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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: hermjakob h. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Kerrien S, et al. Among authors: hermjakob h. BMC Biol. 2007 Oct 9;5:44. doi: 10.1186/1741-7007-5-44. BMC Biol. 2007. PMID: 17925023 Free PMC article.
ENFIN--A European network for integrative systems biology.
Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E. Kahlem P, et al. Among authors: hermjakob h. C R Biol. 2009 Nov;332(11):1050-8. doi: 10.1016/j.crvi.2009.09.003. C R Biol. 2009. PMID: 19909926 Free article. Review.
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: hermjakob h. BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116. BMC Syst Biol. 2013. PMID: 24180668 Free PMC article.
BioModels linked dataset.
Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C. Wimalaratne SM, et al. Among authors: hermjakob h. BMC Syst Biol. 2014 Aug 15;8:91. doi: 10.1186/s12918-014-0091-5. BMC Syst Biol. 2014. PMID: 25182954 Free PMC article.
BioModels: ten-year anniversary.
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C. Chelliah V, et al. Among authors: hermjakob h. Nucleic Acids Res. 2015 Jan;43(Database issue):D542-8. doi: 10.1093/nar/gku1181. Epub 2014 Nov 20. Nucleic Acids Res. 2015. PMID: 25414348 Free PMC article.
SPARQL-enabled identifier conversion with Identifiers.org.
Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C. Wimalaratne SM, et al. Among authors: hermjakob h. Bioinformatics. 2015 Jun 1;31(11):1875-7. doi: 10.1093/bioinformatics/btv064. Epub 2015 Jan 31. Bioinformatics. 2015. PMID: 25638809 Free PMC article.
BioModels: Content, Features, Functionality, and Use.
Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V. Juty N, et al. Among authors: hermjakob h. CPT Pharmacometrics Syst Pharmacol. 2015 Feb;4(2):e3. doi: 10.1002/psp4.3. Epub 2015 Feb 26. CPT Pharmacometrics Syst Pharmacol. 2015. PMID: 26225232 Free PMC article.
Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.
Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N. Swat MJ, et al. Among authors: hermjakob h. CPT Pharmacometrics Syst Pharmacol. 2015 Jun;4(6):316-9. doi: 10.1002/psp4.57. Epub 2015 Jun 15. CPT Pharmacometrics Syst Pharmacol. 2015. PMID: 26225259 Free PMC article.
287 results