Dr. Vinod Scaria

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Open Data, Standards and Tools for Translational Genomics

OpenPGx is a global collaborative endeavour to create an Open Access resource for Pharmacogenomics data in order to 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)

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.

Journals

Advances in Integrative Omics and Applied Biotechnology is an open access, peer-reviewed international journal that publishes approaches to tackling system biology issues, combining various omics disciplines with the perspective of applying such technologies in agriculture, industry, and biomedicine.

Whole Genome Sequencing Initiatives / Collaborations

Indian Human Genome
Sri Lankan Human Genome [overview]

Malaysian Genome

Zebrafish Wild-type Strain

(in collaboration with Dr. Sridhar Sivasubbu, IGIB)

Latest Publications

[Complete list of publications are available here]

Periwal V, Kishtapuram S, Open Source Drug Discovery Consortium and Scaria V
Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets
BMC Pharmacology (2012) In Press

Sati S, Tanwar VS, Kumar KA, Patowary A, Jain V, Ghosh S, Ahmad S, Singh M, S Reddy U, Chandak GR, Raghunath M, Sivasubbu S, Chakraborty K, Scaria V*, Sengupta S*

High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region

PLoS One (2012) In Press

Suryawanshi H, Lalwani MK, Ramsamy Soundhar,Rana R,Scaria V, Sivasubbu S, Maiti S

Antagonism of microRNA function in zebrafish embryos using Locked Nucleic Acid Enzymes(LNAzymes)

ChemBioChem (2012) In Press

Jayaraj GG, Pandey S, Scaria V*, Maiti S*

Potential G-quadruplex forming sequences in the Human non-coding transcriptome

RNA Biology 2012 9:1 In Press

Patowary A, Chauhan RK, Singh M, Shamsudheen KV, Periwal V, Kushwaha KP, Sapkal GN, Bondre VP, Gore MM, Sivasubbu S and Scaria V

De novo identification of viral pathogens from cell culture hologenomes

BMC Research Notes 2012, 5:11

Indian Diabetes Consortium^

INDICO: the development of a resource for epigenomic study of Indians undergoing socioeconomic transition

HUGO Journal (2011) In Press

Periwal V, Jinuraj KR, OSDD Consortium, Jaleel UC and Scaria V*

Predictive models for anti-tubercular molecules using machine learning on high-throughput biological screening datasets

BMC Research Notes 2011 18;4:504.

Karl J Clark, Darius Balciunas, Hans-Martin Pogoda, Yonghe Ding, Stephanie E Westcot, Victoria M Bedell, Tammy M Greenwood, Mark D Urban, Kimberly J Skuster, Andrew M Petzold, Jun Ni, Aubrey L Nielsen, Ashok Patowary, Vinod Scaria, Sridhar Sivasubbu, Xiaolei Xu, Matthias Hammerschmidt & Stephen C Ekker

In vivo protein trapping produces a functional expression codex of the vertebrate proteome

Nature Methods 2011 8(6):506-15. Featured Article [News and views on this article]

Bhardwaj A, Scaria V, Raghava GPS, Lynn AM, Chandra N, Banerjee S, Raghunandanan MV, Pandey V, Taneja B, Yadav J, Dash D, Bhattacharya J, Misra A, Kumar A, Ramachandran S, Thomas Z, Brahmachari SK.

Open source drug discovery: A new paradigm of collaborative research in tuberculosis drug development Tuberculosis 2011 91(5):479-86.

Bhartiya D, Laddha, SV, Mukhopadhyay A, Scaria, V*

miRvar: A Comprehensive Database and Systematic Analysis of Genomic Variations in microRNAs

Human Mutation 2011;32(6):E2226-45

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