|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
|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
|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, 2532, 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
|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
|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), 41, 2014
|Elucidating the interactions between the human gut microbiota and its host through metabolic modeling|
S Shoaie, J Nielsen
Frontiers in genetics 5, 86, 2014
|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
|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
|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
|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
|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
|The human mucosal mycobiome and fungal community interactions|
EA Witherden, S Shoaie, RA Hall, DL Moyes
Journal of Fungi 3 (4), 56, 2017
|Simplified intestinal microbiota to study microbe-diet-host interactions in a mouse model|
P Kovatcheva-Datchary, S Shoaie, S Lee, A Wahlstr÷m, I Nookaew, ...
Cell reports 26 (13), 3772-3783. e6, 2019
|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
|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
|Challenges in modeling the human gut microbiome|
P Babaei, S Shoaie, B Ji, J Nielsen
Nature biotechnology 36 (8), 682-686, 2018
|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
|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
|Postmortem cortical transcriptomics of Lewy body dementia reveal mitochondrial dysfunction and lack of Neuroinflammation|
AP Rajkumar, G Bidkhori, S Shoaie, E Clarke, H Morrin, A Hye, G Williams, ...
The American Journal of Geriatric Psychiatry 28 (1), 75-86, 2020