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Long non-coding RNA (lncRNA) Genomics and Biology

Biomolecular Interaction of lncRNAs with other cellular biomolecules. (A) RNA-Protein interactions (B) Regulation of lncRNAs through formation of ribonucleoprotein complexes (C) lncRNA-interactions with other RNA species including messenger RNA and other ncRNAs (D) lncRNA interaction with DNA motifs (F) Interaction of lncRNAs with small molecules (E) RNA-DNA interactions

Organization of biological interaction networks interconnections between the levels of regulatory networks .The RNA, protein and small molecule mediated interaction networks integrate with the genome, transcriptome and protein interaction networks.

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
The advent of high-throughput genome scale technologies has enabled us to unravel a large amount of the previously unknown transcriptionally active regions of the genome. Recent genome-wide studies have provided annotations of a large repertoire of various classes of non-coding transcripts. Long noncoding RNAs form a major proportion of these novel annotated noncoding transcripts, and presently known to be involved in a number of functionally distinct biological processes. Over 18,000 transcripts are presently annotated as long noncoding RNA, and encompass previously annotated classes of noncoding transcripts including lincRNA, antisense RNA and processed pseudogenes. There is a significant gap in the resources providing a stable annotation, cros-referencing and biologically relevant information. lncRNome has been envisioned with the aim of filling this gap by integrating annotations, on a wide variety of biologically significant information into a comprehensive knowledgebase. To the best of our knowledge, lncRNome is the largest and most comprehensive resource for long noncoding RNAs and is available at URL:

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
Recent Publications

Rajpathak SN, Vellarikkal SK,Patowary A, Scaria V*, Sivasubbu S* and Deobagkar DD*
Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome. 
PLoS ONE (2014) Accepted

Human Mutation (2014) Feb;35(2):192-201

Kaushik K, Leonard VE, Shamsudheen KV, Lalwani MK, Jalali S, Patowary A, Joshi A, Scaria V*and Sivasubbu S*
PLoS ONE (2013) Dec 31;8(12):e83616. 

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*
Database (2013) Jul 11;2013:bat03

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

Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S*, Scaria V*
Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PLoS One (2013) 8(2): e53823. doi:10.1371/journal.pone.0053823

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, Kapoor S, Jalali S, Sati S, Kaushik K, Sachidanandan C, Sivasubbu S, Scaria V
Conceptual approaches for lncRNA drug discovery and future strategies
Expert Opin Drug Discov. 2012 Jun;7(6):503-13.

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 7(2): e31621.

Jayaraj GG, Pandey S, Scaria V*, Maiti S*
Potential G-quadruplex forming sequences in the Human non-coding transcriptome
RNA Biology 2012 9:1