S Kelly

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. doi request reprint Erratum to: OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations.
    Michael P Dunne
    Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
    BMC Genomics 18:488. 2017
  2. doi request reprint OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations
    Michael P Dunne
    Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
    BMC Genomics 18:390. 2017
  3. pmc RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
    Ming Ju Amy Lyu
    CAS MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China
    BMC Evol Biol 15:116. 2015
  4. doi request reprint Exon Skipping Is Correlated with Exon Circularization
    Steven Kelly
    Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK Electronic address
    J Mol Biol 427:2414-7. 2015
  5. pmc SLaP mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes
    Michael Fiebig
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Mol Biochem Parasitol 196:71-4. 2014
  6. pmc Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes
    S Kelly
    Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
    Open Biol 2:120033. 2012
  7. pmc DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments
    Steven Kelly
    Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
    PLoS ONE 8:e58537. 2013
  8. pmc MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments
    Peter W Collingridge
    Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PBDevon, UK
    BMC Bioinformatics 13:117. 2012
  9. pmc Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes
    S Kelly
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Proc Biol Sci 278:1009-18. 2011
  10. pmc Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation
    Steven Kelly
    Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
    PLoS ONE 6:e25666. 2011

Collaborators

Detail Information

Publications15

  1. doi request reprint Erratum to: OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations.
    Michael P Dunne
    Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
    BMC Genomics 18:488. 2017
  2. doi request reprint OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations
    Michael P Dunne
    Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
    BMC Genomics 18:390. 2017
    ..Erroneously unannotated genes can lead to oversights and inaccurate assertions in biological investigations, especially for smaller-scale genome projects, which rely heavily on computational prediction...
  3. pmc RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
    Ming Ju Amy Lyu
    CAS MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China
    BMC Evol Biol 15:116. 2015
    ....
  4. doi request reprint Exon Skipping Is Correlated with Exon Circularization
    Steven Kelly
    Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK Electronic address
    J Mol Biol 427:2414-7. 2015
    ..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. ..
  5. pmc SLaP mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes
    Michael Fiebig
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Mol Biochem Parasitol 196:71-4. 2014
    ..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. ..
  6. pmc Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes
    S Kelly
    Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
    Open Biol 2:120033. 2012
    ..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...
  7. pmc DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments
    Steven Kelly
    Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
    PLoS ONE 8:e58537. 2013
    ..A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/...
  8. pmc MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments
    Peter W Collingridge
    Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PBDevon, UK
    BMC Bioinformatics 13:117. 2012
    ..We present a novel method called MergeAlign which constructs consensus MSAs from multiple independent MSAs and assigns an alignment precision score to each column...
  9. pmc Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes
    S Kelly
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Proc Biol Sci 278:1009-18. 2011
    ..By the same criteria, we also provide evidence in support of an origin for Eukarya either within or as sisters to the Thaumarchaea...
  10. pmc Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation
    Steven Kelly
    Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
    PLoS ONE 6:e25666. 2011
    ..These genomes, though outwardly simple in organisation and gene content, have historically challenged many theories for gene expression regulation in eukaryotes...
  11. pmc Characterization and differential nuclear localization of Nopp140 and a novel Nopp140-like protein in trypanosomes
    S Kelly
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
    Eukaryot Cell 5:876-9. 2006
    ..The restricted occurrence pattern of NoLP proteins reflects an intriguing convergence in evolution, suggestive of a function in nucleoplasmic small nucleolar ribonucleoprotein shuttling...
  12. ncbi request reprint Combined immunophenotyping and FISH identifies the involvement of B-cells in 5q- syndrome
    R J Jaju
    Leukaemia Research Fund Molecular Haematology Unit, Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
    Genes Chromosomes Cancer 29:276-80. 2000
    ..This result suggests that in some cases, MDS arises in a multipotent cell with a capacity to differentiate into both myeloid and lymphoid cells...
  13. pmc A modular and optimized single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor
    S K Poon
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Open Biol 2:110037. 2012
    ....
  14. ncbi request reprint An in silico analysis of trypanosomatid RNA polymerases: insights into their unusual transcription
    S Kelly
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Biochem Soc Trans 33:1435-7. 2005
    ..We propose that these alternative isoforms function in distinct polymerase complexes, and may influence recruitment of the trypanosome RPB4-RPB7 heterodimer...
  15. pmc Loss of both CSF1R (FMS) alleles in patients with myelodysplasia and a chromosome 5 deletion
    J Boultwood
    Department of Haematology, John Radcliffe Hospital, Headington, Oxford, United Kingdom
    Proc Natl Acad Sci U S A 88:6176-80. 1991
    ..The loss of the hemopoietic growth factor receptor gene CSF1R may be important in the pathogenesis of human myeloid leukemia...