When using the UEA sRNA Workbench for your analysis please cite the following paper:

Stocks, M. B., Mohorianu, I., Beckers, M., Paicu, C., Moxon, S., Thody, J., Dalmay, T., & Moulton, V. (2018). The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.
Bioinformatics , Vol. 34, pp. 3382–3384.
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:

PAREsnip2:

Thody, J., Folkes, L., Medina-Calzada, Z., Xu, P., Dalmay, T., & Moulton, V. (2018). PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules.
Nucleic Acids Res, Vol. 46, pp. 8730–8739
PubMed.

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.

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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