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Items: 15

1.

A widely used sampling device in colorectal cancer screening programmes allows for large-scale microbiome studies.

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.

Gut. 2018 Sep 21. pii: gutjnl-2018-316225. doi: 10.1136/gutjnl-2018-316225. [Epub ahead of print] No abstract available.

2.

Challenges in modeling the human gut microbiome.

Babaei P, Shoaie S, Ji B, Nielsen J.

Nat Biotechnol. 2018 Aug 6;36(8):682-686. doi: 10.1038/nbt.4213. No abstract available.

PMID:
30080831
3.

Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling.

Rosario D, Benfeitas R, Bidkhori G, Zhang C, Uhlen M, Shoaie S, Mardinoglu A.

Front Physiol. 2018 Jun 25;9:775. doi: 10.3389/fphys.2018.00775. eCollection 2018.

4.

The Human Mucosal Mycobiome and Fungal Community Interactions.

Witherden EA, Shoaie S, Hall RA, Moyes DL.

J Fungi (Basel). 2017 Oct 7;3(4). pii: E56. doi: 10.3390/jof3040056. Review.

5.

Candidalysin drives epithelial signaling, neutrophil recruitment, and immunopathology at the vaginal mucosa.

Richardson JP, Willems HME, Moyes DL, Shoaie S, Barker KS, Tan SL, Palmer GE, Hube B, Naglik JR, Peters BM.

Infect Immun. 2017 Nov 6. pii: IAI.00645-17. doi: 10.1128/IAI.00645-17. [Epub ahead of print]

6.

Systems biology analysis of hepatitis C virus infection reveals the role of copy number increases in regions of chromosome 1q in hepatocellular carcinoma metabolism.

Elsemman IE, Mardinoglu A, Shoaie S, Soliman TH, Nielsen J.

Mol Biosyst. 2016 Apr 26;12(5):1496-506. doi: 10.1039/c5mb00827a.

PMID:
27040643
7.

The gut microbiota modulates host amino acid and glutathione metabolism in mice.

Mardinoglu A, Shoaie S, Bergentall M, Ghaffari P, Zhang C, Larsson E, Bäckhed F, Nielsen J.

Mol Syst Biol. 2015 Oct 16;11(10):834. doi: 10.15252/msb.20156487.

8.

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome.

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; MICRO-Obes Consortium, Dore J, Dumas ME, Clement K, Bäckhed F, Nielsen J.

Cell Metab. 2015 Aug 4;22(2):320-31. doi: 10.1016/j.cmet.2015.07.001.

9.

Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling.

Ghaffari P, Mardinoglu A, Asplund A, Shoaie S, Kampf C, Uhlen M, Nielsen J.

Sci Rep. 2015 Feb 2;5:8183. doi: 10.1038/srep08183.

10.

Elucidating the interactions between the human gut microbiota and its host through metabolic modeling.

Shoaie S, Nielsen J.

Front Genet. 2014 Apr 22;5:86. doi: 10.3389/fgene.2014.00086. eCollection 2014. Review.

11.

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.

El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, Nielsen J.

BMC Syst Biol. 2014 Apr 3;8:41. doi: 10.1186/1752-0509-8-41.

12.

Understanding the interactions between bacteria in the human gut through metabolic modeling.

Shoaie S, Karlsson F, Mardinoglu A, Nookaew I, Bordel S, Nielsen J.

Sci Rep. 2013;3:2532. doi: 10.1038/srep02532.

13.

The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.

Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J.

PLoS Comput Biol. 2013;9(3):e1002980. doi: 10.1371/journal.pcbi.1002980. Epub 2013 Mar 21.

14.

Dynamic 13C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains.

Hong KK, Hou J, Shoaie S, Nielsen J, Bordel S.

FEMS Yeast Res. 2012 Nov;12(7):741-7. doi: 10.1111/j.1567-1364.2012.00823.x. Epub 2012 Jul 20.

15.

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials.

Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J.

BMC Syst Biol. 2012 Apr 4;6:24. doi: 10.1186/1752-0509-6-24.

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