Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 119

1.

Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig.

Poupin N, Tremblay-Franco M, Amiel A, Canlet C, Rémond D, Debrauwer L, Dardevet D, Thiele I, Aurich MK, Jourdan F, Savary-Auzeloux I, Polakof S.

Sci Rep. 2019 Aug 29;9(1):12527. doi: 10.1038/s41598-019-48997-2.

2.

Intensity modulated terahertz vortex wave generation in air plasma by two-color femtosecond laser pulses.

Ivanov M, Thiele I, Bergé L, Skupin S, Buožius D, Vaičaitis V.

Opt Lett. 2019 Aug 1;44(15):3889-3892. doi: 10.1364/OL.44.003889.

PMID:
31368994
3.

Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome.

Ravcheev DA, Moussu L, Smajic S, Thiele I.

Front Genet. 2019 Jul 4;10:636. doi: 10.3389/fgene.2019.00636. eCollection 2019.

4.

Predicting gastrointestinal drug effects using contextualized metabolic models.

Ben Guebila M, Thiele I.

PLoS Comput Biol. 2019 Jun 26;15(6):e1007100. doi: 10.1371/journal.pcbi.1007100. eCollection 2019 Jun.

5.

Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development.

Peñalver Bernabé B, Thiele I, Galdones E, Siletz A, Chandrasekaran S, Woodruff TK, Broadbelt LJ, Shea LD.

BMC Bioinformatics. 2019 Jun 10;20(1):307. doi: 10.1186/s12859-019-2825-2.

6.

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.

Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I.

Microbiome. 2019 May 15;7(1):75. doi: 10.1186/s40168-019-0689-3.

7.

Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells.

Greenhalgh K, Ramiro-Garcia J, Heinken A, Ullmann P, Bintener T, Pacheco MP, Baginska J, Shah P, Frachet A, Halder R, Fritz JV, Sauter T, Thiele I, Haan S, Letellier E, Wilmes P.

Cell Rep. 2019 Apr 30;27(5):1621-1632.e9. doi: 10.1016/j.celrep.2019.04.001.

8.

Electron Beam Driven Generation of Frequency-Tunable Isolated Relativistic Subcycle Pulses.

Thiele I, Siminos E, Fülöp T.

Phys Rev Lett. 2019 Mar 15;122(10):104803. doi: 10.1103/PhysRevLett.122.104803.

PMID:
30932636
9.

Wavelength scaling of terahertz pulse energies delivered by two-color air plasmas.

Nguyen A, Kaltenecker KJ, Delagnes JC, Zhou B, Cormier E, Fedorov N, Bouillaud R, Descamps D, Thiele I, Skupin S, Jepsen PU, Bergé L.

Opt Lett. 2019 Mar 15;44(6):1488-1491. doi: 10.1364/OL.44.001488.

PMID:
30874683
10.

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.

Nat Protoc. 2019 Mar;14(3):639-702. doi: 10.1038/s41596-018-0098-2.

PMID:
30787451
11.

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities.

Baldini F, Heinken A, Heirendt L, Magnusdottir S, Fleming RMT, Thiele I.

Bioinformatics. 2019 Jul 1;35(13):2332-2334. doi: 10.1093/bioinformatics/bty941.

12.

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.

Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992.

13.

Finding useful biomarkers for Parkinson's disease.

Chen-Plotkin AS, Albin R, Alcalay R, Babcock D, Bajaj V, Bowman D, Buko A, Cedarbaum J, Chelsky D, Cookson MR, Dawson TM, Dewey R, Foroud T, Frasier M, German D, Gwinn K, Huang X, Kopil C, Kremer T, Lasch S, Marek K, Marto JA, Merchant K, Mollenhauer B, Naito A, Potashkin J, Reimer A, Rosenthal LS, Saunders-Pullman R, Scherzer CR, Sherer T, Singleton A, Sutherland M, Thiele I, van der Brug M, Van Keuren-Jensen K, Vaillancourt D, Walt D, West A, Zhang J.

Sci Transl Med. 2018 Aug 15;10(454). pii: eaam6003. doi: 10.1126/scitranslmed.aam6003. Review.

14.

Time trends in stroke incidence and in prevalence of risk factors in Southern Germany, 1989 to 2008/09.

Thiele I, Linseisen J, Heier M, Holle R, Kirchberger I, Peters A, Thorand B, Meisinger C.

Sci Rep. 2018 Aug 10;8(1):11981. doi: 10.1038/s41598-018-30350-8.

15.

From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease.

Bauer E, Thiele I.

NPJ Syst Biol Appl. 2018 Aug 1;4:27. doi: 10.1038/s41540-018-0063-2. eCollection 2018.

16.

Reply to "Challenges in modeling the human gut microbiome".

Magnúsdóttir S, Heinken A, Fleming RMT, Thiele I.

Nat Biotechnol. 2018 Aug 6;36(8):686-691. doi: 10.1038/nbt.4212. No abstract available.

PMID:
30080835
17.

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.

18.

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.

19.

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.

20.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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
28.

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.

29.

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.

30.

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
31.

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.

32.

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.

33.

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
34.

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.

35.

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.

36.

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.

37.

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

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

Microbiome. 2016 Jul 4;4(1):35. No abstract available.

38.

Conditions for duality between fluxes and concentrations in biochemical networks.

Fleming RMT, Vlassis N, Thiele I, Saunders MA.

J Theor Biol. 2016 Nov 21;409:1-10. doi: 10.1016/j.jtbi.2016.06.033. Epub 2016 Jun 23.

39.

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.

40.

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. Review.

PMID:
26677187
41.

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. Erratum in: Microbiome. 2016;4(1):35.

42.

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.

43.

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.

PMID:
26141019
44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

PMID:
25584636
50.

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.

Supplemental Content

Loading ...
Support Center