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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. McMurry JA, et al. Among authors: swainston n. PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun. PLoS Biol. 2017. PMID: 28662064 Free PMC article.
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. Büchel F, et al. Among authors: swainston n. BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116. BMC Syst Biol. 2013. PMID: 24180668 Free PMC article.
biochem4j: Integrated and extensible biochemical knowledge through graph databases.
Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS, Breitling R. Swainston N, et al. PLoS One. 2017 Jul 14;12(7):e0179130. doi: 10.1371/journal.pone.0179130. eCollection 2017. PLoS One. 2017. PMID: 28708831 Free PMC article.
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. Keating SM, et al. Among authors: swainston n. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
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. Carbonell P, et al. Among authors: swainston n. Commun Biol. 2018 Jun 8;1:66. doi: 10.1038/s42003-018-0076-9. eCollection 2018. Commun Biol. 2018. PMID: 30271948 Free PMC article.
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. Hastings J, et al. Among authors: swainston n. Nucleic Acids Res. 2016 Jan 4;44(D1):D1214-9. doi: 10.1093/nar/gkv1031. Epub 2015 Oct 13. Nucleic Acids Res. 2016. PMID: 26467479 Free PMC article.
libChEBI: an API for accessing the ChEBI database.
Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P. Swainston N, et al. J Cheminform. 2016 Mar 1;8:11. doi: 10.1186/s13321-016-0123-9. eCollection 2016. J Cheminform. 2016. PMID: 26933452 Free PMC article.
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. Carbonell P, et al. Among authors: swainston n. Biochem Soc Trans. 2016 Jun 15;44(3):675-7. doi: 10.1042/BST20160009. Biochem Soc Trans. 2016. PMID: 27284023 Free PMC article.
63 results