapa
Virender K. Batish
Draft Genome Sequence of Lactobacillus fermentum Lf1, an Indian Isolate of Human Gut Origin Genome Announcements 2013
Vineet K. Sharma
Naveen Kumar
Tulika Prakash
Todd D. Taylor
Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin PLoS One 2012
Hidehiro Toh
Vineet K. Sharma
Kenshiro Oshima
Shinji Kondo
Masahira Hattori
F. Bruce Ward
Andrew Free
Todd D. Taylor
Complete Genome Sequences of Arcobacter butzleri ED-1 and Arcobacter sp. Strain L, Both Isolated from a Microbial Fuel Cell Journal of Bacteriology 2011
Tulika Prakash
Kenshiro Oshima
Hidetoshi Morita
Shinji Fukuda
Akemi Imaoka
Naveen Kumar
Vineet K. Sharma
Seok-Won Kim
Mahoko Takahashi
Naruya Saitou
Todd D. Taylor
Hiroshi Ohno
Yoshinori Umesaki
Masahira Hattori
Complete Genome Sequences of Rat and Mouse Segmented Filamentous Bacteria, a Potent Inducer of Th17 Cell Differentiation Cell Host and Microbe 2011

Masters Student


  • 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

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.

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

Masters Student


  • Gopal Srivastava