M Ashburner

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc Integrating phenotype ontologies across multiple species
    Christopher J Mungall
    Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 11:R2. 2010
  2. pmc Calling on a million minds for community annotation in WikiProteins
    Barend Mons
    Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
    Genome Biol 9:R89. 2008
  3. pmc The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective
    Joshua S Kaminker
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Genome Biol 3:RESEARCH0084. 2002
  4. pmc Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome
    Casey M Bergman
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
    Genome Biol 7:R112. 2006
  5. pmc The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
  6. pmc Molecular characterization of the singed wings locus of Drosophila melanogaster
    Yuri B Schwartz
    Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090, Russia
    BMC Genet 5:15. 2004
  7. ncbi request reprint A biologist's view of the Drosophila genome annotation assessment project
    M Ashburner
    Department of Genetics, University of Cambridge, England
    Genome Res 10:391-3. 2000
  8. pmc A hat trick--Plasmodium, Anopheles and Homo
    Michael Ashburner
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB3 2EH, UK
    Genome Biol 4:103. 2003
  9. pmc Getting a buzz out of the bee genome
    Michael Ashburner
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
    Genome Biol 7:239. 2006
  10. ncbi request reprint Drosophila melanogaster: a case study of a model genomic sequence and its consequences
    Michael Ashburner
    Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
    Genome Res 15:1661-7. 2005

Detail Information

Publications58

  1. pmc Integrating phenotype ontologies across multiple species
    Christopher J Mungall
    Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Genome Biol 11:R2. 2010
    ..We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology...
  2. pmc Calling on a million minds for community annotation in WikiProteins
    Barend Mons
    Erasmus Medical Centre, Department of Medical Informatics, Rotterdam, The Netherlands
    Genome Biol 9:R89. 2008
    ..We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org...
  3. pmc The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective
    Joshua S Kaminker
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Genome Biol 3:RESEARCH0084. 2002
    ..We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species...
  4. pmc Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome
    Casey M Bergman
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
    Genome Biol 7:R112. 2006
    ..Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the contribution of TEs to genomes sequences...
  5. pmc The Sequence Ontology: a tool for the unification of genome annotations
    Karen Eilbeck
    Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729 3200, USA
    Genome Biol 6:R44. 2005
    ....
  6. pmc Molecular characterization of the singed wings locus of Drosophila melanogaster
    Yuri B Schwartz
    Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090, Russia
    BMC Genet 5:15. 2004
    ..singed wings (swi) is the only gene known in Drosophila melanogaster for which mutations specifically interrupt the transmission of the regulatory signal from early to late ecdysone inducible genes...
  7. ncbi request reprint A biologist's view of the Drosophila genome annotation assessment project
    M Ashburner
    Department of Genetics, University of Cambridge, England
    Genome Res 10:391-3. 2000
  8. pmc A hat trick--Plasmodium, Anopheles and Homo
    Michael Ashburner
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB3 2EH, UK
    Genome Biol 4:103. 2003
    ..This has been a tremendous scientific achievement. But will it offer hope to the millions who die from malaria each year? Yes, but only if combined with political will and social change...
  9. pmc Getting a buzz out of the bee genome
    Michael Ashburner
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
    Genome Biol 7:239. 2006
    ..This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence...
  10. ncbi request reprint Drosophila melanogaster: a case study of a model genomic sequence and its consequences
    Michael Ashburner
    Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
    Genome Res 15:1661-7. 2005
    ..We discuss the impact of the growing number of genome sequences now available in the genus on current Drosophila research, and some of the biological questions that these resources will enable to be solved in the future...
  11. ncbi request reprint Duplication, dicistronic transcription, and subsequent evolution of the Alcohol dehydrogenase and Alcohol dehydrogenase-related genes in Drosophila
    E BETRAN
    Department of Genetics, University of Cambridge, Cambridge, England
    Mol Biol Evol 17:1344-52. 2000
    ..However, why these two genes with clear divergence in the functions of their proteins should remain cotranscribed in groups as divergent as the subgenus Sophophora and the subgenus Scaptodrosophila remains a mystery...
  12. pmc Topological constraints on transvection between white genes within the transposing element TE35B in Drosophila melanogaster
    D Gubb
    Department of Genetics, University of Cambridge, United Kingdom
    Genetics 146:919-37. 1997
    ..Similarly, breakpoints immediately proximal or distal to both w genes give partial suppression. This transvection-dependent downregulation of w genes may result from mis-activation of the X-chromosome dosage compensation mechanism...
  13. pmc A selective screen to recover chromosomal deletions and duplications in Drosophila melanogaster
    D Gubb
    Department of Genetics, University of Cambridge, England
    Genetics 119:377-90. 1988
    ..Such aberration breakpoints can be genetically mapped, as synthetic deletions, and then used as transposon-tagged sites for the recovery of genomic clones...
  14. pmc An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region
    M Ashburner
    Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, England
    Genetics 153:179-219. 1999
    ..Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926..
  15. pmc A novel transvection phenomenon affecting the white gene of Drosophila melanogaster
    D Gubb
    Department of Genetics, University of Cambridge, England
    Genetics 126:167-76. 1990
    ..This effect of rearrangements has been used as the basis for a screen, gamma-ray induced aberrations with at least one breakpoint opposite the TE site were recovered by their suppression of the zeste phenotype...
  16. pmc stress sensitive B encodes an adenine nucleotide translocase in Drosophila melanogaster
    Y Q Zhang
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, England
    Genetics 153:891-903. 1999
    ..This hypothesis is not supported by our study of the ANT genes of D. melanogaster...
  17. ncbi request reprint The Dichaete gene of Drosophila melanogaster encodes a SOX-domain protein required for embryonic segmentation
    S R Russell
    Department of Genetics, University of Cambridge, UK
    Development 122:3669-76. 1996
    ....
  18. pmc The Drosophila melanogaster hybrid male rescue gene causes inviability in male and female species hybrids
    D A Barbash
    Department of Genetics, University of Cambridge, United Kingdom
    Genetics 154:1747-71. 2000
    ..melanogaster mothers. Implications of our findings for understanding Haldane's rule-the observation that hybrid breakdown is often specific to the heterogametic sex-are also discussed...
  19. pmc The Drosophila embargoed gene is required for larval progression and encodes the functional homolog of schizosaccharomyces Crm1
    S Collier
    Department of Genetics, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
    Genetics 155:1799-807. 2000
    ..We see a nuclear accumulation of endogenous actin in the intestinal epithelial cells of the emb mutant larvae, consistent with a role for the emb gene product in nuclear export of actin protein...
  20. pmc Characterization of the FB-NOF transposable element of Drosophila melanogaster
    N Harden
    Department of Genetics, University of Cambridge, England
    Genetics 126:387-400. 1990
    ..These strains also have an increased number of FB elements. The DNA sequence of the NOF region associated with TE146(Z) has been determined...
  21. ncbi request reprint Molecular organization of the Drosophila melanogaster Adh chromosomal region in D. repleta and D. buzzatii, two distantly related species of the Drosophila subgenus
    J Gonzalez
    Department of Genetics, University of Cambridge, UK
    Chromosome Res 8:375-85. 2000
    ..repleta chromosome 2, homologous to D. melanogaster 3R (Muller's element E). Differences in the rate of evolution among chromosomal elements are seemingly persistent in the Drosophila genus over long phylogenetic distances...
  22. pmc From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies
    P V Benos
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Genome Res 11:710-30. 2001
    ....
  23. ncbi request reprint Rescue of hybrid sterility in crosses between D. melanogaster and D. simulans
    A W Davis
    Department of Genetics, University of Cambridge, UK
    Nature 380:157-9. 1996
    ..simulans that produces fertile female hybrids in crosses with D. melanogaster. Our discovery promises to bring the enormous resolution of D. melanogaster genetics to the study of reproductive isolation and species differences...
  24. pmc The Adh-related gene of Drosophila melanogaster is expressed as a functional dicistronic messenger RNA: multigenic transcription in higher organisms
    S Brogna
    Department of Genetics, Downing Street, University of Cambridge, UK
    EMBO J 16:2023-31. 1997
    ..The dicistronic transcript is found in polysomes and the Adhr protein product is detected by antibody staining. We present evidence that the accumulation of the dicistronic mRNA is controlled at the level of the 3' end processing...
  25. ncbi request reprint Speculations on the subject of alcohol dehydrogenase and its properties in Drosophila and other flies
    M Ashburner
    Department of Genetics, University of Cambridge, England
    Bioessays 20:949-54. 1998
    ..I also hint that the ADH enzymes of other flies (e.g., the tephritid fruit flies) may have evolved independently of those of Drosophila, but from a common ancestral gene...
  26. ncbi request reprint The product of the Drosophila gene vasa is very similar to eukaryotic initiation factor-4A
    P F Lasko
    Department of Genetics, University of Cambridge, UK
    Nature 335:611-7. 1988
    ..The predicted amino acid sequence is very similar to those of the translation initiation factor eIF-4A and the human nuclear antigen p68...
  27. pmc FlyBase: enhancing Drosophila Gene Ontology annotations
    Susan Tweedie
    Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
    Nucleic Acids Res 37:D555-9. 2009
    ..Many of these changes stem from our participation in the GO Reference Genome Annotation Project--a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species...
  28. ncbi request reprint The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup
    P S Jeffs
    Department of Genetics, University of Cambridge, England
    Mol Biol Evol 11:287-304. 1994
    ..melanogaster is the sister species to D. simulans, D. sechellia, and D. mauritiana. The evolutionary relationships of the latter three species remain equivocal...
  29. pmc Principles of genome evolution in the Drosophila melanogaster species group
    Jose M Ranz
    Department of Genetics, University of Cambridge, Cambridge, United Kingdom
    PLoS Biol 5:e152. 2007
    ..Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance...
  30. pmc The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster
    Luis Teixeira
    Department of Genetics, University of Cambridge, Cambridge, United Kingdom
    PLoS Biol 6:e2. 2008
    ..melanogaster. The induced resistance to natural viral pathogens may explain Wolbachia prevalence in natural populations and represents a novel Wolbachia-host interaction...
  31. pmc The ribosomal protein genes and Minute loci of Drosophila melanogaster
    Steven J Marygold
    Growth Regulation Laboratory, Cancer Research UK London Research Institute, Lincoln s Inn Fields, London WC2A 3PX, UK
    Genome Biol 8:R216. 2007
    ..While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes...
  32. pmc Entity/quality-based logical definitions for the human skeletal phenome using PATO
    Georgios V Gkoutos
    Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, England
    Conf Proc IEEE Eng Med Biol Soc 2009:7069-72. 2009
    ....
  33. ncbi request reprint Prospects for the genetic transformation of arthropods
    M Ashburner
    Department of Genetics, University of Cambridge, UK
    Insect Mol Biol 7:201-13. 1998
  34. pmc The Drosophila Eip78C gene is not vital but has a role in regulating chromosome puffs
    S R Russell
    Department of Genetics, University of Cambridge, United Kingdom
    Genetics 144:159-70. 1996
    ..These data indicate either that Eip78C function is redundant or that it plays a subtle modulating role in the regulation of chromosome puffing...
  35. pmc FlyMine: an integrated database for Drosophila and Anopheles genomics
    Rachel Lyne
    Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
    Genome Biol 8:R129. 2007
    ..It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists...
  36. ncbi request reprint Informatics--genome and genetic databases
    M Ashburner
    Department of Genetics, University of Cambridge, UK
    Curr Opin Genet Dev 7:750-6. 1997
    ..As comparative genomics develops, however, even databases limited in their scope (e.g. to a single organism) are of great interest to a wider community...
  37. pmc The molecular analysis of the el-noc complex of Drosophila melanogaster
    T Davis
    Department of Genetics, University of Cambridge, England
    Genetics 126:105-19. 1990
    ..No l(2)35Ba-nocA+ aberrations have been found. At the molecular level these loci are found to occupy almost the same region, and are probably identical...
  38. ncbi request reprint Sequence variation database project at the European Bioinformatics Institute
    H Lehvaslaiho
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Hum Mutat 15:52-6. 2000
    ..It is suggested that the hardest problems in unifying mutation databases are related to intellectual property rights. The concept of copylefting is introduced as a potential solution to these...
  39. pmc The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster
    Edward Ryder
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
    Genetics 167:797-813. 2004
    ..In addition, a further 37,000 deletions, selectable by molecular screening, may be generated. We are now using the collection to generate a second-generation deficiency kit that is precisely mapped to the genome sequence...
  40. pmc Drosophila Genomes by the Baker's Dozen. Preface
    Michael Ashburner
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
    Genetics 177:1263-8. 2007
  41. pmc The DrosDel deletion collection: a Drosophila genomewide chromosomal deficiency resource
    Edward Ryder
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
    Genetics 177:615-29. 2007
    ..Finally, we provide a computational resource that facilitates selection of other mapped FRT-bearing elements that, when combined with the DrosDel collection, can theoretically generate over half a million precisely mapped deletions...
  42. pmc Identification of a Drosophila protein similar to rat S13 and archaebacterial S11 ribosomal proteins
    S L McNabb
    Department of Genetics, University of Cambridge, UK
    Nucleic Acids Res 21:2523. 1993
  43. ncbi request reprint Posterior localization of vasa protein correlates with, but is not sufficient for, pole cell development
    P F Lasko
    Department of Genetics, University of Cambridge, UK
    Genes Dev 4:905-21. 1990
    ..These results are discussed with respect to the multiple functions of the vasa gene...
  44. ncbi request reprint Ontologies for biologists: a community model for the annotation of genomic data
    M Ashburner
    Department of Genetics, University of Cambridge and EMBL EBI, Hinxton, Cambridge, United Kingdom
    Cold Spring Harb Symp Quant Biol 68:227-35. 2003
  45. pmc The molecular structure of TE146 and its derivatives in Drosophila melanogaster
    R Lovering
    Department of Genetics, University of Cambridge, England
    Genetics 128:357-72. 1991
    ..We suggest that these FB-FB exchange events occur by mitotic sister-chromatid exchange in the premeiotic germ line...
  46. pmc A novel system of fertility rescue in Drosophila hybrids reveals a link between hybrid lethality and female sterility
    Daniel A Barbash
    Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
    Genetics 163:217-26. 2003
    ..These results also suggest that, while there is some common genetic basis to hybrid lethality and female sterility in D. melanogaster, hybrid females are more sensitive to fertility defects than to lethality...
  47. ncbi request reprint A new hybrid rescue allele in Drosophila melanogaster
    Daniel A Barbash
    Department of Genetics, University of Cambridge, Cambridge, UK
    Genetica 120:261-6. 2004
    ..The structure of Df(1)EP307-1-2 suggests that it was formed by a process similar to P-element induced male recombination...
  48. pmc ChEBI: a database and ontology for chemical entities of biological interest
    Kirill Degtyarenko
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 36:D344-50. 2008
    ..ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi/..
  49. pmc Mapping and identification of essential gene functions on the X chromosome of Drosophila
    Annette Peter
    Max Planck Institut fur biophysikalische Chemie, Abt Molekulare Entwicklungsbiologie, Am Fassberg, 37077 Gottingen, Germany
    EMBO Rep 3:34-8. 2002
    ..The distribution of the P element integration sites, the identified genes and transcription units as well as the expression patterns of the P-element-tagged enhancers is described and discussed...
  50. ncbi request reprint Phenotype ontologies: the bridge between genomics and evolution
    Paula M Mabee
    Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
    Trends Ecol Evol 22:345-50. 2007
    ....
  51. pmc Systematic determination of patterns of gene expression during Drosophila embryogenesis
    Pavel Tomancak
    Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, 539 Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0088. 2002
    ..Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription...
  52. pmc EGASP: the human ENCODE Genome Annotation Assessment Project
    Roderic Guigo
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
    Genome Biol 7:S2.1-31. 2006
    ..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
  53. pmc Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
    Sima Misra
    Department of Molecular and Cell Biology, University of California, Life Sciences Addition, Berkeley, CA 94720 3200, USA
    Genome Biol 3:RESEARCH0083. 2002
    ....
  54. pmc Assessment of genome-wide protein function classification for Drosophila melanogaster
    Huaiyu Mi
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2118-28. 2003
    ..Often, functional associations are made by one method and not the other, indicating that one of the greatest challenges lies in improving the completeness of available ontology associations...
  55. pmc Drosophila crinkled, mutations of which disrupt morphogenesis and cause lethality, encodes fly myosin VIIA
    Daniel P Kiehart
    Department of Biology, Duke University, Durham, North Carolina 27708 1000, USA
    Genetics 168:1337-52. 2004
    ..Together, our data suggest a key role for ck/myoVIIA in the formation of cellular projections and other actin-based functions required for viability...
  56. pmc An ontology for cell types
    Jonathan Bard
    Department of Biomedical Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh, EH8 9XD, UK
    Genome Biol 6:R21. 2005
    ..The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA...
  57. pmc The minimum information about a genome sequence (MIGS) specification
    Dawn Field
    Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford OX1 3SR, UK
    Nat Biotechnol 26:541-7. 2008
    ..As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases...
  58. ncbi request reprint Taking stock of our models: the function and future of stock centres
    Nadia Rosenthal
    Mouse Biology Programme, European Molecular Biology Laboratory, Via Ramarini 32, 00016 Monterotondo, Rome, Italy
    Nat Rev Genet 3:711-7. 2002
    ..But they need forward planning, international cooperation and secure funding to keep pace with the explosion in functional genomics that relies so heavily on them...