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Model-based assessment of mammalian cell metabolic functionalities using omics data.
Richelle A, Kellman BP, Wenzel AT, Chiang AWT, Reagan T, Gutierrez JM, Joshi C, Li S, Liu JK, Masson H, Lee J, Li Z, Heirendt L, Trefois C, Juarez EF, Bath T, Borland D, Mesirov JP, Robasky K, Lewis NE. Richelle A, et al. Among authors: heirendt l. Cell Rep Methods. 2021 Jul 26;1(3):100040. doi: 10.1016/j.crmeth.2021.100040. Epub 2021 Jun 30. Cell Rep Methods. 2021. PMID: 34761247 Free PMC article.
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. Nat Protoc. 2019 Mar;14(3):639-702. doi: 10.1038/s41596-018-0098-2. Nat Protoc. 2019. PMID: 30787451 Free PMC article.
COBREXA.jl: constraint-based reconstruction and exascale analysis.
Kratochvíl M, Heirendt L, Wilken SE, Pusa T, Arreckx S, Noronha A, van Aalst M, Satagopam VP, Ebenhöh O, Schneider R, Trefois C, Gu W. Kratochvíl M, et al. Among authors: heirendt l. Bioinformatics. 2022 Jan 27;38(4):1171-1172. doi: 10.1093/bioinformatics/btab782. Bioinformatics. 2022. PMID: 34791064 Free PMC article.
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease.
Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Daníelsdóttir AD, Krecke M, Merten D, Haraldsdóttir HS, Heinken A, Heirendt L, Magnúsdóttir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Žagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I. Noronha A, et al. Among authors: heirendt l. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. Nucleic Acids Res. 2019. PMID: 30371894 Free PMC article.
15 results