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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).

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

Forthcoming talks

  • These are a tentative list of forthcoming invited talks. The talk title, content and attendance are likely to change.
  • 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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Information 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
Could also register online at crowdomics portal


Whole Genome Sequencing Initiatives / Collaborations
Mycobacterium tuberculosis genomes
(in collaboration with Dr. Sridhar Sivasubbu, IGIB)
Pan Asian Population Genomics Initiative (PAPGI)

Recent Publications 

Giri AK, Khan NM, Narayanan D, INDICO, Basu A, Tandon N, Scaria V*, Bharadwaj D*
Pharmacogenetic landscape of Clopidogrel in North Indians suggest distinct inter-population differences in allele frequencies
Pharmacogenomics (2014) Accepted  

Bhartiya D, Jalali S, Ghosh S, Scaria V*
Distinct patterns of genetic variations in potentially functional elements in long noncoding RNAs
Human Mutation (2014) Feb;35(2):192-201

Singh M, Bhartiya D,Maini J,Sharma M,Singh AR, Subburaj K, Rana R, Sabharwal A, Nanda S, Aravindhakshan R, Mittal A, Kapoor S, Sehgal P, Asad Z, Kaushik K, Vellarikkal SK, Jagga D, Muthulakshmi. M1, Chauhan RK,  Leonard E, Priyadarshini R, Halimani M, Malhotra S, Patowary A, Vishwakarma H, Joshi P, Bhardwaj V,  Bhaumik A,  Bhatt B, Jha A, Kumar A, Budakoti P, Lalwani MK, Meli R, Jalali S, Joshi K, Pal K, Dhiman H, Laddha SV, Jadhav V, Singh N, Pandey V, Sachidanandan C, Ekker SC, Klee EW, Scaria V and Sivasubbu S
The Zebrafish GenomeWiki: A crowdsourcing approach to connect the long tail for zebrafish gene annotation
Database (2014) Accepted 

Joshi KR, Dhiman H, Scaria V
tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis
Database (2014) 2014 : bat083 

Kaushik K, Leonard VE, Shamsudheen KV, Lalwani MK, Jalali S, Patowary A, Joshi A, Scaria V*and Sivasubbu S*
Dynamic Expression of Long Non-coding RNAs (lncRNAs) in Adult Zebrafish
PLoS ONE (2013) Dec 31;8(12):e83616.

Jamal S, Arora S , Scaria V*
Computational analysis and predictive cheminformatics modeling of small molecule inhibitors of epigenetic modifiers 
PLoS ONE (2013) Accepted 

Jamal S, OSDD Consortium, Scaria V*
Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana
BMC Bioinformatics (2013) Nov 19;14:329. .

Vellarikkal S, Singh A, Singh P, Garg P, Katoch V, Katoch K, OSDD Consortium, Chauhan D, Scaria V*, Sivasubbu S*
Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate of the Ural Strain OSDD493 
Genome Announcements (2013)  Nov 7;1(6). pii: e00928-13.

Sivasubbu S*, Sachidanandan C*, Scaria V*
Time for the zebrafish ENCODE
Journal of Genetics (2013) Dec;92(3):695-701.

Salleh MZ*, Teh LK, Lee LS, Ismet RI, Patowary A, Joshi K, Pasha A, Ahmed AZ, Janor MH, Hamzah AS, Adam I, Yusoff K, Hoh BP, Hatta FM, Ismail MI, Scaria V*, Sivasubbu S*
Systematic Pharmacogenomics analysis of a Malay whole genome : Proof of concept for Personalised Medicine.
PLoS ONE (2013) Aug 23;8(8):e71554.

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) Jul 11;2013:bat034.

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]

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