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International Publications and Presentations

Publications

37.A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by human gut microbiota. Sharma AK, Jaiswal S, Chaudhary N, Sharma VK. Scientific Reports 2017. Accepted

36.BioFuelDB: a database and prediction server of enzymes involved in biofuels production. Chaudhary N, Gupta A, Gupta S, Sharma VK PeerJ Journal 2017. Accepted

35. Draft Genome Sequence of Anoxybacillus mongoliensis Strain MB4, a Sulfur-Utilizing Aerobic Thermophile Isolated from a Hot Spring in Tattapani, Central India. Mittal P, Saxena R and Sharma VK. Genome Announc. 2017 Mar 2;5(9). pii: e01709-16. doi: 10.1128/genomeA.01709-16

34. 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. Jaiswal SK, Saxena R, Mittal P, Gupta A, Sharma VK. Genome Announc. 2017 Feb; 5(5): e01527-16.

33.Prediction of Anti-inflammatory proteins/peptides: an insilico approach. Gupta S, Sharma AK, Shastr V, Madhu MK, Sharma VK. J Transl Med. 2017; 15: 7.

32. Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Saxena R, Dhakan DB, Mittal P, Waiker P, Chowdhury A, Ghatak A and Sharma VK. Frontiers in Microbiology 2016; 7: 2123

31. Prediction of Biofilm Inhibiting Peptides: An In Silico Approach. Gupta S, Sharma AK, Jaiswal SK, Sharma VK. Frontiers in Microbiology. 2016. doi: 10.3389/fmicb.2016.00949. Read

30. ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins. Gupta S, Madhu MK, Sharma AK, Sharma VK. Journal of Translational Medicine. 2016. doi: Read

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

28. A Metagenomic Insight into Human Microbiome: Its Implications in Health and Disease. Saxena R, Sharma VK. 2016. Accepted

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

26. Draft Genome Sequence of Tepidimonas taiwanensis Strain MB2, a Chemolithotrophic Thermophile Isolated from a Hot Spring in Central India. Dhakan DB, Saxena, R, Chaudhary N, Sharma VK. Genome Announcements. 2016; 4(1):e01723-15. doi:10.1128/genomeA.01723-15. Read

25. 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 DB, Sharma VK. Genome Announcements. 2015; 3(6):e01295-15. doi: 10.1128/genomeA.01295-15. Read

24. Using the taxon-specific genes for the taxonomic classification of bacterial genomes. Gupta A & Sharma VK. BMC Genomics. 2015; 16(1):396. doi: 10.1186/s12864-015-1542-0. Read

23. Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences. Sharma AK*, Gupta A*, Kumar S, Dhakan DB, Sharma VK. (*: equal authors and contributors). Genomics. 2015; 106(1):1-6. doi:10.1016/j.ygeno.2015.04.001. Read

22. 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. (*: equal authors and contributors). PLoS ONE. 2015; 10(2):e0116106. doi:10.1371/journal.pone.0116106. Read

21. Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. International Glossina Genome Initiative. Science. 2014; 344(6182):380-6. doi: 10.1126/science.1249656. Read

20. MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data. Gupta A, Kapil R, Dhakan DK, Sharma VK. PLoS ONE. 2014; 9(4):e93907. doi: 10.1371/journal.pone.0093907. Read

19. 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). Genome Announcements. 2013; 1(6):e00976-13. doi: 10.1128/genomeA.00976-13. Read

18. 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). Genome Announcements. 2013; 1(6):e00883-13. doi: 10.1128/genomeA.00883-1. Read

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

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

15. 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. Annals of Microbiology. 2014; 64(1):65-74. doi: 10.1007/s13213-013-0633-x. Read

14. Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin. Sharma VK, Kumar N, Prakash T, Taylor TD. PLoS ONE. 2012; 7(4): e34030. doi: 10.1371/journal.pone.0034030. Read

13. 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. Journal of Bacteriology. 2011; 193(22):6411-2. doi: 10.1128/JB.06084-11. Read

12. 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. Cell Host Microbe (Cover page). 2011; 10(3):273-84. doi: 10.1016/j.chom.2011.08.007. Read

11. MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. Sharma VK, Kumar N, Prakash T, Taylor TD, Nucleic Acids Research. 2010; 38. doi: 10.1093/nar/gkp1001. Read

(First resource of commercially useful enzymes (CUEs) and discover them in metagenomic datasets.)

10. 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. PLoS ONE. 2010; 5(10):1-9. doi:10.1371/journal.pone.0013284. Read

9. Genome of an Endosymbiont Coupling N2 Fixation to Cellulolysis Within Protist Cells in Termite Gut. 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). Science. 2008; 322(5904):1108-1109. doi: 10.1126/science.1165578. Read

(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).)

8. 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). Proc Natl Acad Sci USA. 2008; 105(14): 5555-60. doi: 10.1073/pnas.0801389105. Read

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

7. 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. 2007; 31:96-103. doi: 10.1152/physiolgenomics.00183.2006. Read

6. 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 Res. 2007; 14(4):169-181. doi: 10.1093/dnares/dsm018. Read

5. 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. 2006; 7:258-265. doi: 10.1186/1471-2164-7-258. Read

4. (TG/CA)n repeats in human gene families: abundance and selective patterns of distribution. Sharma VK, Brahmachari SK, Ramachandran S. BMC Genomics. 2005; 6(1):83-94. doi: 10.1186/1471-2164-6-83. Read

3. 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. 2005; 21(1):117-123. doi: 10.1152/physiolgenomics.00228.2003. Read

(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.)

2. ArrayD: A general purpose software for Microarray design. Sharma A, Srivastava GP, Sharma VK, Ramachandran S. BMC Bioinformatics. 2004; 5:142-147. doi: 10.1186/1471-2105-5-142. Read

1. (TG/CA)n repeats in human housekeeping genes. Sharma VK, B-Rao C, Sharma A, Brahmachari SK, Ramachandran S. J Bio Mol Str Dyn. 2003; 21(2):303-310. doi: 10.1080/07391102.2003.10506926. Read

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. Mathematical Biology. Sharma VK, Sharma A, Brahmachari SK, Ramachandran S (2005). Editor, Pub: Anamaya Publishers, India.

Presentations

- 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, 13th International Symposium on Microbial Ecology ISME13, Aug 22-27, 2010, Seattle, USA. (Poster)

- Systemic Understanding of our Microbial Planet: A Valiant Metagenomic Initiative, The 2010 GSC Tanabata Meeting, July 15th, 2010, Japan.

- Comparative analysis of (TG/CA)n repeats in the human and chimpanzee genomes, HGM 2010, Montpellier, 18th-22nd May, 2010, France. (Poster)

- iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench, 1st MetaHIT International Conference on Human Metagenomics, 1-3 March 2010, Shenzhen, China. (Talk)

- 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, FEMS2009, June 28th - July 2nd, 2009, Sweden. (Poster)

- iMetaSys: An Integrated Metagenomic and Microbial Systems Analysis Workbench, International Advanced Genomics Workshop, 2009, Tokyo, Japan. (Poster)

- MetaBioME: Comprehensive Metagenomic BioMining Engine to Search Novel Biocatalysts in Metagenomic Datasets, HGM2008, HUGO's 13th Human Genome Meeting, Sep 27-30th, 2008, Hyderabad, India. (Poster)

- MetaBioME: A powerful magnet for finding biocatalyst needles in metagenomic haystacks. International Society for Microbial Ecology (ISME), 12th Symposia, Cairns, Australia, Aug, 2008. (Talk)

- Development of Computational Tools for Metagenomic Data Analysis, Joint Workshop on Computational Science, July7-8th, 2008, Tokyo, Japan. (Poster)

- International Symposium on Current topics in metagenomics and new sequence technologies, University of Tokyo, Tokyo, May 28th, 2008. (Participant)

- 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)

- 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 - Best Poster- Runner's up prize to the presenting author)

- 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)

- Novartis International Biotechnology Leadership Camp 2007. Novartis BIOCAMP 2007. Academy Hills, Roppongi, Tokyo, Japan. 6-8 October, 2007. (Participant- Received award for "Outstanding Performance")

- Tardigrades: Model organisms to study cryptobiosis. The Biology of Genomes. Cold Spring Harbor Laboratory, NY, USA. May 8-12, 2007. (Poster)

- Sixth Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics. Wellcome Trust Conference Centre, Hinxton, UK. September, 2006. (participant)

- 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. Delhi, India. October, 2004. (Poster)

- 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)

- 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)