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Reproducibility in systems biology modelling.
Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H, Malik-Sheriff RS. Tiwari K, et al. Among authors: hermjakob h. Mol Syst Biol. 2021 Feb;17(2):e9982. doi: 10.15252/msb.20209982. Mol Syst Biol. 2021. PMID: 33620773 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: 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.
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.
The evolution of standards and data management practices in systems biology.
Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C. Stanford NJ, et al. Among authors: hermjakob h. Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053. Mol Syst Biol. 2015. PMID: 26700851 Free PMC article.
BioModels: expanding horizons to include more modelling approaches and formats.
Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H. Glont M, et al. Among authors: hermjakob h. Nucleic Acids Res. 2018 Jan 4;46(D1):D1248-D1253. doi: 10.1093/nar/gkx1023. Nucleic Acids Res. 2018. PMID: 29106614 Free PMC article.
Quantifying the impact of public omics data.
Perez-Riverol Y, Zorin A, Dass G, Vu MT, Xu P, Glont M, Vizcaíno JA, Jarnuczak AF, Petryszak R, Ping P, Hermjakob H. Perez-Riverol Y, et al. Among authors: hermjakob h. Nat Commun. 2019 Aug 5;10(1):3512. doi: 10.1038/s41467-019-11461-w. Nat Commun. 2019. PMID: 31383865 Free PMC article.
BioModels-15 years of sharing computational models in life science.
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H. Malik-Sheriff RS, et al. Among authors: hermjakob h. Nucleic Acids Res. 2020 Jan 8;48(D1):D407-D415. doi: 10.1093/nar/gkz1055. Nucleic Acids Res. 2020. PMID: 31701150 Free PMC article.
287 results