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Items: 1 to 50 of 180

1.

"The optimization of superficial planning target volumes (PTVs) with helical tomotherapy". [JACMP, 15 (6), 2014].

Ashburner M, Tudor GS.

J Appl Clin Med Phys. 2017 Jul;18(4):237. doi: 10.1002/acm2.12117. Epub 2017 Jun 12. No abstract available.

2.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

3.

The optimization of superficial planning target volumes (PTVs) with helical tomotherapy.

Ashburner MJ, Tudor S.

J Appl Clin Med Phys. 2014 Sep 8;15(6):4560. doi: 10.1120/jacmp.v15i6.4560. Erratum in: J Appl Clin Med Phys. 2017 Jul;18(4):237.

4.

Intra-fraction motion of the prostate during treatment with helical tomotherapy.

Thomas SJ, Ashburner M, Tudor GS, Treeby J, Dean J, Routsis D, Rimmer YL, Russell SG, Burnet NG.

Radiother Oncol. 2013 Dec;109(3):482-6. doi: 10.1016/j.radonc.2013.09.011. Epub 2013 Oct 12.

PMID:
24128804
5.

Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila.

von Grotthuss M, Ashburner M, Ranz JM.

Genome Res. 2010 Aug;20(8):1084-96. doi: 10.1101/gr.103713.109. Epub 2010 Jul 2.

6.

Integrating phenotype ontologies across multiple species.

Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M.

Genome Biol. 2010 Jan 8;11(1):R2. doi: 10.1186/gb-2010-11-1-r2.

7.

Entity/quality-based logical definitions for the human skeletal phenome using PATO.

Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:7069-72. doi: 10.1109/IEMBS.2009.5333362.

8.

Linking human diseases to animal models using ontology-based phenotype annotation.

Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE.

PLoS Biol. 2009 Nov;7(11):e1000247. doi: 10.1371/journal.pbio.1000247. Epub 2009 Nov 24.

9.

The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster.

Teixeira L, Ferreira A, Ashburner M.

PLoS Biol. 2008 Dec 23;6(12):e2. doi: 10.1371/journal.pbio.1000002.

10.

FlyBase: enhancing Drosophila Gene Ontology annotations.

Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H; FlyBase Consortium.

Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9. doi: 10.1093/nar/gkn788. Epub 2008 Oct 23.

11.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.

Nat Biotechnol. 2008 Aug;26(8):889-96. doi: 10.1038/nbt.1411. No abstract available.

12.

Calling on a million minds for community annotation in WikiProteins.

Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A.

Genome Biol. 2008;9(5):R89. doi: 10.1186/gb-2008-9-5-r89. Epub 2008 May 28.

13.

The minimum information about a genome sequence (MIGS) specification.

Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A.

Nat Biotechnol. 2008 May;26(5):541-7. doi: 10.1038/nbt1360.

14.

Drosophila Genomes by the Baker's Dozen. Preface.

Ashburner M.

Genetics. 2007 Nov;177(3):1263-8. No abstract available.

15.

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S.

Nat Biotechnol. 2007 Nov;25(11):1251-5.

16.

ChEBI: a database and ontology for chemical entities of biological interest.

Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D344-50. Epub 2007 Oct 11.

17.

The ribosomal protein genes and Minute loci of Drosophila melanogaster.

Marygold SJ, Roote J, Reuter G, Lambertsson A, Ashburner M, Millburn GH, Harrison PM, Yu Z, Kenmochi N, Kaufman TC, Leevers SJ, Cook KR.

Genome Biol. 2007;8(10):R216.

18.

The DrosDel deletion collection: a Drosophila genomewide chromosomal deficiency resource.

Ryder E, Ashburner M, Bautista-Llacer R, Drummond J, Webster J, Johnson G, Morley T, Chan YS, Blows F, Coulson D, Reuter G, Baisch H, Apelt C, Kauk A, Rudolph T, Kube M, Klimm M, Nickel C, Szidonya J, Maróy P, Pal M, Rasmuson-Lestander A, Ekström K, Stocker H, Hugentobler C, Hafen E, Gubb D, Pflugfelder G, Dorner C, Mechler B, Schenkel H, Marhold J, Serras F, Corominas M, Punset A, Roote J, Russell S.

Genetics. 2007 Sep;177(1):615-29. Epub 2007 Aug 24.

19.

FlyMine: an integrated database for Drosophila and Anopheles genomics.

Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, Guillier F, Janssens H, Ji W, Mclaren P, North P, Rana D, Riley T, Sullivan J, Watkins X, Woodbridge M, Lilley K, Russell S, Ashburner M, Mizuguchi K, Micklem G.

Genome Biol. 2007;8(7):R129.

20.

Principles of genome evolution in the Drosophila melanogaster species group.

Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM.

PLoS Biol. 2007 Jun;5(6):e152.

21.

Phenotype ontologies: the bridge between genomics and evolution.

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M.

Trends Ecol Evol. 2007 Jul;22(7):345-50. Epub 2007 Apr 9.

PMID:
17416439
22.

Maintenance of a Drosophila laboratory: general procedures.

Ashburner M, Roote J.

CSH Protoc. 2007 Mar 1;2007:pdb.ip35. doi: 10.1101/pdb.ip35.

PMID:
21357030
23.

Culture of Drosophila: the laboratory setup.

Ashburner M, Roote J.

CSH Protoc. 2007 Mar 1;2007:pdb.ip34. doi: 10.1101/pdb.ip34.

PMID:
21357029
24.
25.

Getting a buzz out of the bee genome.

Ashburner M, Kyriacou CP.

Genome Biol. 2006;7(10):239. Epub 2006 Oct 26.

26.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.

Genome Biol. 2006;7 Suppl 1:S2.1-31. Epub 2006 Aug 7. Review.

27.

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge.

Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA.

OMICS. 2006 Summer;10(2):185-98. Review.

PMID:
16901225
28.

Drosophila melanogaster: a case study of a model genomic sequence and its consequences.

Ashburner M, Bergman CM.

Genome Res. 2005 Dec;15(12):1661-7. Review.

29.

Combined evidence annotation of transposable elements in genome sequences.

Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D.

PLoS Comput Biol. 2005 Jul;1(2):166-75. Epub 2005 Jul 29.

30.

The Sequence Ontology: a tool for the unification of genome annotations.

Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M.

Genome Biol. 2005;6(5):R44. Epub 2005 Apr 29.

31.

An ontology for cell types.

Bard J, Rhee SY, Ashburner M.

Genome Biol. 2005;6(2):R21. Epub 2005 Jan 14.

32.

Drosophila crinkled, mutations of which disrupt morphogenesis and cause lethality, encodes fly myosin VIIA.

Kiehart DP, Franke JD, Chee MK, Montague RA, Chen TL, Roote J, Ashburner M.

Genetics. 2004 Nov;168(3):1337-52.

33.

Ontologies for biologists: a community model for the annotation of genomic data.

Ashburner M, Mungall CJ, Lewis SE.

Cold Spring Harb Symp Quant Biol. 2003;68:227-35. Review. No abstract available.

PMID:
15338622
34.

The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster.

Ryder E, Blows F, Ashburner M, Bautista-Llacer R, Coulson D, Drummond J, Webster J, Gubb D, Gunton N, Johnson G, O'Kane CJ, Huen D, Sharma P, Asztalos Z, Baisch H, Schulze J, Kube M, Kittlaus K, Reuter G, Maroy P, Szidonya J, Rasmuson-Lestander A, Ekström K, Dickson B, Hugentobler C, Stocker H, Hafen E, Lepesant JA, Pflugfelder G, Heisenberg M, Mechler B, Serras F, Corominas M, Schneuwly S, Preat T, Roote J, Russell S.

Genetics. 2004 Jun;167(2):797-813.

35.

Molecular characterization of the singed wings locus of Drosophila melanogaster.

Schwartz YB, Boykova T, Belyaeva ES, Ashburner M, Zhimulev IF.

BMC Genet. 2004 Jun 9;5:15.

36.

A new hybrid rescue allele in Drosophila melanogaster.

Barbash DA, Roote J, Johnson G, Ashburner M.

Genetica. 2004 Mar;120(1-3):261-6.

PMID:
15088664
37.

The Gene Ontology (GO) database and informatics resource.

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.

38.

Assessment of genome-wide protein function classification for Drosophila melanogaster.

Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas PD, Ashburner M.

Genome Res. 2003 Sep;13(9):2118-28.

39.

A methodology to migrate the gene ontology to a description logic environment using DAML+OIL.

Wroe CJ, Stevens R, Goble CA, Ashburner M.

Pac Symp Biocomput. 2003:624-35.

41.

On ontologies for biologists: the Gene Ontology--untangling the web.

Ashburner M, Lewis S.

Novartis Found Symp. 2002;247:66-80; discussion 80-3, 84-90, 244-52. Review.

PMID:
12539950
42.

Systematic determination of patterns of gene expression during Drosophila embryogenesis.

Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GM.

Genome Biol. 2002;3(12):RESEARCH0088. Epub 2002 Dec 23.

43.

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.

Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE.

Genome Biol. 2002;3(12):RESEARCH0084. Epub 2002 Dec 23.

44.

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE.

Genome Biol. 2002;3(12):RESEARCH0083. Epub 2002 Dec 31. Review.

45.

A hat trick--Plasmodium, Anopheles and Homo.

Ashburner M.

Genome Biol. 2003;4(1):103. Epub 2002 Dec 17.

46.

Taking stock of our models: the function and future of stock centres.

Rosenthal N, Ashburner M.

Nat Rev Genet. 2002 Sep;3(9):711-7. doi: 10.1038/nrg891. Review.

PMID:
12209145
47.

A quizzical view pays clear dividends.

Ashburner M.

Nature. 2002 Mar 28;416(6879):365. No abstract available.

PMID:
11919599
48.

Mapping and identification of essential gene functions on the X chromosome of Drosophila.

Peter A, Schöttler P, Werner M, Beinert N, Dowe G, Burkert P, Mourkioti F, Dentzer L, He Y, Deak P, Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, Ferraz C, Vidal S, Brun C, Demaille J, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Borkova D, Miñana B, Kafatos FC, Bolshakov S, Sidén-Kiamos I, Papagiannakis G, Spanos L, Louis C, Madueño E, de Pablos B, Modolell J, Bucheton A, Callister D, Campbell L, Henderson NS, McMillan PJ, Salles C, Tait E, Valenti P, Saunders RD, Billaud A, Pachter L, Klapper R, Janning W, Glover DM, Ashburner M, Bellen HJ, Jäckle H, Schäfer U.

EMBO Rep. 2002 Jan;3(1):34-8. Epub 2001 Dec 19.

49.

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies.

Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, Ferraz C, Vidal S, Brun C, Demaille J, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Borkova D, Miñana B, Kafatos FC, Bolshakov S, Sidén-Kiamos I, Papagiannakis G, Spanos L, Louis C, Madueño E, de Pablos B, Modolell J, Peter A, Schöttler P, Werner M, Mourkioti F, Beinert N, Dowe G, Schäfer U, Jäckle H, Bucheton A, Callister D, Campbell L, Henderson NS, McMillan PJ, Salles C, Tait E, Valenti P, Saunders RD, Billaud A, Pachter L, Glover DM, Ashburner M.

Genome Res. 2001 May;11(5):710-30.

50.

Information access. Building a "GenBank" of the published literature.

Roberts RJ, Varmus HE, Ashburner M, Brown PO, Eisen MB, Khosla C, Kirschner M, Nusse R, Scott M, Wold B.

Science. 2001 Mar 23;291(5512):2318-9. No abstract available.

PMID:
11269300

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