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Items: 1 to 50 of 87

1.

Synthetic Biology Open Language (SBOL) Version 2.3.

Madsen C, Goñi Moreno A, P U, Palchick Z, Roehner N, Atallah C, Bartley B, Choi K, Cox RS, Gorochowski T, Grünberg R, Macklin C, McLaughlin J, Meng X, Nguyen T, Pocock M, Samineni M, Scott-Brown J, Tarter Y, Zhang M, Zhang Z, Zundel Z, Beal J, Bissell M, Clancy K, Gennari JH, Misirli G, Myers C, Oberortner E, Sauro H, Wipat A.

J Integr Bioinform. 2019 Jun 13. pii: /j/jib.ahead-of-print/jib-2019-0025/jib-2019-0025.xml. doi: 10.1515/jib-2019-0025. [Epub ahead of print]

PMID:
31199770
2.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1.

Madsen C, Goni Moreno A, Palchick Z, P U, Roehner N, Bartley B, Bhatia S, Bhakta S, Bissell M, Clancy K, Cox RS, Gorochowski T, Grunberg R, Luna A, McLaughlin J, Nguyen T, Le Novere N, Pocock M, Sauro H, Scott-Brown J, Sexton JT, Stan GB, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A.

J Integr Bioinform. 2019 Jun 13. pii: /j/jib.ahead-of-print/jib-2018-0101/jib-2018-0101.xml. doi: 10.1515/jib-2018-0101. [Epub ahead of print]

3.

Regulating, measuring and modelling the viscoelasticity of bacterial biofilms.

Charlton SGV, White MA, Jana S, Eland LE, Jayathilake PG, Burgess JG, Chen J, Wipat A, Curtis TP.

J Bacteriol. 2019 Jun 10. pii: JB.00101-19. doi: 10.1128/JB.00101-19. [Epub ahead of print] Review.

4.

SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information.

Mısırlı G, Taylor R, Goñi-Moreno A, McLaughlin JA, Myers C, Gennari JH, Lord P, Wipat A.

ACS Synth Biol. 2019 Jul 19;8(7):1498-1514. doi: 10.1021/acssynbio.8b00532. Epub 2019 May 14.

PMID:
31059645
5.

Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D.

Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087.

6.

A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.

Waites W, Mısırlı G, Cavaliere M, Danos V, Wipat A.

ACS Synth Biol. 2018 Dec 21;7(12):2812-2823. doi: 10.1021/acssynbio.8b00201. Epub 2018 Nov 20.

7.

sboljs: Bringing the Synthetic Biology Open Language to the Web Browser.

McLaughlin JA, Myers CJ, Zundel Z, Wilkinson N, Atallah C, Wipat A.

ACS Synth Biol. 2019 Jan 18;8(1):191-193. doi: 10.1021/acssynbio.8b00338. Epub 2019 Jan 8.

PMID:
30403869
8.

Species-Specific Detection of C. difficile Using Targeted Antibody Design.

Lawry BM, Johnson CL, Flanagan K, Spoors JA, McNeil CJ, Wipat A, Keegan N.

Anal Chem. 2018 Nov 20;90(22):13475-13482. doi: 10.1021/acs.analchem.8b03349. Epub 2018 Oct 31.

PMID:
30379538
9.

Mild hydrostatic pressure triggers oxidative responses in Escherichia coli.

Guyet A, Dade-Robertson M, Wipat A, Casement J, Smith W, Mitrani H, Zhang M.

PLoS One. 2018 Jul 17;13(7):e0200660. doi: 10.1371/journal.pone.0200660. eCollection 2018.

10.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

Misirli G, Nguyen T, McLaughlin JA, Vaidyanathan P, Jones TS, Densmore D, Myers C, Wipat A.

ACS Synth Biol. 2019 Jul 19;8(7):1548-1559. doi: 10.1021/acssynbio.7b00459. Epub 2018 Jun 5.

PMID:
29782151
11.

Design and modelling of an engineered bacteria-based, pressure-sensitive soil.

Dade-Robertson M, Mitrani H, Corral JR, Zhang M, Hernan L, Guyet A, Wipat A.

Bioinspir Biomim. 2018 May 25;13(4):046004. doi: 10.1088/1748-3190/aabe15.

12.

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A.

J Integr Bioinform. 2018 Apr 2;15(1). pii: /j/jib.2018.15.issue-1/jib-2018-0001/jib-2018-0001.xml. doi: 10.1515/jib-2018-0001.

13.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.

Cox RS, Madsen C, McLaughlin J, Nguyen T, Roehner N, Bartley B, Bhatia S, Bissell M, Clancy K, Gorochowski T, Grünberg R, Luna A, Le Novère N, Pocock M, Sauro H, Sexton JT, Stan GB, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A.

J Integr Bioinform. 2018 Mar 19;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0074/jib-2017-0074.xml. doi: 10.1515/jib-2017-0074.

14.

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.

McLaughlin JA, Myers CJ, Zundel Z, Mısırlı G, Zhang M, Ofiteru ID, Goñi-Moreno A, Wipat A.

ACS Synth Biol. 2018 Feb 16;7(2):682-688. doi: 10.1021/acssynbio.7b00403. Epub 2018 Jan 30.

PMID:
29316788
15.

Impact of Age-Related Mitochondrial Dysfunction and Exercise on Intestinal Microbiota Composition.

Houghton D, Stewart CJ, Stamp C, Nelson A, Aj Ami NJ, Petrosino JF, Wipat A, Trenell MI, Turnbull DM, Greaves LC.

J Gerontol A Biol Sci Med Sci. 2018 Apr 17;73(5):571-578. doi: 10.1093/gerona/glx197.

16.

Heterogeneity in Pure Microbial Systems: Experimental Measurements and Modeling.

González-Cabaleiro R, Mitchell AM, Smith W, Wipat A, Ofiţeru ID.

Front Microbiol. 2017 Sep 20;8:1813. doi: 10.3389/fmicb.2017.01813. eCollection 2017. Review.

17.

A standard-enabled workflow for synthetic biology.

Myers CJ, Beal J, Gorochowski TE, Kuwahara H, Madsen C, McLaughlin JA, Mısırlı G, Nguyen T, Oberortner E, Samineni M, Wipat A, Zhang M, Zundel Z.

Biochem Soc Trans. 2017 Jun 15;45(3):793-803. doi: 10.1042/BST20160347. Review.

PMID:
28620041
18.

CSBB: synthetic biology research at Newcastle University.

Goñi-Moreno A, Wipat A, Krasnogor N.

Biochem Soc Trans. 2017 Jun 15;45(3):781-783. doi: 10.1042/BST20160437.

19.

SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design.

Zhang M, McLaughlin JA, Wipat A, Myers CJ.

ACS Synth Biol. 2017 Jul 21;6(7):1150-1160. doi: 10.1021/acssynbio.6b00275. Epub 2017 May 12.

PMID:
28441476
20.

Synthetic Biology Open Language (SBOL) Version 2.1.0.

Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari J, Myers C, Sauro H, Wipat A.

J Integr Bioinform. 2016 Dec 18;13(3):291. doi: 10.2390/biecoll-jib-2016-291.

PMID:
28187407
21.

A Visual Language for Protein Design.

Cox RS 3rd, McLaughlin JA, Grünberg R, Beal J, Wipat A, Sauro HM.

ACS Synth Biol. 2017 Jul 21;6(7):1120-1123. doi: 10.1021/acssynbio.6b00286. Epub 2017 Mar 7.

22.

Data Integration and Mining for Synthetic Biology Design.

Mısırlı G, Hallinan J, Pocock M, Lord P, McLaughlin JA, Sauro H, Wipat A.

ACS Synth Biol. 2016 Oct 21;5(10):1086-1097. Epub 2016 Jun 20.

23.

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

Madsen C, McLaughlin JA, Mısırlı G, Pocock M, Flanagan K, Hallinan J, Wipat A.

ACS Synth Biol. 2016 Jun 17;5(6):487-97. doi: 10.1021/acssynbio.5b00210. Epub 2016 Jun 8.

24.

An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations.

Mullen J, Cockell SJ, Woollard P, Wipat A.

PLoS One. 2016 May 19;11(5):e0155811. doi: 10.1371/journal.pone.0155811. eCollection 2016.

25.

Sharing Structure and Function in Biological Design with SBOL 2.0.

Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grünberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, Gennari JH, Wipat A, Sauro HM, Myers CJ.

ACS Synth Biol. 2016 Jun 17;5(6):498-506. doi: 10.1021/acssynbio.5b00215. Epub 2016 May 4.

PMID:
27111421
26.

Mining integrated semantic networks for drug repositioning opportunities.

Mullen J, Cockell SJ, Tipney H, Woollard PM, Wipat A.

PeerJ. 2016 Jan 19;4:e1558. doi: 10.7717/peerj.1558. eCollection 2016.

27.

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

McLaughlin JA, Pocock M, Mısırlı G, Madsen C, Wipat A.

ACS Synth Biol. 2016 Aug 19;5(8):874-6. doi: 10.1021/acssynbio.5b00244. Epub 2016 Feb 9.

PMID:
26808703
28.

A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome.

James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Hindmarsh V, Locke J, Mitchell S, Lendrem D, Bowman S, Price E, Pease CT, Emery P, Lanyon P, Hunter JA, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Griffiths B; UK Primary Sjögren’s Syndrome registry, Wipat A, Newton J, Jones DE, Isaacs J, Hallinan J, Ng WF.

PLoS One. 2015 Dec 22;10(12):e0143970. doi: 10.1371/journal.pone.0143970. eCollection 2015.

29.

SBOL Visual: A Graphical Language for Genetic Designs.

Quinn JY, Cox RS 3rd, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari AJ, McLaughlin JA, Myers CJ, P U, Pocock M, Rodriguez C, Soldatova L, Stan GB, Swainston N, Wipat A, Sauro HM.

PLoS Biol. 2015 Dec 3;13(12):e1002310. doi: 10.1371/journal.pbio.1002310. eCollection 2015 Dec.

30.

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.

Misirli G, Cavaliere M, Waites W, Pocock M, Madsen C, Gilfellon O, Honorato-Zimmer R, Zuliani P, Danos V, Wipat A.

Bioinformatics. 2016 Mar 15;32(6):908-17. doi: 10.1093/bioinformatics/btv660. Epub 2015 Nov 11.

31.

Synthetic Biology Open Language (SBOL) Version 2.0.0.

Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H.

J Integr Bioinform. 2015 Sep 4;12(2):272. doi: 10.2390/biecoll-jib-2015-272.

PMID:
26528570
32.

Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES).

Relton CL, Gaunt T, McArdle W, Ho K, Duggirala A, Shihab H, Woodward G, Lyttleton O, Evans DM, Reik W, Paul YL, Ficz G, Ozanne SE, Wipat A, Flanagan K, Lister A, Heijmans BT, Ring SM, Davey Smith G.

Int J Epidemiol. 2015 Aug;44(4):1181-90. doi: 10.1093/ije/dyv072. Epub 2015 May 19. No abstract available.

33.

Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons.

Best A, James K, Dalgliesh C, Hong E, Kheirolahi-Kouhestani M, Curk T, Xu Y, Danilenko M, Hussain R, Keavney B, Wipat A, Klinck R, Cowell IG, Cheong Lee K, Austin CA, Venables JP, Chabot B, Santibanez Koref M, Tyson-Capper A, Elliott DJ.

Nat Commun. 2014 Sep 11;5:4760. doi: 10.1038/ncomms5760.

34.

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species.

Misirli G, Hallinan J, Röttger R, Baumbach J, Wipat A.

J Integr Bioinform. 2014 Jul 8;11(2):244. doi: 10.2390/biecoll-jib-2014-244.

PMID:
25001169
35.

Probabilistic latent semantic analysis applied to whole bacterial genomes identifies common genomic features.

Rusakovica J, Hallinan J, Wipat A, Zuliani P.

J Integr Bioinform. 2014 Jun 30;11(2):243. doi: 10.2390/biecoll-jib-2014-243.

PMID:
24980693
36.

A distributed computational search strategy for the identification of diagnostics targets: application to finding aptamer targets for methicillin-resistant staphylococci.

Flanagan K, Cockell S, Harwood C, Hallinan J, Nakjang S, Lawry B, Wipat A.

J Integr Bioinform. 2014 Jun 30;11(2):242. doi: 10.2390/biecoll-jib-2014-242.

PMID:
24980620
37.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM.

Nat Biotechnol. 2014 Jun;32(6):545-50. doi: 10.1038/nbt.2891. Epub 2014 Jun 6.

PMID:
24911500
38.

Proposed data model for the next version of the synthetic biology open language.

Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ.

ACS Synth Biol. 2015 Jan 16;4(1):57-71. doi: 10.1021/sb500176h. Epub 2014 Jun 16.

PMID:
24896221
39.

Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins.

Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM.

Proteomics. 2013 Nov;13(22):3298-308. doi: 10.1002/pmic.201300183. Epub 2013 Oct 27.

PMID:
24115457
40.

BacillOndex: an integrated data resource for systems and synthetic biology.

Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan JS.

J Integr Bioinform. 2013 Apr 10;10(2):224. doi: 10.2390/biecoll-jib-2013-224.

PMID:
23571273
41.

Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud.

Flanagan K, Nakjang S, Hallinan J, Harwood C, Hirt RP, Pocock MR, Wipat A.

J Integr Bioinform. 2012 Sep 24;9(2):212. doi: 10.2390/biecoll-jib-2012-212.

PMID:
23001322
42.

Is newer better?--evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae.

James K, Wipat A, Hallinan J.

Integr Biol (Camb). 2012 Jul;4(7):715-27. doi: 10.1039/c2ib00123c. Epub 2012 Apr 23.

PMID:
22526920
43.

Bayesian integration of networks without gold standards.

Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ.

Bioinformatics. 2012 Jun 1;28(11):1495-500. doi: 10.1093/bioinformatics/bts154. Epub 2012 Apr 6.

44.

Data mining the human gut microbiota for therapeutic targets.

Collison M, Hirt RP, Wipat A, Nakjang S, Sanseau P, Brown JR.

Brief Bioinform. 2012 Nov;13(6):751-68. doi: 10.1093/bib/bbs002. Epub 2012 Mar 24. Review.

PMID:
22445903
45.

Genome-wide analysis to identify pathways affecting telomere-initiated senescence in budding yeast.

Chang HY, Lawless C, Addinall SG, Oexle S, Taschuk M, Wipat A, Wilkinson DJ, Lydall D.

G3 (Bethesda). 2011 Aug;1(3):197-208. doi: 10.1534/g3.111.000216. Epub 2011 Aug 1.

46.

A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes.

Nakjang S, Ndeh DA, Wipat A, Bolam DN, Hirt RP.

PLoS One. 2012;7(1):e30287. doi: 10.1371/journal.pone.0030287. Epub 2012 Jan 27.

47.

Network approaches to the functional analysis of microbial proteins.

Hallinan JS, James K, Wipat A.

Adv Microb Physiol. 2011;59:101-33. doi: 10.1016/B978-0-12-387661-4.00005-7. Review.

PMID:
22114841
48.

Automatic extraction of microorganisms and their habitats from free text using text mining workflows.

Kolluru B, Nakjang S, Hirt RP, Wipat A, Ananiadou S.

J Integr Bioinform. 2011 Oct 10;8(2):184. doi: 10.2390/biecoll-jib-2011-184.

PMID:
21987583
49.

Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant.

Stadler LK, Hoffmann T, Tomlinson DC, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner SD, Knowles MA, Davis JJ, Keegan N, Ferrigno PK.

Protein Eng Des Sel. 2011 Sep;24(9):751-63. doi: 10.1093/protein/gzr019. Epub 2011 May 25.

PMID:
21616931
50.

Keratinocyte apoptosis in epidermal remodeling and clearance of psoriasis induced by UV radiation.

Weatherhead SC, Farr PM, Jamieson D, Hallinan JS, Lloyd JJ, Wipat A, Reynolds NJ.

J Invest Dermatol. 2011 Sep;131(9):1916-26. doi: 10.1038/jid.2011.134. Epub 2011 May 26.

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