Awards and Achievements

portertoaststicksBiotechnology

Oct 23, 2013 (3 years and 7 months ago)

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Tab
1
: Home

Personal Details

Designation

:
Assistant

Professor

Department

:
Biological

Sciences

E
-
Mail

:
vineetks[at]iiserb.ac.in

Phone

:
+91
-
755
-
4092323
,

Fax

:
+91
-
755
-
4092392


Awards and
Achievements



Awarded with
prestigious
Khorana Fellowship to attend
a two week 'Technology Transfer Course' 2012 at
University of Wisconsin
-

Madison (USA), sponsored by Department of Biotechnology, India, Indo
-
US Science
and Technology Forum (IUSSTF) and University of Wisconsin, Madison.



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, Japa
n
.



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.


Education

Ph.D. in Bioinformatics

2000
-
2005, f
rom 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 Biom
edical 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



Tab 2: Research

MetaBioSys

lab at IISER Bhopal, primarily focus on Metagenomics,
Bioinformatics and
Systems
B
iology. Metagenomics has emerged as a culture independent approach to directly extract and
sequence the microbes from

their environment which cannot be cultured by conventi onal
methods.

We are carrying out interesting and challenging metagenomics projects at our lab.

Current research interests

1. Metagenomic analysis of various environments such as human gut, soil,
sediment etc.

2. Complete genome sequencing and analysis of novel bacteria.

3. Development of computational tools for metagenomic and genomic data analysis.

4.
Metabiolic pathway re
-
construction

in newly sequenced genomes.

5. Human genome analysis.

Past p
rojects

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 micr
obiomes 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, Biot
echnology, 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
G
ene 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.



Tab 3: Publicat
i
ons


Publications

in International Journals

1. Fast and Accurate Taxonomic Assi
gnments of Metagenomic Sequences Using MetaBin. Sharma VK, Kumar N,
Prakash T, Taylor TD. 2012.

PLoS ONE
. 7(4): e34030.

2. 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.

3. Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell
differentiation. Prakash T, Oshima K, Mor
ita 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.

4. MetaBioME: a database to explore commercially useful enzymes in metagenomic dataset
s. Sharma VK, Kumar N,
Prakash T, Taylor TD, 2010.

Nucleic Acids Research

doi: 10.1093/nar/gkp1001.

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

5. Expression of Conjoined Genes: Another Mechanism for Ge
netic 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.

6. Complete genome of the N2
-
fixing intra
cellular 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 geno
me 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).)

7. 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)

8. Abundance of dinucleotide repeats and gene expression are inversely correlated: a ro
le for gene function in
addition to intron length. Sharma VK, Kumar N, Brahmachari SK, Ramachandran S, 2007,
Physiological
Genomics

31: 96
-
103.

9. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. Kurokawa K, Itoh
T, Ku
wahara 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.

10. Expoldb: EXpression linked POLymorphi
sm 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.

11. (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.

12. 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.)

13. ArrayD: A general purpose software for Microarray design. Sharma A, Srivastava GP, Sharma VK, Ramachandran
S, 2004,

BMC Bioinformatics

5:142
-
147.

14. (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

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


CopyRights

-

MetaBin: Software for phylogenetic binning of metagenomic sequences, 2010, RIKEN

-

ConjoinG: Database of Conjoined Genes, 2009,

RIKEN

-

iMetaSys: Integrated Metagenomic Analysis Pipeline, 2008, RIKEN

-

SuperGene: Software for finding genes in metagenomic sequences, 2008, RIKEN

-

MetaBioME: Comprehensive metagenomic biomining engine, 2008, RIKEN

-

ArrayD: A general purpose software

for Microarray design, 2004, IGIB

-

EXPOLDB: Expression Linked Polymorphism Database, 2002, IGIB

-

Collective algorithms for repeat analysis, 2002, IGIB


Selected Presentations

-

MetaBin: a program for fast, accurate and highly sensitive taxonomic assignm
ents 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 c
himpanzee 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. (Ta
lk)

-

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,
200
9, 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), 1
2th Symposia, Cairns, Australia, Aug, 2008. (Talk)

-

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
Adva
nced 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. So
uth 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, Rop
pongi,
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. A
pril 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 Biolog
y. Indian Institute of Technology,
Kanpur, India. 2004. (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 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 a
nd Integrative Biology, Delhi, India. 2000.
(Talk)



Tab4
:
Group

Resources at

MetaBioSys

(
Metagenomics, Bioinformatics and
Systems Biology
)

Lab
oratory

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
Ins
titute's
facility
which will provide support for the computat
i
onal work at our lab.

People at MetaBioSys Lab @ IISER Bhopal

Graduate
Students



Darshan Kumar, PhD Student

Master's Students



Ankit

Gupta



Rohan

Kapil

Past
Project
Students



Enosh Philips, MTech Thesis (6
months) Student
,
Thesis Title: Text Mining of NCBI PubMed Database Using
a Bioinformatics Approach.


Software and Databases

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

Taxonomic assignment of seq
uence 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 Bla
stx, 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, creati
on 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 know
n 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 k
nown
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 prote
ins and enzymes in the metagenomic datasets.