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Zebrafish Encyclopedia of DNA Elements (ZENCODE)

About the Zebrafish ENCODE
Genomics research in recent years, especially the human ENCODE project, have made great strides in understanding the genomic and epigenomic structure and organization of humans. These advances promise a new era of precision medicine, through a better understanding of the genomic correlates of human physiology and promise to offer precise and personalized preventive and therapeutic options. The translation of genome-scale maps of genomic and epigenomic markers to clinically relevant information and further to medical practice await functional validation of the genomic features identified through these large-scale efforts. Such studies must essentially be done in model systems where it is possible to model physiological and pathological processes and enquire how they could be modulated by genomic elements and epigenomic signatures. The availability of large number of personal genomes and maps of genomic variations at population scale has created an acute necessity for model systems to model phenotypic and molecular effects of variations, especially in regulatory regions. We realise that the enormous wealth of disease models and excellent tools to engineer genomes in zebrafish could be effectively capitalized towards making it an effective and widely used model system for precision medicine. This would be possible only through a concerted and systematic effort to create orthologous genomic and epigenomic maps for zebrafish. [>Read More]
The Zebrafish ENCODE Collaborative Network
The ZENCODE is envisaged to be a collaborative initiative with contributions from across the globe in terms of data points and expert analysis support. As also briefly mentioned in the overview paper, we would embrace the concepts of open-source and collaboration between the groups.

We are in the process of creating a track-hub for the genome annotations as part of the ZENCODE programme. For individuals interested in contributing to the tracks, please contact us Vinod Scaria OR Sridhar Sivasubbu You can also access the ZENCODE Data Hub and Genome Browser

A number of complementary resources have been developed as part of this initiative apart from resources on zebrafish genomics developed as part of previous projects.
The ongoing activities of ZENCODE is supported by the funding from the Council of Scientific and Industrial Research (CSIR) India through Grants CARDIOMED and GENCODE-C 


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

Kaushik K, Leonard VE, Shamsudheen KV, Lalwani MK, Jalali S, Patowary A, Joshi A, Scaria V, Sivasubbu S.
Dynamic Expression of Long Non-Coding RNAs (lncRNAs) in Adult Zebrafish.
PLoS One. 2013 Dec 31;8(12):e83616. doi: 10.1371/journal.pone.0083616.

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) 2014 : bau011

Haque S,  Kaushik K, Leonard VE, Kapoor S, Sivadas A, Joshi A, Scaria V, Sivasubbu S
Short stories on zebrafish long noncoding RNAs
Zebrafish (2014) Accepted