Chris P Ponting

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc Duplication and positive selection among hominin-specific PRAME genes
    Zoë Birtle
    Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
    BMC Genomics 6:120. 2005
  2. pmc Diverse spatial, temporal, and sexual expression of recently duplicated androgen-binding protein genes in Mus musculus
    Christina M Laukaitis
    Department of Biological Sciences, Butler University, 4600 Sunset Ave, Indianapolis, Indiana 46208, USA
    BMC Evol Biol 5:40. 2005
  3. pmc Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction
    C P Ponting
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Biochem J 351:527-35. 2000
  4. pmc Novel domains and orthologues of eukaryotic transcription elongation factors
    Chris P Ponting
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Nucleic Acids Res 30:3643-52. 2002
  5. ncbi request reprint Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution
    C P Ponting
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
    Genome Res 11:1996-2008. 2001
  6. ncbi request reprint Genome cartography through domain annotation
    C P Ponting
    MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford OX13QX, UK
    Genome Biol 2:Comment 2006. 2001
  7. ncbi request reprint Issues in predicting protein function from sequence
    C P Ponting
    Department of Human Anatomy and Genetics, University of Oxford, UK
    Brief Bioinform 2:19-29. 2001
  8. ncbi request reprint Plagiarized bacterial genes in the human book of life
    C P Ponting
    MRC Functional Genetics Unit, Dept of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK OX1 3QX
    Trends Genet 17:235-7. 2001
  9. ncbi request reprint Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all beta-trefoil proteins
    C P Ponting
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, UK
    J Mol Biol 302:1041-7. 2000
  10. ncbi request reprint A novel domain suggests a ciliary function for ASPM, a brain size determining gene
    Chris P Ponting
    MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics South Parks Road, Oxford OX1 3QX, UK
    Bioinformatics 22:1031-5. 2006

Detail Information

Publications101 found, 100 shown here

  1. pmc Duplication and positive selection among hominin-specific PRAME genes
    Zoë Birtle
    Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
    BMC Genomics 6:120. 2005
    ..PRAME-like genes are expressed in the testis and in a large number of tumours, and are thought to possess roles in spermatogenesis and oogenesis...
  2. pmc Diverse spatial, temporal, and sexual expression of recently duplicated androgen-binding protein genes in Mus musculus
    Christina M Laukaitis
    Department of Biological Sciences, Butler University, 4600 Sunset Ave, Indianapolis, Indiana 46208, USA
    BMC Evol Biol 5:40. 2005
    ..This makes ABP an appropriate model system with which to investigate how recent adaptive evolution of paralogous genes results in functional innovation (neofunctionalization)...
  3. pmc Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction
    C P Ponting
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Biochem J 351:527-35. 2000
    ..This finding hints at the mechanism by which Ire1p may sense extended unfolded proteins at the expense of compact folded molecules...
  4. pmc Novel domains and orthologues of eukaryotic transcription elongation factors
    Chris P Ponting
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Nucleic Acids Res 30:3643-52. 2002
    ..These findings imply that much of the transcription elongation machinery of eukaryotes has been acquired subsequent to their divergence from prokaryotes...
  5. ncbi request reprint Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution
    C P Ponting
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
    Genome Res 11:1996-2008. 2001
    ..These findings demonstrate how completely sequenced genomes can be exploited to further understand the relationships between molecular structure, function, and evolution...
  6. ncbi request reprint Genome cartography through domain annotation
    C P Ponting
    MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford OX13QX, UK
    Genome Biol 2:Comment 2006. 2001
    ..To account for the great diversity of domain contexts and an unexpected paucity of ortholog conservation, we must categorize the coding regions of completely sequenced genomes into domain families, as well as protein families...
  7. ncbi request reprint Issues in predicting protein function from sequence
    C P Ponting
    Department of Human Anatomy and Genetics, University of Oxford, UK
    Brief Bioinform 2:19-29. 2001
    ..Pitfalls in database searching methods arising from amino acid compositional bias and database size effects are also discussed...
  8. ncbi request reprint Plagiarized bacterial genes in the human book of life
    C P Ponting
    MRC Functional Genetics Unit, Dept of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK OX1 3QX
    Trends Genet 17:235-7. 2001
    ..So how did the human 'book of life' evolve to be a chimaera, part animal and part bacterium? And what was the probable evolutionary impact of such gene plagiarism?..
  9. ncbi request reprint Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all beta-trefoil proteins
    C P Ponting
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, UK
    J Mol Biol 302:1041-7. 2000
    ..The combined analysis of structure and sequence databases for detecting significant similarities is suggested as a highly sensitive approach to determining the common ancestry of extremely divergent homologues...
  10. ncbi request reprint A novel domain suggests a ciliary function for ASPM, a brain size determining gene
    Chris P Ponting
    MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics South Parks Road, Oxford OX1 3QX, UK
    Bioinformatics 22:1031-5. 2006
    ..ASPM's rapid evolution may thus reflect selective pressures on ciliary function, rather than pressures on mitosis during neurogenesis...
  11. pmc Mammalian BEX, WEX and GASP genes: coding and non-coding chimaerism sustained by gene conversion events
    Eitan E Winter
    Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
    BMC Evol Biol 5:54. 2005
    ....
  12. pmc Genome assembly quality: assessment and improvement using the neutral indel model
    Stephen Meader
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 20:675-84. 2010
    ..Our approach contributes a new fine-scale quality metric for assemblies that should facilitate development of improved genome sequencing and assembly strategies...
  13. pmc The genomic landscape shaped by selection on transposable elements across 18 mouse strains
    Christoffer Nellåker
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
    Genome Biol 13:R45. 2012
    ..Despite their high prevalence, the different genomic and gene properties controlling whether TEs are preferentially purged from, or are retained by, genetic drift or positive selection in mammalian genomes remain poorly defined...
  14. pmc Variable strength of translational selection among 12 Drosophila species
    Andreas Heger
    MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genetics 177:1337-48. 2007
    ..The strength of translational selection was predicted to have varied between species largely according to their phylogeny, with the D. melanogaster group species exhibiting the strongest degree of selection...
  15. pmc Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa
    Peter L Oliver
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000753. 2009
    ..We suggest that Prdm9 should be investigated as a candidate gene in other instances of hybrid sterility in metazoans...
  16. pmc OPTIC: orthologous and paralogous transcripts in clades
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK
    Nucleic Acids Res 36:D267-70. 2008
    ..Gene predictions, multiple alignments and phylogenetic trees are freely available to browse and download from http://genserv.anat.ox.ac.uk/clades. Further genomes and clades will be added in the future...
  17. pmc Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
    Ana C Marques
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, UK
    Genome Biol 10:R124. 2009
    ..This apparent difference may account for the surprisingly small fraction (11%) of transcripts that are represented in both catalogues. Here we sought to resolve the reported discrepancy between the evolutionary rates for these two sets...
  18. pmc GAT: a simulation framework for testing the association of genomic intervals
    Andreas Heger
    MRC CGAT Programme and Functional Genomics Unit, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
    Bioinformatics 29:2046-8. 2013
    ..This question arises, for example, when interpreting ChIP-Seq or RNA-Seq data in functional terms. Because genome organization is complex, answering this question is non-trivial...
  19. ncbi request reprint Structure-function mapping of BbCRASP-1, the key complement factor H and FHL-1 binding protein of Borrelia burgdorferi
    Frank S Cordes
    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Int J Med Microbiol 296:177-84. 2006
    ..This work demonstrates that pathogens interact with complement regulators in ways that are distinct from the mechanisms used by the host and are thus obvious targets for drug design...
  20. pmc Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes
    Rebecca A Chodroff
    Department of Physiology, Anatomy, and Genetics, Le Gros Clark Building South Parks Road, University of Oxford, Oxford OX1 3QX, UK
    Genome Biol 11:R72. 2010
    ..This dearth of information is partially attributable to a lack of established non-protein-coding RNA (ncRNA) orthologs among birds and mammals within sequence and expression databases...
  21. pmc Comparative evolutionary genomics of androgen-binding protein genes
    Richard D Emes
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 14:1516-29. 2004
    ..We propose a role for ABPalpha/beta/gamma proteins as pheromones, or in modulating odorant detection. This would account for the extraordinary adaptive evolution of these genes, and surrounding genomic regions, in murid rodents...
  22. pmc A transcriptomic atlas of mouse neocortical layers
    T Grant Belgard
    MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
    Neuron 71:605-16. 2011
    ....
  23. ncbi request reprint Meisetz and the birth of the KRAB motif
    Zoë Birtle
    Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford South Parks Road, Oxford OX1 3QX, UK
    Bioinformatics 22:2841-5. 2006
    ..Finally, we present evidence that KRAB motifs derive from a novel family of KRI (KRAB Interior) motifs that were present in the last common ancestor of animals, plants and fungi...
  24. pmc Massive turnover of functional sequence in human and other mammalian genomes
    Stephen Meader
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 20:1335-43. 2010
    ..This suggests that, rather than genome size or protein-coding gene complement, it is the number of functional bases that might best mirror our naïve preconceptions of organismal complexity...
  25. ncbi request reprint The long and the short of RNA maps
    Jasmina Ponjavic
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, UK
    Bioessays 29:1077-80. 2007
    ..These results suggest that a proportion of these RNAs might have roles in the cis-regulation of neighbouring protein-coding genes' expression...
  26. pmc Accelerated evolution of PAK3- and PIM1-like kinase gene families in the zebra finch, Taeniopygia guttata
    Lesheng Kong
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 27:1923-34. 2010
    ..Nevertheless, our results show how ancient and conserved intracellular signaling molecules can be co-opted, following duplication, thereby resulting in lineage-specific functions, presumably affecting the zebra finch testis and brain...
  27. ncbi request reprint TRAM, LAG1 and CLN8: members of a novel family of lipid-sensing domains?
    Eitan Winter
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK OX1 3QX
    Trends Biochem Sci 27:381-3. 2002
    ..The identification of these homologues has potential implications for our understanding of ceramide synthesis, lipid regulation and protein translocation in the endoplasmic reticulum...
  28. pmc Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 17:1837-49. 2007
    ..Duplications were significantly more frequent among trypsin-like proteases and DM8 putative lipid-binding domain proteins...
  29. pmc Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human
    Leo Goodstadt
    Medical Research Council Functional Genetics Unit, University of Oxford, Department of Physiology, Anatomy, and Genetics, Oxford, United Kingdom
    PLoS Comput Biol 2:e133. 2006
    ..PhyOP will be particularly useful in predicting orthology for mammalian genomes that have been incompletely sequenced, and for large families of rapidly duplicating genes...
  30. pmc THoR: a tool for domain discovery and curation of multiple alignments
    Nicholas J Dickens
    MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
    Genome Biol 4:R52. 2003
    ..THoR has been benchmarked for accuracy using the SMART and pufferfish genome databases...
  31. pmc Reduced purifying selection prevails over positive selection in human copy number variant evolution
    Duc Quang Nguyen
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, United Kingdom
    Genome Res 18:1711-23. 2008
    ..In contrast, SD sequences that appear fixed in the human population lie more frequently within low G+C sequence. These findings provide an overarching view of how CNVs arise and segregate in the human population...
  32. pmc Hotspots of mutation and breakage in dog and human chromosomes
    Caleb Webber
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 15:1787-97. 2005
    ..Rather, we propose that high G+C sequences are found preferentially within dog subtelomeres as a direct consequence of chromosomal fission occurring more frequently within regions elevated in G+C...
  33. ncbi request reprint Comparison of the genomes of human and mouse lays the foundation of genome zoology
    Richard D Emes
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Hum Mol Genet 12:701-9. 2003
    ..We predict that the availability of numerous animal genomes will give rise to a new field of genome zoology in which differences in animal physiology and ethology are illuminated by the study of genomic sequence variations...
  34. doi request reprint Separating derived from ancestral features of mouse and human genomes
    Chris P Ponting
    Department of Physiology, MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
    Biochem Soc Trans 37:734-9. 2009
    ..Nevertheless, many such genes may be under little or no selection...
  35. pmc Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents
    Richard D Emes
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
    Genome Res 14:591-602. 2004
    ..We predict that these contribute to physicochemical and functional diversity within pheromone-receptor interaction sites...
  36. pmc Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes
    Martin S Taylor
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
    Genome Res 14:555-66. 2004
    ..There is a specific enrichment of CpG dinucleotides in close proximity to insertion events, and both insertions and deletions are more common in higher G+C content sequences...
  37. pmc Forging links between human mental retardation-associated CNVs and mouse gene knockout models
    Caleb Webber
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000531. 2009
    ..This study is the first to demonstrate how the power of mouse knockout data can be systematically exploited to better understand genetically heterogeneous neurological disorders...
  38. doi request reprint A common ancestry for BAP1 and Uch37 regulators
    Luis Sanchez-Pulido
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
    Bioinformatics 28:1953-6. 2012
    ..Our analysis demonstrates a common ancestry for BAP1 and Uch37 regulators in PR-DUB, INO80 chromatin remodelling and proteosome complexes...
  39. doi request reprint Nprl3 is required for normal development of the cardiovascular system
    Monika S Kowalczyk
    MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK
    Mamm Genome 23:404-15. 2012
    ..NPRL3 is a candidate gene for harbouring mutations in individuals with developmental abnormalities of the cardiovascular system...
  40. pmc Wrangling for microRNAs provokes much crosstalk
    Ana C Marques
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, UK
    Genome Biol 12:132. 2011
    ..Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks...
  41. doi request reprint Structure and evolutionary history of DISC1
    Luis Sanchez-Pulido
    Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, South Parks Road, Oxford, UK
    Hum Mol Genet 20:R175-81. 2011
    ..One common missense variant in DISC1 (L607F) lies within the second DISC1 UVR-like domain. These observations should assist in delineating the functional regions of the DISC1 protein...
  42. pmc Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
    Jasmina Ponjavic
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 17:556-65. 2007
    ..2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality. Our findings should now provide an incentive for the experimental investigation of these macroRNAs' functions...
  43. pmc An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes
    Leo Goodstadt
    MRC Functional Genetics Unit, University of Oxford, Department of Physiology, Oxford, UK
    Genome Res 17:969-81. 2007
    ..In particular, we propose that the higher G+C content of the Monodelphis X chromosome is a direct consequence of its small size relative to the giant autosomes...
  44. pmc Bias of selection on human copy-number variants
    Duc Quang Nguyen
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 2:e20. 2006
    ..It thus appears that CNV differences among mouse strains do not provide an appropriate model for large-scale sequence variations in the human population...
  45. ncbi request reprint The natural history of protein domains
    Chris P Ponting
    Department of Human Anatomy and Genetics, University of Oxford, MRC Functional Genetics Unit, South Parks Road, Oxford OX1 3QX, UK
    Annu Rev Biophys Biomol Struct 31:45-71. 2002
    ..These parallels illustrate how the concept of domains can be applied to provide insights into evolutionary biology...
  46. pmc Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
    Jasmina Ponjavic
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000617. 2009
    ....
  47. doi request reprint Accurate estimation of gene evolutionary rates using XRATE, with an application to transmembrane proteins
    Andreas Heger
    Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, UK
    Mol Biol Evol 26:1715-21. 2009
    ..Less stringent purifying selection is thus a general property of the extracellular milieu, rather than being specific to only soluble and secreted proteins...
  48. pmc Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence
    Chris M Rands
    Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK
    BMC Genomics 14:95. 2013
    ..Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris...
  49. doi request reprint Identification and functional analysis of an ovarian form of the egg activation factor phospholipase C zeta (PLCζ) in pufferfish
    Kevin Coward
    Department of Obstetrics and Gynaecology, John Radcliffe Hospital, Headington, Oxford, UK
    Mol Reprod Dev 78:48-56. 2011
    ....
  50. doi request reprint Evolution and functions of long noncoding RNAs
    Chris P Ponting
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford, OX1 3QX, UK
    Cell 136:629-41. 2009
    ..Here, we review the evolution of lncRNAs and their roles in transcriptional regulation, epigenetic gene regulation, and disease...
  51. doi request reprint The functional repertoires of metazoan genomes
    Chris P Ponting
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, UK
    Nat Rev Genet 9:689-98. 2008
    ..Yet it is here, encoded in lineage-specific and functional sequence, that we expect physiological differences between species to be most concentrated...
  52. pmc Elevated rates of protein secretion, evolution, and disease among tissue-specific genes
    Eitan E Winter
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
    Genome Res 14:54-61. 2004
    ..These findings illuminate major selective pressures that have shaped the gene repertoires expressed in different mammalian tissues...
  53. ncbi request reprint Signatures of adaptive evolution within human non-coding sequence
    Chris P Ponting
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Hum Mol Genet 15:R170-5. 2006
    ..Illuminating the functions of this adaptive dark matter will lead to a better understanding of the sequence changes that have shaped the innovative biology of our species...
  54. pmc Genome-wide identification of human functional DNA using a neutral indel model
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 2:e5. 2006
    ..The ability to identify elements under heterogeneous selection enables, for the first time, the genome-wide investigation of positive selection on functional elements other than protein-coding genes...
  55. pmc A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution
    Sreeram V Ramagopalan
    Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
    Genome Res 20:1352-60. 2010
    ..ChIP-seq determination of transcription factor binding, in combination with GWA data, provides a powerful approach to further understanding the molecular bases of complex diseases...
  56. ncbi request reprint Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9
    Andrew R Bassett
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
    Biol Open . 2013
    ..This technology enables controlled genetic manipulation in Drosophila cell lines, and its simplicity offers the opportunity to study cellular phenotypes genome-wide...
  57. pmc Network topologies and convergent aetiologies arising from deletions and duplications observed in individuals with autism
    Hyun Ji Noh
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy, and Genetics, Oxford, United Kingdom
    PLoS Genet 9:e1003523. 2013
    ....
  58. pmc Cofilin-1: a modulator of anxiety in mice
    Martin Goodson
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 8:e1002970. 2012
    ..Our results indicate that similarity of function of mammalian genes can be used to recognize key genetic regulators of anxiety and potentially of other emotional behaviours...
  59. doi request reprint Rapid turnover of functional sequence in human and other genomes
    Chris P Ponting
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Annu Rev Genomics Hum Genet 12:275-99. 2011
    ..In contrast to the slow rate at which protein-coding sequence changes, functional noncoding sequence appears to change or be turned over at rapid rates in mammals...
  60. ncbi request reprint Vitamin K epoxide reductase: homology, active site and catalytic mechanism
    Leo Goodstadt
    MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford, OX1 3QX, UK
    Trends Biochem Sci 29:289-92. 2004
    ..These might reduce disulfide bonds of VKORC1-like enzymes as a prerequisite for their catalytic activities...
  61. pmc Transcribed dark matter: meaning or myth?
    Chris P Ponting
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK
    Hum Mol Genet 19:R162-8. 2010
    ..These issues will only be resolved upon the demonstration, or otherwise, that organismal or cellular phenotypes frequently result when non-coding RNA loci are disrupted...
  62. ncbi request reprint Genes and homology
    Caleb Webber
    MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
    Curr Biol 14:R332-3. 2004
  63. pmc The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase
    Thomas Gerken
    Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, Oxon OX1 3TA, UK
    Science 318:1469-72. 2007
    ..Studies can now be directed toward determining the physiologically relevant FTO substrate and how nucleic acid methylation status is linked to increased fat mass...
  64. pmc What fraction of the human genome is functional?
    Chris P Ponting
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 21:1769-76. 2011
    ..Experimental investigations focusing on lineage-specific, noncoding, and functional sequence are now essential if we are to appreciate the complete functional repertoire of the human genome...
  65. ncbi request reprint Identification of a novel family of presenilin homologues
    Chris P Ponting
    MRC Functional Genetics Unit, University of Oxford, Department of Human Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
    Hum Mol Genet 11:1037-44. 2002
    ..Based on these findings, we propose that PSs and PSHs represent different sub-branches of a larger family of polytopic membrane-associated aspartyl proteases...
  66. doi request reprint What are the genomic drivers of the rapid evolution of PRDM9?
    Chris P Ponting
    Medical Research Council Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
    Trends Genet 27:165-71. 2011
    ....
  67. doi request reprint Cdc45: the missing RecJ ortholog in eukaryotes?
    Luis Sanchez-Pulido
    Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
    Bioinformatics 27:1885-8. 2011
    ..The likely orthology between Cdc45 and RecJ reveals new lines of enquiry into DNA replication mechanisms in eukaryotes...
  68. ncbi request reprint Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma
    Youming Zhang
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
    Nat Genet 34:181-6. 2003
    ..We also found association with these variants to severe clinical asthma. The gene product (PHF11) contains two PHD zinc fingers and probably regulates transcription. Distinctive splice variants were expressed in immune tissues and cells...
  69. ncbi request reprint Brain, know thy transcriptome, know thyself
    Chris P Ponting
    MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy, and Genetics, Oxford OX1 3PT, UK
    Neuron 75:543-5. 2012
    ..The data provide an initial opportunity for linking genomic and brain differences among these primate species...
  70. pmc Mutations in BMP4 cause eye, brain, and digit developmental anomalies: overlap between the BMP4 and hedgehog signaling pathways
    Preeti Bakrania
    Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Am J Hum Genet 82:304-19. 2008
    ..Our finding of low-penetrant variants in BMP4 and HH signaling partners is suggestive of an interaction between the two pathways in humans...
  71. pmc Genome analysis of the platypus reveals unique signatures of evolution
    Wesley C Warren
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 453:175-83. 2008
    ..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation...
  72. ncbi request reprint Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  73. pmc InterPro, progress and status in 2005
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 33:D201-5. 2005
    ..The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  74. ncbi request reprint A SNP map of the rat genome generated from cDNA sequences
    Heike Zimdahl
    Max Delbrück Center for Molecular Medicine MDC, Robert Rossle Str 10, 13092 Berlin Buch, Germany
    Science 303:807. 2004
  75. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  76. ncbi request reprint Evolutionary biology: human brain gene wins genome race
    Chris P Ponting
    Nature 443:149-50. 2006
  77. pmc Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes
    Hui Huang
    Department of Bioinformatics, Genome Therapeutics Corporation, Waltham, MA 02453, USA
    Genome Biol 5:R47. 2004
    ..Here, we investigate whether human disease genes differ significantly from their rodent orthologs with respect to their overall levels of conservation and their rates of evolutionary change...
  78. ncbi request reprint Cadherin-like domains in alpha-dystroglycan, alpha/epsilon-sarcoglycan and yeast and bacterial proteins
    Nicholas J Dickens
    Curr Biol 12:R197-9. 2002
  79. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  80. pmc Systematic identification of novel protein domain families associated with nuclear functions
    Tobias Doerks
    European Molecular Biology Laboratory, 69114 Heidelberg, Germany
    Genome Res 12:47-56. 2002
    ....
  81. ncbi request reprint Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
  82. ncbi request reprint GIFT domains: linking eukaryotic intraflagellar transport and glycosylation to bacterial gliding
    Scott Beatson
    Microbial Genomics Group, Institute for Biomedical Research, Division of Immunity and Infection, Medical School, University of Birmingham, Birmingham, UK B15 2TT
    Trends Biochem Sci 29:396-9. 2004
    ..A distant evolutionary relationship to periplasmic-binding proteins hints that GIFT domains might possess oligosaccharide-binding functions...
  83. pmc Recent improvements to the SMART domain-based sequence annotation resource
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 30:242-4. 2002
    ..SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk...
  84. ncbi request reprint OPR, PC and AID: all in the PB1 family
    Chris P Ponting
    Trends Biochem Sci 27:10. 2002
  85. pmc SMART 4.0: towards genomic data integration
    Ivica Letunic
    EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nucleic Acids Res 32:D142-4. 2004
    ..Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries...
  86. pmc Defensins and the convergent evolution of platypus and reptile venom genes
    Camilla M Whittington
    Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia
    Genome Res 18:986-94. 2008
    ..Convergent evolution has repeatedly selected genes coding for proteins containing specific structural motifs as templates for venom molecules...
  87. pmc Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals
    Christina M Laukaitis
    Department of Medical Genetics, University of Washington, Seattle, USA and Division of Human Biology, Fred Hutchinson CancerResearch Center, Seattle, USA
    BMC Evol Biol 8:46. 2008
    ..Questions arise from imperfections in the initial mouse genome assembly and a dearth of information about the gene family structure in other rodents and mammals...
  88. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  89. ncbi request reprint UBA domain containing proteins in fission yeast
    Rasmus Hartmann-Petersen
    August Krogh Institute, University of Copenhagen, Universitetsparken 13, DK 2100, Copenhagen, Denmark
    Int J Biochem Cell Biol 35:629-36. 2003
    ..The proteins display remarkable differences in their domain organisation, indicating that these potential ubiquitin binding proteins are involved in various cell activities...
  90. ncbi request reprint The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains
    Sebastian Maurer-Stroh
    Research Institute of Molecular Pathology, Dr Bohr Gasse 7, A 1030 Vienna, Austria
    Trends Biochem Sci 28:69-74. 2003
    ..In addition, we have revealed pairs of tandem repeats in the fragile X mental retardation protein (FMRP) family that are also members of this Tudor domain 'Royal Family'...
  91. pmc Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
    Roderic Guigo
    Research Group in Biomedical Informatics, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra Centre de Regulació Genòmica, E08003 Barcelona, Catalonia, Spain
    Proc Natl Acad Sci U S A 100:1140-5. 2003
    ..This is likely to constitute a significant fraction of the previously unknown, multiexon mammalian genes...
  92. pmc The InterPro Database, 2003 brings increased coverage and new features
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 31:315-8. 2003
    ..The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  93. ncbi request reprint Sequence analysis of multidomain proteins: past perspectives and future directions
    Richard R Copley
    Adv Protein Chem 61:75-98. 2002
  94. ncbi request reprint InterPro: an integrated documentation resource for protein families, domains and functional sites
    Nicola J Mulder
    EMBL Outstation, European Bioinformatics Institute, Hinxton, Cambridge, UK
    Brief Bioinform 3:225-35. 2002
    ..Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (2,141,621 InterPro hits from 586,124 SWISS-PROT and TrEMBL protein sequences). The database is freely accessible for text- and sequence-based searches...
  95. pmc Predicting protein cellular localization using a domain projection method
    Richard Mott
    Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom
    Genome Res 12:1168-74. 2002
    ..This method is complementary to approaches that use amino-acid composition or identify sorting sequences; these methods may be combined to further enhance prediction accuracy...
  96. ncbi request reprint EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer
    Luke Hughes-Davies
    Cancer Research UK Wellcome Trust Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
    Cell 115:523-35. 2003
    ..The remarkable clinical overlap between sporadic EMSY amplification and familial BRCA2 deletion implicates a BRCA2 pathway in sporadic breast and ovarian cancer...
  97. ncbi request reprint Structural and mechanistic insights into ras association domains of phospholipase C epsilon
    Tom D Bunney
    Cancer Research UK Centre for Cell and Molecular Biology, Chester Beatty Laboratories, The Institute of Cancer Research, Fulham Road, London SW3 6JB, United Kingdom
    Mol Cell 21:495-507. 2006
    ..Studies of PLCepsilon regulation suggest that, in a cellular context, the RA2 domain, in a mode specific to PLCepsilon, has a role in membrane targeting with further regulatory impact on PLC activity...
  98. ncbi request reprint Positional cloning of a novel gene influencing asthma from chromosome 2q14
    Maxine Allen
    Oxagen, Milton Park, Oxfordshire, UK
    Nat Genet 35:258-63. 2003
    ..6 kb (DPP10), which extends over 1 Mb of genomic DNA. DPP10 encodes a homolog of dipeptidyl peptidases (DPPs) that cleave terminal dipeptides from cytokines and chemokines, and it presents a potential new target for asthma therapy...
  99. pmc A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms
    Gane Ka Shu Wong
    Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China
    Nature 432:717-22. 2004
    ..In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases...
  100. pmc Mutations in TOPORS cause autosomal dominant retinitis pigmentosa with perivascular retinal pigment epithelium atrophy
    Christina F Chakarova
    Institute of Ophthalmology, University College London, London, UK
    Am J Hum Genet 81:1098-103. 2007
    ....