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Biological and Chemical Sciences

Prof Ines Thiele

M.Sc., PhD

Contact Details

Personal Professor
Orbsen Building
E: ines.thiele@nuigalway.ie
www.thielelab.eu
 
researcher
 

Biography

Prof Ines Thiele is the principal investigator of the Molecular Systems Physiology group at the National University of Ireland, Galway. Her research aims to improve the understanding of how diet influences human health. Therefore, she uses a computational modelling approach, termed constraint-based modelling, which has gained increasing importance in systems biology. Her group builds comprehensive models of human cells and human-associated microbes; then employs them together with experimental data to investigate how nutrition and genetic predisposition can affect one's health. In particular, she is interested in applying her computational modelling approach for better understanding of inherited and neurodegenerative diseases. Ines Thiele has been pioneering models and methods allowing large-scale computational modelling of the human gut microbiome and its metabolic effect on human metabolism.

Prof Ines Thiele earned her PhD in bioinformatics from the University of California, San Diego, in 2009. From 2009 until 2013, Ines Thiele was an Assistant Professor at the University of Iceland. From April 2013 until January 2019, she was an Associate Professor at the University of Luxembourg. Since February 2019, Ines Thiele is a Professor for Systems Biomedicine at the National University of Ireland, Galway. In 2013, Ines Thiele received the ATTRACT fellowship from the Fonds National de la Recherche (Luxembourg). In 2015, she was elected as EMBO Young Investigator. In 2017, she was awarded the prestigious ERC starting grant. She is an author of over 80 international scientific papers and reviewer for multiple journals and funding agencies.  
Prof Ines Thiele is the principal investigator of the Molecular Systems Physiology group at the National University of Ireland, Galway. Her research aims to improve the understanding of how diet influences human health. Therefore, she uses a computational modelling approach, termed constraint-based modelling, which has gained increasing importance in systems biology. Her group builds comprehensive models of human cells and human-associated microbes; then employs them together with experimental data to investigate how nutrition and genetic predisposition can affect one's health. In particular, she is interested in applying her computational modelling approach for better understanding of inherited and neurodegenerative diseases. Ines Thiele has been pioneering models and methods allowing large-scale computational modelling of the human gut microbiome and its metabolic effect on human metabolism.

Prof Ines Thiele earned her PhD in bioinformatics from the University of California, San Diego, in 2009. From 2009 until 2013, Ines Thiele was an Assistant Professor at the University of Iceland. From April 2013 until January 2019, she was an Associate Professor at the University of Luxembourg. Since February 2019, Ines Thiele is a Professor for Systems Biomedicine at the National University of Ireland, Galway. In 2013, Ines Thiele received the ATTRACT fellowship from the Fonds National de la Recherche (Luxembourg). In 2015, she was elected as EMBO Young Investigator. In 2017, she was awarded the prestigious ERC starting grant. She is an author of over 80 international scientific papers and reviewer for multiple journals and funding agencies.  

Research Interests

The Molecular Systems Physiology group, headed by Prof. Ines Thiele, aims to improve our understanding of how diet influences human health. 

We use a computational modelling approach, termed constraint-based modelling, which has gained increasing importance in systems biology. In this approach, comprehensive computational models are assembled in a bottom-up manner from literature and genomic information. These models describe in a stoichiometric accurate format biochemical transformations occurring in a target organism. Once assembled, various omics data sets can be integrated and analyzed with these models, expanding currently available analysis tools and thus providing mechanistically based insight into complex multi-dimensional data sets. Moreover, these models can be used to predict the impact of genetic alterations (e.g., enzyme deficiencies) and of changed environment conditions (e.g., changes in diet composition) on the metabolic state of the target organism. The molecular systems physiology group builds comprehensive models of human cells and human-associated microbes. We then employ these models together with experimental data to investigate how nutrition and genetic predisposition can affect one’s health. In particular, we are interested in applying our computational modelling approach for better understanding of inherited and neurodegenerative diseases. 

Research Projects

  Project Start Date End Date
ImprovAFish: Improving aquaculture sustainability by modulating the feed-microbiome-host axis in Fish 01-SEP-20 31-AUG-28
Subaward with Duke University_Alzheimer's Gut Microbiome Project (Core 2) 13-DEC-19 31-AUG-25
Gut Liver Brain biochemical Axis in Alzheimer's Disease 01-FEB-19 31-JAN-24
International Research Support Services Agreement with Duke University 01-JAN-19 30-JUN-20
PoLiMeR - Polymers in the Liver: Metabolism and Regulation 01-OCT-18 30-SEP-22
BugTheDrug - PREDICTING THE EFFECTS OF GUT MIRCROBIOTA AND DIET ON AN INDIVIDUAL'S DRUG RESPONSE AND SAFETY 01-APR-18 31-MAR-23

Peer Reviewed Journals

  Year Publication
(2020) 'Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions'
Baldini, F;Hertel, J;Sandt, E;Thinnes, CC;Neuberger-Castillo, L;Pavelka, L;Betsou, F;Kruger, R;Thiele, I (2020) 'Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions'. Bmc Biology, 18 [DOI] [Details]
(2020) 'Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome'
Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich, Ronan MT Fleming (2020) 'Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome'. Molecular Systems Biology, 16 (5) [Details]
(2019) 'Predicting the gastrointestinal side effects of drugs using contextualized metabolic models'
Ben Guebila, M., Thiele, I. (2019) 'Predicting the gastrointestinal side effects of drugs using contextualized metabolic models'. Plos Computational Biology, 15 (6) [Details]
(2019) 'Integrated in vitro and in silico modelling delineates the molecular effects of a synbiotic regimen on colorectal cancer-derived cells'
Greenhalgh, K., Ramiro-Garcia, J., Heinken, A., Ullmann, P., Bintener, T., Pires Pacheco, M., Baginska, J., Shah, P., Frachet, A., Halder, R., Fritz, J.V., Sauter, T., Thiele, I., Haan, S., Letellier, E., Wilmes, P. (2019) 'Integrated in vitro and in silico modelling delineates the molecular effects of a synbiotic regimen on colorectal cancer-derived cells'. Cell Reports, 27 (5):1621-1632 [Details]
(2019) '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; (2019) 'Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development'. BMC Bioinformatics, 20 (1) [DOI] [Details]
(2019) 'Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease'
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;Mollenhauer B;Thiele I; (2019) 'Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease'. Cell Reports, 29 (7) [DOI] [ARAN Link] [Details]
(2019) '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;¿agare 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; (2019) 'Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0'. Nature Protocols, 14 (3) [DOI] [Details]
(2019) 'The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease'
Noronha, A., Modamio, J., Jarosz, Y., Sompairac, N., Gonzalez, G., Danielsdottir, A.D., Krecke, M., Merten, D., Haraldsdottir, H.S., , A., Heirendt, L., Magnusdottir, S., Ravcheev, D.A., Sahoo, S., Gawron, P., Guerard, E., Friscioni, L., Garcia, B., Prendergast, M., Rodrigues, M., Roy, A., Rouquaya, M., Wiltgen, L., Zagare, A., John, E., Krueger, M., Kuperstein, I., Zinovyev, A., Schneider, R., Fleming, R.M.T., Thiele, I. (2019) 'The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease'. Nucleic Acid Research, 47 (D1):D614-D624 [Details]
(2019) 'Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals'
Heinken, A., Ravcheev, D.A., Baldini, F., Heirendt, L., Fleming, R.M.T., Thiele, I. (2019) 'Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals'. Microbiome, 7 (75) [Details]
(2019) 'Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome'
Ravcheev, DA;Moussu, L;Smajic, S;Thiele, I (2019) 'Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome'. Frontiers in Genetics, 10 [DOI] [Details]
(2019) 'The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities'
Baldini, Federico and Heinken, Almut Katrin and Heirendt, Laurent and Magnusdottir, Stefania and Fleming, Ronan and Thiele, Ines (2019) 'The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities'. Bioinformatics, [Details]
(2018) 'Modeling metabolism of the human gut microbiome'
Magn\'usd\'ottir, Stefan\'\ia and Thiele, Ines (2018) 'Modeling metabolism of the human gut microbiome'. Current opinion in biotechnology, 51 :90-96 [Details]
(2018) 'Recon3D enables a three-dimensional view of gene variation in human metabolism'
Brunk, Elizabeth and Sahoo, Swagatika and Zielinski, Daniel C and Altunkaya, Ali and Dr\"ager, Andreas and Mih, Nathan and Gatto, Francesco and Nilsson, Avlant and Gonzalez, German Andres Preciat and Aurich, Maike Kathrin and others (2018) 'Recon3D enables a three-dimensional view of gene variation in human metabolism'. Nature biotechnology, 36 (3) [Details]
(2018) 'From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease'
Bauer, Eugen and Thiele, Ines (2018) 'From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease'. NPJ systems biology and applications, 4 (1) [Details]
(2018) 'Gut microbiota functions: metabolism of nutrients and other food components'
Rowland, Ian and Gibson, Glenn and Heinken, Almut and Scott, Karen and Swann, Jonathan and Thiele, Ines and Tuohy, Kieran (2018) 'Gut microbiota functions: metabolism of nutrients and other food components'. European journal of nutrition, 57 (1):1-24 [Details]
(2018) 'Finding useful biomarkers for Parkinson’s disease'
Chen-Plotkin, Alice S and Albin, Roger and Alcalay, Roy and Babcock, Debra and Bajaj, Vikram and Bowman, Dubois and Buko, Alex and Cedarbaum, Jesse and Chelsky, Daniel and Cookson, Mark R and others (2018) 'Finding useful biomarkers for Parkinson’s disease'. Science translational medicine, 10 (454) [Details]
(2018) 'Reply to Challenges in modeling the human gut microbiome'
Magnusdottir, Stefania and Heinken, Almut and Fleming, Ronan MT and Thiele, Ines (2018) 'Reply to Challenges in modeling the human gut microbiome'. Nature Biotechnology, 36\ (8\) [Details]
(2018) 'Reply to Challenges in modeling the human gut microbiome'
Magnusdottir, Stefania and Heinken, Almut and Fleming, Ronan MT and Thiele, Ines (2018) 'Reply to Challenges in modeling the human gut microbiome'. Nature biotechnology, 36 (8) [Details]
(2017) 'ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software'
Heirendt, Laurent and Arreckx, Sylvain and Trefois, Christophe and Yarosz, Yohan and Vyas, Maharshi and Satagopam, Venkata P and Schneider, Reinhard and Thiele, Ines and Fleming, Ronan MT (2017) 'ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software'. arXiv preprint arXiv:1712.05236, [Details]
(2017) 'DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia'
Heirendt, Laurent and Thiele, Ines, Fleming Ronan MT (2017) 'DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia'. Bioinformatics, [Details]
(2017) 'Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota'
Magn\'usd\'ottir, Stefan\'\ia and Heinken, Almut and Kutt, Laura and Ravcheev, Dmitry A and Bauer, Eugen and Noronha, Alberto and Greenhalgh, Kacy and J\"ager, Christian and Baginska, Joanna and Wilmes, Paul and others (2017) 'Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota'. Nature biotechnology, 35 (1) [Details]
(2017) 'CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models'
Haraldsd\'ottir, Hulda S and Cousins, Ben and Thiele, Ines and Fleming, Ronan MT and Vempala, Santosh (2017) 'CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models'. Bioinformatics, 33 (11):1741-1743 [Details]
(2017) 'Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression'
Ma, Ding and Yang, Laurence and Fleming, Ronan MT and Thiele, Ines and Palsson, Bernhard O and Saunders, Michael A (2017) 'Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression'. Scientific reports, 7 [Details]
(2017) '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'
Ravcheev, Dmitry A and Thiele, Ines (2017) '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 [Details]
(2017) 'BacArena: individual-based metabolic modeling of heterogeneous microbes in complex communities'
Bauer, Eugen and Zimmermann, Johannes and Baldini, Federico and Thiele, Ines and Kaleta, Christoph (2017) 'BacArena: individual-based metabolic modeling of heterogeneous microbes in complex communities'. PLoS computational biology, 13 (5) [Details]
(2017) 'Leigh Map: a novel diagnostic resource for mitochondrial disease'
Rahman, J and Noronha, A and Thiele, I and Rahman, S (2017) 'Leigh Map: a novel diagnostic resource for mitochondrial disease'. Neuromuscular Disorders, 27 [Details]
(2017) 'Quantitative systems pharmacology and the personalized drug--microbiota--diet axis'
Thiele, Ines and Clancy, Catherine M and Heinken, Almut and Fleming, Ronan MT (2017) 'Quantitative systems pharmacology and the personalized drug--microbiota--diet axis'. Current Opinion in Systems Biology, 4 :43-52 [Details]
(2017) 'Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D'
Gonzalez, German A Preciat and El Assal, Lemmer RP and Noronha, Alberto and Thiele, Ines and Haraldsd\'ottir, Hulda S and Fleming, Ronan MT (2017) 'Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D'. Journal of cheminformatics, 9 (1) [Details]
(2017) 'A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines'
Aurich, Maike K and Fleming, Ronan MT and Thiele, Ines (2017) 'A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines'. PLoS computational biology, 13 (8) [Details]
(2016) 'ReconMap: an interactive visualization of human metabolism'
Noronha, Alberto and Dan\'\ielsd\'ottir, Anna Dr\"ofn and Gawron, Piotr and J\'ohannsson, Freyr and J\'onsd\'ottir, Soff\'\ia and Jarlsson, Sindri and Gunnarsson, J\'on P\'etur and Brynj\'olfsson, Sigur\dhur and Schneider, Reinhard and Thiele, Ines and others (2016) 'ReconMap: an interactive visualization of human metabolism'. Bioinformatics, 33 (4):605-607 [Details]
(2016) 'Metabolomics enables precision medicine:“a white paper, community perspective”'
Beger, Richard D and Dunn, Warwick and Schmidt, Michael A and Gross, Steven S and Kirwan, Jennifer A and Cascante, Marta and Brennan, Lorraine and Wishart, David S and Oresic, Matej and Hankemeier, Thomas and others (2016) 'Metabolomics enables precision medicine:“a white paper, community perspective”'. Metabolomics, 12 (9) [Details]
(2016) 'The Human Gutome: Journey of Microbes and Health'
Dimitrov, Dimiter and Thiele, Ines and Ferguson, Lynnette Robin (2016) 'The Human Gutome: Journey of Microbes and Health'. Frontiers in Genetics, [Details]
(2016) 'Systems biology of bacteria-host interactions'
Heinken, Almut and Ravcheev, Dmitry A and Thiele, Ines (2016) 'Systems biology of bacteria-host interactions'. The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology, [Details]
(2016) 'MetaboTools: a comprehensive toolbox for analysis of genome-scale metabolic models'
Aurich, Maike K and Fleming, Ronan MT and Thiele, Ines (2016) 'MetaboTools: a comprehensive toolbox for analysis of genome-scale metabolic models'. Frontiers in physiology, 7 [Details]
(2016) 'Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis'
Ravcheev, Dmitry A and Thiele, Ines (2016) 'Genomic analysis of the human gut microbiome suggests novel enzymes involved in quinone biosynthesis'. Frontiers in microbiology, 7 [Details]
(2016) 'Conditions for duality between fluxes and concentrations in biochemical networks'
Fleming, Ronan MT and Vlassis, Nikos and Thiele, Ines and Saunders, Michael A (2016) 'Conditions for duality between fluxes and concentrations in biochemical networks'. Journal of theoretical biology, 409 :1-10 [Details]
(2016) 'Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients'
Guebila, Marouen Ben and Thiele, Ines (2016) 'Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients'. NPJ systems biology and applications, 2 [Details]
(2015) 'Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes'
Magn\'usd\'ottir, Stefan\'\ia and Ravcheev, Dmitry and de Cr\'ecy-Lagard, Val\'erie and Thiele, Ines (2015) 'Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes'. Frontiers in genetics, 6 [Details]
(2015) 'Anoxic conditions promote species-specific mutualism between gut microbes in silico'
Heinken, Almut and Thiele, Ines (2015) 'Anoxic conditions promote species-specific mutualism between gut microbes in silico'. Appl. Environ. Microbiol, 81 (12):4049-4061 [Details]
(2015) 'Systems biology of host--microbe metabolomics'
Heinken, Almut and Thiele, Ines (2015) 'Systems biology of host--microbe metabolomics'. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 7 (4):195-219 [Details]
(2015) 'Do genome-scale models need exact solvers or clearer standards?'
Ebrahim, Ali and Almaas, Eivind and Bauer, Eugen and Bordbar, Aarash and Burgard, Anthony P and Chang, Roger L and Dr\"ager, Andreas and Famili, Iman and Feist, Adam M and Fleming, Ronan MT and others (2015) 'Do genome-scale models need exact solvers or clearer standards?'. Molecular systems biology, 11 (10) [Details]
(2015) 'Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires'
Bauer, Eugen and Laczny, Cedric Christian and Magnusdottir, Stefania and Wilmes, Paul and Thiele, Ines (2015) 'Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires'. Microbiome, 3 (1) [Details]
(2015) 'Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework'
Heinken, Almut and Thiele, Ines (2015) 'Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework'. Gut Microbes, 6 (2):120-130 [Details]
(2015) 'Prediction of intracellular metabolic states from extracellular metabolomic data'
Aurich, Maike K and Paglia, Giuseppe and Rolfsson, \'Ottar and Hrafnsd\'ottir, Sigr\'un and Magn\'usd\'ottir, Manuela and Stefaniak, Magdalena M and Palsson, Bernhard \O and Fleming, Ronan MT and Thiele, Ines (2015) 'Prediction of intracellular metabolic states from extracellular metabolomic data'. Metabolomics, 11 (3):603-619 [Details]
(2015) 'Modeling the effects of commonly used drugs on human metabolism'
Sahoo, Swagatika and Haraldsd\'ottir, Hulda S and Fleming, Ronan MT and Thiele, Ines (2015) 'Modeling the effects of commonly used drugs on human metabolism'. The FEBS journal, 282 (2):297-317 [Details]
(2014) 'Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe'
Heinken, Almut and Khan, M Tanweer and Paglia, Giuseppe and Rodionov, Dmitry A and Harmsen, Hermie JM and Thiele, Ines (2014) 'Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe'. Journal of bacteriology, 196 (18):3289-3302 [Details]
(2014) 'Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia'
Edwards, Lindsay M and Sigurdsson, Martin I and Robbins, Peter A and Weale, Michael E and Cavalleri, Gianpiero L and Montgomery, Hugh E and Thiele, Ines (2014) 'Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia'. Circulation: Cardiovascular Genetics, 7 (4):407-415 [Details]
(2014) 'fastGapFill: efficient gap filling in metabolic networks'
Thiele, Ines and Vlassis, Nikos and Fleming, Ronan MT (2014) 'fastGapFill: efficient gap filling in metabolic networks'. Bioinformatics, 30 (17):2529-2531 [Details]
(2014) 'Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2'
Haraldsd\'ottir, Hulda S and Thiele, Ines and Fleming, Ronan MT (2014) 'Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2'. Journal of cheminformatics, 6 (1) [Details]
(2014) 'Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease'
Sahoo, Swagatika and Aurich, Maike Kathrin and Jonsson, Jon Johannes and Thiele, Ines (2014) 'Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease'. Frontiers in physiology, 5 [Details]
(2014) 'Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota'
Ravcheev, Dmitry A and Thiele, Ines (2014) 'Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota'. Frontiers in microbiology, 5 [Details]
(2013) 'A community-driven global reconstruction of human metabolism'
Thiele, Ines and Swainston, Neil and Fleming, Ronan MT and Hoppe, Andreas and Sahoo, Swagatika and Aurich, Maike K and Haraldsdottir, Hulda and Mo, Monica L and Rolfsson, Ottar and Stobbe, Miranda D and others (2013) 'A community-driven global reconstruction of human metabolism'. Nature biotechnology, 31 (5) [Details]
(2013) 'Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks'
Nogales, Juan and Gudmundsson, Steinn and Thiele, Ines (2013) 'Toward systems metabolic engineering in cyanobacteria: opportunities and bottlenecks'. Bioengineered, 4 (3):158-163 [Details]
(2013) 'A systems biology approach to studying the role of microbes in human health'
Thiele, Ines and Heinken, Almut and Fleming, Ronan MT (2013) 'A systems biology approach to studying the role of microbes in human health'. Current opinion in biotechnology, 24 (1):4-12 [Details]
(2013) 'Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut'
Heinken, Almut and Sahoo, Swagatika and Fleming, Ronan MT and Thiele, Ines (2013) 'Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut'. Gut microbes, 4 (1):28-40 [Details]
(2013) 'Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells'
Sahoo, Swagatika and Thiele, Ines (2013) 'Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells'. Human molecular genetics, 22 (13):2705-2722 [Details]
(2013) 'Robust flux balance analysis of multiscale biochemical reaction networks'
Sun, Yuekai and Fleming, Ronan MT and Thiele, Ines and Saunders, Michael A (2013) 'Robust flux balance analysis of multiscale biochemical reaction networks'. BMC bioinformatics, 14 (1) [Details]
(2013) 'Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity'
Rolfsson, Ottar and Paglia, Giuseppe and Magnusdottir, Manuela and Palsson, Bernhard O and Thiele, Ines (2013) 'Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity'. Biochemical Journal, 449 (2):427-435 [Details]
(2013) 'Consensus and conflict cards for metabolic pathway databases'
Stobbe, Miranda D and Swertz, Morris A and Thiele, Ines and Rengaw, Trebor and Van Kampen, Antoine HC and Moerland, Perry D (2013) 'Consensus and conflict cards for metabolic pathway databases'. BMC systems biology, 7 (1) [Details]
(2013) 'Applying systems biology methods to the study of human physiology in extreme environments'
Edwards, Lindsay M and Thiele, Ines (2013) 'Applying systems biology methods to the study of human physiology in extreme environments'. Extreme physiology \& medicine, 2 (1) [Details]
(2012) 'Contextualization procedure and modeling of monocyte specific TLR signaling'
Aurich, Maike K and Thiele, Ines (2012) 'Contextualization procedure and modeling of monocyte specific TLR signaling'. PloS one, 7 (12) [Details]
(2012) 'Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage'
Thiele, Ines and Fleming, Ronan MT and Que, Richard and Bordbar, Aarash and Diep, Dinh and Palsson, Bernhard O (2012) 'Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage'. PloS one, 7 (9) [Details]
(2012) 'Intracellular metabolite profiling of platelets: Evaluation of extraction processes and chromatographic strategies'
Paglia, Giuseppe and Magn\'usd\'ottir, Manuela and Thorlacius, Steinunn and Sigurj\'onsson, \'Olafur E and Gu\dhmundsson, Sveinn and Palsson, Bernhard \O and Thiele, Ines (2012) 'Intracellular metabolite profiling of platelets: Evaluation of extraction processes and chromatographic strategies'. Journal of Chromatography B, 898 :111-120 [Details]
(2012) 'Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration'
Fleming, Ronan MT and Thiele, Ines (2012) 'Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration'. Journal of theoretical biology, 314 :173-181 [Details]
(2012) 'Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis'
Nogales, Juan and Gudmundsson, Steinn and Knight, Eric M and Palsson, Bernhard O and Thiele, Ines (2012) 'Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis'. Proceedings of the National Academy of Sciences, 109 (7):2678-2683 [Details]
(2012) 'Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction'
Haraldsd\'ottir, HS and Thiele, Ines and Fleming, Ronan MT (2012) 'Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction'. Biophysical journal, 102 (8):1703-1711 [Details]
(2012) 'An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production'
Nogales, Juan and Gudmundsson, Steinn and Thiele, Ines (2012) 'An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production'. international journal of hydrogen energy, 37 (17):12205-12218 [Details]
(2012) 'Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole--time of flight mass spectrometry (UPLC--Q--ToF-MS)'
Paglia, Giuseppe and Hrafnsd\'ottir, Sigr\'un and Magn\'usd\'ottir, Manuela and Fleming, Ronan MT and Thorlacius, Steinunn and Palsson, Bernhard \O and Thiele, Ines (2012) 'Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole--time of flight mass spectrometry (UPLC--Q--ToF-MS)'. Analytical and bioanalytical chemistry, 402 (3):1183-1198 [Details]
(2012) 'A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm'
Sigurdsson, Gunnar and Fleming, Ronan MT and Heinken, Almut and Thiele, Ines (2012) 'A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm'. PLoS One, 7 (4) [Details]
(2012) 'A compendium of inborn errors of metabolism mapped onto the human metabolic network'
Sahoo, Swagatika and Franzson, Leifur and Jonsson, Jon J and Thiele, Ines (2012) 'A compendium of inborn errors of metabolism mapped onto the human metabolic network'. Molecular bioSystems, 8 (10):2545-2558 [Details]
(2011) 'rBioNet: A COBRA toolbox extension for r econstructing high-quality bio chemical net works'
Thorleifsson, Stefan Gretar and Thiele, Ines (2011) 'rBioNet: A COBRA toolbox extension for r econstructing high-quality bio chemical net works'. Bioinformatics, 27 (14):2009-2010 [Details]
(2011) 'The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions'
Rolfsson, Ottar and Palsson, Bernhard \O and Thiele, Ines (2011) 'The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions'. BMC systems biology, 5 (1) [Details]
(2011) 'Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0'
Schellenberger, Jan and Que, Richard and Fleming, Ronan MT and Thiele, Ines and Orth, Jeffrey D and Feist, Adam M and Zielinski, Daniel C and Bordbar, Aarash and Lewis, Nathan E and Rahmanian, Sorena and others (2011) 'Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0'. Nature protocols, 6 (9) [Details]
(2011) 'A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2'
Thiele, Ines and Hyduke, Daniel R and Steeb, Benjamin and Fankam, Guy and Allen, Douglas K and Bazzani, Susanna and Charusanti, Pep and Chen, Feng-Chi and Fleming, Ronan MT and Hsiung, Chao A and others (2011) 'A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2'. BMC systems biology, 5 (1) [Details]
(2010) 'What is flux balance analysis?'
Orth, Jeffrey D and Thiele, Ines and Palsson, Bernhard \O (2010) 'What is flux balance analysis?'. Nature biotechnology, 28 (3) [Details]
(2010) 'A protocol for generating a high-quality genome-scale metabolic reconstruction'
Thiele, Ines and Palsson, Bernhard \O (2010) 'A protocol for generating a high-quality genome-scale metabolic reconstruction'. Nature protocols, 5 (1) [Details]
(2010) 'Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism'
Fleming, Ronan MT and Thiele, Ines and Provan, G and Nasheuer, HP (2010) 'Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism'. Journal of theoretical biology, 264 (3):683-692 [Details]
(2010) 'Reconstruction annotation jamborees: a community approach to systems biology'
Thiele, Ines and Palsson, Bernhard \O (2010) 'Reconstruction annotation jamborees: a community approach to systems biology'. Molecular systems biology, 6 (1) [Details]
(2010) 'A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1'
Sigurdsson, Martin I and Jamshidi, Neema and Steingrimsson, Eirikur and Thiele, Ines and Palsson, Bernhard \O (2010) 'A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1'. BMC systems biology, 4 (1) [Details]
(2010) 'Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery'
Thiele, Ines and Fleming, Ronan MT and Bordbar, Aarash and Schellenberger, Jan and Palsson, Bernhard \O (2010) 'Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery'. Biophysical journal, 98 (10):2072-2081 [Details]
(2010) 'von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models'
Fleming, Ronan MT and Thiele, Ines (2010) 'von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models'. Bioinformatics, 27 (1):142-143 [Details]
(2010) 'Computationally efficient flux variability analysis'
Gudmundsson, Steinn and Thiele, Ines (2010) 'Computationally efficient flux variability analysis'. BMC bioinformatics, 11 (1) [Details]
(2009) 'Three-dimensional structural view of the central metabolic network of Thermotoga maritima'
Zhang, Ying and Thiele, Ines and Weekes, Dana and Li, Zhanwen and Jaroszewski, Lukasz and Ginalski, Krzysztof and Deacon, Ashley M and Wooley, John and Lesley, Scott A and Wilson, Ian A and others (2009) 'Three-dimensional structural view of the central metabolic network of Thermotoga maritima'. Science, 325 (5947):1544-1549 [Details]
(2009) 'Metabolic Systems Biology'
Lewis, Nathan E and Jamshidi, Neema and Thiele, Ines and Palsson, Bernhard \O (2009) 'Metabolic Systems Biology'. Encyclopedia of Complexity and Systems Science, :5535-5552 [Details]
(2009) 'Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli'
Fleming, Ronan MT and Thiele, Ines and Nasheuer, HP (2009) 'Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli'. Biophysical chemistry, 145 (2-3):47-56 [Details]
(2009) 'Identification of potential pathway mediation targets in Toll-like receptor signaling'
Li, Fan and Thiele, Ines and Jamshidi, Neema and Palsson, Bernhard \O (2009) 'Identification of potential pathway mediation targets in Toll-like receptor signaling'. PLoS computational biology, 5 (2) [Details]
(2009) 'Metabolic network analysis integrated with transcript verification for sequenced genomes'
Manichaikul, Ani and Ghamsari, Lila and Hom, Erik FY and Lin, Chenwei and Murray, Ryan R and Chang, Roger L and Balaji, S and Hao, Tong and Shen, Yun and Chavali, Arvind K and others (2009) 'Metabolic network analysis integrated with transcript verification for sequenced genomes'. Nature methods, 6 (8) [Details]
(2009) 'Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization'
Thiele, Ines and Jamshidi, Neema and Fleming, Ronan MT and Palsson, Bernhard \O (2009) '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 (3) [Details]
(2009) 'Genome-Scale Reconstruction, Modeling, and Simulation of E. coli's Metabolic Network'
Feist, Adam M and Thiele, Ines and Palsson, Bernhard \O (2009) 'Genome-Scale Reconstruction, Modeling, and Simulation of E. coli's Metabolic Network'. Systems Biology and Biotechnology of Escherichia coli, :149-176 [Details]
(2009) 'Reconstruction of biochemical networks in microorganisms'
Feist, Adam M and Herrg\aard, Markus J and Thiele, Ines and Reed, Jennie L and Palsson, Bernhard \O (2009) 'Reconstruction of biochemical networks in microorganisms'. Nature Reviews Microbiology, 7 (2) [Details]
(2008) 'A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory'
Nogales, Juan and Palsson, Bernhard and Thiele, Ines (2008) 'A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory'. BMC systems biology, 2 (1) [Details]
(2007) 'Estimation of the number of extreme pathways for metabolic networks'
Yeung, Matthew and Thiele, Ines and Palsson, Bernard \O (2007) 'Estimation of the number of extreme pathways for metabolic networks'. BMC bioinformatics, 8 (1) [Details]
(2007) 'Global reconstruction of the human metabolic network based on genomic and bibliomic data'
Duarte, Natalie C and Becker, Scott A and Jamshidi, Neema and Thiele, Ines and Mo, Monica L and Vo, Thuy D and Srivas, Rohith and Palsson, Bernhard \O (2007) 'Global reconstruction of the human metabolic network based on genomic and bibliomic data'. Proceedings of the National Academy of Sciences, 104 (6):1777-1782 [Details]
(2006) 'Candidate states of Helicobacter pylori’s genome-scale metabolic network upon application of “loop law” thermodynamic constraints'
Price, Nathan D and Thiele, Ines and Palsson, Bernhard \O (2006) 'Candidate states of Helicobacter pylori’s genome-scale metabolic network upon application of “loop law” thermodynamic constraints'. Biophysical journal, 90 (11):3919-3928 [Details]
(2006) 'Towards multidimensional genome annotation'
Reed, Jennifer L and Famili, Iman and Thiele, Ines and Palsson, Bernhard O (2006) 'Towards multidimensional genome annotation'. Nature Reviews Genetics, 7 (2) [Details]
(2005) 'Candidate metabolic network states in human mitochondria impact of diabetes, ischemia, and diet'
Thiele, Ines and Price, Nathan D and Vo, Thuy D and Palsson, Bernhard \O (2005) 'Candidate metabolic network states in human mitochondria impact of diabetes, ischemia, and diet'. Journal of Biological Chemistry, 280 (12):11683-11695 [Details]
(2005) 'Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single-and double-deletion mutants'
Thiele, Ines and Vo, Thuy D and Price, Nathan D and Palsson, Bernhard \O (2005) '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 (16):5818-5830 [Details]
(2005) 'The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes'
Overbeek, Ross and Begley, Tadhg and Butler, Ralph M and Choudhuri, Jomuna V and Chuang, Han-Yu and Cohoon, Matthew and de Cr\'ecy-Lagard, Val\'erie and Diaz, Naryttza and Disz, Terry and Edwards, Robert and others (2005) 'The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes'. Nucleic acids research, 33 (17):5691-5702 [Details]

Book Chapters

  Year Publication
(2016) 'Computational modeling of human metabolism and its application to systems biomedicine'
Aurich, Maike K and Thiele, Ines (2016) 'Computational modeling of human metabolism and its application to systems biomedicine' In: Humana Press, New York, NY. [Details]
(2007) 'Bringing genomes to life: the use of genome-scale in silico models'
Thiele, Ines and Palsson, Bernhard \O (2007) 'Bringing genomes to life: the use of genome-scale in silico models' In: Humana Press. [Details]

Honours and Awards

  Year Title Awarding Body
2018 NUI Galway Foundation Research Leadership Programme Awardee NUI Galway Foundation
2018 ERC Starting Grant European Research Council
2017 Future Leaders Programme of the STS Forum Annual Meeting STS Forum
2015 EMBO Young Investigator Lecturer A-IBMN
2015 EMBO Young Investigator EMBO
2013 Attract Fellowship Fonds National de la Recherche, Luxembourg
2012 Emerging Investigator Molecular BioSystems

Employment

  Employer Position From / To
University of Iceland Assistant Professor 01-JUN-09 / 30-JUN-12
University of Iceland Associate Professor 01-JUL-12 / 31-MAR-13
University of Luxembourg Associate Professor 01-APR-13 / 31-JAN-19
National University of Ireland, Galway Personal Professor 01-FEB-19 /

Education

  Year Institution Qualification Subject
2009 University of California, San Diego PhD Bioinformatics
2007 University of California, San Diego MSc Bioinformatics
2004 Ecole Superieure de Biotechnologie de Strasbourg MSc Biotechnology

Languages

  Language
German
English
French

Teaching Interests

Systems Biology; Constraint-based metabolic modelling