Peter W H Holland

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc 4273π: bioinformatics education on low cost ARM hardware
    Daniel Barker
    Sir Harold Mitchell Building, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
    BMC Bioinformatics 14:243. 2013
  2. doi request reprint Evolution of homeobox genes
    Peter W H Holland
    Department of Zoology, University of Oxford, OX1 3PS, UK
    Wiley Interdiscip Rev Dev Biol 2:31-45. 2013
  3. pmc The dynamics of vertebrate homeobox gene evolution: gain and loss of genes in mouse and human lineages
    Ying Fu Zhong
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    BMC Evol Biol 11:169. 2011
  4. pmc Protein evolution of ANTP and PRD homeobox genes
    Nuno A Fonseca
    Instituto de Biologia Molecular e Celular IBMC, University of Porto, Rua do Campo Alegre 823, 4150 180 Porto, Portugal
    BMC Evol Biol 8:200. 2008
  5. pmc Comparative genomics of chondrichthyan Hoxa clusters
    John F Mulley
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX13PS UK
    BMC Evol Biol 9:218. 2009
  6. pmc Classification and nomenclature of all human homeobox genes
    Peter W H Holland
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    BMC Biol 5:47. 2007
  7. pmc The origin and evolution of ARGFX homeobox loci in mammalian radiation
    Guang Li
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    BMC Evol Biol 10:182. 2010
  8. ncbi request reprint A Gbx homeobox gene in amphioxus: insights into ancestry of the ANTP class and evolution of the midbrain/hindbrain boundary
    L Filipe C Castro
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Dev Biol 295:40-51. 2006
  9. doi request reprint Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization
    Jerome H L Hui
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 29:157-65. 2012
  10. doi request reprint Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster
    Jerome H L Hui
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Evol Dev 10:725-30. 2008

Collaborators

Detail Information

Publications46

  1. pmc 4273π: bioinformatics education on low cost ARM hardware
    Daniel Barker
    Sir Harold Mitchell Building, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
    BMC Bioinformatics 14:243. 2013
    ..We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access...
  2. doi request reprint Evolution of homeobox genes
    Peter W H Holland
    Department of Zoology, University of Oxford, OX1 3PS, UK
    Wiley Interdiscip Rev Dev Biol 2:31-45. 2013
    ..WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. Conflict of interest: The author declares that he has no conflicts of interest. ..
  3. pmc The dynamics of vertebrate homeobox gene evolution: gain and loss of genes in mouse and human lineages
    Ying Fu Zhong
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    BMC Evol Biol 11:169. 2011
    ..Comparison of homeobox genes between species may provide insights into the evolution of developmental mechanisms...
  4. pmc Protein evolution of ANTP and PRD homeobox genes
    Nuno A Fonseca
    Instituto de Biologia Molecular e Celular IBMC, University of Porto, Rua do Campo Alegre 823, 4150 180 Porto, Portugal
    BMC Evol Biol 8:200. 2008
    ..Although homeobox genes have been the subject of many studies, little is known about the main amino acid changes that occurred early in the evolution of genes belonging to different classes...
  5. pmc Comparative genomics of chondrichthyan Hoxa clusters
    John F Mulley
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX13PS UK
    BMC Evol Biol 9:218. 2009
    ....
  6. pmc Classification and nomenclature of all human homeobox genes
    Peter W H Holland
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    BMC Biol 5:47. 2007
    ..Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described...
  7. pmc The origin and evolution of ARGFX homeobox loci in mammalian radiation
    Guang Li
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    BMC Evol Biol 10:182. 2010
    ..Here we ask when and how this locus originated and examine its pattern of molecular evolution...
  8. ncbi request reprint A Gbx homeobox gene in amphioxus: insights into ancestry of the ANTP class and evolution of the midbrain/hindbrain boundary
    L Filipe C Castro
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Dev Biol 295:40-51. 2006
    ..Comparison with hemichordates suggests that anterior Otx and posterior Gbx domains were probably overlapping in the ancestral deuterostome and came to abut at the MHB early in the chordate lineage before MHB organizer properties evolved...
  9. doi request reprint Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization
    Jerome H L Hui
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 29:157-65. 2012
    ..dumerilii and chordates. This implies a very low rate of interchromosomal genome rearrangement in the lineages leading to P. dumerilii and the chordate ancestor since the time of the PDA...
  10. doi request reprint Do cnidarians have a ParaHox cluster? Analysis of synteny around a Nematostella homeobox gene cluster
    Jerome H L Hui
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Evol Dev 10:725-30. 2008
    ..This proves that the duplication that gave rise to the Hox and ParaHox regions of bilaterians occurred before the origin of cnidarians, and the cnidarian N. vectensis has bona fide Hox and ParaHox loci...
  11. pmc Parallel retention of Pdx2 genes in cartilaginous fish and coelacanths
    John F Mulley
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 27:2386-91. 2010
    ..The Pdx2 gene has been lost independently in ray-finned fish and in tetrapods...
  12. doi request reprint A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus?
    Jordi Paps
    Department of Zoology, University of Oxford, UK
    Brief Funct Genomics 11:177-86. 2012
    ..We conclude that, at least in terms of transcription factor gene complexity, the genome of amphioxus has experienced remarkable stasis compared to the genomes of other chordates...
  13. ncbi request reprint Annotation, nomenclature and evolution of four novel homeobox genes expressed in the human germ line
    H Anne F Booth
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Gene 387:7-14. 2007
    ..Deducing the evolutionary origins of these genes is not straightforward, but we propose that TPRX1, DPRX and DUXA are highly divergent derivatives of the CRX gene, itself a member of the Otx homeobox gene family...
  14. pmc Breakup of a homeobox cluster after genome duplication in teleosts
    John F Mulley
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 103:10369-72. 2006
    ..We propose that this homeobox gene cluster is held together in chordates by the existence of interdigitated control regions that could be separated after locus duplication in the teleost fish...
  15. ncbi request reprint Amphioxus and ascidian Dmbx homeobox genes give clues to the vertebrate origins of midbrain development
    Tokiharu Takahashi
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Development 131:3285-94. 2004
    ..We discuss the evolution of midbrain development in relation to the ancestry of the tripartite neural ground plan and the origin of the MHB organiser...
  16. ncbi request reprint Eleven daughters of NANOG
    H Anne F Booth
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Genomics 84:229-38. 2004
    ..The mouse genome has two processed pseudogenes, which are not clear orthologues of the primate pseudogenes...
  17. ncbi request reprint A degenerate ParaHox gene cluster in a degenerate vertebrate
    Rebecca F Furlong
    Department of Zoology, Oxford University, Oxford, United Kingdom
    Mol Biol Evol 24:2681-6. 2007
    ..Furthermore, our phylogenetic analyses suggest that hagfishes may have diverged from the vertebrate lineage before the duplications, which created the multiple ParaHox clusters in jawed vertebrates...
  18. ncbi request reprint Buddenbrockia is a cnidarian worm
    Eva Jimenez-Guri
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Science 317:116-8. 2007
    ..This active muscular worm increases the known diversity in cnidarian body plans and demonstrates that a muscular, wormlike form can evolve in the absence of overt bilateral symmetry...
  19. ncbi request reprint An antecedent of the MHC-linked genomic region in amphioxus
    L Filipe C Castro
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Immunogenetics 55:782-4. 2004
    ..The composition of the MHC-linked genomic region, therefore, pre-dates vertebrate origins...
  20. doi request reprint Asymmetry in a pterobranch hemichordate and the evolution of left-right patterning
    Atsuko Sato
    Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
    Dev Dyn 237:3634-9. 2008
    ..Together with previous studies, our results suggest that hemichordates have undergone degeneration in the precision of asymmetry from an ancestral asymmetrical condition that existed before the divergence of deuterostomes...
  21. pmc Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression
    Thomas Butts
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Proc Biol Sci 277:3381-9. 2010
    ..In the case of these homeobox genes, we propose that this has occurred in relation to the evolution of the chordate pharynx and brain...
  22. doi request reprint The urbilaterian Super-Hox cluster
    Thomas Butts
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Trends Genet 24:259-62. 2008
    ..Here we show that this cluster was embedded within a larger homeobox gene cluster, the Super-Hox cluster, in the ancestral bilaterian. This Super-Hox cluster contained at least eight genes alongside the core Hox genes ('EuHox' genes)...
  23. ncbi request reprint Origin and evolution of a myxozoan worm
    Eva Jimenez-Guri
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6BX, UK
    Integr Comp Biol 47:752-8. 2007
    ..bryozoides or T. bryosalmonae. Implications for the evolution of worm-like body plans in the Myxozoa are discussed...
  24. pmc A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates
    Alan O Marron
    Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
    Proc Biol Sci 280:20122543. 2013
    ....
  25. pmc Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, UK
    Biol Lett 4:370-4. 2008
    ..The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence...
  26. ncbi request reprint The evolution of homeobox genes: Implications for the study of brain development
    Peter W H Holland
    Department of Zoology, University of Oxford, UK
    Brain Res Bull 66:484-90. 2005
    ..We argue that understanding evolutionary history is important for establishing consistent gene nomenclature, and for comparing gene expression patterns and gene functions between species and between gene families...
  27. doi request reprint Developmental biology of pterobranch hemichordates: history and perspectives
    Atsuko Sato
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Genesis 46:587-91. 2008
    ..Given that the larval and adult forms differ from enteropneusts, we suggest that molecular developmental studies of pterobranchs may offer new insights into chordate origins...
  28. pmc Degenerate evolution of the hedgehog gene in a hemichordate lineage
    Atsuko Sato
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 106:7491-4. 2009
    ..We conclude that the Hh sequence and expression in S. kowalevskii represent the derived state for deuterostomes, and we argue that functional evolution accompanied secondary reduction of the central nervous system in harrimaniids...
  29. doi request reprint How are comparative genomics and the study of microRNAs changing our views on arthropod endocrinology and adaptations to the environment?
    Nathan J Kenny
    Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
    Gen Comp Endocrinol 188:16-22. 2013
    ....
  30. pmc HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology
    Ying Fu Zhong
    Department of Zoology, University of Oxford, Oxford, UK
    Evol Dev 13:567-8. 2011
    ..HomeoDB2 provides a resource for studying the dynamics of homeobox gene evolution, and is freely accessible at http://homeodb.zoo.ox.ac.uk...
  31. ncbi request reprint The evolution of multicellularity and early animal genomes
    Nina M Brooke
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Curr Opin Genet Dev 13:599-603. 2003
    ..The homeobox and kinase gene families have been further analysed in basal animals, although more data are required to enable detailed comparison with Bilateria...
  32. pmc The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens
    Christoph Loenarz
    Chemistry Research Laboratory and the Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
    EMBO Rep 12:63-70. 2011
    ..Cross-genomic analyses rationalize the relative importance of HIF system components, and imply that the HIF system is likely to be present in all animals, but is unique to this kingdom...
  33. ncbi request reprint Bayesian phylogenetic analysis supports monophyly of ambulacraria and of cyclostomes
    Rebecca F Furlong
    School of Animal and Microbial Sciences, The University of Reading, Whiteknoghts, UK
    Zoolog Sci 19:593-9. 2002
    ..Using robust Bayesian statistical analysis of 18S ribosomal DNA, mitochondrial genes and nuclear protein-coding DNA, we find strong support for a hemichordate-echinoderm clade, and for monophyly of the cyclostomes...
  34. ncbi request reprint Ciona intestinalis ParaHox genes: evolution of Hox/ParaHox cluster integrity, developmental mode, and temporal colinearity
    David E K Ferrier
    School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading, RG6 6AJ, UK
    Mol Phylogenet Evol 24:412-7. 2002
    ..This disintegration may be mediated by the invasion of transposable elements into the clusters, and subsequent genomic rearrangements...
  35. ncbi request reprint More genes in vertebrates?
    Peter W H Holland
    School of Animal and Microbial Sciences, The University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, United Kingdom
    J Struct Funct Genomics 3:75-84. 2003
    ..These data confirm that vertebrates have more genes than their closest invertebrate relatives, acquired through gene duplication...
  36. ncbi request reprint An orphan PRD class homeobox gene expressed in mouse brain and limb development
    Tokiharu Takahashi
    School of Animal and Microbial Science, The University of Reading, Whiteknights, Reading, RG6 6AJ, UK
    Dev Genes Evol 212:293-7. 2002
    ..Unusually for homeobox genes, there is no orthologue in the Drosophila or Caenorhabditis genomes; we argue this reflects secondary loss...
  37. pmc Dispersal of NK homeobox gene clusters in amphioxus and humans
    Graham N Luke
    School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, United Kingdom
    Proc Natl Acad Sci U S A 100:5292-5. 2003
    ..This evolutionary pattern is in marked contrast to the Hox and ParaHox gene clusters, which are compact in amphioxus and vertebrates, but have been disrupted in Drosophila...
  38. ncbi request reprint Phylogenomics of eukaryotes: impact of missing data on large alignments
    Hervé Philippe
    School of Animal and Microbial Sciences, The University of Reading, Reading, UK
    Mol Biol Evol 21:1740-52. 2004
    ....
  39. pmc Were vertebrates octoploid?
    Rebecca F Furlong
    School of Animal and Microbial Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, UK
    Philos Trans R Soc Lond B Biol Sci 357:531-44. 2002
    ..We propose that early vertebrates passed through an autoautooctoploid phase in the evolution of their genomes...
  40. pmc No more than 14: the end of the amphioxus Hox cluster
    Carolina Minguillon
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona Av Diagonal, 645 E 08028, Barcelona, Spain
    Int J Biol Sci 1:19-23. 2005
    ..We suggest that 14 is the end...
  41. pmc An unusual choanoflagellate protein released by Hedgehog autocatalytic processing
    Elizabeth A Snell
    School of Animal and Microbial Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, UK
    Proc Biol Sci 273:401-7. 2006
    ..Since Hh-C and Hoglet-C are homologous, but Hh-N and Hoglet-N are not, we argue that metazoan hedgehog genes evolved by fusion of two distinct genes...
  42. pmc Patterns of conservation and change in honey bee developmental genes
    Peter K Dearden
    Laboratory for Evolution and Development, Biochemistry Department, University of Otago, Dunedin, Aotearoa New Zealand
    Genome Res 16:1376-84. 2006
    ....
  43. doi request reprint The amphioxus genome and the evolution of the chordate karyotype
    Nicholas H Putnam
    Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
    Nature 453:1064-71. 2008
    ..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution...
  44. pmc The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    Linda Z Holland
    Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093 0202, USA
    Genome Res 18:1100-11. 2008
    ..Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates...
  45. ncbi request reprint The origins of multicellularity: a multi-taxon genome initiative
    Inaki Ruiz-Trillo
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Trends Genet 23:113-8. 2007
    ..Here, we introduce this initiative and the biological questions that underpin it, summarize the rationale guiding the choice of organisms and discuss the anticipated benefits to the broader scientific community...
  46. ncbi request reprint Orphan worm finds a home: Buddenbrockia is a myxozoan
    Ana Sara Monteiro
    Mol Biol Evol 19:968-71. 2002