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Items: 1 to 50 of 59

1.

Systems biology in hepatology: approaches and applications.

Mardinoglu A, Boren J, Smith U, Uhlen M, Nielsen J.

Nat Rev Gastroenterol Hepatol. 2018 Apr 23. doi: 10.1038/s41575-018-0007-8. [Epub ahead of print] Review.

PMID:
29686404
2.

Identification of Discriminating Metabolic Pathways and Metabolites in Human PBMCs Stimulated by Various Pathogenic Agents.

Zhang X, Mardinoglu A, Joosten LAB, Kuivenhoven JA, Li Y, Netea MG, Groen AK.

Front Physiol. 2018 Feb 27;9:139. doi: 10.3389/fphys.2018.00139. eCollection 2018.

3.

Combined ASRGL1 and p53 immunohistochemistry as an independent predictor of survival in endometrioid endometrial carcinoma.

Huvila J, Laajala TD, Edqvist PH, Mardinoglu A, Talve L, Pontén F, Grénman S, Carpén O, Aittokallio T, Auranen A.

Gynecol Oncol. 2018 Apr;149(1):173-180. doi: 10.1016/j.ygyno.2018.02.016. Epub 2018 Mar 2.

PMID:
29486992
4.

Translational study reveals a two-faced role of RBM3 in pancreatic cancer and suggests its potential value as a biomarker for improved patient stratification.

Karnevi E, Dror LB, Mardinoglu A, Elebro J, Heby M, Olofsson SE, Nodin B, Eberhard J, Gallagher W, Uhlén M, Jirström K.

Oncotarget. 2017 Dec 15;9(5):6188-6200. doi: 10.18632/oncotarget.23486. eCollection 2018 Jan 19.

5.

An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans.

Mardinoglu A, Wu H, Bjornson E, Zhang C, Hakkarainen A, Räsänen SM, Lee S, Mancina RM, Bergentall M, Pietiläinen KH, Söderlund S, Matikainen N, Ståhlman M, Bergh PO, Adiels M, Piening BD, Granér M, Lundbom N, Williams KJ, Romeo S, Nielsen J, Snyder M, Uhlén M, Bergström G, Perkins R, Marschall HU, Bäckhed F, Taskinen MR, Borén J.

Cell Metab. 2018 Mar 6;27(3):559-571.e5. doi: 10.1016/j.cmet.2018.01.005. Epub 2018 Feb 15.

PMID:
29456073
6.

Broad Views of Non-alcoholic Fatty Liver Disease.

Mardinoglu A, Uhlen M, Borén J.

Cell Syst. 2018 Jan 24;6(1):7-9. doi: 10.1016/j.cels.2018.01.004.

PMID:
29401451
7.

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP.

Cell Syst. 2018 Feb 28;6(2):157-170.e8. doi: 10.1016/j.cels.2017.12.013. Epub 2018 Jan 17.

PMID:
29361466
8.

Letter: dose-response analysis revealed closer relationship between obesity and perioperative outcomes in patients after liver transplantation.

Liu Z, Mardinoglu A, Que S.

Aliment Pharmacol Ther. 2018 Jan;47(2):310-312. doi: 10.1111/apt.14425. No abstract available.

PMID:
29265455
9.

Elevated Plasma Levels of 3-Hydroxyisobutyric Acid Are Associated With Incident Type 2 Diabetes.

Mardinoglu A, Gogg S, Lotta LA, Stančáková A, Nerstedt A, Boren J, Blüher M, Ferrannini E, Langenberg C, Wareham NJ, Laakso M, Smith U.

EBioMedicine. 2018 Jan;27:151-155. doi: 10.1016/j.ebiom.2017.12.008. Epub 2017 Dec 7.

10.

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.

Nucleic Acids Res. 2018 Jan 4;46(D1):D595-D600. doi: 10.1093/nar/gkx994.

11.

The effect of the TM6SF2 E167K variant on liver steatosis and fibrosis in patients with chronic hepatitis C: a meta-analysis.

Liu Z, Que S, Zhou L, Zheng S, Romeo S, Mardinoglu A, Valenti L.

Sci Rep. 2017 Aug 24;7(1):9273. doi: 10.1038/s41598-017-09548-9.

12.

Network analyses identify liver-specific targets for treating liver diseases.

Lee S, Zhang C, Liu Z, Klevstig M, Mukhopadhyay B, Bergentall M, Cinar R, Ståhlman M, Sikanic N, Park JK, Deshmukh S, Harzandi AM, Kuijpers T, Grøtli M, Elsässer SJ, Piening BD, Snyder M, Smith U, Nielsen J, Bäckhed F, Kunos G, Uhlen M, Boren J, Mardinoglu A.

Mol Syst Biol. 2017 Aug 21;13(8):938. doi: 10.15252/msb.20177703.

13.

A pathology atlas of the human cancer transcriptome.

Uhlen M, Zhang C, Lee S, Sjöstedt 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 JM, Brunnström H, Glimelius B, Sjöblom T, Edqvist PH, Djureinovic D, Micke P, Lindskog C, Mardinoglu A, Ponten F.

Science. 2017 Aug 18;357(6352). pii: eaan2507. doi: 10.1126/science.aan2507.

PMID:
28818916
14.

Plasma Mannose Levels Are Associated with Incident Type 2 Diabetes and Cardiovascular Disease.

Mardinoglu A, Stančáková A, Lotta LA, Kuusisto J, Boren J, Blüher M, Wareham NJ, Ferrannini E, Groop PH, Laakso M, Langenberg C, Smith U.

Cell Metab. 2017 Aug 1;26(2):281-283. doi: 10.1016/j.cmet.2017.07.006.

PMID:
28768165
15.

New Challenges to Study Heterogeneity in Cancer Redox Metabolism.

Benfeitas R, Uhlen M, Nielsen J, Mardinoglu A.

Front Cell Dev Biol. 2017 Jul 11;5:65. doi: 10.3389/fcell.2017.00065. eCollection 2017. Review.

16.

Improving the economics of NASH/NAFLD treatment through the use of systems biology.

Bosley J, Boren C, Lee S, Grøtli M, Nielsen J, Uhlen M, Boren J, Mardinoglu A.

Drug Discov Today. 2017 Oct;22(10):1532-1538. doi: 10.1016/j.drudis.2017.07.005. Epub 2017 Jul 20. Review.

PMID:
28736156
17.

Rediscussion on linearity between fibrosis stages and mortality risk in nonalcoholic fatty liver disease patients.

Liu Z, Que S, Mardinoglu A.

Hepatology. 2017 Oct;66(4):1357-1358. doi: 10.1002/hep.29390. Epub 2017 Sep 4. No abstract available.

PMID:
28727167
18.

Predicting growth of the healthy infant using a genome scale metabolic model.

Nilsson A, Mardinoglu A, Nielsen J.

NPJ Syst Biol Appl. 2017 Jan 31;3:3. doi: 10.1038/s41540-017-0004-5. eCollection 2017.

19.

A subcellular map of the human proteome.

Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, Alm T, Asplund A, Björk L, Breckels LM, Bäckström A, Danielsson F, Fagerberg L, Fall J, Gatto L, Gnann C, Hober S, Hjelmare M, Johansson F, Lee S, Lindskog C, Mulder J, Mulvey CM, Nilsson P, Oksvold P, Rockberg J, Schutten R, Schwenk JM, Sivertsson Å, Sjöstedt E, Skogs M, Stadler C, Sullivan DP, Tegel H, Winsnes C, Zhang C, Zwahlen M, Mardinoglu A, Pontén F, von Feilitzen K, Lilley KS, Uhlén M, Lundberg E.

Science. 2017 May 26;356(6340). pii: eaal3321. doi: 10.1126/science.aal3321. Epub 2017 May 11.

PMID:
28495876
20.

AUP1 (Ancient Ubiquitous Protein 1): A Molecular Link Between Hepatic Lipid Mobilization and VLDL Secretion.

Mardinoglu A, Borén J.

Arterioscler Thromb Vasc Biol. 2017 Apr;37(4):609-610. doi: 10.1161/ATVBAHA.117.309152. No abstract available.

21.

Personal model-assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLD.

Mardinoglu A, Bjornson E, Zhang C, Klevstig M, Söderlund S, Ståhlman M, Adiels M, Hakkarainen A, Lundbom N, Kilicarslan M, Hallström BM, Lundbom J, Vergès B, Barrett PH, Watts GF, Serlie MJ, Nielsen J, Uhlén M, Smith U, Marschall HU, Taskinen MR, Boren J.

Mol Syst Biol. 2017 Mar 2;13(3):916. doi: 10.15252/msb.20167422.

22.

Editorial: The Impact of Systems Medicine on Human Health and Disease.

Mardinoglu A, Nielsen J.

Front Physiol. 2016 Nov 24;7:552. eCollection 2016. No abstract available.

23.

Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus.

Casey JR, Mardinoglu A, Nielsen J, Karl DM.

mSystems. 2016 Nov 15;1(6). pii: e00065-16. eCollection 2016 Nov-Dec.

24.

Mitochondria-related transcriptional signature is downregulated in adipocytes in obesity: a study of young healthy MZ twins.

Heinonen S, Muniandy M, Buzkova J, Mardinoglu A, Rodríguez A, Frühbeck G, Hakkarainen A, Lundbom J, Lundbom N, Kaprio J, Rissanen A, Pietiläinen KH.

Diabetologia. 2017 Jan;60(1):169-181. Epub 2016 Oct 12.

PMID:
27734103
25.

ARAP2 promotes GLUT1-mediated basal glucose uptake through regulation of sphingolipid metabolism.

Chaudhari A, Håversen L, Mobini R, Andersson L, Ståhlman M, Lu E, Rutberg M, Fogelstrand P, Ekroos K, Mardinoglu A, Levin M, Perkins R, Borén J.

Biochim Biophys Acta. 2016 Nov;1861(11):1643-1651. doi: 10.1016/j.bbalip.2016.07.009. Epub 2016 Jul 27.

PMID:
27476102
26.

Investigating the Combinatory Effects of Biological Networks on Gene Co-expression.

Zhang C, Lee S, Mardinoglu A, Hua Q.

Front Physiol. 2016 May 2;7:160. doi: 10.3389/fphys.2016.00160. eCollection 2016.

27.

Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance.

Lee S, Zhang C, Kilicarslan M, Piening BD, Bjornson E, Hallström BM, Groen AK, Ferrannini E, Laakso M, Snyder M, Blüher M, Uhlen M, Nielsen J, Smith U, Serlie MJ, Boren J, Mardinoglu A.

Cell Metab. 2016 Jul 12;24(1):172-84. doi: 10.1016/j.cmet.2016.05.026. Epub 2016 Jun 23.

28.

Liver: Phenotypic and genetic variance: a systems approach to the liver.

Mardinoglu A, Uhlén M.

Nat Rev Gastroenterol Hepatol. 2016 Aug;13(8):439-40. doi: 10.1038/nrgastro.2016.93. Epub 2016 Jun 22. No abstract available.

PMID:
27329803
29.

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.

Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J.

Nucleic Acids Res. 2016 Jul 8;44(12):5529-39. doi: 10.1093/nar/gkw462. Epub 2016 May 23.

30.

Transcriptomics resources of human tissues and organs.

Uhlén M, Hallström BM, Lindskog C, Mardinoglu A, Pontén F, Nielsen J.

Mol Syst Biol. 2016 Apr 4;12(4):862. doi: 10.15252/msb.20155865. Review.

31.

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
32.

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes.

Väremo L, Scheele C, Broholm C, Mardinoglu A, Kampf C, Asplund A, Nookaew I, Uhlén M, Pedersen BK, Nielsen J.

Cell Rep. 2016 Feb 16;14(6):1567. doi: 10.1016/j.celrep.2016.01.054. Epub 2016 Feb 16. No abstract available.

33.

Personalized Cardiovascular Disease Prediction and Treatment-A Review of Existing Strategies and Novel Systems Medicine Tools.

Björnson E, Borén J, Mardinoglu A.

Front Physiol. 2016 Jan 26;7:2. doi: 10.3389/fphys.2016.00002. eCollection 2016. Review.

34.

Confounding Effects of Metformin on the Human Gut Microbiome in Type 2 Diabetes.

Mardinoglu A, Boren J, Smith U.

Cell Metab. 2016 Jan 12;23(1):10-2. doi: 10.1016/j.cmet.2015.12.012.

35.

Cancer Metabolism: A Modeling Perspective.

Ghaffari P, Mardinoglu A, Nielsen J.

Front Physiol. 2015 Dec 16;6:382. doi: 10.3389/fphys.2015.00382. eCollection 2015. Review.

36.

Stratification of Hepatocellular Carcinoma Patients Based on Acetate Utilization.

Björnson E, Mukhopadhyay B, Asplund A, Pristovsek N, Cinar R, Romeo S, Uhlen M, Kunos G, Nielsen J, Mardinoglu A.

Cell Rep. 2015 Dec 1;13(9):2014-26. doi: 10.1016/j.celrep.2015.10.045. Epub 2015 Nov 19.

37.

Kinetic Studies to Elucidate Impaired Metabolism of Triglyceride-rich Lipoproteins in Humans.

Adiels M, Mardinoglu A, Taskinen MR, Borén J.

Front Physiol. 2015 Nov 20;6:342. doi: 10.3389/fphys.2015.00342. eCollection 2015. Review.

38.

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.

39.

Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue.

Mardinoglu A, Heiker JT, Gärtner D, Björnson E, Schön MR, Flehmig G, Klöting N, Krohn K, Fasshauer M, Stumvoll M, Nielsen J, Blüher M.

Sci Rep. 2015 Oct 5;5:14841. doi: 10.1038/srep14841.

40.

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.

41.

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.

Lindskog C, Linné J, Fagerberg L, Hallström BM, Sundberg CJ, Lindholm M, Huss M, Kampf C, Choi H, Liem DA, Ping P, Väremo L, Mardinoglu A, Nielsen J, Larsson E, Pontén F, Uhlén M.

BMC Genomics. 2015 Jun 25;16:475. doi: 10.1186/s12864-015-1686-y.

42.

Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes.

Väremo L, Scheele C, Broholm C, Mardinoglu A, Kampf C, Asplund A, Nookaew I, Uhlén M, Pedersen BK, Nielsen J.

Cell Rep. 2015 May 12;11(6):921-933. doi: 10.1016/j.celrep.2015.04.010. Epub 2015 Apr 30. Erratum in: Cell Rep. 2016 Feb 16;14(6):1567.

43.

Modelling the effect of SPION size in a stent assisted magnetic drug targeting system with interparticle interactions.

Mardinoglu A, Cregg PJ.

ScientificWorldJournal. 2015;2015:618658. doi: 10.1155/2015/618658. Epub 2015 Mar 1.

44.

Logical transformation of genome-scale metabolic models for gene level applications and analysis.

Zhang C, Ji B, Mardinoglu A, Nielsen J, Hua Q.

Bioinformatics. 2015 Jul 15;31(14):2324-31. doi: 10.1093/bioinformatics/btv134. Epub 2015 Mar 2.

PMID:
25735769
45.

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.

46.

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.

Science. 2015 Jan 23;347(6220):1260419. doi: 10.1126/science.1260419.

47.

New paradigms for metabolic modeling of human cells.

Mardinoglu A, Nielsen J.

Curr Opin Biotechnol. 2015 Aug;34:91-7. doi: 10.1016/j.copbio.2014.12.013. Epub 2015 Jan 2. Review.

PMID:
25559199
48.

Toxicogenomics directory of chemically exposed human hepatocytes.

Grinberg M, Stöber RM, Edlund K, Rempel E, Godoy P, Reif R, Widera A, Madjar K, Schmidt-Heck W, Marchan R, Sachinidis A, Spitkovsky D, Hescheler J, Carmo H, Arbo MD, van de Water B, Wink S, Vinken M, Rogiers V, Escher S, Hardy B, Mitic D, Myatt G, Waldmann T, Mardinoglu A, Damm G, Seehofer D, Nüssler A, Weiss TS, Oberemm A, Lampen A, Schaap MM, Luijten M, van Steeg H, Thasler WE, Kleinjans JC, Stierum RH, Leist M, Rahnenführer J, Hengstler JG.

Arch Toxicol. 2014 Dec;88(12):2261-87. doi: 10.1007/s00204-014-1400-x. Epub 2014 Nov 16.

PMID:
25399406
49.

Defining the human adipose tissue proteome to reveal metabolic alterations in obesity.

Mardinoglu A, Kampf C, Asplund A, Fagerberg L, Hallström BM, Edlund K, Blüher M, Pontén F, Uhlen M, Nielsen J.

J Proteome Res. 2014 Nov 7;13(11):5106-19. doi: 10.1021/pr500586e. Epub 2014 Sep 25.

PMID:
25219818
50.

Defining the human gallbladder proteome by transcriptomics and affinity proteomics.

Kampf C, Mardinoglu A, Fagerberg L, Hallström BM, Danielsson A, Nielsen J, Pontén F, Uhlen M.

Proteomics. 2014 Nov;14(21-22):2498-507. doi: 10.1002/pmic.201400201. Epub 2014 Oct 9.

PMID:
25175928

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