Scientist

Institute of Genomics and Integrative Biology

Research Interest: Functional Genomics

Contact: s.sivasubbu@igib.res.in

                sridhar@igib.in

Education

Ph.D - Manonmaniam Sundaranar University, India (2001)

M.Sc -St. Xavier's College, Palayamkottai, India (1996)

Research

Genome sequencing projects in a variety of organisms have led to the unprecedented accumulation of sequence information. While biological information for many of these genes has been documented, functional annotation of the tens of thousands of protein-encoding, non-coding RNA including micro-RNA genes of unknown in vivo function still remains a major challenge to biology. Zebrafish provides a near ideal vertebrate genetic system to identify and annotate the biological role(s) of these novel genes because of their optical transparency, rapid embryonic development, short generation time and rapidly advancing genomic manipulation tools.  This vertebrate model organism provides novel opportunities for biological studies, such as functional genomics, organogenesis, and drug discovery.

The mission of the laboratory is to exploit the advantages of zebrafish to dissect molecular mechanisms of gene function, regulation and genome organization in vertebrates.

Zebrafish Genome Resources

FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of zebrafish. (in collaboration with Dr. Vinod Scaria, IGIB)

Laboratory Address

IGIB Extension  Center at Naraina,

A93-94 Naraina Inds Area, Phase 1,

Naraina, New Delhi -110 028, India.

Ph- +91-11-25895615, 45073677/88/99

Fax no: +91-11-2766 7471

News and Events

Genes define why we crave nicotine - Nicotine Response Genetics in Zebrafish published in PNAS. For more information see http://www.pnas.org/content/early/2009/10/23/0908247106.abstract

Institute of Genomics and Integrative Biology (IGIB), which is a constituent laboratory of the Council of Scientific and Industrial Research (CSIR) has completed the whole genome sequencing of a Wildtype Strain of Zebrafish (Danio rerio). This work marks India’s entry into the arena of whole genome sequencing of animals. For more information see http://genome.igib.res.in
(in collaboration with Dr. Vinod Scaria, IGIB)
See press coverage of the genome release.

Selected Publications

Petzold AM, Balciunas D, Sivasubbu S, Clark KJ, Bedell VM, Westcot SE, Myers SR, Moulder GL, Thomas MJ, Ekker SC.
Nicotine response genetics in the zebrafish.
Proc Natl Acad Sci U S A. 2009 Oct 26

Kumar N, Patowary A, Sivasubbu S, Petersen M, Maiti S.
Silencing c-MYC expression by targeting quadruplex in P1 promoter using locked nucleic acid trap.
Biochemistry. 2008 Dec 16;47(50):13179-88.

Meli R, Prasad A, Patowary A, Lalwani MK, Maini MK, Sharma M,
Singh AR, Kumar G, Jadhav V, Scaria V*, Sivasubbu S*.
FishMap: A community resource for Zebrafish genomics.
Zebrafish June 1, 2008, 5(2): 125-130
Cover Article

Indian Genome Variation Consortium*
Genetic Landscape of the People of India: a Canvas for Disease Gene Exploration
J Genetics 2008 (*as co-author of the consortia)
Cover Article

Sivasubbu S, Balciunas D, Amsterdam A, Ekker SC.
Insertional mutagenesis strategies in zebrafish.
Genome Biol. 2007;8 Suppl 1:S9. Review.

Pickart MA, Klee EW, Nielsen AL, Sivasubbu S, Mendenhall EM, Bill BR, Chen E, Eckfeldt CE, Knowlton M, Robu ME, Larson JD, Deng Y, Schimmenti LA, Ellis LB, Verfaillie CM, Hammerschmidt M, Farber SA, Ekker SC.
Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome.
PLoS ONE. 2006 Dec 20;1:e104.

Balciunas D, Wangensteen KJ, Wilber A, Bell J, Geurts A, Sivasubbu S, Wang X, Hackett PB, Largaespada DA, McIvor RS, Ekker SC.
Harnessing a high cargo-capacity transposon for genetic applications in vertebrates.
PLoS Genet. 2006 Nov 10;2(11):e169. Epub 2006 Aug 28.

Sivasubbu S, Balciunas D, Davidson AE, Pickart MA, Hermanson SB, Wangensteen KJ, Wolbrink DC, Ekker SC.
Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval development.
Mech Dev. 2006 Jul;123(7):513-29. Epub 2006 Jun 9.

Hermanson S, Davidson AE, Sivasubbu S, Balciunas D, Ekker SC.
Sleeping Beauty transposon for efficient gene delivery.
Methods Cell Biol. 2004;77:349-62.

Pickart MA, Sivasubbu S, Nielsen AL, Shriram S, King RA, Ekker SC.
Functional genomics tools for the analysis of zebrafish pigment. Pigment Cell Res. 2004 Oct;17(5):461-70.

Balciunas D, Davidson AE, Sivasubbu S, Hermanson SB, Welle Z, Ekker SC.
Enhancer trapping in zebrafish using the Sleeping Beauty transposon.
BMC Genomics. 2004 Sep 3;5(1):62.

Davidson AE, Balciunas D, Mohn D, Shaffer J, Hermanson S, Sivasubbu S, Cliff MP, Hackett PB, Ekker SC.
Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon.
Dev Biol. 2003 Nov 15;263(2):191-202.