Saeed Shoaie
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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
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
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
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
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
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
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
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
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
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
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
Elucidating the interactions between the human gut microbiota and its host through metabolic modeling
S Shoaie, J Nielsen
Frontiers in genetics 5, 86, 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
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
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, 352912, 2018
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
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
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
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
The human mucosal mycobiome and fungal community interactions
EA Witherden, S Shoaie, RA Hall, DL Moyes
Journal of Fungi 3 (4), 56, 2017
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Articles 1–20