Research output per year
Research output per year
- 17 results
Search results
-
2024
The Toolbox for Microbial and Individualized GEMs, Reactobiome and Community Network Modelling
Bidkhori, G. & Shoaie, S., Mar 2024, In: Metabolites. 14, 3, 132.Research output: Contribution to journal › Article › peer-review
Open Access2 Citations (Scopus) -
Transient colonizing microbes promote gut dysbiosis and functional impairment
Lee, S., Meslier, V., Bidkhori, G., Garcia-Guevara, F., Etienne-Mesmin, L., Clasen, F., Park, J., Plaza Oñate, F., Cai, H., Le Chatelier, E., Pons, N., Pereira, M., Seifert, M., Boulund, F., Engstrand, L., Lee, D., Proctor, G., Mardinoglu, A., Blanquet-Diot, S., Moyes, D., & 4 others, 8 Sept 2024, In: npj Biofilms and Microbiomes. 10, 1, p. 80Research output: Contribution to journal › Article › peer-review
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2023
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment
Ezzamouri, B., Rosario, D., Bidkhori, G., Lee, S., Uhlen, M. & Shoaie, S., Dec 2023, In: npj Systems Biology and Applications. 9, 1, 2.Research output: Contribution to journal › Article › peer-review
Open Access8 Citations (Scopus) -
Systematic diet composition swap in a mouse genome-scale metabolic model reveals determinants of obesogenic diet metabolism in liver cancer
Clasen, F., Nunes, P. M., Bidkhori, G., Bah, N., Boeing, S., Shoaie, S. & Anastasiou, D., 17 Feb 2023, In: iScience. 26, 2, 106040.Research output: Contribution to journal › Article › peer-review
Open Access3 Citations (Scopus) -
2022
Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders
Proffitt, C., Bidkhori, G., Lee, S., Tebani, A., Mardinoglu, A., Uhlen, M., Moyes, D. L. & Shoaie, S., 15 Jul 2022, In: iScience. 25, 7, 104513.Research output: Contribution to journal › Article › peer-review
Open Access20 Citations (Scopus) -
Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment
Ezzamouri, B., Rosario, D., Bidkhori, R., Lee, S., Uhlen, M. & Shoaie, S., 1 Nov 2022, (Accepted/In press) In: npj Systems Biology and Applications.Research output: Contribution to journal › Article › peer-review
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2021
Acute kidney injury leading to CKD is associated with a persistence of metabolic dysfunction and hypertriglyceridemia
Harzandi, A., Lee, S., Bidkhori, R., Saha, S., Hendry, B., Mardinoglu, A., Shoaie, S. & Sharpe, C., 19 Feb 2021, In: iScience. 24, 2, 102046.Research output: Contribution to journal › Article › peer-review
Open Access24 Citations (Scopus) -
Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease
Rosario, D., Bidkhori, G., Lee, S., Bedarf, J., Hildebrand, F., Le Chatelier, E., Uhlen, M., Ehrlich, S. D., Proctor, G., Wüllner, U., Mardinoglu, A. & Shoaie, S., 2 Mar 2021, In: Cell Reports. 34, 9, 108807.Research output: Contribution to journal › Article › peer-review
Open Access79 Citations (Scopus) -
2020
Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals
Vaga, S., Lee, S., Ji, B., Andreasson, A., Talley, N. J., Agréus, L., Bidkhori, G., Kovatcheva-Datchary, P., Park, J., Lee, D., Proctor, G., Ehrlich, S. D., Nielsen, J., Engstrand, L. & Shoaie, S., 1 Dec 2020, In: Scientific Reports. 10, 1, 14977.Research output: Contribution to journal › Article › peer-review
Open Access84 Citations (Scopus) -
Disease, Drugs and Dysbiosis: Understanding Microbial Signatures in Metabolic Disease and Medical Interventions
Proffitt, C., Shoaie, S., Bidkhori, R. & Moyes, D., 9 Sept 2020, In: Microorganisms. 8, 9, p. 1-16 16 p., 1381.Research output: Contribution to journal › Review article › peer-review
Open Access13 Citations (Scopus) -
Postmortem Cortical Transcriptomics of Lewy Body Dementia Reveal Mitochondrial Dysfunction and Lack of Neuroinflammation
Rajkumar, A. P., Bidkhori, G., Shoaie, S., Clarke, E., Morrin, H., Hye, A., Williams, G., Ballard, C., Francis, P. & Aarsland, D., 1 Jan 2020, In: American Journal of Geriatric Psychiatry. 28, 1, p. 75-86 12 p.Research output: Contribution to journal › Article › peer-review
40 Citations (Scopus) -
The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease
Zhang, C., Bjornson, E., Arif, M., Tebani, A., Lovric, A., Benfeitas, R., Ozcan, M., Juszczak, K., Kim, W., Kim, J. T., Bidkhori, G., Ståhlman, M., Bergh, P. O., Adiels, M., Turkez, H., Taskinen, M. R., Bosley, J., Marschall, H. U., Nielsen, J., Uhlén, M., & 2 others, 1 Apr 2020, In: Molecular Systems Biology. 16, 4, p. e9495 e9495.Research output: Contribution to journal › Article › peer-review
Open Access29 Citations (Scopus) -
2018
ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling
Zhang, C., Bidkhori, G., Benfeitas, R., Lee, S., Arif, M., Uhlen, M. & Mardinoglu, A., 28 Sept 2018, In: Frontiers in Physiology. 9Research output: Contribution to journal › Article › peer-review
Open Access8 Citations (Scopus) -
High Cell Density Perfusion Culture has a Maintained Exoproteome and Metabolome
Zamani, L., Lundqvist, M., Zhang, Y., Aberg, M., Edfors, F., Bidkhori, G., Lindahl, A., Mie, A., Mardinoglu, A., Field, R., Turner, R., Rockberg, J. & Chotteau, V., Oct 2018, In: Biotechnology Journal. 13, 10, 1800036.Research output: Contribution to journal › Article › peer-review
Open Access17 Citations (Scopus) -
Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma
Bidkhori, G., Benfeitas, R., Elmas, E., Kararoudi, M. N., Arif, M., Uhlen, M., Nielsen, J. & Mardinoglu, A., 17 Jul 2018, In: Frontiers in Physiology. 9Research output: Contribution to journal › Article › peer-review
Open Access35 Citations (Scopus) -
TCSBN: a database of tissue and cancer specific biological networks
Lee, S., Zhang, C., Arif, M., Liu, Z., Benfeitas, R., Bidkhori, G., Deshmukh, S., Al Shobky, M., Lovric, A., Boren, J., Nielsen, J., Uhlen, M. & Mardinoglu, A., 4 Jan 2018, In: Nucleic Acids Research. 46, D1, p. D595-D600Research output: Contribution to journal › Article › peer-review
Open Access44 Citations (Scopus) -
2017
A pathology atlas of the human cancer transcriptome
Uhlen, M., Zhang, C., Lee, S., Sjostedt, E., Fagerberg, L., Bidkhori, G., Benfeitas, R., Arif, M., Liu, Z., Edfors, F., Sanli, K., von Feilitzen, K., Oksvold, P., Lundberg, E., Hober, S., Nilsson, P., Mattsson, J., Schwenk, J. M., Brunnstrom, H., Glimelius, B., & 7 others, 18 Aug 2017, In: Science. 357, 6352, 13 p., eaan2507.Research output: Contribution to journal › Article › peer-review
2256 Citations (Scopus)