Personal Details
- Name: Prof. Vineet K. Sharma
- Designation: Professor
- Department: Biological Sciences
- E-Mail: vineetks[AT]iiserb.ac.in
- Phone: +91 755 269 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 |
|---|---|---|---|
| Aditya Malwe Gopal Srivastava Vineet K Sharma |
GutBug: A tool for prediction of human gut bacteria mediated biotransformation of biotic and xenobiotic molecules using machine learning | Journal of Molecular Biology | 2023 |
| Vineet K Sharma Abhisek Chakraborty Manohar Bisht Shruti Mahajan Joby Pullikan |
Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds | Genes and Genomics | 2023 |
| Shruti Mahajan Abhisek Chakraborty Manohar Bisht Vineet K Sharma |
Genome of Phyllanthus emblica: the medicinal plant Amla with super antioxidant properties | Frontiers in Plant Science | 2023 |
| Deepthi Arvind Vineet K Sharma Tony Grace |
Exploring variation in the fecal microbial communities of Kasaragod Dwarf and Holstein crossbred cattle. | Antonie Van Leeuwenhoek | 2022 |
| Vineet K Sharma Vishnu Prasoodanan PK Rituja Saxena Sonia V Gupta Sudheer Gupta Prashant waikar Atul Samaiya Ashok K Sharma |
Assessing the effect of smokeless tobacco-consumption on oral microbiome in healthy and oral cancer patients | Frontiers in Cellular and Infection Microbiology | 2022 |
| Ankit Gupta Aditya Malwe Gopal Srivastava Parikshit Thodum Keshav Hibare Vineet K. Sharma |
MP4: A machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets | BMC Bioinformatics | 2022 |
| Abhisek Chakraborty Shruti Mahajan Manohar Singh Bisht Vineet K Sharma |
Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity | iScience | 2022 |
| Abhisek Chakraborty Manohar Bisht Shruti Mahajan Rituja Saxena Joby Pulikkan Vineet K Sharma |
Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds | bioRxiv | 2022 |
| Vishnu Prasoodanan Ashok Sharma Shruti Mahajan Darshan Dhakan Abhijit Maji Joy Scaria Vineet K Sharma |
Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis | Nature Biofilms and Microbiomes | 2021 |
| Vishnu Prasoodanan Shruti Menon Rituja Saxena Prashant waiker Vineet k sharma |
Draft genome assembly data of Anoxybacillus sp. strain MB8 isolated from Tattapani hot springs, India | bioRxiv | 2021 |
| Abhisek Chakraborty Shruti Mahajan Shubham Jaiswal Vineet K Sharma |
Genome sequencing of turmeric provides evolutionary insights into its medicinal properties | Nature Communications Biology | 2021 |
| Shruti Mahajan Abhisek Chakraborty Vineet K Sharma |
Genome sequencing and assembly of Tinospora cordifolia (Giloy) plant | bioRxiv | 2021 |
| Shubham Jaiswal Ankit Gupta Aaron Shafer Vishnu Prasoodanan Nagarjun Vijay Vineet K Sharma |
Genomic Insights Into the Molecular Basis of Sexual Selection in Birds | Frontiers in Ecology and Evolution | 2021 |
| Shubham Jaiswal Ankit Gupta Aaron Shafer Vishnu Prasoodanan Nagarjun Vijay Vineet K. Sharma |
Genomic insights into the molecular basis of sexual selection in birds | Frontiers in Ecology and Evolution | 2021 |
| Shubham Jaiswal Shruti Mahajan Abhisek Chakraborty Sudhir Kumar Vineet K. Sharma |
The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms | iScience | 2021 |
| Rituja Saxena Parul Mittal Cecile Clavaud Darshan Dhakan Nita Roy Lionel Breton Namita Misra Vineet K Sharma |
Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals | Scientific Reports | 2021 |
| Vineet K Sharma Gopal Srivastava Aditya Malve |
Molib: A machine learning based classification tool for the prediction of biofilm inhibitory molecules | Genomics | 2020 |
| Parul Mittal Rituja Saxena Atul Gupta Shruti Mahajan Vineet K Sharma |
The gene catalogue and comparative analysis of gut microbiome of big cats provide new insights on Panthera species | Frontiers in Microbiology | 2020 |
| Shubham K. Jaiswal Abhisek Chakraborty Shruti Mahajan Sudhir Kumar Vineet K. Sharma |
The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms | bioRxiv | 2020 |
| Abhisek Chakraborty Shruti Mahajan Shubham K. Jaiswal Vineet K. Sharma |
Genome sequencing of turmeric provides evolutionary insights into its medicinal properties | bioRxiv | 2020 |
| Shubham K. Jaiswal Shitij Agarwal Parikshit Thakur Vineet K. Sharma |
SkinBug: An artificial intelligence approach to predict human skin microbiome-mediated metabolsim of biotics and xenobiotics. | iScience | 2020 |
| Vineet Kumar Sharma Ankit Gupta Darshan Dhakan Abhijit Maji Rituja Saxena Joby Pulikkan Vishnu Prasoodanan Jacob Kurian Andres Gomez Joy Scaria Kathrine Amato Ashok Sharma |
Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India | mSystems | 2019 |
| Parul Mittal Vishnu Prasoodanan PK Darshan B Dhakkan Sanjiv Kumar Vineet K Sharma |
Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes | Environmental Microbiome | 2019 |
| Ankit Gupta Ahmad Ahmad Dipesh Chowthe Midhun K Madhu Shireesh Srivastava Vineet K Sharma |
Genome-scale metabolic reconstruction and metabolic versatility of an obligate methanotroph Methylococcus capsulatus str. Bath | PeerJ | 2019 |
| Vineet Kumar Sharma Parul Mittal Shubham Jaiswal Rituja Saxena Nagarjun Vijay Vineet Sharma |
Comparative analysis of corrected tiger genome provides clues to its neuronal evolution | Scientific Reports | 2019 |
| Vineet K Sharma Kundan Kumar Gaurao Dhoke Ashok K Sharma Shubham Jaiswal |
Mechanistic elucidation of amphetamine metabolism by tyramine oxidase from human gut microbiota using molecular dynamics simulations | JOURNAL OF CELLULAR BIOCHEMISTRY | 2019 |
| Darshan Dhakan Abhijit Maji Ashok Sharma Rituja Saxena Joy Scaria Andres Gomez Tony Grace Joby Pulikkan Vineet K Sharma |
The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches | GigaScience | 2019 |
| 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 |
| Vineet K. Sharma Shubham Jaiswal Ankit Gupta Rituja Saxena vishnu Prasoodanan Ashok Sharma Parul Mittal Ankita Roy Aaron Shafer Nagarjun Vijay Vineet K. Sharma |
Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird | Frontiers in Genetics | 2018 |
| Rituja Saxena Parul Mittal Cecile Clavaud Darshan Dhakan Prashant Hegde Mahesh M. Subarna Saha Luc Souverain Nita Roy Lionel Breton Namita Misra Vineet K. Sharma |
Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health | Front. Cell. Infect. Microbiol. | 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 |
| Rituja Saxena Parul Mittal Cecile Clavaud Namita Misra Vineet K. Sharma |
The microbial and functional diversity of the microflora present on the scalps of Indian subjects with and without dandruff | Journal of Investigative Dermatalogy | 2017 |
| Rituja Saxena Parul Mittal Namita Misra Cecile clavaud |
The microbial and functional diversity of the microflora present on the scalps of Indian subjects with and without dandruff | Journal of Investigative Dermatology | 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 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