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.
PubMed.

The following paper gives extra information:

Mohorianu, I.; Stocks, M.B.; Applegate, C.S.; Folkes, L.; Moulton, V. (2017) The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.
Methods in Molecular Biology, Vol. 1580, pp. 193-224.
PubMed.

When using the following tools or workflows please cite these papers:

CoLIde

Mohorianu, I.; Stocks, M.B.; Wood, J.; Dalmay, T. and Moulton, V. (2013) CoLIde: A bioinformatics tool for CO-expression based small RNA Loci Identification using high-throughput sequencing data.
RNA biology, Vol. 10, pp. 1221-1230.
PubMed.

miRCat2:

Paicu, C.; Mohorianu, I.; Stocks, M. B.; Xu, P.; Coince, A.; Billmeier, M.; Dalmay, T.; Moulton, V.; Moxon, S. (2017) miRCat2: Accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.
Bioinformatics, Vol. 33, pp. 2446-2454.
PubMed.

PAREsnip:

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.
PubMed.

Quality Checking, Normalisation and Differential Expression workflow:

Beckers, M. L.; Mohorianu, I.; Stocks M. B.; Applegate, C.; Dalmay, T.; Moulton, V. (2017)  Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench.
RNA,  Vol. 23, pp. 823-835.
PubMed.

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