| 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 Comput Biol 9 (3), e1002980, 2013 | 352 | 2013 |
| 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 | 255 | 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), 1-10, 2013 | 206 | 2013 |
| 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 | 201 | 2015 |
| 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 | 124 | 2012 |
| 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 | 101* | 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), 1-11, 2014 | 73 | 2014 |
| 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), 2018 | 71 | 2018 |
| 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 | 69 | 2019 |
| Elucidating the interactions between the human gut microbiota and its host through metabolic modeling S Shoaie, J Nielsen Frontiers in genetics 5, 86, 2014 | 68 | 2014 |
| 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), 1-10, 2015 | 51 | 2015 |
| 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 | 27 | 2018 |
| 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 | 23 | 2019 |
| The human mucosal mycobiome and fungal community interactions EA Witherden, S Shoaie, RA Hall, DL Moyes Journal of Fungi 3 (4), 56, 2017 | 21 | 2017 |
| Integrating the “immunome” in the stratification of myelodysplastic syndromes and future clinical trial design S Winter, S Shoaie, S Kordasti, U Platzbecker J Clin Oncol 38 (15), 1723-1735, 2020 | 15 | 2020 |
| Challenges in modeling the human gut microbiome P Babaei, S Shoaie, B Ji, J Nielsen Nature biotechnology 36 (8), 682-686, 2018 | 15 | 2018 |
| Systems biology analysis of hepatitis C virus infection reveals the role of copy number increases in regions of chromosome 1q in hepatocellular carcinoma metabolism IE Elsemman, A Mardinoglu, S Shoaie, TH Soliman, J Nielsen Molecular BioSystems 12 (5), 1496-1506, 2016 | 15 | 2016 |
| Dynamic13C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains KK Hong, J Hou, S Shoaie, J Nielsen, S Bordel FEMS yeast research 12 (7), 741-747, 2012 | 15 | 2012 |
| 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), 1-10, 2020 | 10 | 2020 |
| Using systems biology approaches to elucidate cause and effect in host–microbiome interactions EA Witherden, DL Moyes, KD Bruce, SD Ehrlich, S Shoaie Current Opinion in Systems Biology 3, 141-146, 2017 | 9 | 2017 |
Jens NielsenProfessor in Systems Biology, Chalmers University of Technology, SwedenVerified email at chalmers.se
