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Items: 1 to 50 of 76

1.

Enabling precision medicine via standard communication of HTS provenance, analysis, and results.

Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R.

PLoS Biol. 2018 Dec 31;16(12):e3000099. doi: 10.1371/journal.pbio.3000099. eCollection 2018 Dec.

2.

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals.

Carbonell P, Jervis AJ, Robinson CJ, Yan C, Dunstan M, Swainston N, Vinaixa M, Hollywood KA, Currin A, Rattray NJW, Taylor S, Spiess R, Sung R, Williams AR, Fellows D, Stanford NJ, Mulherin P, Le Feuvre R, Barran P, Goodacre R, Turner NJ, Goble C, Chen GG, Kell DB, Micklefield J, Breitling R, Takano E, Faulon JL, Scrutton NS.

Commun Biol. 2018 Jun 8;1:66. doi: 10.1038/s42003-018-0076-9. eCollection 2018.

3.

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).

Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E.

Stand Genomic Sci. 2018 Aug 9;13:17. doi: 10.1186/s40793-018-0320-4. eCollection 2018.

4.

ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G.

F1000Res. 2017 Jun 21;6. pii: ELIXIR-952. doi: 10.12688/f1000research.11837.1. eCollection 2017.

5.

Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.

Pawlik A, van Gelder CWG, Nenadic A, Palagi PM, Korpelainen E, Lijnzaad P, Marek D, Sansone SA, Hancock J, Goble C.

F1000Res. 2017 Jul 3;6. pii: ELIXIR-1040. doi: 10.12688/f1000research.11718.1. eCollection 2017.

6.

Four simple recommendations to encourage best practices in research software.

Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017.

7.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun.

8.

An open and transparent process to select ELIXIR Node Services as implemented by ELIXIR-UK.

Hancock JM, Game A, Ponting CP, Goble CA.

Version 2. F1000Res. 2016 Dec 21 [revised 2017 Jan 1];5. pii: ELIXIR-2894. doi: 10.12688/f1000research.10473.2. eCollection 2016.

9.

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

Wolstencroft K, Krebs O, Snoep JL, Stanford NJ, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, van Niekerk DD, Williams AR, Malmström L, Rinn B, Müller W, Goble C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.

10.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

Hardisty AR, Bacall F, Beard N, Balcázar-Vargas MP, Balech B, Barcza Z, Bourlat SJ, De Giovanni R, de Jong Y, De Leo F, Dobor L, Donvito G, Fellows D, Guerra AF, Ferreira N, Fetyukova Y, Fosso B, Giddy J, Goble C, Güntsch A, Haines R, Ernst VH, Hettling H, Hidy D, Horváth F, Ittzés D, Ittzés P, Jones A, Kottmann R, Kulawik R, Leidenberger S, Lyytikäinen-Saarenmaa P, Mathew C, Morrison N, Nenadic A, de la Hidalga AN, Obst M, Oostermeijer G, Paymal E, Pesole G, Pinto S, Poigné A, Fernandez FQ, Santamaria M, Saarenmaa H, Sipos G, Sylla KH, Tähtinen M, Vicario S, Vos RA, Williams AR, Yilmaz P.

BMC Ecol. 2016 Oct 20;16(1):49.

11.

SYNBIOCHEM Synthetic Biology Research Centre, Manchester - A UK foundry for fine and speciality chemicals production.

Ra LF, P C, A C, M D, D F, Aj J, Njw R, Cj R, N S, M V, A W, C Y, P B, R B, Gg C, Jl F, C G, R G, Db K, J M, Ns S, P S, E T, Nj T.

Synth Syst Biotechnol. 2016 Aug 25;1(4):271-275. doi: 10.1016/j.synbio.2016.07.001. eCollection 2016 Dec.

12.

SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals.

Carbonell P, Currin A, Dunstan M, Fellows D, Jervis A, Rattray NJ, Robinson CJ, Swainston N, Vinaixa M, Williams A, Yan C, Barran P, Breitling R, Chen GG, Faulon JL, Goble C, Goodacre R, Kell DB, Feuvre RL, Micklefield J, Scrutton NS, Shapira P, Takano E, Turner NJ.

Biochem Soc Trans. 2016 Jun 15;44(3):675-7. doi: 10.1042/BST20160009.

13.

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

Nickerson D, Atalag K, de Bono B, Geiger J, Goble C, Hollmann S, Lonien J, Müller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P.

Interface Focus. 2016 Apr 6;6(2):20150103. doi: 10.1098/rsfs.2015.0103. Review.

14.

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.

15.

Natural Language Search Interfaces: Health Data Needs Single-Field Variable Search.

Jay C, Harper S, Dunlop I, Smith S, Sufi S, Goble C, Buchan I.

J Med Internet Res. 2016 Jan 14;18(1):e13. doi: 10.2196/jmir.4912.

16.

The evolution of standards and data management practices in systems biology.

Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C.

Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053. No abstract available.

17.

SEEK: a systems biology data and model management platform.

Wolstencroft K, Owen S, Krebs O, Nguyen Q, Stanford NJ, Golebiewski M, Weidemann A, Bittkowski M, An L, Shockley D, Snoep JL, Mueller W, Goble C.

BMC Syst Biol. 2015 Jul 11;9:33. doi: 10.1186/s12918-015-0174-y.

18.

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control.

Mathew C, Güntsch A, Obst M, Vicario S, Haines R, Williams AR, de Jong Y, Goble C.

Biodivers Data J. 2014 Dec 11;(2):e4221. doi: 10.3897/BDJ.2.e4221. eCollection 2014.

19.

BIFI: a Taverna plugin for a simplified and user-friendly workflow platform.

Yildiz A, Dilaveroglu E, Visne I, Günay B, Sefer E, Weinhausel A, Rattay F, Goble CA, Pandey RV, Kriegner A.

BMC Res Notes. 2014 Oct 20;7:740. doi: 10.1186/1756-0500-7-740.

20.

Structuring research methods and data with the research object model: genomics workflows as a case study.

Hettne KM, Dharuri H, Zhao J, Wolstencroft K, Belhajjame K, Soiland-Reyes S, Mina E, Thompson M, Cruickshank D, Verdes-Montenegro L, Garrido J, de Roure D, Corcho O, Klyne G, van Schouwen R, 't Hoen PA, Bechhofer S, Goble C, Roos M.

J Biomed Semantics. 2014 Sep 18;5(1):41. doi: 10.1186/2041-1480-5-41. eCollection 2014.

21.

Distilling structure in Taverna scientific workflows: a refactoring approach.

Cohen-Boulakia S, Chen J, Missier P, Goble C, Williams AR, Froidevaux C.

BMC Bioinformatics. 2014;15 Suppl 1:S12. doi: 10.1186/1471-2105-15-S1-S12. Epub 2014 Jan 10.

22.

Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications.

Clark T, Ciccarese PN, Goble CA.

J Biomed Semantics. 2014 Jul 4;5:28. doi: 10.1186/2041-1480-5-28. eCollection 2014.

23.

PAV ontology: provenance, authoring and versioning.

Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray AJ, Goble C, Clark T.

J Biomed Semantics. 2013 Nov 22;4(1):37. doi: 10.1186/2041-1480-4-37.

24.

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.

Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, Soiland-Reyes S, Dunlop I, Nenadic A, Fisher P, Bhagat J, Belhajjame K, Bacall F, Hardisty A, Nieva de la Hidalga A, Balcazar Vargas MP, Sufi S, Goble C.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W557-61. doi: 10.1093/nar/gkt328. Epub 2013 May 2.

25.

The potential hazards of barefoot running: proceed with caution.

Goble C, Wegler J, Forest CP.

JAAPA. 2013 Mar;26(3):49-53. Review. No abstract available.

PMID:
23520806
26.

Opening new gateways to workflows for life scientists.

Karasavvas K, Wolstencroft K, Mina E, Cruickshank D, Williams A, De Roure D, Goble C, Roos M.

Stud Health Technol Inform. 2012;175:131-41.

PMID:
22942004
27.

Open PHACTS: semantic interoperability for drug discovery.

Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, Willighagen EL, Evelo CT, Blomberg N, Ecker G, Goble C, Mons B.

Drug Discov Today. 2012 Nov;17(21-22):1188-98. doi: 10.1016/j.drudis.2012.05.016. Epub 2012 Jun 7. Review.

28.

Toward interoperable bioscience data.

Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W.

Nat Genet. 2012 Jan 27;44(2):121-6. doi: 10.1038/ng.1054.

29.

The SEEK: a platform for sharing data and models in systems biology.

Wolstencroft K, Owen S, du Preez F, Krebs O, Mueller W, Goble C, Snoep JL.

Methods Enzymol. 2011;500:629-55. doi: 10.1016/B978-0-12-385118-5.00029-3.

PMID:
21943917
30.

RightField: embedding ontology annotation in spreadsheets.

Wolstencroft K, Owen S, Horridge M, Krebs O, Mueller W, Snoep JL, du Preez F, Goble C.

Bioinformatics. 2011 Jul 15;27(14):2021-2. doi: 10.1093/bioinformatics/btr312. Epub 2011 May 26.

PMID:
21622664
31.

Community-driven computational biology with Debian Linux.

Möller S, Krabbenhöft HN, Tille A, Paleino D, Williams A, Wolstencroft K, Goble C, Holland R, Belhachemi D, Plessy C.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S5. doi: 10.1186/1471-2105-11-S12-S5.

32.

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Database (Oxford). 2011 Jan 4;2011:baq027. doi: 10.1093/database/baq027. Print 2011.

33.

Systematic integration of experimental data and models in systems biology.

Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW.

BMC Bioinformatics. 2010 Nov 29;11:582. doi: 10.1186/1471-2105-11-582.

34.

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Nucleic Acids Res. 2011 Jan;39(Database issue):D7-10. doi: 10.1093/nar/gkq1173. Epub 2010 Nov 18.

35.

CaGrid Workflow Toolkit: a Taverna based workflow tool for cancer grid.

Tan W, Madduri R, Nenadic A, Soiland-Reyes S, Sulakhe D, Foster I, Goble CA.

BMC Bioinformatics. 2010 Nov 2;11:542. doi: 10.1186/1471-2105-11-542.

36.

Elements of a computational infrastructure for social simulation.

Birkin M, Procter R, Allan R, Bechhofer S, Buchan I, Goble C, Hudson-Smith A, Lambert P, De Roure D, Sinnott R.

Philos Trans A Math Phys Eng Sci. 2010 Aug 28;368(1925):3797-812. doi: 10.1098/rsta.2010.0145.

PMID:
20643677
37.

A Comparison of Using Taverna and BPEL in Building Scientific Workflows: the case of caGrid.

Tan W, Missier P, Foster I, Madduri R, Goble C.

Concurr Comput. 2010 Jun 25;22(9):1098-1117.

38.

myExperiment: a repository and social network for the sharing of bioinformatics workflows.

Goble CA, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D, Borkum M, Bechhofer S, Roos M, Li P, De Roure D.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W677-82. doi: 10.1093/nar/gkq429. Epub 2010 May 25.

39.

BioCatalogue: a universal catalogue of web services for the life sciences.

Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W689-94. doi: 10.1093/nar/gkq394. Epub 2010 May 19.

40.

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE; Coordination of Mouse Informatics Resources (CASIMIR); Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC.

Genome Biol. 2010;11(3):R27. doi: 10.1186/gb-2010-11-3-r27. Epub 2010 Mar 9.

41.

Data curation + process curation=data integration + science.

Goble C, Stevens R, Hull D, Wolstencroft K, Lopez R.

Brief Bioinform. 2008 Nov;9(6):506-17. doi: 10.1093/bib/bbn034. Epub 2008 Dec 6.

PMID:
19060304
42.

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

Li P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, Owen S, Withers D, Oinn T, Pocock MR, Goble CA, Oliver SG, Kell DB.

BMC Bioinformatics. 2008 Aug 7;9:334. doi: 10.1186/1471-2105-9-334.

43.

The Montagues and the Capulets.

Goble C, Wroe C.

Comp Funct Genomics. 2004;5(8):623-32. doi: 10.1002/cfg.442.

44.

Building ontologies in DAML + OIL.

Stevens R, Wroe C, Bechhofer S, Lord P, Rector A, Goble C.

Comp Funct Genomics. 2003;4(1):133-41. doi: 10.1002/cfg.233.

45.

The low down on e-science and grids for biology.

Goble C.

Comp Funct Genomics. 2001;2(6):365-70. doi: 10.1002/cfg.115.

46.

A roadmap for caGrid, an enterprise Grid architecture for biomedical research.

Saltz J, Hastings S, Langella S, Oster S, Kurc T, Payne P, Ferreira R, Plale B, Goble C, Ervin D, Sharma A, Pan T, Permar J, Brezany P, Siebenlist F, Madduri R, Foster I, Shanbhag K, Mead C, Chue Hong N.

Stud Health Technol Inform. 2008;138:224-37.

47.

ISPIDER Central: an integrated database web-server for proteomics.

Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, Goble CA, Oliver SG, Stevens R, Zamboulis L, Martin N, Poulovassillis A, Jones P, Côté R, Hermjakob H, Pentony MM, Jones DT, Orengo CA, Hubbard SJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W485-90. doi: 10.1093/nar/gkn196. Epub 2008 Apr 25.

48.

State of the nation in data integration for bioinformatics.

Goble C, Stevens R.

J Biomed Inform. 2008 Oct;41(5):687-93. doi: 10.1016/j.jbi.2008.01.008. Epub 2008 Feb 5. Review.

49.

The (my)Grid ontology: bioinformatics service discovery.

Wolstencroft K, Alper P, Hull D, Wroe C, Lord PW, Stevens RD, Goble CA.

Int J Bioinform Res Appl. 2007;3(3):303-25.

PMID:
18048194
50.

Using provenance to manage knowledge of in silico experiments.

Stevens R, Zhao J, Goble C.

Brief Bioinform. 2007 May;8(3):183-94. Epub 2007 May 14.

PMID:
17502335

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