| The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum R Agren, L Liu, S Shoaie, W Vongsangnak, I Nookaew, J Nielsen PLoS computational biology 9 (3), e1002980, 2013 | 465 | 2013 |
| 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 | 432* | 2020 |
| Quantifying diet-induced metabolic changes of the human gut microbiome S Shoaie, P Ghaffari, P Kovatcheva-Datchary, A Mardinoglu, P Sen, ... Cell metabolism 22 (2), 320-331, 2015 | 405 | 2015 |
| The gut microbiota modulates host amino acid and glutathione metabolism in mice A Mardinoglu#, S Shoaie#, M Bergentall, P Ghaffari, C Zhang, E Larsson, ... Molecular Systems Biology 11 (10), 834, 2015 | 358 | 2015 |
| Understanding the interactions between bacteria in the human gut through metabolic modeling S Shoaie, F Karlsson, A Mardinoglu, I Nookaew, S Bordel, J Nielsen Scientific reports 3 (1), 2532, 2013 | 294 | 2013 |
| The intestine harbors functionally distinct homeostatic tissue-resident and inflammatory Th17 cells S Omenetti, C Bussi, A Metidji, A Iseppon, S Lee, M Tolaini, Y Li, G Kelly, ... Immunity 51 (1), 77-89. e6, 2019 | 278 | 2019 |
| Candidalysin drives epithelial signaling, neutrophil recruitment, and immunopathology at the vaginal mucosa JP Richardson, HME Willems, DL Moyes, S Shoaie, KS Barker, SL Tan, ... Infection and immunity 86 (2), 10.1128/iai. 00645-17, 2018 | 182 | 2018 |
| Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials L Caspeta#, S Shoaie#, R Agren, I Nookaew, ... BMC systems biology 6 (1), 24, 2012 | 141 | 2012 |
| Rifaximin-α reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial VC Patel, S Lee, MJW McPhail, K Da Silva, S Guilly, A Zamalloa, ... Journal of hepatology 76 (2), 332-342, 2022 | 136 | 2022 |
| Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals S Vaga, S Lee, B Ji, A Andreasson, NJ Talley, L Agréus, G Bidkhori, ... Scientific reports 10 (1), 14977, 2020 | 125 | 2020 |
| Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction IE El-Semman, FH Karlsson, S Shoaie, I Nookaew, TH Soliman, J Nielsen BMC systems biology 8, 1-11, 2014 | 111 | 2014 |
| Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s disease D Rosario, G Bidkhori, S Lee, J Bedarf, F Hildebrand, E Le Chatelier, ... Cell reports 34 (9), 2021 | 102 | 2021 |
| Elucidating the interactions between the human gut microbiota and its host through metabolic modeling S Shoaie, J Nielsen Frontiers in genetics 5, 86, 2014 | 95 | 2014 |
| Understanding the representative gut microbiota dysbiosis in metformin-treated type 2 diabetes patients using genome-scale metabolic modeling D Rosario, R Benfeitas, G Bidkhori, C Zhang, M Uhlen, S Shoaie, ... Frontiers in physiology 9, 775, 2018 | 85 | 2018 |
| Integrating the “immunome” in the stratification of myelodysplastic syndromes and future clinical trial design S Winter, S Shoaie, S Kordasti, U Platzbecker Journal of Clinical Oncology 38 (15), 1723-1735, 2020 | 82 | 2020 |
| Combined metabolic activators accelerates recovery in mild‐to‐moderate COVID‐19 O Altay, M Arif, X Li, H Yang, M Aydın, G Alkurt, W Kim, D Akyol, C Zhang, ... Advanced Science 8 (17), 2101222, 2021 | 73 | 2021 |
| Simplified intestinal microbiota to study microbe-diet-host interactions in a mouse model P Kovatcheva-Datchary, S Shoaie, S Lee, A Wahlström, I Nookaew, ... Cell reports 26 (13), 3772-3783. e6, 2019 | 73 | 2019 |
| Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling P Ghaffari, A Mardinoglu, A Asplund, S Shoaie, C Kampf, M Uhlen, ... Scientific reports 5 (1), 8183, 2015 | 73 | 2015 |
| Abundance and diversity of resistomes differ between healthy human oral cavities and gut VR Carr, EA Witherden, S Lee, S Shoaie, P Mullany, GB Proctor, ... Nature communications 11 (1), 693, 2020 | 71 | 2020 |
| The human mucosal mycobiome and fungal community interactions EA Witherden, S Shoaie, RA Hall, DL Moyes Journal of Fungi 3 (4), 56, 2017 | 59 | 2017 |
Jens NielsenProfessor in Systems Biology, Chalmers University of Technology, SwedenVerified email at chalmers.se
