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Items: 1 to 20 of 103

1.

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota.

Bauer E, Thiele I.

mSystems. 2018 Mar 27;3(3). pii: e00209-17. doi: 10.1128/mSystems.00209-17. eCollection 2018 May-Jun. Review.

2.

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.

Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19.

PMID:
29457794
3.

Modeling metabolism of the human gut microbiome.

Magnúsdóttir S, Thiele I.

Curr Opin Biotechnol. 2018 Jun;51:90-96. doi: 10.1016/j.copbio.2017.12.005. Epub 2017 Dec 16. Review.

4.

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

Preciat Gonzalez GA, El Assal LRP, Noronha A, Thiele I, Haraldsdóttir HS, Fleming RMT.

J Cheminform. 2017 Jun 14;9(1):39. doi: 10.1186/s13321-017-0223-1.

6.

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines.

Aurich MK, Fleming RMT, Thiele I.

PLoS Comput Biol. 2017 Aug 14;13(8):e1005698. doi: 10.1371/journal.pcbi.1005698. eCollection 2017 Aug.

7.

Model-based dietary optimization for late-stage, levodopa-treated, Parkinson's disease patients.

Guebila MB, Thiele I.

NPJ Syst Biol Appl. 2016 Jun 16;2:16013. doi: 10.1038/npjsba.2016.13. eCollection 2016.

8.

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities.

Bauer E, Zimmermann J, Baldini F, Thiele I, Kaleta C.

PLoS Comput Biol. 2017 May 22;13(5):e1005544. doi: 10.1371/journal.pcbi.1005544. eCollection 2017 May.

9.

DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia.

Heirendt L, Thiele I, Fleming RMT.

Bioinformatics. 2017 May 1;33(9):1421-1423. doi: 10.1093/bioinformatics/btw838.

10.

Gut microbiota functions: metabolism of nutrients and other food components.

Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K.

Eur J Nutr. 2018 Feb;57(1):1-24. doi: 10.1007/s00394-017-1445-8. Epub 2017 Apr 9. Review.

11.

Spectral dynamics of THz pulses generated by two-color laser filaments in air: the role of Kerr nonlinearities and pump wavelength.

Nguyen A, González de Alaiza Martínez P, Déchard J, Thiele I, Babushkin I, Skupin S, Bergé L.

Opt Express. 2017 Mar 6;25(5):4720-4740. doi: 10.1364/OE.25.004720.

PMID:
28380743
12.

CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models.

Haraldsdóttir HS, Cousins B, Thiele I, Fleming RMT, Vempala S.

Bioinformatics. 2017 Jun 1;33(11):1741-1743. doi: 10.1093/bioinformatics/btx052.

13.

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression.

Ma D, Yang L, Fleming RM, Thiele I, Palsson BO, Saunders MA.

Sci Rep. 2017 Jan 18;7:40863. doi: 10.1038/srep40863.

14.

Theory of terahertz emission from femtosecond-laser-induced microplasmas.

Thiele I, Nuter R, Bousquet B, Tikhonchuk V, Skupin S, Davoine X, Gremillet L, Bergé L.

Phys Rev E. 2016 Dec;94(6-1):063202. doi: 10.1103/PhysRevE.94.063202. Epub 2016 Dec 6.

PMID:
28085420
15.

ReconMap: an interactive visualization of human metabolism.

Noronha A, Daníelsdóttir AD, Gawron P, Jóhannsson F, Jónsdóttir S, Jarlsson S, Gunnarsson JP, Brynjólfsson S, Schneider R, Thiele I, Fleming RM.

Bioinformatics. 2017 Feb 15;33(4):605-607. doi: 10.1093/bioinformatics/btw667.

16.

Leigh map: A novel computational diagnostic resource for mitochondrial disease.

Rahman J, Noronha A, Thiele I, Rahman S.

Ann Neurol. 2017 Jan;81(1):9-16. doi: 10.1002/ana.24835. No abstract available.

17.

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RM, Thiele I.

Nat Biotechnol. 2017 Jan;35(1):81-89. doi: 10.1038/nbt.3703. Epub 2016 Nov 28.

PMID:
27893703
18.

Editorial: The Human Gutome: Nutrigenomics of Host-Microbiome Interactions.

Dimitrov D, Thiele I, Ferguson LR.

Front Genet. 2016 Sep 6;7:158. doi: 10.3389/fgene.2016.00158. eCollection 2016. No abstract available.

19.

Metabolomics enables precision medicine: "A White Paper, Community Perspective".

Beger RD, Dunn W, Schmidt MA, Gross SS, Kirwan JA, Cascante M, Brennan L, Wishart DS, Oresic M, Hankemeier T, Broadhurst DI, Lane AN, Suhre K, Kastenmüller G, Sumner SJ, Thiele I, Fiehn O, Kaddurah-Daouk R; for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative.

Metabolomics. 2016;12(10):149. Epub 2016 Sep 2.

20.

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models.

Aurich MK, Fleming RM, Thiele I.

Front Physiol. 2016 Aug 3;7:327. doi: 10.3389/fphys.2016.00327. eCollection 2016.

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