Thiele, Ines

What is flux balance analysis?

Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 3,903

Gut microbiota functions: metabolism of nutrients and other food components

Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2018) · European Journal of Nutrition

Gut microbiota and healthMicrobial Metabolites in Food Biotechnology

Cited by 2,878

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 1,835

A protocol for generating a high-quality genome-scale metabolic reconstruction

Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 1,789

Global reconstruction of the human metabolic network based on genomic and bibliomic data

Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., & Palsson, B. Ø. (2007) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 1,374

A community-driven global reconstruction of human metabolism

Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 1,019

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

Magnúsdóttir, S., Ravcheev, D., de Crécy-Lagard, V., & Thiele, I. (2015) · Frontiers in Genetics

Gut microbiota and healthFolate and B Vitamins Research

Cited by 876

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

Magnúsdóttir, S., Heinken, A., Kutt, L., Ravcheev, D. A., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., et al. (2017) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionGut microbiota and health

Cited by 798

Metabolomics enables precision medicine: “A White Paper, Community Perspective”

for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative, Beger, R. D., Dunn, W., Schmidt, M. A., Gross, S. S., Kirwan, J. A., Cascante, M., Brennan, L., Wishart, D. S., Oresic, M., et al. (2016) · Metabolomics

Metabolomics and Mass Spectrometry StudiesHealth, Environment, Cognitive Aging

Cited by 592

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

Nogales, J., Gudmundsson, S., Knight, E. M., Palsson, B. O., & Thiele, I. (2012) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionPhotosynthetic Processes and Mechanisms

Cited by 301

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

Thiele, I., Jamshidi, N., Fleming, R. M. T., & Palsson, B. Ø. (2009) · PLoS Computational Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 182

Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease

Hertel, J., Harms, A. C., Heinken, A., Baldini, F., Thinnes, C. C., Glaab, E., Vasco, D. A., Pietzner, M., Stewart, I. D., Wareham, N. J., et al. (2019) · Cell Reports

Gut microbiota and healthParkinson's Disease Mechanisms and Treatments

Cited by 162

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

Sigurdsson, M. I., Jamshidi, N., Steingrimsson, E., Thiele, I., & Palsson, B. Ø. (2010) · BMC Systems Biology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 154

Modeling metabolism of the human gut microbiome

Magnúsdóttir, S., & Thiele, I. (2018) · Current Opinion in Biotechnology

Microbial Metabolic Engineering and BioproductionGut microbiota and health

Cited by 127

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

Heinken, A., & Thiele, I. (2015) · Applied and Environmental Microbiology

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 123

A systems biology approach to studying the role of microbes in human health

Thiele, I., Heinken, A., & Fleming, R. M. (2013) · Current Opinion in Biotechnology

Microbial Metabolic Engineering and BioproductionGut microbiota and health

Cited by 114

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

Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, A., Famili, I., Feist, A. M., Fleming, R. M., et al. (2015) · Molecular Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 57

Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism

Cheng, Y., Schlosser, P., Hertel, J., Sekula, P., Oefner, P. J., Spiekerkoetter, U., Mielke, J., Freitag, D. F., Schmidts, M., GCKD Investigators, et al. (2021) · Nature Communications

Metabolism and Genetic DisordersGenomics and Rare Diseases

Cited by 37

Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data

Jo, T., Kim, J., Bice, P., Huynh, K., Wang, T., Arnold, M., Meikle, P. J., Giles, C., Kaddurah-Daouk, R., Saykin, A. J., et al. (2023) · eBioMedicine

Dementia and Cognitive Impairment ResearchMetabolomics and Mass Spectrometry Studies

Cited by 15