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Results: 1 to 20 of 24

1.

SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution.

Currin A, Swainston N, Day PJ, Kell DB.

Protein Eng Des Sel. 2014 Sep;27(9):273-80. doi: 10.1093/protein/gzu029. Epub 2014 Aug 9.

PMID:
25108914
[PubMed - in process]
Free PMC Article
2.

GeneGenie: optimized oligomer design for directed evolution.

Swainston N, Currin A, Day PJ, Kell DB.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W395-400. doi: 10.1093/nar/gku336. Epub 2014 Apr 29.

PMID:
24782527
[PubMed - indexed for MEDLINE]
Free Article
3.

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

PMID:
24180668
[PubMed - indexed for MEDLINE]
Free Article
4.

An analysis of a 'community-driven' reconstruction of the human metabolic network.

Swainston N, Mendes P, Kell DB.

Metabolomics. 2013 Aug;9(4):757-764. Epub 2013 Jul 12.

PMID:
23888127
[PubMed]
Free PMC Article
5.

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.

Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JE, Paton NW, Westerhoff HV, Kell DB, Mendes P.

FEBS Lett. 2013 Sep 2;587(17):2832-41. doi: 10.1016/j.febslet.2013.06.043. Epub 2013 Jul 4.

PMID:
23831062
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A community-driven global reconstruction of human metabolism.

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ.

Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3.

PMID:
23455439
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Improving metabolic flux predictions using absolute gene expression data.

Lee D, Smallbone K, Dunn WB, Murabito E, Winder CL, Kell DB, Mendes P, Swainston N.

BMC Syst Biol. 2012 Jun 19;6:73. doi: 10.1186/1752-0509-6-73.

PMID:
22713172
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.

Swainston N, Smallbone K, Mendes P, Kell D, Paton N.

J Integr Bioinform. 2011 Nov 18;8(2):186. doi: 10.2390/biecoll-jib-2011-186.

PMID:
22095399
[PubMed - indexed for MEDLINE]
9.

Sustainable model building the role of standards and biological semantics.

Krause F, Schulz M, Swainston N, Liebermeister W.

Methods Enzymol. 2011;500:371-95. doi: 10.1016/B978-0-12-385118-5.00019-0.

PMID:
21943907
[PubMed - indexed for MEDLINE]
10.

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D.

BMC Syst Biol. 2011 Jan 18;5:8. doi: 10.1186/1752-0509-5-8.

PMID:
21244678
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A QconCAT informatics pipeline for the analysis, visualization and sharing of absolute quantitative proteomics data.

Swainston N, Jameson D, Carroll K.

Proteomics. 2011 Jan;11(2):329-33. doi: 10.1002/pmic.201000454. Epub 2010 Dec 17.

PMID:
21204260
[PubMed - indexed for MEDLINE]
12.

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.

PMID:
21114840
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Further developments towards a genome-scale metabolic model of yeast.

Dobson PD, Smallbone K, Jameson D, Simeonidis E, Lanthaler K, Pir P, Lu C, Swainston N, Dunn WB, Fisher P, Hull D, Brown M, Oshota O, Stanford NJ, Kell DB, King RD, Oliver SG, Stevens RD, Mendes P.

BMC Syst Biol. 2010 Oct 28;4:145. doi: 10.1186/1752-0509-4-145.

PMID:
21029416
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Enzyme kinetics informatics: from instrument to browser.

Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Müller W, Paton NW, Rojas I.

FEBS J. 2010 Sep;277(18):3769-79. doi: 10.1111/j.1742-4658.2010.07778.x. Epub 2010 Aug 3.

PMID:
20738395
[PubMed - indexed for MEDLINE]
15.

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks.

Radrich K, Tsuruoka Y, Dobson P, Gevorgyan A, Swainston N, Baart G, Schwartz JM.

BMC Syst Biol. 2010 Aug 16;4:114. doi: 10.1186/1752-0509-4-114.

PMID:
20712863
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Towards a genome-scale kinetic model of cellular metabolism.

Smallbone K, Simeonidis E, Swainston N, Mendes P.

BMC Syst Biol. 2010 Jan 28;4:6. doi: 10.1186/1752-0509-4-6.

PMID:
20109182
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Information management for high content live cell imaging.

Jameson D, Turner DA, Ankers J, Kennedy S, Ryan S, Swainston N, Griffiths T, Spiller DG, Oliver SG, White MR, Kell DB, Paton NW.

BMC Bioinformatics. 2009 Jul 21;10:226. doi: 10.1186/1471-2105-10-226.

PMID:
19622144
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics.

Brown M, Dunn WB, Dobson P, Patel Y, Winder CL, Francis-McIntyre S, Begley P, Carroll K, Broadhurst D, Tseng A, Swainston N, Spasic I, Goodacre R, Kell DB.

Analyst. 2009 Jul;134(7):1322-32. doi: 10.1039/b901179j. Epub 2009 Apr 9.

PMID:
19562197
[PubMed - indexed for MEDLINE]
19.

libAnnotationSBML: a library for exploiting SBML annotations.

Swainston N, Mendes P.

Bioinformatics. 2009 Sep 1;25(17):2292-3. doi: 10.1093/bioinformatics/btp392. Epub 2009 Jun 26.

PMID:
19561017
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB.

Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492.

PMID:
18846089
[PubMed - indexed for MEDLINE]
Free PMC Article

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