S Kelly


Affiliation: University of Oxford
Country: UK


  1. request reprint
    Catarino B, Hetherington A, Emms D, Kelly S, Dolan L. The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Mol Biol Evol. 2016;33:2815-2819 pubmed
    ..These findings reveal that the majority of innovation in plant and metazoan TF families occurred in the Precambrian before the Phanerozoic radiation of land plants and metazoans. ..
  2. Ebenezer T, Zoltner M, Burrell A, Nenarokova A, Novák Vanclová A, Prasad B, et al. Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biol. 2019;17:11 pubmed publisher
    ..We also suggest that euglenids possess unique regulatory mechanisms for achieving extreme adaptability, through mechanisms of paralog expansion and gene acquisition. ..
  3. Abu Jamous B, Kelly S. Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data. Genome Biol. 2018;19:172 pubmed publisher
    ..Additionally, clust can simultaneously cluster multiple datasets, enabling users to leverage the large quantity of public expression data for novel comparative analysis. Clust is available at https://github.com/BaselAbujamous/clust . ..
  4. Kelly S, Wickstead B, Gull K. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc Biol Sci. 2011;278:1009-18 pubmed publisher
    ..By the same criteria, we also provide evidence in support of an origin for Eukarya either within or as sisters to the Thaumarchaea. ..
  5. Kelly S, Wickstead B, Maini P, Gull K. Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation. PLoS ONE. 2011;6:e25666 pubmed publisher
    ..The nature of the elements discovered reinforces the hypothesis that context dependant RNA secondary structure has an important influence on gene expression regulation in Trypanosoma brucei. ..
  6. Seward E, Kelly S. Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria. Genome Biol. 2018;19:102 pubmed publisher
    ..These findings reveal how optimization of resource allocation to messenger RNA synthesis is a critical factor that determines both the evolution and composition of genes. ..
  7. Emms D, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157 pubmed publisher
    ..Furthermore, we demonstrate the utility of OrthoFinder by providing a complete classification of transcription factor gene families in plants revealing 6.9 million previously unobserved relationships. ..
  8. Seward E, Kelly S. Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms. Genome Biol. 2016;17:226 pubmed
  9. Dunne M, Kelly S. Erratum to: OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations. BMC Genomics. 2017;18:488 pubmed publisher

More Information


  1. 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. ..
  2. 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. ..
  3. 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. ..
  4. 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. ..
  5. 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. ..
  6. 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. ..
  7. 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. ..
  8. Carrington M, Dóró E, Forlenza M, Wiegertjes G, Kelly S. Transcriptome Sequence of the Bloodstream Form of Trypanoplasma borreli, a Hematozoic Parasite of Fish Transmitted by Leeches. Genome Announc. 2017;5: pubmed publisher
  9. 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. ..
  10. 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. ..
  11. 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...