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Carr, VR, Witherden, E, Lee, S, Shoaie, S, Mullany, P, Proctor, GB, Gomez-Cabrero, D & Moyes, DL 2020, 'Abundance and diversity of resistomes differ between healthy human oral cavities and gut', Nature Communications.


Winter, S, Shoaie, S, Kordasti, S & Platzbecker, U 2020, 'Integrating the "Immunome" in the Stratification of Myelodysplastic Syndromes and Future Clinical Trial Design: Systems immunology; a way forward in MDS', Journal of clinical oncology : official journal of the American Society of Clinical Oncology.


Rajkumar, AP, Bidkhori, G, Shoaie, S, Clarke, E, Morrin, H, Hye, A, Williams, G, Ballard, C, Francis, P & Aarsland, D 2020, 'Postmortem Cortical Transcriptomics of Lewy Body Dementia Reveal Mitochondrial Dysfunction and Lack of Neuroinflammation', American Journal of Geriatric Psychiatry, vol. 28, no. 1, pp. 75-86.


Kovatcheva-Datchary, P, Shoaie, S, Lee, S, Wahlstrom, A, Nookaew, I, Hallen, A, Perkins, R, Nielsen, J & Bäckhed, F 2019, 'Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model', Cell Reports, vol. 26, no. 13, pp. 3772-3783.e6.


Omenetti, S, Bussi, C, Metidji, A, Iseppon, A, Lee, S, Tolaini, M, Li, Y, Kelly, G, Chakravarty, P, Shoaie, S, G. Gutierrez, M & Stockinger, B 2019, 'The Intestine Harbors Functionally Distinct Homeostatic Tissue-Resident and Inflammatory Th17 Cells', Immunity, vol. 51, no. 1, pp. 77-89.e6.


Gudra, D, Shoaie, S, Fridmanis, D, Klovins, J, Wefer, H, Silamikelis, I, Peculis, R, Kalnina, I, Elbere, I, Radovica-Spalvina, I, Hultcrantz, R, Šķenders, Ģ, Leja, M & Engstrand, L 2018, 'A widely used sampling device in colorectal cancer screening programmes allows for large-scale microbiome studies', Gut.


Richardson, JP, Willems, HME, Moyes, DL, Shoaie, S, Barker, KS, Tan, SL, Palmer, GE, Hube, B, Naglik, JR & Peters, BM 2018, 'Candidalysin drives epithelial signaling, neutrophil recruitment, andimmunopathology at the vaginal mucosa', Infection and Immunity, vol. 86.


Babaei, P, Shoaie, S, Ji, B & Nielsen, J 2018, 'Challenges in modeling the human gut microbiome', Nature Biotechnology, vol. 36, pp. 682–686.


Rosário, D, Benfeitas, R, Bidkhori, G, Zhang, C, Uhlen, M, Shoaie, S & Mardinoglu, A 2018, 'Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling', Frontiers in Physiology, vol. 9, 775.


Witherden, EA, Shoaie, S, Hall, R & Moyes, DL 2017, 'The Human Mucosal Mycobiome and Fungal Community Interactions', Journal of Fungi, vol. 3, no. 4, 56.


Witherden, EA, Moyes, D, Bruce, K, Ehrlich, S & Shoaie, S 2017, 'Using systems biology approaches to elucidate cause and effect in host-microbiome interactions', Current Opinion in Systems Biology, pp. 141-146.


Ghaffari, P, Mardinoglu, A, Asplund, A, Shoaie, S, Kampf, C, Uhlen, M & Nielsen, J 2015, 'Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling', Scientific Reports, vol. 5, 8183.


Shoaie, S, Ghaffari, P, Kovatcheva-Datchary, P, Mardinoglu, A, Sen, P, Pujos-Guillot, E, de Wouters, T, Juste, C, Rizkalla, S, Chilloux, J, Hoyles, L, Nicholson, JK, Dore, J, Dumas, ME, Clement, K, Bäckhed, F, Nielsen, J & MICRO-Obes Consortium 2015, 'Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome', CELL METABOLISM, vol. 22, no. 2, pp. 320–331.


El-Semman, IE, Karlsson, FH, Shoaie, S, Nookaew, I, Soliman, TH & Nielsen, J 2014, 'Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction', Bmc Systems Biology, vol. 8, pp. 41.


Agren, R, Liu, L, Shoaie, S, Vongsangnak, W, Nookaew, I & Nielsen, J 2013, 'The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum', PL o S Computational Biology, vol. 9, no. 3, pp. e1002980.


Hong, K-K, Hou, J, Shoaie, S, Nielsen, J & Bordel, S 2012, 'Dynamic 13C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains', FEMS YEAST RESEARCH, vol. 12, no. 7, pp. 741-7.


Caspeta, L, Shoaie, S, Agren, R, Nookaew, I & Nielsen, J 2012, 'Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials', Bmc Systems Biology, vol. 6, pp. 24.

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