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Minimum information requested in the annotation of biochemical models (MIRIAM).
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Le Novère N, et al. Among authors: klipp e. Nat Biotechnol. 2005 Dec;23(12):1509-15. doi: 10.1038/nbt1156. Nat Biotechnol. 2005. PMID: 16333295
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. Herrgård MJ, et al. Among authors: klipp e. Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492. Nat Biotechnol. 2008. PMID: 18846089 Free PMC article.
Minimum Information About a Simulation Experiment (MIASE).
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. Waltemath D, et al. Among authors: klipp e. PLoS Comput Biol. 2011 Apr;7(4):e1001122. doi: 10.1371/journal.pcbi.1001122. Epub 2011 Apr 28. PLoS Comput Biol. 2011. PMID: 21552546 Free PMC article. No abstract available.
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. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
MEMOTE for standardized genome-scale metabolic model testing.
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Malik Sheriff RS, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. Lieven C, et al. Among authors: klipp e. Nat Biotechnol. 2020 Mar;38(3):272-276. doi: 10.1038/s41587-020-0446-y. Nat Biotechnol. 2020. PMID: 32123384 Free PMC article. No abstract available.
Bridging the gaps in systems biology.
Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M. Cvijovic M, et al. Among authors: klipp e. Mol Genet Genomics. 2014 Oct;289(5):727-34. doi: 10.1007/s00438-014-0843-3. Epub 2014 Apr 13. Mol Genet Genomics. 2014. PMID: 24728588 Review.
175 results