| Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0 J Schellenberger, R Que, RMT Fleming, I Thiele, JD Orth, AM Feist, ... Nature protocols 6 (9), 1290-1307, 2011 | 1694 | 2011 |
| A community-driven global reconstruction of human metabolism I Thiele, N Swainston, RMT Fleming, A Hoppe, S Sahoo, MK Aurich, ... Nature biotechnology 31 (5), 419-425, 2013 | 1230 | 2013 |
| Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices S Halldorsson, E Lucumi, R Gómez-Sjöberg, RMT Fleming Biosensors and Bioelectronics 63, 218–231, 2015 | 1211 | 2015 |
| Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0 L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ... Nature protocols 14 (3), 639-702, 2019 | 1191 | 2019 |
| Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota S Magnúsdóttir, A Heinken, L Kutt, DA Ravcheev, E Bauer, A Noronha, ... Nature biotechnology 35 (1), 81-89, 2017 | 790 | 2017 |
| Recon3D enables a three-dimensional view of gene variation in human metabolism E Brunk, S Sahoo, DC Zielinski, A Altunkaya, A Dräger, N Mih, F Gatto, ... Nature biotechnology 36 (3), 272-281, 2018 | 718 | 2018 |
| MEMOTE for standardized genome-scale metabolic model testing C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ... Nature biotechnology 38 (3), 272-276, 2020 | 469* | 2020 |
| Derivation of human midbrain-specific organoids from neuroepithelial stem cells AS Monzel, LM Smits, K Hemmer, S Hachi, EL Moreno, T van Wuellen, ... Stem cell reports 8 (5), 1144-1154, 2017 | 427 | 2017 |
| The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease A Noronha, J Modamio, Y Jarosz, E Guerard, N Sompairac, G Preciat, ... Nucleic acids research 47 (D1), D614-D624, 2019 | 367 | 2019 |
| Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide JD Orth, RMT Fleming, BØ Palsson EcoSal plus 4 (1), 10.1128/ecosalplus. 10.2. 1, 2010 | 325 | 2010 |
| Consistent estimation of Gibbs energy using component contributions E Noor, HS Haraldsdóttir, R Milo, RMT Fleming PLoS computational biology 9 (7), e1003098, 2013 | 320 | 2013 |
| Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease A Heinken, DA Ravcheev, F Baldini, L Heirendt, RMT Fleming, I Thiele Microbiome 7, 1-18, 2019 | 287 | 2019 |
| Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut A Heinken, S Sahoo, RMT Fleming, I Thiele Gut microbes 4 (1), 28-40, 2013 | 254 | 2013 |
| SBML Level 3: an extensible format for the exchange and reuse of biological models SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ... Molecular systems biology 16 (8), e9110, 2020 | 253 | 2020 |
| Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its … I Thiele, N Jamshidi, RMT Fleming, BØ Palsson PLoS computational biology 5 (3), e1000312, 2009 | 246 | 2009 |
| Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome I Thiele, S Sahoo, A Heinken, J Hertel, L Heirendt, MK Aurich, ... Molecular systems biology 16 (5), e8982, 2020 | 205* | 2020 |
| Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine A Heinken, J Hertel, G Acharya, DA Ravcheev, M Nyga, OE Okpala, ... Nature Biotechnology 41 (9), 1320-1331, 2023 | 193* | 2023 |
| Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture EL Moreno, S Hachi, K Hemmer, SJ Trietsch, AS Baumuratov, ... Lab on a Chip 15 (11), 2419-2428, 2015 | 175 | 2015 |
| A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 I Thiele, DR Hyduke, B Steeb, G Fankam, DK Allen, S Bazzani, ... BMC systems biology 5, 1-9, 2011 | 173 | 2011 |
| Integrated analyses of microbiome and longitudinal metabolome data reveal microbial-host interactions on sulfur metabolism in Parkinson’s disease J Hertel, AC Harms, A Heinken, F Baldini, CC Thinnes, E Glaab, ... Cell reports 29 (7), 1767-1777. e8, 2019 | 150 | 2019 |
Ines ThieleUniversity of GalwayVerified email at universityofgalway.ie
