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Predicting growth of the healthy infant using a genome scale metabolic model.
Nilsson A, Mardinoglu A, Nielsen J. Nilsson A, et al. NPJ Syst Biol Appl. 2017 Jan 31;3:3. doi: 10.1038/s41540-017-0004-5. eCollection 2017. NPJ Syst Biol Appl. 2017. PMID: 28649430 Free PMC article.
We used a human genome scale metabolic model to simulate the mechanisms of growth and integrate data about breast-milk intake and composition with the infant's biomass and energy expenditure of major organs. ...The model and simulation method were integrated to a pl …
We used a human genome scale metabolic model to simulate the mechanisms of growth and integrate data about breast-milk intake and com …
Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase.
Nilsson A, Nielsen J. Nilsson A, et al. Sci Rep. 2016 Mar 1;6:22264. doi: 10.1038/srep22264. Sci Rep. 2016. PMID: 26928598 Free PMC article.
Only a fraction of cellular protein can, however, be allocated to enzymes of intermediary metabolism and consequently metabolic trade-offs may take place. ...And that the switch to fermentation at high growth rates therefore is a consequence of a high ATP pro …
Only a fraction of cellular protein can, however, be allocated to enzymes of intermediary metabolism and consequently metabolic trade …
Genome scale metabolic modeling of cancer.
Nilsson A, Nielsen J. Nilsson A, et al. Metab Eng. 2017 Sep;43(Pt B):103-112. doi: 10.1016/j.ymben.2016.10.022. Epub 2016 Nov 4. Metab Eng. 2017. PMID: 27825806 Review.
A genome scale metabolic model (GEM) is a mathematical formalization of metabolism which allows simulation and hypotheses testing of metabolic strategies. ...
A genome scale metabolic model (GEM) is a mathematical formalization of metabolism which allows simulation and hypotheses test
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.
Sánchez BJ, Zhang C, Nilsson A, Lahtvee PJ, Kerkhoven EJ, Nielsen J. Sánchez BJ, et al. Mol Syst Biol. 2017 Aug 3;13(8):935. doi: 10.15252/msb.20167411. Mol Syst Biol. 2017. PMID: 28779005 Free PMC article.
Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to …
Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each m …
Metabolic Models of Protein Allocation Call for the Kinetome.
Nilsson A, Nielsen J, Palsson BO. Nilsson A, et al. Cell Syst. 2017 Dec 27;5(6):538-541. doi: 10.1016/j.cels.2017.11.013. Cell Syst. 2017. PMID: 29284126
To move further, the scientific community needs to measure the kinetics of all enzymes in a systematic way....
To move further, the scientific community needs to measure the kinetics of all enzymes in a systematic way....
Recon3D enables a three-dimensional view of gene variation in human metabolism.
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. Brunk E, et al. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. Nat Biotechnol. 2018. PMID: 29457794 Free PMC article.
Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. ...These data provide a unique resource for investigating molecular mechani …
Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enab …
Complex I is bypassed during high intensity exercise.
Nilsson A, Björnson E, Flockhart M, Larsen FJ, Nielsen J. Nilsson A, et al. Nat Commun. 2019 Nov 7;10(1):5072. doi: 10.1038/s41467-019-12934-8. Nat Commun. 2019. PMID: 31699973 Free PMC article.
A metabolic bypass of mitochondrial complex I is found to increase the ATP synthesis rate per gram of protein compared to full respiration. To test if this metabolic mode occurs in vivo, we conduct a high resolved incremental exercise tests for five subjects. Their
A metabolic bypass of mitochondrial complex I is found to increase the ATP synthesis rate per gram of protein compared to full respir
An atlas of human metabolism.
Robinson JL, Kocabaş P, Wang H, Cholley PE, Cook D, Nilsson A, Anton M, Ferreira R, Domenzain I, Billa V, Limeta A, Hedin A, Gustafsson J, Kerkhoven EJ, Svensson LT, Palsson BO, Mardinoglu A, Hansson L, Uhlén M, Nielsen J. Robinson JL, et al. Sci Signal. 2020 Mar 24;13(624):eaaz1482. doi: 10.1126/scisignal.aaz1482. Sci Signal. 2020. PMID: 32209698
Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. ...We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Hum …
Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of om …
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis.
Nilsson A, Haanstra JR, Engqvist M, Gerding A, Bakker BM, Klingmüller U, Teusink B, Nielsen J. Nilsson A, et al. Proc Natl Acad Sci U S A. 2020 May 12;117(19):10294-10304. doi: 10.1073/pnas.1919250117. Epub 2020 Apr 27. Proc Natl Acad Sci U S A. 2020. PMID: 32341162 Free PMC article.
Here, we dynamically profile the uptake and excretion fluxes of a liver cancer cell line (HepG2) and use genome-scale metabolic modeling for in-depth analysis. ...
Here, we dynamically profile the uptake and excretion fluxes of a liver cancer cell line (HepG2) and use genome-scale metabolic model …
A dedicated database system for handling multi-level data in systems biology.
Pornputtapong N, Wanichthanarak K, Nilsson A, Nookaew I, Nielsen J. Pornputtapong N, et al. Source Code Biol Med. 2014 Jul 10;9:17. doi: 10.1186/1751-0473-9-17. eCollection 2014. Source Code Biol Med. 2014. PMID: 25053973 Free PMC article.
METHODS: To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a
METHODS: To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data ma …
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