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Liver: Phenotypic and genetic variance: a systems approach to the liver.
Mardinoglu A, Uhlén M. Mardinoglu A, et al. Nat Rev Gastroenterol Hepatol. 2016 Aug;13(8):439-40. doi: 10.1038/nrgastro.2016.93. Epub 2016 Jun 22. Nat Rev Gastroenterol Hepatol. 2016. PMID: 27329803 No abstract available.
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C, Dräger A, Ebert BE, Edirisinghe JN, Faria JP, Feist AM, Fengos G, Fleming RMT, García-Jiménez B, Hatzimanikatis V, van Helvoirt W, Henry CS, Hermjakob H, Herrgård MJ, Kaafarani A, Kim HU, King Z, Klamt S, Klipp E, Koehorst JJ, König M, Lakshmanan M, Lee DY, Lee SY, Lee S, Lewis NE, Liu F, Ma H, Machado D, Mahadevan R, Maia P, Mardinoglu A, Medlock GL, Monk JM, Nielsen J, Nielsen LK, Nogales J, Nookaew I, Palsson BO, Papin JA, Patil KR, Poolman M, Price ND, Resendis-Antonio O, Richelle A, Rocha I, Sánchez BJ, Schaap PJ, Sheriff RSM, Shoaie S, Sonnenschein N, Teusink B, Vilaça P, Vik JO, Wodke JAH, Xavier JC, Yuan Q, Zakhartsev M, Zhang C. Lieven C, et al. Nat Biotechnol. 2020 Apr;38(4):504. doi: 10.1038/s41587-020-0477-4. Nat Biotechnol. 2020. PMID: 32265554 Free PMC article.
An amendment to this paper has been published and can be accessed via a link at the top of the paper....
An amendment to this paper has been published and can be accessed via a link at the top of the paper....
Systems medicine and metabolic modelling.
Mardinoglu A, Nielsen J. Mardinoglu A, et al. J Intern Med. 2012 Feb;271(2):142-54. doi: 10.1111/j.1365-2796.2011.02493.x. J Intern Med. 2012. PMID: 22142312 Review.
Genome-scale modeling of human metabolism - a systems biology approach.
Mardinoglu A, Gatto F, Nielsen J. Mardinoglu A, et al. Biotechnol J. 2013 Sep;8(9):985-96. doi: 10.1002/biot.201200275. Epub 2013 Apr 24. Biotechnol J. 2013. PMID: 23613448 Review.
Genome-scale metabolic models (GEMs) have been employed for studying human metabolism in a systematic manner, as well as for understanding complex human diseases. ...Finally, recent advancements in genome-scale modeling and the future challenge of developing a model …
Genome-scale metabolic models (GEMs) have been employed for studying human metabolism in a systematic manner, as well as for understa …
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.
Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto CA, Skogs M, Takanen JO, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk JM, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson A, von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M. Fagerberg L, et al. Mol Cell Proteomics. 2014 Feb;13(2):397-406. doi: 10.1074/mcp.M113.035600. Epub 2013 Dec 5. Mol Cell Proteomics. 2014. PMID: 24309898 Free PMC article.
Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. ...The …
Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a r …
Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease.
Mardinoglu A, Agren R, Kampf C, Asplund A, Uhlen M, Nielsen J. Mardinoglu A, et al. Nat Commun. 2014;5:3083. doi: 10.1038/ncomms4083. Nat Commun. 2014. PMID: 24419221
Here we reconstruct a consensus GEM for hepatocytes, which we call iHepatocytes2322, that extends previous models by including an extensive description of lipid metabolism. ...
Here we reconstruct a consensus GEM for hepatocytes, which we call iHepatocytes2322, that extends previous models by including an ext …
The human liver-specific proteome defined by transcriptomics and antibody-based profiling.
Kampf C, Mardinoglu A, Fagerberg L, Hallström BM, Edlund K, Lundberg E, Pontén F, Nielsen J, Uhlen M. Kampf C, et al. FASEB J. 2014 Jul;28(7):2901-14. doi: 10.1096/fj.14-250555. Epub 2014 Mar 19. FASEB J. 2014. PMID: 24648543
We identified in total 477 protein-coding genes with elevated expression in the liver: 179 genes have higher expression as compared to all the other analyzed tissues; 164 genes have elevated transcript levels in the liver shared with at least one other tissue type; and an additio …
We identified in total 477 protein-coding genes with elevated expression in the liver: 179 genes have higher expression as compared to all t …
Proteomics. Tissue-based map of the human proteome.
Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Uhlén M, et al. Science. 2015 Jan 23;347(6220):1260419. doi: 10.1126/science.1260419. Science. 2015. PMID: 25613900
Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down …
Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics …
Logical transformation of genome-scale metabolic models for gene level applications and analysis.
Zhang C, Ji B, Mardinoglu A, Nielsen J, Hua Q. Zhang C, et al. Bioinformatics. 2015 Jul 15;31(14):2324-31. doi: 10.1093/bioinformatics/btv134. Epub 2015 Mar 2. Bioinformatics. 2015. PMID: 25735769
RESULTS: Here, we propose a framework named logic transformation of model (LTM) that is able to simplify the gene-reaction associations and enables integration with other developed methods for gene level applications. ...
RESULTS: Here, we propose a framework named logic transformation of model (LTM) that is able to simplify the gene-reaction associatio …
Modelling the effect of SPION size in a stent assisted magnetic drug targeting system with interparticle interactions.
Mardinoglu A, Cregg PJ. Mardinoglu A, et al. ScientificWorldJournal. 2015;2015:618658. doi: 10.1155/2015/618658. Epub 2015 Mar 1. ScientificWorldJournal. 2015. PMID: 25815370 Free PMC article.
Cancer is a leading cause of death worldwide and it is caused by the interaction of genomic, environmental, and lifestyle factors. ...Here, we develop a mathematical model for studying the interactions between the MDCPs enriched with three different diameters of SPI …
Cancer is a leading cause of death worldwide and it is caused by the interaction of genomic, environmental, and lifestyle factors. .. …
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