Affiliation: University of Oxford
- Dunne M, Kelly S. OMGene: mutual improvement of gene models through optimisation of evolutionary conservation. BMC Genomics. 2018;19:307 pubmed publisher..We show that significant improvements in the accuracy of gene model annotations can be made, both in established and in de novo annotated genomes, by leveraging information from multiple species. ..
- Kelly S, Greenman C, Cook P, Papantonis A. Exon Skipping Is Correlated with Exon Circularization. J Mol Biol. 2015;427:2414-7 pubmed publisher..We find that circularization of exons is widespread and correlates with exon skipping, a feature that adds considerably to the regulatory complexity of the human transcriptome. ..
- Fiebig M, Gluenz E, Carrington M, Kelly S. SLaP mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes. Mol Biochem Parasitol. 2014;196:71-4 pubmed publisher..SLaP mapper is an easy to use, platform independent webserver that is freely available for use at http://www.stevekellylab.com/software/slap. Example files are provided on the website. ..
- Emms D, Covshoff S, Hibberd J, Kelly S. Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species. Mol Biol Evol. 2016;33:1796-806 pubmed publisher..C4 photosynthesis, gene duplication, gene families, parallel evolution. ..
- Lyu M, Gowik U, Kelly S, Covshoff S, Mallmann J, Westhoff P, et al. RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evol Biol. 2015;15:116 pubmed publisher..The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C4 photosynthesis in the Flavaria clade. ..
- Seward E, Votypka J, Kment P, Lukes J, Kelly S. Description of Phytomonas oxycareni n. sp. from the Salivary Glands of Oxycarenus lavaterae. Protist. 2017;168:71-79 pubmed publisher..Finally, phylogenetic analyses of small subunit ribosomal RNA genes revealed that this species is sister to other species within the genus Phytomonas, providing new insight into the evolutionary history of the clade. ..
- Butler C, Jaskowska E, Kelly S. Genome Sequence of Phytomonas françai, a Cassava (Manihot esculenta) Latex Parasite. Genome Announc. 2017;5: pubmed publisher..françai infection is linked with the yield-loss disease "chochamento de raizes" (empty roots) in the Unha variety of cassava, a disease characterized by poor root development and chlorosis of the leaves. ..
- Ebenezer T, Carrington M, Lebert M, Kelly S, Field M. Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features. Adv Exp Med Biol. 2017;979:125-140 pubmed publisher..Finally, as a preliminary view of the genome architecture, we discuss the tubulin and calmodulin genes, which highlight potential novel splicing mechanisms. ..
- Dunne M, Kelly S. OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations. BMC Genomics. 2017;18:390 pubmed publisher..We show that significant improvements in the completeness of genome annotations can be made by leveraging information from multiple species. ..
- Kelly S, Kramer S, Schwede A, Maini P, Gull K, Carrington M. Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes. Open Biol. 2012;2:120033 pubmed publisher..This work provides evidence that the genome in trypanosomes is organized to facilitate co-coordinated temporal control of gene expression in the absence of selective promoters...