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Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis.

Ravcheev DA, Thiele I.

Front Microbiol. 2016 Feb 9;7:128. doi: 10.3389/fmicb.2016.00128. eCollection 2016.


Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine.

Aurich MK, Thiele I.

Methods Mol Biol. 2016;1386:253-81. doi: 10.1007/978-1-4939-3283-2_12.


Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

Bauer E, Laczny CC, Magnusdottir S, Wilmes P, Thiele I.

Microbiome. 2015 Nov 30;3:55. doi: 10.1186/s40168-015-0121-6.


Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


Associations between calcium and vitamin D supplement use as well as their serum concentrations and subclinical cardiovascular disease phenotypes.

Thiele I, Linseisen J, Meisinger C, Schwab S, Huth C, Peters A, Perz S, Meitinger T, Kronenberg F, Lamina C, Thiery J, Koenig W, Rathmann W, Kääb S, Then C, Seissler J, Thorand B.

Atherosclerosis. 2015 Aug;241(2):743-51. doi: 10.1016/j.atherosclerosis.2015.06.032. Epub 2015 Jun 19.


Prediction of intracellular metabolic states from extracellular metabolomic data.

Aurich MK, Paglia G, Rolfsson Ó, Hrafnsdóttir S, Magnúsdóttir M, Stefaniak MM, Palsson BØ, Fleming RM, Thiele I.

Metabolomics. 2015;11(3):603-619. Epub 2014 Aug 14.


Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes.

Magnúsdóttir S, Ravcheev D, de Crécy-Lagard V, Thiele I.

Front Genet. 2015 Apr 20;6:148. doi: 10.3389/fgene.2015.00148. eCollection 2015.


Systems biology of host-microbe metabolomics.

Heinken A, Thiele I.

Wiley Interdiscip Rev Syst Biol Med. 2015 Jul-Aug;7(4):195-219. doi: 10.1002/wsbm.1301. Epub 2015 Apr 30. Review.


Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework.

Heinken A, Thiele I.

Gut Microbes. 2015;6(2):120-30. doi: 10.1080/19490976.2015.1023494.


Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico.

Heinken A, Thiele I.

Appl Environ Microbiol. 2015 Jun 15;81(12):4049-61. doi: 10.1128/AEM.00101-15. Epub 2015 Apr 3.


Enhancing second harmonic generation in gold nanoring resonators filled with lithium niobate.

Lehr D, Reinhold J, Thiele I, Hartung H, Dietrich K, Menzel C, Pertsch T, Kley EB, Tünnermann A.

Nano Lett. 2015 Feb 11;15(2):1025-30. doi: 10.1021/nl5038819. Epub 2015 Jan 14.


Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota.

Ravcheev DA, Thiele I.

Front Microbiol. 2014 Dec 5;5:674. doi: 10.3389/fmicb.2014.00674. eCollection 2014.


Modeling the effects of commonly used drugs on human metabolism.

Sahoo S, Haraldsdóttir HS, Fleming RM, Thiele I.

FEBS J. 2015 Jan;282(2):297-317. doi: 10.1111/febs.13128. Epub 2014 Nov 21.


Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe.

Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJ, Thiele I.

J Bacteriol. 2014 Sep;196(18):3289-302. doi: 10.1128/JB.01780-14. Epub 2014 Jul 7.


Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia.

Edwards LM, Sigurdsson MI, Robbins PA, Weale ME, Cavalleri GL, Montgomery HE, Thiele I.

Circ Cardiovasc Genet. 2014 Aug;7(4):407-15. doi: 10.1161/CIRCGENETICS.113.000269. Epub 2014 May 29.


fastGapFill: efficient gap filling in metabolic networks.

Thiele I, Vlassis N, Fleming RM.

Bioinformatics. 2014 Sep 1;30(17):2529-31. doi: 10.1093/bioinformatics/btu321. Epub 2014 May 7.


Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease.

Sahoo S, Aurich MK, Jonsson JJ, Thiele I.

Front Physiol. 2014 Mar 11;5:91. doi: 10.3389/fphys.2014.00091. eCollection 2014. Review.


Phospholipase A2 receptor autoantibodies and clinical outcome in patients with primary membranous nephropathy.

Hoxha E, Thiele I, Zahner G, Panzer U, Harendza S, Stahl RA.

J Am Soc Nephrol. 2014 Jun;25(6):1357-66. doi: 10.1681/ASN.2013040430. Epub 2014 Mar 7.


Robust flux balance analysis of multiscale biochemical reaction networks.

Sun Y, Fleming RM, Thiele I, Saunders MA.

BMC Bioinformatics. 2013 Jul 30;14:240. doi: 10.1186/1471-2105-14-240.

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