Publications

List of publications on RNA from the UEA Computational Biology Laboratory (most recent first):

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.

Paicu, C.; Mohorianu, I.; Stocks, M.; 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.

Beckers, M.; Mohorianu, I.; Stocks, M.; 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.

Collins, D.; Mohorianu, I.; Beckers, M.; Moulton, V.; Dalmay, T.; Bourke, A. (2017) MicroRNAs associated with caste determination and differentiation in a primitively eusocial insect,
Scientific Reports, 7, 45674.
PubMed.

Mohorianu, I.; Stocks, M.; Wood, J.; Dalmay, T.; 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.

Mapleson, D.; Moxon, S.; Dalmay, T.; Moulton, V. (2013) MirPlex: A tool for identifying miRNAs in high-throughput sRNA datasets without a genome,
Journal of Experimental Zoology: Part B, 320(1), 47-56.
PubMed.

Stocks, M.; Moxon, S.; Mapleson, D.; Woolfenden, H.; Mohorianu, I.; Folkes, L.; Schwach, F.; Dalmay, T.; Moulton, V. (2012) The UEA sRNA Workbench: A suite of tools for analysing and visualising next generation sequencing microRNA and small RNA datasets,
Bioinformatics , Vol. 28, pp. 2059-2061.
PubMed.

Folkes, L.; Moxon, S.; Woolfenden, H.; Stocks, M.; 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.

Sorefan, K.; Pais, H.; Hall, A.; Kozomara, A.; Griffith-Jones, S.; Moulton, V.; Dalmay, T. (2012) Reducing ligation bias of small RNAs in libraries for next generation sequencing,
Silence, 3:4.
PubMed.

Mohorianu, I.; Lopez-Gomollon, S.; Schwach, F.; Dalmay, T.; Moulton, V. (2012) FiRePat – Finding Regulatory Patterns between sRNAs and putative target genes,
WIREs Data Mining and Knowledge Discovery, 2, 273-284.

Mohorianu, I.; Jing, R.; Schwach, F.; Lopez-Gomollon, S.; Szittya, G.; Moxon, S.; Sorefan, K.; Moulton, V.; Dalmay, T. (2011) Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns,
Plant Journal, 67(2), 232-246.

Nicolas, F.; Pais, H.; Schwach, F.; Lindow, M.; Kauppinen, S.; Moulton, V.; Dalmay, T. (2011) mRNA expression profiling reveals conserved and non-conserved miR-140 targets,
RNA Biology, 8(4), 607-615.

Pantaleo, V.; Szittya, G.; Moxon, S.; Miozzi, L.; Moulton, V.; Dalmay, T.; Burgyan, J. (2010) Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis,
Plant Journal, 62(6), 960-976.

Nicolas, F.; Moxon, S.; Haro, J.; Calo, S.; Grigoriev, I.; Torres-Martinez, S.; Moulton, V.; Ruiz-Vazquez, R.; Dalmay, T. (2010) Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides,
Nucleic Acids Research, 38(16), 5535-5541.

Pais, H.; Nicolas, F.; Soond, S.; Swingler, T.; Clark, I.; Chantry, A.; Moulton, V.; Dalmay, T. (2010) Analysing mRNA expression identifies Smad3 as a microRNA-140 target regulated only at protein level,
RNA, 16, 489-494.

MacLean, D.; Moulton, V.; Studholme, D. (2010) Finding sRNA generative locales from high-throughput sequencing data with NiBLS,
BMC Bioinformatics, 11:93.

Szittya, G.; Moxon, S.; Pantaleo, V.; Toth, G.; Pilcher, R.; Moulton, V.; Burgyan, J.; Dalmay, T. (2010) Structural and functional analysis of viral siRNAs,
PLoS Pathogens, 6(4): e1000838.

Rathjen, T.; Pais, H.; Sweetman, D.; Moulton, V.; Munsterberg, A.; Dalmay, T. (2009) High throughput sequencing of microRNAs in chicken somites,
FEBS Letters, 583(9), 1422-1426.

Molina, F.; Pais, H.; Schwach, F.; Lindow, M.; Kauppinen, S.; Moulton, V.; Dalmay, T. (2008) Experimental identification of microRNA-140 targets by suppressing and over-expressing microRNA-140,
RNA, 14, 2513-2520.

Szittya, G.; Moxon, S.; Santos, D.; Jing, R.; Fevereiro, M.; Moulton, V.; Dalmay, T. (2008) High-throughput sequencing of Medicago truncatula short RNAs,
BMC Genomics, 9:593.

Moxon, S.; Schwach, F.; MacLean, D.; Dalmay, T.; Studholme, D.; Moulton, V. (2008) A toolkit for analysing large-scale plant small RNA datasets,
Bioinformatics, 24, 2252 – 2253.

Moxon, S.; Jing, R.; Szittya, G.; Schwach, F.; Pilcher, R.; Moulton, V.; Dalmay, T. (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening,
Genome Research, 18, 1602-1609.

Rusholme, R.; Moxon, S.; Pakseresht, N.; Moulton, V.; Mannington, K.; Seymour, G.; Dalmay, T. (2007) Identification of novel short RNAs in tomato (Solanum lycopersicum),
Planta, 3, 709-717.

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices