| Year |
Citation |
Score |
| 2023 |
Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O'Brolchain A, O'Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, ... ... Thiele I, et al. APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. Biorxiv : the Preprint Server For Biology. PMID 37873072 DOI: 10.1101/2023.10.02.560573 |
0.771 |
|
| 2023 |
Hertel J, Heinken A, Fässler D, Thiele I. Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses. Cell Reports Methods. 3: 100615. PMID 37848031 DOI: 10.1016/j.crmeth.2023.100615 |
0.747 |
|
| 2023 |
Martinelli F, Heinken A, Henning AK, Wörheide MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston M, Johnson S, Kastenmüller G, ... ... Thiele I, et al. Whole-body modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease. Research Square. PMID 37720019 DOI: 10.21203/rs.3.rs-3306891/v1 |
0.669 |
|
| 2023 |
Ternes D, Tsenkova M, Pozdeev VI, Meyers M, Koncina E, Atatri S, Schmitz M, Karta J, Schmoetten M, Heinken A, Rodriguez F, Delbrouck C, Gaigneaux A, Ginolhac A, Nguyen TTD, ... ... Thiele I, et al. Author Correction: The gut microbial metabolite formate exacerbates colorectal cancer progression. Nature Metabolism. PMID 37709964 DOI: 10.1038/s42255-023-00898-5 |
0.669 |
|
| 2023 |
van der Spek A, Stewart ID, Kühnel B, Pietzner M, Alshehri T, Gauß F, Hysi PG, MahmoudianDehkordi S, Heinken A, Luik AI, Ladwig KH, Kastenmüller G, Menni C, Hertel J, Ikram MA, ... ... Thiele I, et al. Circulating metabolites modulated by diet are associated with depression. Molecular Psychiatry. PMID 37495887 DOI: 10.1038/s41380-023-02180-2 |
0.681 |
|
| 2023 |
Basile A, Heinken A, Hertel J, Smarr L, Li W, Treu L, Valle G, Campanaro S, Thiele I. Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics. Gut Microbes. 15: 2226921. PMID 37438876 DOI: 10.1080/19490976.2023.2226921 |
0.748 |
|
| 2023 |
Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ. Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta. Plos Biology. 21: e3002125. PMID 37205710 DOI: 10.1371/journal.pbio.3002125 |
0.784 |
|
| 2023 |
Weston BR, Thiele I. A nutrition algorithm to optimize feed and medium composition using genome-scale metabolic models. Metabolic Engineering. PMID 36724839 DOI: 10.1016/j.ymben.2023.01.010 |
0.349 |
|
| 2023 |
Heinken A, Hertel J, Acharya G, Ravcheev DA, Nyga M, Okpala OE, Hogan M, Magnúsdóttir S, Martinelli F, Nap B, Preciat G, Edirisinghe JN, Henry CS, Fleming RMT, Thiele I. Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nature Biotechnology. PMID 36658342 DOI: 10.1038/s41587-022-01628-0 |
0.832 |
|
| 2023 |
Kindschuh WF, Baldini F, Liu MC, Liao J, Meydan Y, Lee HH, Heinken A, Thiele I, Thaiss CA, Levy M, Korem T. Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome. Nature Microbiology. PMID 36635575 DOI: 10.1038/s41564-022-01293-8 |
0.772 |
|
| 2022 |
Thiele I, Preciat G, Fleming RMT. MetaboAnnotator: An efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions. Bioinformatics (Oxford, England). PMID 36047841 DOI: 10.1093/bioinformatics/btac596 |
0.391 |
|
| 2022 |
Hertel J, Fässler D, Heinken A, Weiß FU, Rühlemann M, Bang C, Franke A, Budde K, Henning AK, Petersmann A, Völker U, Völzke H, Thiele I, Grabe HJ, Lerch MM, et al. NMR Metabolomics Reveal Urine Markers of Microbiome Diversity and Identify Benzoate Metabolism as a Mediator between High Microbial Alpha Diversity and Metabolic Health. Metabolites. 12. PMID 35448495 DOI: 10.3390/metabo12040308 |
0.731 |
|
| 2022 |
Ternes D, Tsenkova M, Pozdeev VI, Meyers M, Koncina E, Atatri S, Schmitz M, Karta J, Schmoetten M, Heinken A, Rodriguez F, Delbrouck C, Gaigneaux A, Ginolhac A, Nguyen TTD, ... ... Thiele I, et al. The gut microbial metabolite formate exacerbates colorectal cancer progression. Nature Metabolism. 4: 458-475. PMID 35437333 DOI: 10.1038/s42255-022-00558-0 |
0.687 |
|
| 2022 |
Heinken A, Thiele I. Microbiome Modelling Toolbox 2.0: Efficient, tractable modelling of microbiome communities. Bioinformatics (Oxford, England). PMID 35157025 DOI: 10.1093/bioinformatics/btac082 |
0.702 |
|
| 2021 |
Ben Guebila M, Thiele I. Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes. Nature Computational Science. 1: 348-361. PMID 38217214 DOI: 10.1038/s43588-021-00074-3 |
0.312 |
|
| 2021 |
Heinken A, Magnúsdóttir S, Fleming RMT, Thiele I. DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. Bioinformatics (Oxford, England). PMID 34473240 DOI: 10.1093/bioinformatics/btab622 |
0.793 |
|
| 2021 |
Heinken A, Basile A, Hertel J, Thinnes C, Thiele I. Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine. Annual Review of Microbiology. PMID 34314593 DOI: 10.1146/annurev-micro-060221-012134 |
0.755 |
|
| 2021 |
Hertel J, Heinken A, Martinelli F, Thiele I. Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of spp. on community butyrate production. Gut Microbes. 13: 1-23. PMID 34057024 DOI: 10.1080/19490976.2021.1915673 |
0.759 |
|
| 2021 |
Heinken A, Hertel J, Thiele I. Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis. Npj Systems Biology and Applications. 7: 19. PMID 33958598 DOI: 10.1038/s41540-021-00178-6 |
0.738 |
|
| 2021 |
Cheng Y, Schlosser P, Hertel J, Sekula P, Oefner PJ, Spiekerkoetter U, Mielke J, Freitag DF, Schmidts M, Kronenberg F, Eckardt KU, Thiele I, Li Y, Köttgen A. Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism. Nature Communications. 12: 964. PMID 33574263 DOI: 10.1038/s41467-020-20877-8 |
0.334 |
|
| 2020 |
Baloni P, Funk CC, Yan J, Yurkovich JT, Kueider-Paisley A, Nho K, Heinken A, Jia W, Mahmoudiandehkordi S, Louie G, Saykin AJ, Arnold M, Kastenmüller G, Griffiths WJ, Thiele I, et al. Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease. Cell Reports. Medicine. 1: 100138. PMID 33294859 DOI: 10.1016/j.xcrm.2020.100138 |
0.81 |
|
| 2020 |
Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R, Thiele I. Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions. Bmc Biology. 18: 62. PMID 32517799 DOI: 10.1186/S12915-020-00775-7 |
0.601 |
|
| 2020 |
Thiele I, Sahoo S, Heinken A, Hertel J, Heirendt L, Aurich MK, Fleming RM. Personalized whole-body models integrate metabolism, physiology, and the gut microbiome. Molecular Systems Biology. 16: e8982. PMID 32463598 DOI: 10.15252/Msb.20198982 |
0.85 |
|
| 2019 |
Hertel J, Harms AC, Heinken A, Baldini F, Thinnes CC, Glaab E, Vasco DA, Pietzner M, Stewart ID, Wareham NJ, Langenberg C, Trenkwalder C, Krüger R, Hankemeier T, Fleming RMT, ... ... Thiele I, et al. Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease. Cell Reports. 29: 1767-1777.e8. PMID 31722195 DOI: 10.1016/J.Celrep.2019.10.035 |
0.79 |
|
| 2019 |
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. Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig. Scientific Reports. 9: 12527. PMID 31467335 DOI: 10.1038/S41598-019-48997-2 |
0.81 |
|
| 2019 |
Ravcheev DA, Moussu L, Smajic S, Thiele I. Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome. Frontiers in Genetics. 10: 636. PMID 31333721 DOI: 10.3389/Fgene.2019.00636 |
0.46 |
|
| 2019 |
Ben Guebila M, Thiele I. Predicting gastrointestinal drug effects using contextualized metabolic models. Plos Computational Biology. 15: e1007100. PMID 31242176 DOI: 10.1371/Journal.Pcbi.1007100 |
0.425 |
|
| 2019 |
Peñalver Bernabé B, Thiele I, Galdones E, Siletz A, Chandrasekaran S, Woodruff TK, Broadbelt LJ, Shea LD. Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. Bmc Bioinformatics. 20: 307. PMID 31182013 DOI: 10.1186/S12859-019-2825-2 |
0.435 |
|
| 2019 |
Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome. 7: 75. PMID 31092280 DOI: 10.1186/S40168-019-0689-3 |
0.833 |
|
| 2019 |
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, et al. Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells. Cell Reports. 27: 1621-1632.e9. PMID 31042485 DOI: 10.1016/J.Celrep.2019.04.001 |
0.721 |
|
| 2019 |
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, ... ... Thiele I, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/S41596-018-0098-2 |
0.784 |
|
| 2018 |
Baldini F, Heinken A, Heirendt L, Magnusdottir S, Fleming RMT, Thiele I. The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. Bioinformatics (Oxford, England). PMID 30462168 DOI: 10.1093/Bioinformatics/Bty941 |
0.796 |
|
| 2018 |
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, ... ... Thiele I, et al. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research. PMID 30371894 DOI: 10.1093/Nar/Gky992 |
0.832 |
|
| 2018 |
Bauer E, Thiele I. From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease. Npj Systems Biology and Applications. 4: 27. PMID 30083388 DOI: 10.1038/s41540-018-0063-2 |
0.76 |
|
| 2018 |
Magnúsdóttir S, Heinken A, Fleming RMT, Thiele I. Reply to "Challenges in modeling the human gut microbiome". Nature Biotechnology. 36: 686-691. PMID 30080835 DOI: 10.1038/Nbt.4212 |
0.8 |
|
| 2018 |
Bauer E, Thiele I. From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota. Msystems. 3. PMID 29600286 DOI: 10.1128/mSystems.00209-17 |
0.812 |
|
| 2018 |
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, ... ... Thiele I, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology. PMID 29457794 DOI: 10.1038/Nbt.4072 |
0.818 |
|
| 2017 |
Thiele I, Clancy CM, Heinken A, Fleming RMT. Quantitative systems pharmacology and the personalized drug-microbiota-diet axis. Current Opinion in Systems Biology. 4: 43-52. PMID 32984662 DOI: 10.1016/J.Coisb.2017.06.001 |
0.711 |
|
| 2017 |
Magnúsdóttir S, Thiele I. Modeling metabolism of the human gut microbiome. Current Opinion in Biotechnology. 51: 90-96. PMID 29258014 DOI: 10.1016/J.Copbio.2017.12.005 |
0.848 |
|
| 2017 |
Preciat Gonzalez GA, El Assal LRP, Noronha A, Thiele I, Haraldsdóttir HS, Fleming RMT. Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. Journal of Cheminformatics. 9: 39. PMID 29086112 DOI: 10.1186/S13321-017-0223-1 |
0.793 |
|
| 2017 |
Ravcheev DA, Thiele I. Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. Frontiers in Genetics. 8: 111. PMID 28912798 DOI: 10.3389/Fgene.2017.00111 |
0.397 |
|
| 2017 |
Aurich MK, Fleming RMT, Thiele I. A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines. Plos Computational Biology. 13: e1005698. PMID 28806730 DOI: 10.1371/Journal.Pcbi.1005698 |
0.821 |
|
| 2017 |
Bauer E, Zimmermann J, Baldini F, Thiele I, Kaleta C. BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities. Plos Computational Biology. 13: e1005544. PMID 28531184 DOI: 10.1371/Journal.Pcbi.1005544 |
0.835 |
|
| 2017 |
Heirendt L, Thiele I, Fleming RMT. DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia. Bioinformatics (Oxford, England). 33: 1421-1423. PMID 28453682 DOI: 10.1093/Bioinformatics/Btw838 |
0.325 |
|
| 2017 |
Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K. Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition. PMID 28393285 DOI: 10.1007/S00394-017-1445-8 |
0.773 |
|
| 2017 |
Haraldsdóttir HS, Cousins B, Thiele I, Fleming RM, Vempala S. CHRR: Coordinate hit-and-run with rounding for uniform sampling of constraint-based models. Bioinformatics (Oxford, England). PMID 28158334 DOI: 10.1093/Bioinformatics/Btx052 |
0.422 |
|
| 2017 |
Ma D, Yang L, Fleming RM, Thiele I, Palsson BO, Saunders MA. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. Scientific Reports. 7: 40863. PMID 28098205 DOI: 10.1038/Srep40863 |
0.54 |
|
| 2017 |
Rahman J, Noronha A, Thiele I, Rahman S. Leigh Map: a novel diagnostic resource for mitochondrial disease Neuromuscular Disorders. 27: S19. DOI: 10.1016/S0960-8966(17)30274-2 |
0.763 |
|
| 2017 |
Thiele I, Clancy CM, Heinken A, Fleming RM. Quantitative systems pharmacology and the personalized drug–microbiota–diet axis Current Opinion in Systems Biology. 4: 43-52. DOI: 10.1016/J.COISB.2017.06.001 |
0.623 |
|
| 2016 |
Guebila MB, Thiele I. Model-based dietary optimization for late-stage, levodopa-treated, Parkinson's disease patients. Npj Systems Biology and Applications. 2: 16013. PMID 28725472 DOI: 10.1038/npjsba.2016.13 |
0.787 |
|
| 2016 |
Noronha A, Daníelsdóttir AD, Gawron P, Jóhannsson F, Jónsdóttir S, Jarlsson S, Gunnarsson JP, Brynjólfsson S, Schneider R, Thiele I, Fleming RM. ReconMap: an interactive visualization of human metabolism. Bioinformatics (Oxford, England). PMID 27993782 DOI: 10.1093/Bioinformatics/Btw667 |
0.825 |
|
| 2016 |
Rahman J, Noronha A, Thiele I, Rahman S. Leigh Map: A Novel Computational Diagnostic Resource for Mitochondrial Disease. Annals of Neurology. PMID 27977873 DOI: 10.1002/Ana.24835 |
0.786 |
|
| 2016 |
Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, Fleming RM, Thiele I. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology. PMID 27893703 DOI: 10.1038/Nbt.3703 |
0.837 |
|
| 2016 |
Dimitrov D, Thiele I, Ferguson LR. Editorial: The Human Gutome: Nutrigenomics of Host-Microbiome Interactions. Frontiers in Genetics. 7: 158. PMID 27656194 DOI: 10.3389/Fgene.2016.00158 |
0.35 |
|
| 2016 |
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, et al. Metabolomics enables precision medicine: "A White Paper, Community Perspective". Metabolomics : Official Journal of the Metabolomic Society. 12: 149. PMID 27642271 DOI: 10.1007/S11306-016-1094-6 |
0.446 |
|
| 2016 |
Aurich MK, Fleming RM, Thiele I. MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models. Frontiers in Physiology. 7: 327. PMID 27536246 DOI: 10.3389/Fphys.2016.00327 |
0.831 |
|
| 2016 |
Bauer E, Laczny CC, Magnusdottir S, Wilmes P, Thiele I. Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Microbiome. 4: 35. PMID 27377779 DOI: 10.1186/s40168-016-0180-3 |
0.822 |
|
| 2016 |
Fleming RM, Vlassis N, Thiele I, Saunders MA. Conditions for duality between fluxes and concentrations in biochemical networks. Journal of Theoretical Biology. PMID 27345817 DOI: 10.1016/J.Jtbi.2016.06.033 |
0.714 |
|
| 2016 |
Ravcheev DA, Thiele I. Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. Frontiers in Microbiology. 7: 128. PMID 26904004 DOI: 10.3389/Fmicb.2016.00128 |
0.404 |
|
| 2016 |
Aurich MK, Thiele I. Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine. Methods in Molecular Biology (Clifton, N.J.). 1386: 253-81. PMID 26677187 DOI: 10.1007/978-1-4939-3283-2_12 |
0.854 |
|
| 2015 |
Bauer E, Laczny CC, Magnusdottir S, Wilmes P, Thiele I. Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Microbiome. 3: 55. PMID 26617277 DOI: 10.1186/S40168-015-0121-6 |
0.831 |
|
| 2015 |
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, ... ... Thiele I, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284 DOI: 10.15252/Msb.20156157 |
0.733 |
|
| 2015 |
Aurich MK, Paglia G, Rolfsson Ó, Hrafnsdóttir S, Magnúsdóttir M, Stefaniak MM, Palsson BØ, Fleming RM, Thiele I. Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics : Official Journal of the Metabolomic Society. 11: 603-619. PMID 25972769 DOI: 10.1007/S11306-014-0721-3 |
0.848 |
|
| 2015 |
Magnúsdóttir S, Ravcheev D, de Crécy-Lagard V, Thiele I. Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Frontiers in Genetics. 6: 148. PMID 25941533 DOI: 10.3389/Fgene.2015.00148 |
0.776 |
|
| 2015 |
Heinken A, Thiele I. Systems biology of host-microbe metabolomics. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 7: 195-219. PMID 25929487 DOI: 10.1002/Wsbm.1301 |
0.765 |
|
| 2015 |
Heinken A, Thiele I. Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework. Gut Microbes. 6: 120-30. PMID 25901891 DOI: 10.1080/19490976.2015.1023494 |
0.789 |
|
| 2015 |
Heinken A, Thiele I. Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico. Applied and Environmental Microbiology. 81: 4049-61. PMID 25841013 DOI: 10.1128/Aem.00101-15 |
0.721 |
|
| 2015 |
Sahoo S, Haraldsdóttir HS, Fleming RM, Thiele I. Modeling the effects of commonly used drugs on human metabolism. The Febs Journal. 282: 297-317. PMID 25345908 DOI: 10.1111/Febs.13128 |
0.687 |
|
| 2014 |
Ravcheev DA, Thiele I. Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. Frontiers in Microbiology. 5: 674. PMID 25538694 DOI: 10.3389/Fmicb.2014.00674 |
0.422 |
|
| 2014 |
Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJ, Thiele I. Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. Journal of Bacteriology. 196: 3289-302. PMID 25002542 DOI: 10.1128/Jb.01780-14 |
0.799 |
|
| 2014 |
Edwards LM, Sigurdsson MI, Robbins PA, Weale ME, Cavalleri GL, Montgomery HE, Thiele I. Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia. Circulation. Cardiovascular Genetics. 7: 407-15. PMID 24873932 DOI: 10.1161/Circgenetics.113.000269 |
0.372 |
|
| 2014 |
Thiele I, Vlassis N, Fleming RM. fastGapFill: efficient gap filling in metabolic networks. Bioinformatics (Oxford, England). 30: 2529-31. PMID 24812336 DOI: 10.1093/Bioinformatics/Btu321 |
0.756 |
|
| 2014 |
Sahoo S, Aurich MK, Jonsson JJ, Thiele I. Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease. Frontiers in Physiology. 5: 91. PMID 24653705 DOI: 10.3389/Fphys.2014.00091 |
0.832 |
|
| 2014 |
Haraldsdóttir HS, Thiele I, Fleming RM. Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. Journal of Cheminformatics. 6: 2. PMID 24468196 DOI: 10.1186/1758-2946-6-2 |
0.509 |
|
| 2014 |
Ravcheev D, Thiele I. Genomics analysis of the respiratory capacities of the human intestinal microbiota F1000research. 5. DOI: 10.7490/F1000Research.1096811.1 |
0.345 |
|
| 2013 |
Sun Y, Fleming RM, Thiele I, Saunders MA. Robust flux balance analysis of multiscale biochemical reaction networks. Bmc Bioinformatics. 14: 240. PMID 23899245 DOI: 10.1186/1471-2105-14-240 |
0.406 |
|
| 2013 |
Edwards LM, Thiele I. Applying systems biology methods to the study of human physiology in extreme environments. Extreme Physiology & Medicine. 2: 8. PMID 23849719 DOI: 10.1186/2046-7648-2-8 |
0.388 |
|
| 2013 |
Stobbe MD, Swertz MA, Thiele I, Rengaw T, van Kampen AH, Moerland PD. Consensus and conflict cards for metabolic pathway databases. Bmc Systems Biology. 7: 50. PMID 23803311 DOI: 10.1186/1752-0509-7-50 |
0.451 |
|
| 2013 |
Sahoo S, Thiele I. Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. Human Molecular Genetics. 22: 2705-22. PMID 23492669 DOI: 10.1093/Hmg/Ddt119 |
0.725 |
|
| 2013 |
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/Nbt.2488 |
0.835 |
|
| 2013 |
Nogales J, Gudmundsson S, Thiele I. Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks. Bioengineered. 4: 158-63. PMID 23138691 DOI: 10.4161/Bioe.22792 |
0.75 |
|
| 2013 |
Thiele I, Heinken A, Fleming RM. A systems biology approach to studying the role of microbes in human health. Current Opinion in Biotechnology. 24: 4-12. PMID 23102866 DOI: 10.1016/J.Copbio.2012.10.001 |
0.776 |
|
| 2013 |
Rolfsson Ó, Paglia G, Magnusdóttir M, Palsson BØ, Thiele I. Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity. The Biochemical Journal. 449: 427-35. PMID 23067238 DOI: 10.1042/Bj20120980 |
0.65 |
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| 2013 |
Heinken A, Sahoo S, Fleming RM, Thiele I. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes. 4: 28-40. PMID 23022739 DOI: 10.4161/Gmic.22370 |
0.844 |
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| 2012 |
Aurich MK, Thiele I. Contextualization procedure and modeling of monocyte specific TLR signaling. Plos One. 7: e49978. PMID 23236359 DOI: 10.1371/Journal.Pone.0049978 |
0.775 |
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| 2012 |
Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson BO. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. Plos One. 7: e45635. PMID 23029152 DOI: 10.1371/Journal.Pone.0045635 |
0.716 |
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| 2012 |
Haraldsdóttir HS, Thiele I, Fleming RM. Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction. Biophysical Journal. 102: 1703-11. PMID 22768925 DOI: 10.1016/J.Bpj.2012.02.032 |
0.412 |
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| 2012 |
Sahoo S, Franzson L, Jonsson JJ, Thiele I. A compendium of inborn errors of metabolism mapped onto the human metabolic network. Molecular Biosystems. 8: 2545-58. PMID 22699794 DOI: 10.1039/C2Mb25075F |
0.73 |
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| 2012 |
Sigurdsson G, Fleming RM, Heinken A, Thiele I. A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm. Plos One. 7: e34337. PMID 22523548 DOI: 10.1371/Journal.Pone.0034337 |
0.714 |
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| 2012 |
Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I. Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proceedings of the National Academy of Sciences of the United States of America. 109: 2678-83. PMID 22308420 DOI: 10.1073/Pnas.1117907109 |
0.733 |
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| 2012 |
Nogales J, Gudmundsson S, Thiele I. An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production International Journal of Hydrogen Energy. 37: 12205-12218. DOI: 10.1016/J.Ijhydene.2012.06.032 |
0.35 |
|
| 2011 |
Rolfsson O, Palsson BØ, Thiele I. The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. Bmc Systems Biology. 5: 155. PMID 21962087 DOI: 10.1186/1752-0509-5-155 |
0.656 |
|
| 2011 |
Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols. 6: 1290-307. PMID 21886097 DOI: 10.1038/Nprot.2011.308 |
0.824 |
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| 2011 |
Thorleifsson SG, Thiele I. rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks. Bioinformatics (Oxford, England). 27: 2009-10. PMID 21596791 DOI: 10.1093/Bioinformatics/Btr308 |
0.383 |
|
| 2011 |
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, et al. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. Bmc Systems Biology. 5: 8. PMID 21244678 DOI: 10.1186/1752-0509-5-8 |
0.795 |
|
| 2011 |
Fleming RM, Thiele I. von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics (Oxford, England). 27: 142-3. PMID 21115436 DOI: 10.1093/Bioinformatics/Btq607 |
0.434 |
|
| 2011 |
Hyduke D, Schellenberger J, Que R, Fleming R, Thiele I, Orth J, Feist A, Zielinski D, Bordbar A, Lewis N, Rahmanian S, Kang J, Palsson B. COBRA Toolbox 2.0 Protocol Exchange. DOI: 10.1038/Protex.2011.234 |
0.741 |
|
| 2011 |
Thiele I, Fleming RMT, Que R, Bordbar A, Palsson BO. A Systems Biology Approach to the Evolution of Codon Use Pattern Nature Precedings. DOI: 10.1038/Npre.2011.6312.1 |
0.611 |
|
| 2010 |
Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ. A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. Bmc Systems Biology. 4: 140. PMID 20959003 DOI: 10.1186/1752-0509-4-140 |
0.753 |
|
| 2010 |
Gudmundsson S, Thiele I. Computationally efficient flux variability analysis. Bmc Bioinformatics. 11: 489. PMID 20920235 DOI: 10.1186/1471-2105-11-489 |
0.4 |
|
| 2010 |
Thiele I, Fleming RM, Bordbar A, Schellenberger J, Palsson BØ. Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. Biophysical Journal. 98: 2072-81. PMID 20483314 DOI: 10.1016/J.Bpj.2010.01.060 |
0.788 |
|
| 2010 |
Thiele I, Palsson BØ. Reconstruction annotation jamborees: a community approach to systems biology. Molecular Systems Biology. 6: 361. PMID 20393581 DOI: 10.1038/Msb.2010.15 |
0.574 |
|
| 2010 |
Fleming RM, Thiele I, Provan G, Nasheuer HP. Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. Journal of Theoretical Biology. 264: 683-92. PMID 20230840 DOI: 10.1016/J.Jtbi.2010.02.044 |
0.46 |
|
| 2010 |
Orth JD, Thiele I, Palsson BO. What is flux balance analysis? Nature Biotechnology. 28: 245-248. PMID 20212490 DOI: 10.1038/Nbt.1614 |
0.78 |
|
| 2010 |
Thiele I, Palsson BØ. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols. 5: 93-121. PMID 20057383 DOI: 10.1038/Nprot.2009.203 |
0.602 |
|
| 2010 |
Thiele I, Fleming R, Rolfsson O, Palsson B. A systems biology approach for human metabolism in health and disease New Biotechnology. 27: S80. DOI: 10.1016/J.Nbt.2010.01.224 |
0.552 |
|
| 2009 |
Fleming RM, Thiele I, Nasheuer HP. Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophysical Chemistry. 145: 47-56. PMID 19783351 DOI: 10.1016/J.Bpc.2009.08.007 |
0.383 |
|
| 2009 |
Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science (New York, N.Y.). 325: 1544-9. PMID 19762644 DOI: 10.1126/Science.1174671 |
0.557 |
|
| 2009 |
Manichaikul A, Ghamsari L, Hom EF, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan C, Mello E, Hill DE, et al. Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods. 6: 589-92. PMID 19597503 DOI: 10.1038/Nmeth.1348 |
0.781 |
|
| 2009 |
Thiele I, Jamshidi N, Fleming RM, Palsson BØ. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. Plos Computational Biology. 5: e1000312. PMID 19282977 DOI: 10.1371/Journal.Pcbi.1000312 |
0.651 |
|
| 2009 |
Li F, Thiele I, Jamshidi N, Palsson BØ. Identification of potential pathway mediation targets in Toll-like receptor signaling. Plos Computational Biology. 5: e1000292. PMID 19229310 DOI: 10.1371/Journal.Pcbi.1000292 |
0.665 |
|
| 2009 |
Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ. Reconstruction of biochemical networks in microorganisms. Nature Reviews. Microbiology. 7: 129-43. PMID 19116616 DOI: 10.1038/Nrmicro1949 |
0.793 |
|
| 2009 |
Li F, Thiele I, Jamshidi N, Palsson BØ. Correction: Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling Plos Computational Biology. 5. DOI: 10.1371/Annotation/5Cc0D918-83B8-44E4-9778-B96A249D4099 |
0.628 |
|
| 2009 |
Feist AM, Thiele I, Palsson B. Genome-scale reconstruction, modeling, and simulation of E. coli's metabolic network Systems Biology and Biotechnology of Escherichia Coli. 149-176. DOI: 10.1007/978-1-4020-9394-4_9 |
0.703 |
|
| 2008 |
Nogales J, Palsson BØ, Thiele I. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. Bmc Systems Biology. 2: 79. PMID 18793442 DOI: 10.1186/1752-0509-2-79 |
0.781 |
|
| 2007 |
Yeung M, Thiele I, Palsson BO. Estimation of the number of extreme pathways for metabolic networks. Bmc Bioinformatics. 8: 363. PMID 17897474 DOI: 10.1186/1471-2105-8-363 |
0.502 |
|
| 2007 |
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences of the United States of America. 104: 1777-82. PMID 17267599 DOI: 10.1073/Pnas.0610772104 |
0.849 |
|
| 2007 |
Thiele I, Palsson BO. Bringing genomes to life: The use of genome-scale in silico models Introduction to Systems Biology. 14-36. DOI: 10.1007/978-1-59745-531-2_2 |
0.405 |
|
| 2006 |
Price ND, Thiele I, Palsson BØ. Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophysical Journal. 90: 3919-28. PMID 16533855 DOI: 10.1529/Biophysj.105.072645 |
0.653 |
|
| 2006 |
Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nature Reviews. Genetics. 7: 130-41. PMID 16418748 DOI: 10.1038/Nrg1769 |
0.786 |
|
| 2005 |
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, ... ... Thiele I, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research. 33: 5691-702. PMID 16214803 DOI: 10.1093/Nar/Gki866 |
0.789 |
|
| 2005 |
Thiele I, Vo TD, Price ND, Palsson BØ. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. Journal of Bacteriology. 187: 5818-30. PMID 16077130 DOI: 10.1128/Jb.187.16.5818-5830.2005 |
0.793 |
|
| 2005 |
Thiele I, Price ND, Vo TD, Palsson BØ. Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. The Journal of Biological Chemistry. 280: 11683-95. PMID 15572364 DOI: 10.1074/Jbc.M409072200 |
0.784 |
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