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Constraint Based Modeling Going Multicellular.
Martins Conde Pdo R, Sauter T, Pfau T. Martins Conde Pdo R, et al. Among authors: pfau t. Front Mol Biosci. 2016 Feb 10;3:3. doi: 10.3389/fmolb.2016.00003. eCollection 2016. Front Mol Biosci. 2016. PMID: 26904548 Free PMC article. Review.
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.
A dynamic multi-tissue model to study human metabolism.
Martins Conde P, Pfau T, Pires Pacheco M, Sauter T. Martins Conde P, et al. Among authors: pfau t. NPJ Syst Biol Appl. 2021 Jan 22;7(1):5. doi: 10.1038/s41540-020-00159-1. NPJ Syst Biol Appl. 2021. PMID: 33483512 Free PMC article.
Systems approaches to modelling pathways and networks.
Pfau T, Christian N, Ebenhöh O. Pfau T, et al. Brief Funct Genomics. 2011 Sep;10(5):266-79. doi: 10.1093/bfgp/elr022. Epub 2011 Sep 8. Brief Funct Genomics. 2011. PMID: 21903724 Review.
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT. Heirendt L, et al. Among authors: pfau t. Nat Protoc. 2019 Mar;14(3):639-702. doi: 10.1038/s41596-018-0098-2. Nat Protoc. 2019. PMID: 30787451 Free PMC article.
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