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Open Data, Standards and Tools for Translational Genomics

OpenPGx is a global collaborative endeavour to create an Open Access resource and toolkit for personal genome data analysis . We hope this would enable the application of advances in science and technology to clinical settings with the overall aim and impact of improving patient health care. (more about OpenPGx).

Forthcoming talks

  • These are a tentative list of forthcoming invited talks. The talk title, content and attendance are likely to change.[complete list]
  • International Conference on Human Genetics and 39th Annual Meeting of the Indian Society of Human Genetics Conference URL: http://www.ishg2014.org/International Conference on Human Genetics and 39th Annual Meeting of the Indian Society of Human GeneticsAhmedabad Management Association, Ahmedabad, India, from 23rd - 25th ...
    Posted May 17, 2013, 4:34 AM by Vinod Scaria
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For Potential Interns and Summer Students

I have only limited opportunities for Interns/Summer students, usually 2 at a time. As an Institute policy the duration should be more than 3 months, and I would prefer someone for 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. This need not be on something I generally work on. To make sure you are a legitimate applicant and not a spammer, please add "[Internship]" in your subject. I generally would not need unsolicited recommendations.

Attractive oppurtunity to participate in Collaborative Cheminformatics Research and work closely with a number of researchers across the country as part of the Open Source Drug Discovery Initiative

Crowd Computing for Scientific Research

We have been recently experimenting with crowd computing for addressing and solving various scientific problems. One of the active areas of interest have been using wisdom of the crowd to create methodologies for chemical data-mining. Read more about our projects 2C4C and 3C4TB

Whole Genome Sequencing Initiatives / Collaborations
Indian Human Genome
Sri Lankan Human Genome [overview]
Malaysian Genome
Zebrafish Wild-type Strain [Data/Resources] 
(in collaboration with Dr. Sridhar Sivasubbu, IGIB)

Pan Asian Population Genomics Initiative (PAPGI)



Recent Publications
[Complete list of publications are available here]

Pore SK, Choudhary A, Rathore B, Ganguly A, Sujitha P , Kumar CG, Agawane SB, Kumar JM ,Scaria V, Pillai B, Banerjee R.
Hsp90-targeted miRNA-liposomal formulation for systemic antitumor effect
Biomaterials (2013) Accepted

Bhartiya D,Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B, Jain S, Sati S, Sengupta S, Sachidanandan C, Raghava GPS, Sivasubbu S and Scaria V*
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
 Database (2013) Accepted

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*
Zebrafish (2013) 10(1): 15-20. [cover article]

Mole S, Jalali S, Scaria V, Bhardwaj A
MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variation
PLoS ONE (2013) Accepted

Jamal S, Periwal V, OSDD Consortium and Scaria V*
Predictive cheminformatics analysis of anti-malarial molecules inhibiting apicoplast formation
BMC Bioinformatics 2013, 14:55

Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S*, Scaria V*
Systematic transcriptome wide analysis of lncRNA-miRNA interactions. 
PLoS ONE (2013) 8(2): e53823.

Scaria V*, Pasha A
Long noncoding RNAs in infection biology
Front. Genet.3:308 (2012)

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

Jamal S, Periwal V, OSDD Consortium, Scaria V*
Computational analysis and predictive modeling of small molecule modulators of microRNA
Journal of Cheminformatics 2012, 4:16

Sati S, Ghosh S; Jain V, Scaria V*, Sengupta S*
Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci
Nucl. Acids Res. (2012) 40 (20):10018-10031.

Jalali S, Jayaraj GG, Scaria V*
Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs
Biology Direct  2012, 7:25

Bhartiya D, Talwar J, Hasija Y, Scaria V*
Systematic curation and analysis of genomic variations and their potential functional consequences in snoRNA loci
Human Mutation (2012), 33: E2367–E2374.

Bargaje R, Alam P, Patowary A, Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S, Brahmachari V, Pillai B 
Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain.
Nucl. Acids Res. (2012) 40 (18):8965-8978.

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. Mutat., 33: 1133–1140.  [Genome Browser]

(*as communicating/co-communicating author)(^as member of consortium)