Resources

Find further details on the TarpiD website
TarPiD (Targets of piRNA Database) that offers comprehensive information on piRNA and its targets,
including their expression, methodologies (high-throughput or low-throughput) for target identification/validation,
cells/tissue types, diseases, target regulation types, target binding regions, and important biological functions driven by piRNAs through target interactions.
Published in: To be updated soon.

Find further details our cancerome NGS data on the GEO website.
Our RNAi laboratory has performed next-generation sequencing of small RNA and transcriptomes in tissues and cell lines of multiple cancer types to decode the cancerome with an aim to develop novel diagnostic and therapeutic strategies.
GEO accession nos. of our cancerome NGS data are GSE197508, GSE196674, GSE196688, GSE83945, GSE83794, GSE85075.

Click here to download the standalone version of the SoCeR tool.
SoCeR predict, gauge, and compare the propensity of the ceRNAs of a gene of interest based on a miRNA-mediated ‘tug-of-war’ model
and precisely envisages which among a ceRNA pair exerts a stronger pull on the shared miRNA pool.
This predict ceRNAs in 32 cancer types with true positive rate of 79%.

Published in: miRNA-mediated 'tug-of-war' model reveals ceRNA propensity of genes in cancers. Arpit Chandan Swain, Bibekanand Mallick
Molecular Oncology. 12(6):855-868, 2018

Find further details on the STarMir website.
StarMir predicts both seed and seedless target sites in all three regions of target mRNAs (5’UTR, CDS, 3’UTR)
using prediction model based on V-CLIP (human), HITS-CLIP (mouse) and ALG1-CLIP (worm).
This was developed while working at Wadsworth Center, NY as a postdoc.
Published in: CLIP-based prediction of mammalian microRNA binding sites Chaochun Liu, Bibekanand Mallick, Dang Long, William A. Rennie, Adam Wolenc, C. Steven Carmack, Ye Ding.
Nucleic Acids Res. 41(14): e138. 2013.
STarMirDB: a database of microRNA binding sites William Rennie, Shaveta Kanoria, Chaochun Liu, Bibekanand Mallick, Dang Long, Adam Wolenc, C. Steven Carmack, Jun Lu & Ye Ding. RNA Biology 13 (6), 554-560, 2016.

Click here to download installation file of RiNAcyc (RNA interacting Nodes in Acyclic Path) as well as its prerequisite.
Published in:
Unraveling novel TF-miRNA regulatory crosstalk in metastasis of Soft Tissue Sarcoma. Devyani Samantarrai, Mousumi Sahu, Jyoti Roy, Bedanta Ballav Mohanty, Garima Singh, Chandra Bhushan & Bibekanand Mallick
Sci Rep 5, 9742, 2015.