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Items: 1 to 50 of 67

1.

A design framework and exemplar metrics for FAIRness.

Wilkinson MD, Sansone SA, Schultes E, Doorn P, Bonino da Silva Santos LO, Dumontier M.

Sci Data. 2018 Jun 26;5:180118. doi: 10.1038/sdata.2018.118. No abstract available.

2.

Preparing Data at the Source to Foster Interoperability across Rare Disease Resources.

Roos M, López Martin E, Wilkinson MD.

Adv Exp Med Biol. 2017;1031:165-179. doi: 10.1007/978-3-319-67144-4_9. Review.

PMID:
29214571
3.

Feruloylation and structure of arabinoxylan in wheat endosperm cell walls from RNAi lines with suppression of genes responsible for backbone synthesis and decoration.

Freeman J, Ward JL, Kosik O, Lovegrove A, Wilkinson MD, Shewry PR, Mitchell RAC.

Plant Biotechnol J. 2017 Nov;15(11):1429-1438. doi: 10.1111/pbi.12727. Epub 2017 Apr 21.

4.

Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae.

Illana A, Marconi M, Rodríguez-Romero J, Xu P, Dalmay T, Wilkinson MD, Ayllón MÁ, Sesma A.

Arch Virol. 2017 Mar;162(3):891-895. doi: 10.1007/s00705-016-3144-9. Epub 2016 Nov 17.

PMID:
27858291
5.

Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base.

Rodríguez-Iglesias A, Rodríguez-González A, Irvine AG, Sesma A, Urban M, Hammond-Kosack KE, Wilkinson MD.

Front Plant Sci. 2016 May 12;7:641. doi: 10.3389/fpls.2016.00641. eCollection 2016.

6.

The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18.

7.

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

Aranguren ME, Wilkinson MD.

Gigascience. 2015 Dec 3;4:59. doi: 10.1186/s13742-015-0092-3. eCollection 2015.

8.

VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock.

Nakada TA, Boyd JH, Russell JA, Aguirre-Hernández R, Wilkinson MD, Thair SA, Nakada E, McConechy MK, Fjell CD, Walley KR.

J Innate Immun. 2015;7(5):545-53. doi: 10.1159/000381265. Epub 2015 Apr 17.

9.

Clinical Applications of Cine Balanced Steady-State Free Precession MRI for the Evaluation of the Subarachnoid Spaces.

Li AE, Wilkinson MD, McGrillen KM, Stoodley MA, Magnussen JS.

Clin Neuroradiol. 2015 Dec;25(4):349-60. doi: 10.1007/s00062-015-0383-1. Epub 2015 Apr 9. Review.

PMID:
25854921
10.

Effect of suppression of arabinoxylan synthetic genes in wheat endosperm on chain length of arabinoxylan and extract viscosity.

Freeman J, Lovegrove A, Wilkinson MD, Saulnier L, Shewry PR, Mitchell RA.

Plant Biotechnol J. 2016 Jan;14(1):109-16. doi: 10.1111/pbi.12361. Epub 2015 Mar 27.

11.

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples.

Pawluczyk M, Weiss J, Links MG, Egaña Aranguren M, Wilkinson MD, Egea-Cortines M.

Anal Bioanal Chem. 2015 Mar;407(7):1841-8. doi: 10.1007/s00216-014-8435-y. Epub 2015 Jan 11.

PMID:
25577362
12.

The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus.

Hily JM, García A, Moreno A, Plaza M, Wilkinson MD, Fereres A, Fraile A, García-Arenal F.

PLoS Pathog. 2014 Nov 6;10(11):e1004492. doi: 10.1371/journal.ppat.1004492. eCollection 2014 Nov.

13.

Executing SADI services in Galaxy.

Aranguren ME, González AR, Wilkinson MD.

J Biomed Semantics. 2014 Sep 22;5(1):42. doi: 10.1186/2041-1480-5-42. eCollection 2014.

14.

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.

Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, Wilkinson MD, Hoehndorf R.

J Biomed Semantics. 2014 Mar 6;5(1):14. doi: 10.1186/2041-1480-5-14.

15.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

16.

Automatically exposing OpenLifeData via SADI semantic Web Services.

González AR, Callahan A, Cruz-Toledo J, Garcia A, Egaña Aranguren M, Dumontier M, Wilkinson MD.

J Biomed Semantics. 2014 Nov 19;5:46. doi: 10.1186/2041-1480-5-46. eCollection 2014.

17.

The emergent discipline of health web science.

Luciano JS, Cumming GP, Wilkinson MD, Kahana E.

J Med Internet Res. 2013 Aug 22;15(8):e166. doi: 10.2196/jmir.2499.

18.

RNA interference suppression of genes in glycosyl transferase families 43 and 47 in wheat starchy endosperm causes large decreases in arabinoxylan content.

Lovegrove A, Wilkinson MD, Freeman J, Pellny TK, Tosi P, Saulnier L, Shewry PR, Mitchell RA.

Plant Physiol. 2013 Sep;163(1):95-107. doi: 10.1104/pp.113.222653. Epub 2013 Jul 22.

19.

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions.

Vandervalk B, McCarthy EL, Cruz-Toledo J, Klein A, Baker CJ, Dumontier M, Wilkinson MD.

JMIR Res Protoc. 2013 Apr 5;2(1):e14. doi: 10.2196/resprot.2315.

20.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T.

J Biomed Semantics. 2013 Feb 11;4(1):6. doi: 10.1186/2041-1480-4-6.

21.

Analysis of a multilevel diagnosis decision support system and its implications: a case study.

Rodríguez-González A, Torres-Niño J, Mayer MA, Alor-Hernandez G, Wilkinson MD.

Comput Math Methods Med. 2012;2012:367345. doi: 10.1155/2012/367345. Epub 2012 Dec 23.

22.

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows.

Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, Wilkinson MD.

J Biomed Semantics. 2013 Jan 4;4(1):2. doi: 10.1186/2041-1480-4-2.

23.

Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web.

Samadian S, McManus B, Wilkinson MD.

J Biomed Semantics. 2012 Jul 20;3(1):6. doi: 10.1186/2041-1480-3-6.

24.

Genomics data resources: frameworks and standards.

Wilkinson MD.

Methods Mol Biol. 2012;856:489-511. doi: 10.1007/978-1-61779-585-5_20.

PMID:
22399472
25.

Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses.

Anders N, Wilkinson MD, Lovegrove A, Freeman J, Tryfona T, Pellny TK, Weimar T, Mortimer JC, Stott K, Baker JM, Defoin-Platel M, Shewry PR, Dupree P, Mitchell RA.

Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):989-93. doi: 10.1073/pnas.1115858109. Epub 2012 Jan 3.

26.

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

Wilkinson MD, Vandervalk B, McCarthy L.

J Biomed Semantics. 2011 Oct 24;2(1):8. doi: 10.1186/2041-1480-2-8.

27.

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T.

J Biomed Semantics. 2011 Aug 2;2:4. doi: 10.1186/2041-1480-2-4.

28.

SADI, SHARE, and the in silico scientific method.

Wilkinson MD, McCarthy L, Vandervalk B, Withers D, Kawas E, Samadian S.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S7. doi: 10.1186/1471-2105-11-S12-S7.

29.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.

30.

OWL2Perl: creating Perl modules from OWL class definitions.

Kawas E, Wilkinson MD.

Bioinformatics. 2010 Sep 15;26(18):2357-8. doi: 10.1093/bioinformatics/btq416. Epub 2010 Jul 13.

31.

Temporal and spatial changes in cell wall composition in developing grains of wheat cv. Hereward.

Toole GA, Le Gall G, Colquhoun IJ, Nemeth C, Saulnier L, Lovegrove A, Pellny T, Wilkinson MD, Freeman J, Mitchell RA, Mills EN, Shewry PR.

Planta. 2010 Aug;232(3):677-89. doi: 10.1007/s00425-010-1199-5. Epub 2010 Jun 13.

PMID:
20549231
32.

Down-regulation of the CSLF6 gene results in decreased (1,3;1,4)-beta-D-glucan in endosperm of wheat.

Nemeth C, Freeman J, Jones HD, Sparks C, Pellny TK, Wilkinson MD, Dunwell J, Andersson AA, Aman P, Guillon F, Saulnier L, Mitchell RA, Shewry PR.

Plant Physiol. 2010 Mar;152(3):1209-18. doi: 10.1104/pp.109.151712. Epub 2010 Jan 20.

33.

Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics.

Good BM, Tennis JT, Wilkinson MD.

BMC Bioinformatics. 2009 Sep 25;10:313. doi: 10.1186/1471-2105-10-313.

34.

Transgenic approach to improve wheat (Triticum aestivum L.) nutritional quality.

Tamás C, Kisgyörgy BN, Rakszegi M, Wilkinson MD, Yang MS, Láng L, Tamás L, Bedo Z.

Plant Cell Rep. 2009 Jul;28(7):1085-94. doi: 10.1007/s00299-009-0716-0. Epub 2009 May 24.

PMID:
19466426
35.

Moby and Moby 2: creatures of the deep (web).

Vandervalk BP, McCarthy EL, Wilkinson MD.

Brief Bioinform. 2009 Mar;10(2):114-28. doi: 10.1093/bib/bbn051. Epub 2009 Jan 16.

PMID:
19151099
36.

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

BioMoby Consortium, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano M, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A.

Brief Bioinform. 2008 May;9(3):220-31. doi: 10.1093/bib/bbn003. Epub 2008 Jan 31. Review.

PMID:
18238804
37.

Decreased shoot stature and grain alpha-amylase activity following ectopic expression of a gibberellin 2-oxidase gene in transgenic wheat.

Appleford NE, Wilkinson MD, Ma Q, Evans DJ, Stone MC, Pearce SP, Powers SJ, Thomas SG, Jones HD, Phillips AL, Hedden P, Lenton JR.

J Exp Bot. 2007;58(12):3213-26. Epub 2007 Oct 4.

PMID:
17916639
38.

DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs.

Song YC, Kawas E, Good BM, Wilkinson MD, Tebbutt SJ.

Bioinformatics. 2007 Mar 15;23(6):780-2. Epub 2007 Jan 18.

PMID:
17237074
39.

Vcsa1 gene peptides for the treatment of inflammatory and allergic reactions.

Morris K, Kuo B, Wilkinson MD, Davison JS, Befus AD, Mathison RD.

Recent Pat Inflamm Allergy Drug Discov. 2007 Jun;1(2):124-32. Review.

PMID:
19075974
40.

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website.

Good BM, Kawas EA, Kuo BY, Wilkinson MD.

BMC Bioinformatics. 2006 Dec 15;7:534.

41.

BioMoby extensions to the Taverna workflow management and enactment software.

Kawas E, Senger M, Wilkinson MD.

BMC Bioinformatics. 2006 Nov 30;7:523.

42.

Fast, cheap and out of control: a zero curation model for ontology development.

Good BM, Tranfield EM, Tan PC, Shehata M, Singhera GK, Gosselink J, Okon EB, Wilkinson MD.

Pac Symp Biocomput. 2006:128-39.

43.

The Life Sciences Semantic Web is full of creeps!

Good BM, Wilkinson MD.

Brief Bioinform. 2006 Sep;7(3):275-86. Epub 2006 Aug 9. Review.

PMID:
16899496
44.

Comparison of ESTs from juvenile and adult phases of the giant unicellular green alga Acetabularia acetabulum.

Henry IM, Wilkinson MD, Hernandez JM, Schwarz-Sommer Z, Grotewold E, Mandoli DF.

BMC Plant Biol. 2004 Mar 12;4:3.

45.

FDG PET imaging of metastatic gastrointestinal stromal tumor.

Wilkinson MD, Fulham MJ.

Clin Nucl Med. 2003 Sep;28(9):780-1. Review.

PMID:
12973009
46.

Differentiation of synchronous tumors using FDG positron emission tomography.

Wilkinson MD, Fulham MJ, McCaughan BC, Constable CJ.

Clin Nucl Med. 2003 Jun;28(6):489-91. No abstract available.

PMID:
12917532
47.

FDG-PET in paraneoplastic neuropathy.

Wilkinson MD, Fulham MJ, Heard RN, McCaughan BC, McCarthy SW.

Neurology. 2003 May 27;60(10):1668. No abstract available.

PMID:
12771260
48.

Invasive aspergillosis mimicking stage IIIA non-small-cell lung cancer on FDG positron emission tomography.

Wilkinson MD, Fulham MJ, McCaughan BC, Constable CJ.

Clin Nucl Med. 2003 Mar;28(3):234-5. No abstract available.

PMID:
12592137
49.

Neuroimaging findings in a suprasellar granular cell tumor.

Wilkinson MD, Fulham MJ, Besser M.

J Comput Assist Tomogr. 2003 Jan-Feb;27(1):26-9.

PMID:
12544238
50.

FDG positron emission tomographic imaging of a large abdominal aortic aneurysm.

Wilkinson MD, Szeto E, Fulham M, Constable CJ, McCaughan BC.

Clin Nucl Med. 2003 Feb;28(2):130-1. No abstract available.

PMID:
12544133

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