When using the UEA sRNA Workbench for your analysis please cite the following paper:
Stocks, M. B.; Moxon, S.; Mapleson, D.; Woolfenden, H. C.; Mohorianu, I.; Folkes, L.; Schwach, F.; Dalmay, T. & Moulton, V. (2012) The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics ,Vol. 28,pp. 2059-2061
When using the PAREsnip tool please also cite:
Folkes, L.; Moxon, S.; Woolfenden, H. C.; Stocks, M. B.; Szittya, G.; Dalmay, T. & Moulton, V. (2012) PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Res, Vol. 40, pp. e103
When using the CoLIde tool please also cite:
I. Mohorianu, M. B. Stocks, J. Wood, T. Dalmay, and V. Moulton, “CoLIde: A bioinformatics tool for CO-expression based small RNA Loci Identification using high-throughput sequencing data.,” RNA biology, vol. 10, no. 7, Jun. 2013.
http://www.landesbioscience.com/journals/rnabiology/toc/volume/10/issue/7/
@article{Mohorianu2013,
abstract = {Small RNAs (sRNAs) are 20-25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci. To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk.},
author = {Mohorianu, Irina and Stocks, Matthew Benedict and Wood, John and Dalmay, Tamas and Moulton, Vincent},
issn = {1555-8584},
journal = {RNA biology},
month = jun,
number = {7},
pmid = {23851377},
title = {{CoLIde: A bioinformatics tool for CO-expression based small RNA Loci Identification using high-throughput sequencing data.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23851377},
volume = {10},
year = {2013}
}
Our Licence File
Follow this link for a PDF of our licence file