In-Vivo Protein Trap Expression in Zebrafish
Whole Genome Sequencing Initiatives

Zebrafish Wild-type Strain Genome
First Indian Human Genome
First Sri Lankan Human Genome
First Malaysian Personal Human Genome 
Mycobacterium tuberculosis Genomes
(in collaboration with Dr. Vinod Scaria, CSIR-IGIB)

Zebrafish Genome Biology @ CSIR-IGIB

For Potential Interns and Summer Students
I have only limited opportunities for Interns/Summer students, usually 2 at a time. I would prefer someone who can spend 6 months or more. Please note that all prospective Interns and Summer Students need to write a short proposal (a paragraph would do) on an innovative idea they think could be performed during their internship. Interested candidates may please send the short proposal through email with the tag "Internship proposal" in the subject line.
Selected Publications
[Complete list is available here]

Zebrafish Genetics and Genomics:

Patowary A, Purkanti R, Singh M, Chauhan R,Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher J, Clark KJ, Stemple DL, Klee EW, Ekker SC*, Scaria V*, Sivasubbu S*
A sequence-based variation map of zebrafish.
Zebrafish. 2013 Mar;10(1):15-20 [Highlighted on the cover of the journal]
For more information see http://zebrafish.igib.in/aswt-genome

Clark KJ, Balciunas D, Pogoda HM, Ding Y, Westcot SE, Bedell VM, Greenwood TM, Urban MD, Skuster KJ, Petzold AM, Ni J, Nielsen AL, Patowary A, Scaria V, Sivasubbu S, Xu X, Hammerschmidt M, Ekker SC.
In vivo protein trapping produces a functional expression codex of the vertebrate proteome.
Nat Methods. 2011 Jun;8(6):506-15.

Lalwani MK, Sharma M, Singh AR, Chauhan RK, Patowary A, Singh N, Scaria V*, Sivasubbu S*.
Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity.
PLoS One. 2012;7(12):e52588.

Kaushik K, Leonard VE, Kv S, Lalwani MK, Jalali S, Patowary A, Joshi A, ScariaV*, Sivasubbu S*.
Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish.
PLoS One. 2013 Dec 31;8(12):e83616.

Singh AR, Sivadas A, Sabharwal A, Vellarikal SK, Jayarajan R, Verma A, Kapoor S, Joshi A, Scaria V*, Sivasubbu S*
Chamber specific gene expression landscape of the zebrafish heart.
PLoS One. 2016 Jan 27;11(1):e0147823

Personalized and Precision Medicine in Humans:

Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, Chauhan G, Bharadwaj D, Sivasubbu S*, Scaria V*.
Systematic analysis and functional annotation of variations in the genome of an Indian individual.
Hum Mutation. 2012 Jul;33(7):1133-40

Salleh MZ*, Teh LK, Lee LS, Ismet RI, Patowary A, Joshi K, Pasha A, Ahmed AZ, Janor RM, Hamzah AS, Adam A, Yusoff K, Hoh BP, Hatta FH, Ismail MI, Scaria V*, Sivasubbu S*.
Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine.
PLoS One. 2013 Aug 23;8(8):e71554.

Vellarikkal SK, Dhiman H, Joshi K, Hasija Y, Sivasubbu S*, Scaria V*.
mit-o-matic: a comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets.
Hum Mutation. 2015 Apr;36 (4):419-24

Aayush Gupta, Yugal Sharma, Kirti Deo, Shamsudheen Vellarikkal, Rijith Jayarajan, Vishal Dixit, Ankit Verma, Vinod Scaria*, Sridhar Sivasubbu*.
Case Report: Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis.
F1000Res. 2015 Jul 31;4:446. doi: 10.12688/f1000research.6779.1. eCollection 2015.

Shehata BM, Cundiff CA, Lee K, Sabharwal A, Lalwani MK, Davis AK, Agrawal V, Sivasubbu S, Iannucci GJ, Gibson G.
Exome sequencing of patients with histiocytoid cardiomyopathy reveals a de novo NDUFB11 mutation that plays a role in the pathogenesis of histiocytoid cardiomyopathy.
Am J Med Genet A. 2015 Sep;167A(9):2114-21

( * Indicates Corresponding Author)