Penny Coggill

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis
    Debanu Das
    Joint Center for Structural Genomics, La Jolla, CA, USA
    BMC Bioinformatics 15:75. 2014
  2. pmc LUD, a new protein domain associated with lactate utilization
    William C Hwang
    Joint Center for Structural Genomics, La Jolla, CA 92037, USA
    BMC Bioinformatics 14:341. 2013
  3. pmc New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily
    Christine B Trame
    Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
    BMC Bioinformatics 15:1. 2014
  4. pmc Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
    Penelope Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    BMC Bioinformatics 14:265. 2013
  5. pmc The YARHG domain: an extracellular domain in search of a function
    Penny Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 7:e35575. 2012
  6. pmc The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes
    Changsoo Chang
    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
    BMC Struct Biol 9:75. 2009
  7. pmc Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
    Eleni M Tomazou
    UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
    BMC Med Genomics 1:19. 2008
  8. pmc The tammar wallaby major histocompatibility complex shows evidence of past genomic instability
    Hannah V Siddle
    Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
    BMC Genomics 12:421. 2011
  9. pmc MHC-linked and un-linked class I genes in the wallaby
    Hannah V Siddle
    Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
    BMC Genomics 10:310. 2009
  10. pmc Evolution and comparative analysis of the MHC Class III inflammatory region
    Janine E Deakin
    ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia
    BMC Genomics 7:281. 2006

Collaborators

Detail Information

Publications16

  1. pmc Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis
    Debanu Das
    Joint Center for Structural Genomics, La Jolla, CA, USA
    BMC Bioinformatics 15:75. 2014
    ..CA_C2195 was chosen for crystal structure determination for structure-based function annotation of novel protein sequence space...
  2. pmc LUD, a new protein domain associated with lactate utilization
    William C Hwang
    Joint Center for Structural Genomics, La Jolla, CA 92037, USA
    BMC Bioinformatics 14:341. 2013
    ..Based on our analysis of its sequence, structure, and recent experimental evidence reported by other groups, we hereby redefine DUF162 as the LUD domain family...
  3. pmc New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily
    Christine B Trame
    Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
    BMC Bioinformatics 15:1. 2014
    ..The Acel_2062 protein was chosen by the Joint Center for Structural Genomics for crystal structure determination to explore novel protein sequence space and structure-based function annotation...
  4. pmc Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
    Penelope Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    BMC Bioinformatics 14:265. 2013
    ..Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology...
  5. pmc The YARHG domain: an extracellular domain in search of a function
    Penny Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 7:e35575. 2012
    ..The large number of different domains that are found associated with YARHG suggests that it is a useful functional module that nature has recombined multiple times...
  6. pmc The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes
    Changsoo Chang
    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
    BMC Struct Biol 9:75. 2009
    ..Streptococcus pyogenes, closely related to LAB, is one of the most common human pathogens, so knowledge of how it competes against other LAB species is likely to prove invaluable...
  7. pmc Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis
    Eleni M Tomazou
    UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
    BMC Med Genomics 1:19. 2008
    ..Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics...
  8. pmc The tammar wallaby major histocompatibility complex shows evidence of past genomic instability
    Hannah V Siddle
    Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
    BMC Genomics 12:421. 2011
    ..The tammar wallaby (Macropus eugenii), an Australian marsupial, provides a unique model for understanding MHC gene evolution, as many of its antigen presenting genes are not linked to the MHC, but are scattered around the genome...
  9. pmc MHC-linked and un-linked class I genes in the wallaby
    Hannah V Siddle
    Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
    BMC Genomics 10:310. 2009
    ..We investigated this hypothesis by characterizing the class I genes of the tammar wallaby, a model marsupial that has a novel MHC organization, with class I genes located within the MHC and 10 other chromosomal locations...
  10. pmc Evolution and comparative analysis of the MHC Class III inflammatory region
    Janine E Deakin
    ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia
    BMC Genomics 7:281. 2006
    ..We also discuss the extent of sequence conservation across the entire region and identify elements conserved in evolution...
  11. pmc Identification of the ancestral killer immunoglobulin-like receptor gene in primates
    Jennifer G Sambrook
    Immunogenomics Laboratory, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 ISA, UK
    BMC Genomics 7:209. 2006
    ..Since few KIR remain orthologous between species, with only one of them, KIR2DL4, shown to be common to human, apes and monkeys, the evolution of the KIR gene family in primates remains unclear...
  12. pmc The Pfam protein families database
    Robert D Finn
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 38:D211-22. 2010
    ..Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/)...
  13. pmc The challenge of increasing Pfam coverage of the human proteome
    Jaina Mistry
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Database (Oxford) 2013:bat023. 2013
    ..New families will also be built, prioritizing those that have been experimentally functionally characterized. Database URL: http://pfam.sanger.ac.uk/..
  14. pmc DUFs: families in search of function
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, England
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1148-52. 2010
    ..In particular, the important role that structural genomics can play in identifying potential function is evaluated...
  15. ncbi request reprint Identifying protein domains with the Pfam database
    Penny Coggill
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Curr Protoc Bioinformatics . 2008
    ..Details on running Pfam, both remotely and locally are presented...
  16. pmc InterPro in 2011: new developments in the family and domain prediction database
    Sarah Hunter
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, UK
    Nucleic Acids Res 40:D306-12. 2012
    ..Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces...