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Items: 1 to 20 of 32

1.

Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle.

Carbonell P, Currin A, Jervis AJ, Rattray NJ, Swainston N, Yan C, Takano E, Breitling R.

Nat Prod Rep. 2016 May 17. [Epub ahead of print]

PMID:
27185383
2.

libChEBI: an API for accessing the ChEBI database.

Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P.

J Cheminform. 2016 Mar 1;8:11. doi: 10.1186/s13321-016-0123-9. eCollection 2016.

3.

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.

4.

ChEBI in 2016: Improved services and an expanding collection of metabolites.

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1214-9. doi: 10.1093/nar/gkv1031. Epub 2015 Oct 13.

5.

RobOKoD: microbial strain design for (over)production of target compounds.

Stanford NJ, Millard P, Swainston N.

Front Cell Dev Biol. 2015 Mar 24;3:17. doi: 10.3389/fcell.2015.00017. eCollection 2015.

6.

A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs.

O Hagan S, Swainston N, Handl J, Kell DB.

Metabolomics. 2015;11(2):323-339. Epub 2014 Sep 19.

7.

Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis.

Kell DB, Swainston N, Pir P, Oliver SG.

Trends Biotechnol. 2015 Apr;33(4):237-46. doi: 10.1016/j.tibtech.2015.02.001. Epub 2015 Mar 3. Review.

8.

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.

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

Chem Soc Rev. 2015 Mar 7;44(5):1172-239. doi: 10.1039/c4cs00351a. Review.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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
17.

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
18.

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.

19.

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
20.

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.

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