.

Publications

KEY PUBLICATIONS

Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation
Jin, H., Zhang, C., Zwahlen M., von Feilitzen K., Karlsson M., Shi M., Yuan M., Song X., Li X., Yang H., Turkez H., Fagerberg L., Uhlén M., Mardinoglu A.
Nat Commun. 2023 Sep 5;14(1):5417.

Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19
Altay, O., M. Arif, X. Li, H. Yang, M. Aydin, G. Alkurt, W. Kim, D. Akyol, C. Zhang, G. Dinler-Doganay, H. Turkez, S. Shoaie, J. Nielsen, J. Boren, O. Olmuscelik, L. Doganay, M. Uhlen, and A. Mardinoglu
Adv Sci (Weinh), 8: e2101222.

Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction
Arif, M., M. Klevstig, R. Benfeitas, S. Doran, H. Turkez, M. Uhlen, M. Clausen, J. Wikstrom, D. Etal, C. Zhang, M. Levin, A. Mardinoglu, and J. Boren
Elife, 10.
Highlighted at eLife

Addressing the heterogeneity in liver diseases using biological networks
Lam, S., S. Doran, H. H. Yuksel, O. Altay, H. Turkez, J. Nielsen, J. Boren, M. Uhlen, and A. Mardinoglu
Brief Bioinform, 22: 1751-66.

iNetModels 2.0: an interactive visualization and database of multi-omics data
Arif, M., C. Zhang, X. Li, C. Gungor, B. Cakmak, M. Arslanturk, A. Tebani, B. Ozcan, O. Subas, W. Zhou, B. Piening, H. Turkez, L. Fagerberg, N. Price, L. Hood, M. Snyder, J. Nielsen, M. Uhlen, and A. Mardinoglu
Nucleic Acids Res, 49: W271-W76.

Multi-omics approaches for revealing the complexity of cardiovascular disease
Doran, S., M. Arif, S. Lam, A. Bayraktar, H. Turkez, M. Uhlen, J. Boren, and A. Mardinoglu
Brief Bioinform, 22.

Systems biology in hepatology: approaches and applications
Mardinoglu, A., J. Boren, U. Smith, M. Uhlen, and J. Nielsen
Nat Rev Gastroenterol Hepatol, 15: 365-77.

Broad Views of Non-alcoholic Fatty Liver Disease
Mardinoglu, A., M. Uhlen, and J. Boren
Cell Syst, 6(1):7-9.

TCSBN: a database of tissue and cancer specific biological networks
Lee, S., C. Zhang, M. Arif, Z. Liu, R. Benfeitas, G. Bidkhori, S. Deshmukh, M. Al Shobky, A. Lovric, J. Boren, J. Nielsen, M. Uhlen, and A. Mardinoglu
Nucleic Acids Res, 46: D595-D600.

An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans
A. Mardinoglu, Hao Wu, Elias Bjornson, Cheng Zhang, Antti Hakkarainen, Sari M. Rasanen, Sunjae lee, Rosellina M. Mancina, Matthias Bergentall, Kirsi H. Pietilainen, Sanni Soderlund, Niina Matikainen, Marcus Stahlman, Per-Olof Bergh, Martin Adiels, Brian D. Piening, Marit Graner, Nina Lundbom, Kevin J. Williams, Stefano Romeo, Jens Nielsen, Michael Snyder, Mathias Uhlen, Goran Bergstrom, Rosie Perkins, Hanns-Ulrich Marschall, Fredrik Backhed, Marja-Riitta Taskinen, Jan Boren
Cell Metabolism
Highlighted at SCIENCE TRANSLATIONAL MEDICINE

Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes
Gholamreza Bidkhori, Rui Benfeitas, Martina Klevstig, Cheng Zhang, Jens Nielsen, Mathias Uhlen, Jan Boren, Adil Mardinoglu
PNAS (Proceedings of the National Academy of Sciences)

A pathology atlas of the human cancer transcriptome
M. Uhlén, C. Zhang, S. Lee, E. Sjöstedt, L. Fagerberg, G. Bidkhori, R. Benfeitas, M. Arif, Z. Liu, F. Edfors, K. Sanli, K. von Feilitzen, P. Oksvold, E. Lundberg, S. Hober, P. Nilsson, J. Mattsson, J. M. Schwenk, H. Brunnström, B. Glimelius, T. Sjöblom, P. Edqvist, D. Djureinovic, P. Micke, C. Lindskog, A. Mardinoglu, F.Ponten
Science
Highlighted at NATURE

Network analyses identify liver-specific targets for treating liver diseases
S. Lee, C. Zhang, Z. Liu, M. Klevstig, B. Mukhopadhyay, M. Bergentall, R. Cinar, M. Ståhlman, N. Sikanic, J. K. Park, S. Deshmukh, A. M. Harzandi, T. Kuijpers, M. Grøtli, S. J. Elsässer, B. D. Piening, M. Snyder, U. Smith, J. Nielsen, F. Bäckhed, G. Kunos, M. Uhlen, J. Boren, A. Mardinoglu,
Molecular Systems Biology, 13:938

Plasma Mannose Levels Are Associated with Incident Type 2 Diabetes and Cardiovascular Disease
A Mardinoglu, A Stančáková, L A Lotta, J Kuusisto, J Boren, M Blüher, N J Wareham, E Ferrannini, …
Cell Metabolism 26 (2), 281-283

Personal model‐assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLD
A Mardinoglu, E Bjornson, C Zhang, M Klevstig, S Söderlund, M Ståhlman, …
Molecular systems biology 13 (3), 916
Highlighted at SCIENCE TRANSLATIONAL MEDICINE

Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance
S Lee, C Zhang, M Kilicarslan, BD Piening, E Björnson, BM Hallström, …
Cell Metabolism 24(1), 172-184
Highlighted at NATURE REVIEWS ENDOCRINOLOGY

ALL PUBLICATIONS

209) Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation
Jin, H., Zhang, C., Zwahlen M., von Feilitzen K., Karlsson M., Shi M., Yuan M., Song X., Li X., Yang H., Turkez H., Fagerberg L., Uhlén M., Mardinoglu A.
Nat Commun. 2023 Sep 5;14(1):5417.

208) Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection
Ambikan AT, Elaldi N, Svensson-Akusjärvi S, Bagci B, Pektas AN, Hewson R, Bagci G, Arasli M, Appelberg S, Mardinoglu A, Sood V, Végvári Á, Benfeitas R, Gupta S, Cetin I, Mirazimi A, Neogi U.
Proc Natl Acad Sci U S A. 2023 Sep 12;120(37):e2304722120.

207) Tissue pleiotropic effect of biotin and prebiotic supplementation in established obesity
Voland L, Yuan M, Lecoutre S, Debédat J, Pelloux V, Pradeau M, Coles E, Merabtene F, Zhang C, Mardinoglu A, Le Roy T, Soula H, Clément K.
Am J Physiol Endocrinol Metab. 2023 Aug 30.

206) Next generation pan-cancer blood proteome profiling using proximity extension assay
Álvez MB, Edfors F, von Feilitzen K, Zwahlen M, Mardinoglu A, Edqvist PH, Sjöblom T, Lundin E, Rameika N, Enblad G, Lindman H, Höglund M, Hesselager G, Stålberg K, Enblad M, Simonson OE, Häggman M, Axelsson T, Åberg M, Nordlund J, Zhong W, Karlsson M, Gyllensten U, Ponten F, Fagerberg L, Uhlén M.
Nat Commun. 2023 Jul 18;14(1):4308.

205) The acute effect of different NAD+ precursors included in the combined metabolic activators
Li X, Yang H, Jin H, Turkez H, Ozturk G, Doganay HL, Zhang C, Nielsen J, Uhlén M, Borén J, Mardinoglu A.
Free Radic Biol Med. 2023 Jun 2;205:77-89.

204) Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators
Yang H, Li X, Jin H, Turkez H, Ozturk G, Doganay HL, Zhang C, Nielsen J, Uhlén M, Borén J, Mardinoglu A.
Free Radic Biol Med. 2023 Aug 1;204:347-358.

203) Exploration of Novel Urolithin C Derivatives as Non-Competitive Inhibitors of Liver Pyruvate Kinase
Battisti UM, Monjas L, Akladios F, Matic J, Andresen E, Nagel CH, Hagkvist M, Håversen L, Kim W, Uhlen M, Borén J, Mardinoğlu A, Grøtli M.
Pharmaceuticals (Basel). 2023 Apr 28;16(5):668.

202) Drug repositioning targeting glutaminase reveals drug candidates for the treatment of Alzheimer’s disease patients
Bayraktar A, Li X, Kim W, Zhang C, Turkez H, Shoaie S, Mardinoglu A.
J Transl Med. 2023 May 20;21(1):332.

201) Revisiting the role of serine metabolism in hepatic lipogenesis
Yang H, Zhang C, Turkez H, Uhlen M, Boren J, Mardinoglu A.
Nat Metab. 2023 May;5(5):760-761.

200) Normalization of hepatic ChREBP activity does not protect against liver disease progression in a mouse model for Glycogen Storage Disease type Ia
Rutten MGS, Lei Y, Hoogerland JH, Bloks VW, Yang H, Bos T, Krishnamurthy KA, Bleeker A, Koster MH, Thomas RE, Wolters JC, van den Bos H, Mithieux G, Rajas F, Mardinoglu A, Spierings DCJ, de Bruin A, van de Sluis B, Oosterveer MH.
Cancer Metab. 2023 Apr 21;11(1):5.

199) Costunolide and Parthenolide Ameliorate MPP+ Induced Apoptosis in the Cellular Parkinson’s Disease Model
Arslan ME, Türkez H, Sevim Y, Selvitopi H, Kadi A, Öner S, Mardinoğlu A.
Cells. 2023 Mar 24;12(7):992.

198) Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma
Graves OK, Kim W, Özcan M, Ashraf S, Turkez H, Yuan M, Zhang C, Mardinoglu A, Li X.
Biomed Pharmacother. 2023 Mar 10;161:114486.

197) Cardiomyocyte-specific PCSK9 deficiency compromises mitochondrial bioenergetics and heart function
Laudette M, Lindbom M, Arif M, Cinato M, Ruiz M, Doran S, Miljanovic A, Rutberg M, Andersson L, Klevstig M, Henricsson M, Bergh PO, Bollano E, Aung N, Smith JG, Pilon M, Hyötyläinen T, Orešič M, Perkins R, Mardinoglu A, Levin MC, Borén J.
Cardiovasc Res. 2023 Mar 6:cvad041.

196) Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection
Mikaeloff F, Gelpi M, Benfeitas R, Knudsen AD, Vestad B, Høgh J, Hov JR, Benfield T, Murray D, Giske CG, Mardinoglu A, Trøseid M, Nielsen SD, Neogi U.
Elife. 2023 Feb 16;12:e82785.

195) Ellagic Acid and Its Metabolites as Potent and Selective Allosteric Inhibitors of Liver Pyruvate Kinase
Battisti UM, Gao C, Akladios F, Kim W, Yang H, Bayram C, Bolat I, Kiliclioglu M, Yuksel N, Tozlu OO, Zhang C, Sebhaoui J, Iqbal S, Shoaie S, Hacimuftuoglu A, Yildirim S, Turkez H, Uhlen M, Boren J, Mardinoglu A, Grøtli M.
Nutrients. 2023 Jan 22;15(3):577.

194) Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial
Yulug B, Altay O, Li X, Hanoglu L, Cankaya S, Lam S, Velioglu HA, Yang H, Coskun E, Idil E, Nogaylar R, Ozsimsek A, Bayram C, Bolat I, Oner S, Tozlu OO, Arslan ME, Hacimuftuoglu A, Yildirim S, Arif M, Shoaie S, Zhang C, Nielsen J, Turkez H, Borén J, Uhlén M, Mardinoglu A.
Transl Neurodegener. 2023 Jan 26;12(1):4.

193) Lipoic Acid Conjugated Boron Hybrids Enhance Wound Healing and Antimicrobial Processes
Türkez H, Yıldırım ÖÇ, Öner S, Kadı A, Mete A, Arslan ME, Şahin İO, Yapça ÖE, Mardinoğlu A.
Pharmaceutics. 2022 Dec 31;15(1):149.

192) Combined metabolic activators improve metabolic functions in the animal models of neurodegenerative diseases
Turkez H, Altay O, Yildirim S, Li X, Yang H, Bayram C, Bolat I, Oner S, Tozlu OO, Arslan ME, Arif M, Yulug B, Hanoglu L, Cankaya S, Lam S, Velioglu HA, Coskun E, Idil E, Nogaylar R, Ozsimsek A, Hacimuftuoglu A, Shoaie S, Zhang C, Nielsen J, Borén J, Uhlén M, Mardinoglu A.
Life Sci. 2023 Feb 1;314:121325.

191) In Vitro Transcriptome Analysis of Cobalt Boride Nanoparticles on Human Pulmonary Alveolar Cells
Arslan ME, Tatar A, Yıldırım ÖÇ, Şahin İO, Ozdemir O, Sonmez E, Hacımuftuoglu A, Acikyildiz M, Geyikoğlu F, Mardinoğlu A, Türkez H.
Materials (Basel). 2022 Dec 6;15(23):8683.

190) Toxicity of Glycyl-l-Prolyl-l-Glutamate Pseudotripeptides: Cytotoxic, Oxidative, Genotoxic, and Embryotoxic Perspectives
Turkez H, Ozdemir Tozlu O, Tatar A, Arslan ME, Cadirci K, Marinelli L, Yapca OE, Cacciatore I, Di Stefano A, Mardinoglu A.
J Toxicol. 2022 Nov 19;2022:3775194.

189) Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase
Battisti UM, Gao C, Nilsson O, Akladios F, Lulla A, Bogucka A, Nain-Perez A, Håversen L, Kim W, Boren J, Hyvönen M, Uhlen M, Mardinoglu A, Grøtli M.
Chembiochem. 2023 Jan 3;24(1):e202200339.

188) Editorial: Application of systems biology in molecular characterization and diagnosis of cancer, Volume II
Wei Y, Zhang C, Mardinoglu A, Zhang P.
Front Mol Biosci. 2022 Nov 25;9:1089463.

187) In Vitro and In Vivo Neuroprotective Effects of Sarcosine
Tanas A, Tozlu ÖÖ, Gezmiş T, Hacimüftüoğlu A, Abd El-Aty AM, Ceylan O, Mardinoğlu A, Türkez H.
Biomed Res Int. 2022 Oct 15;2022:5467498.

186) Assessment of the neuroprotective potential of d-cycloserine and l-serine in aluminum chloride-induced experimental models of Alzheimer’s disease: In vivo and in vitro studies
Tozlu, Ö. Ö., Türkez, H., Okkay, U., Ceylan, O., Bayram, C., Hacımüftüoğlu, A., & Mardinoğlu, A.
Front Nutr. 2022 Sep 8;9:981889.

185) Boron Compounds Exhibit Protective Effects against Aluminum-Induced Neurotoxicity and Genotoxicity: In Vitro and In Vivo Study
Turkez, H., Yildirim, S., Sahin, E., Arslan, M. E., Emsen, B., Tozlu, O. O., Alak, G., Ucar, A., Tatar, A., Hacimuftuoglu, A., Keles, M. S., Geyikoglu, F., Atamanalp, M., Saruhan, F. and Mardinoglu, A.
Toxics. 2022 Jul 28;10(8).

184) Ameliorative Effects by Hexagonal Boron Nitride Nanoparticles against Beta Amyloid Induced Neurotoxicity
Aydin, N., Turkez, H., Tozlu, O. O., Arslan, M. E., Yavuz, M., Sonmez, E., Ozpolat, O. F., Cacciatore, I., Di Stefano, A. and Mardinoglu, A.
Nanomaterials (Basel). 2022 Aug 5;12(15).

183) Boron Nitride Nanoparticles Loaded with a Boron-Based Hybrid as a Promising Drug Carrier System for Alzheimer’s Disease Treatment
Yildirim, O. C., Arslan, M. E., Oner, S., Cacciatore, I., Di Stefano, A., Mardinoglu, A. and Turkez, H.
Int J Mol Sci. 2022 Jul 26;23(15).

182) Molecular Genetics and Cytotoxic Responses to Titanium Diboride and Zinc Borate Nanoparticles on Cultured Human Primary Alveolar Epithelial Cells
Turkez, H., Arslan, M. E., Tatar, A., Ozdemir, O., Sonmez, E., Cadirci, K., Hacimuftuoglu, A., Ceylan, B., Acikyildiz, M., Kahraman, C. Y., Geyikoglu, F., Tatar, A. and Mardinoglu, A.
Materials (Basel). 2022 Mar 22;15(7).

181) A Gene Co-Expression Network-Based Drug Repositioning Approach Identifies Candidates for Treatment of Hepatocellular Carcinoma
Yuan, M., Shong, K., Li, X., Ashraf, S., Shi, M., Kim, W., Nielsen, J., Turkez, H., Shoaie, S., Uhlen, M., Zhang, C. and Mardinoglu, A.
Cancers (Basel). 2022 Mar 19;14(6).

180) Development of l-Dopa-containing diketopiperazines as blood-brain barrier shuttle
Cornacchia, C., Marinelli, L., Di Rienzo, A., Dimmito, M. P., Serra, F., Di Biase, G., De Filippis, B., Turkez, H., Mardinoglu, A., Bellezza, I., Di Stefano, A. and Cacciatore, I.
Eur J Med Chem. 2022 Sep 8;243:114746.

179) BMP4 and Gremlin 1 regulate hepatic cell senescence during clinical progression of NAFLD/NASH
Baboota, R. K., Rawshani, A., Bonnet, L., Li, X., Yang, H., Mardinoglu, A., Tchkonia, T., Kirkland, J. L., Hoffmann, A., Dietrich, A., Boucher, J., Bluher, M. and Smith, U.
Nat Metab. 2022 Aug;4(8):1007-1021.

178) Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning
Zhang, C., Shi, M., Kim, W., Arif, M., Klevstig, M., Li, X., Yang, H., Bayram, C., Bolat, I., Tozlu, O. O., Hacimuftuoglu, A., Yildirim, S., Sebhaoui, J., Iqbal, S., Wei, Y., Shi, X., Nielsen, J., Turkez, H., Uhlen, M., Boren, J. and Mardinoglu, A.
EBioMedicine. 2022 Sep;83:104214.

177) Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity
Ambikan, A. T., Yang, H., Krishnan, S., Svensson Akusjarvi, S., Gupta, S., Lourda, M., Sperk, M., Arif, M., Zhang, C., Nordqvist, H., Ponnan, S. M., Sonnerborg, A., Treutiger, C. J., O’Mahony, L., Mardinoglu, A., Benfeitas, R. and Neogi, U.
Cell Syst. 2022 Aug 17;13(8):665-681.e4.

176) Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
Mahdessian, D., Cesnik, A. J., Gnann, C., Danielsson, F., Stenstrom, L., Arif, M., Zhang, C., Le, T., Johansson, F., Schutten, R., Backstrom, A., Axelsson, U., Thul, P., Cho, N. H., Carja, O., Uhlen, M., Mardinoglu, A., Stadler, C., Lindskog, C., Ayoglu, B., Leonetti, M. D., Ponten, F., Sullivan, D. P. and Lundberg, E.
Nature. 2022 Aug;608(7924):E32.

175) Chronic hyperinsulinemia promotes human hepatocyte senescence
Baboota, R. K., Spinelli, R., Erlandsson, M. C., Brandao, B. B., Lino, M., Yang, H., Mardinoglu, A., Bokarewa, M. I., Boucher, J., Kahn, C. R. and Smith, U.
Mol Metab. 2022 Oct;64:101558.

174) MRI characterization of skeletal muscle size and fatty infiltration in long-term trained and untrained inliiduals
Emanuelsson, E. B., Berry, D. B., Reitzner, S. M., Arif, M., Mardinoglu, A., Gustafsson, T., Ward, S. R., Sundberg, C. J. and Chapman, M. A.
Physiol Rep. 2022 Jul;10(14):e15398.

173) Repositioning of Anti-Inflammatory Drugs for the Treatment of Cervical Cancer Sub-Types
Kori, M., Arga, K. Y., Mardinoglu, A. and Turanli, B.
Front Pharmacol. 2022 Jun 13;13:884548.

172) 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. and Shoaie, S.
iScience. 2022 Jun 2;25(7):104513.

171) Machine Learning Analysis Reveals Biomarkers for the Detection of Neurological Diseases
Lam, S., Arif, M., Song, X., Uhlen, M. and Mardinoglu, A.
Front Mol Neurosci. 2022 May 31;15:889728.

170) Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation
Liu, Z., Xu, J., Que, S., Geng, L., Zhou, L., Mardinoglu, A. and Zheng, S.
J Clin Transl Hepatol. 2022 Apr 28;10(2):363-373.

169) Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach
Li, X., Shong, K., Kim, W., Yuan, M., Yang, H., Sato, Y., Kume, H., Ogawa, S., Turkez, H., Shoaie, S., Boren, J., Nielsen, J., Uhlen, M., Zhang, C. and Mardinoglu, A.
EBioMedicine. 2022 Apr;78:103963.

168) Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase
Nain-Perez, A., Foller Fuchtbauer, A., Haversen, L., Lulla, A., Gao, C., Matic, J., Monjas, L., Rodriguez, A., Brear, P., Kim, W., Hyvonen, M., Boren, J., Mardinoglu, A., Uhlen, M. and Grotli, M.
Eur J Med Chem. 2022 Apr 15;234:114270.

167) Stratification of the Gut Microbiota Composition Landscape across the Alzheimer’s Disease Continuum in a Turkish Cohort
Yildirim, S., Nalbantoglu, O. U., Bayraktar, A., Ercan, F. B., Gundogdu, A., Velioglu, H. A., Gol, M. F., Soylu, A. E., Koc, F., Gulpinar, E. A., Kadak, K. S., Arikan, M., Mardinoglu, A., Kocak, M., Koseoglu, E. and Hanoglu, L.
mSystems. 2022 Feb 22;7(1):e0000422.

166) Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis
Zeybel, M., Arif, M., Li, X., Altay, O., Yang, H., Shi, M., Akyildiz, M., Saglam, B., Gonenli, M. G., Yigit, B., Ulukan, B., Ural, D., Shoaie, S., Turkez, H., Nielsen, J., Zhang, C., Uhlen, M., Boren, J. and Mardinoglu, A.
Adv Sci (Weinh). 2022 Apr;9(11):e2104373.

165) Correction to: Toxicogenomics directory of chemically exposed human hepatocytes
Grinberg, M., Stober, R. M., 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, M. D., van de Water, B., Wink, S., Vinken, M., Rogiers, V., Escher, S., Hardy, B., Mitic, D., Apic, G., Myatt, G., Waldmann, T., Mardinoglu, A., Damm, G., Seehofer, D., Nussler, A., Weiss, T. S., Oberemm, A., Lampen, A., Schaap, M. M., Luijten, M., van Steeg, H., Thasler, W. E., Kleinjans, J. C. S., Stierum, R. H., Leist, M., Rahnenfuhrer, J. and Hengstler, J. G.
Arch Toxicol. 2022 Mar;96(3):945-946.

164) Genome-wide annotation of protein-coding genes in pig
Karlsson, M., Sjostedt, E., Oksvold, P., Sivertsson, A., Huang, J., Alvez, M. B., Arif, M., Li, X., Lin, L., Yu, J., Ma, T., Xu, F., Han, P., Jiang, H., Mardinoglu, A., Zhang, C., von Feilitzen, K., Xu, X., Wang, J., Yang, H., Bolund, L., Zhong, W., Fagerberg, L., Lindskog, C., Ponten, F., Mulder, J., Luo, Y. and Uhlen, M.
BMC Biol. 2022 Jan 25;20(1):25.

163) Improvement of the performance of anticancer peptides using a drug repositioning pipeline
Mohammadi, E., Tahmoorespur, M., Benfeitas, R., Altay, O., Javadmanesh, A., Lam, S., Mardinoglu, A. and Sekhavati, M. H.
Biotechnol J. 2022 Jan;17(1):e2100417.

162) Boron-based hybrids as novel scaffolds for the development of drugs with neuroprotective properties
Cacciatore, I., H. Turkez, A. Di Rienzo, M. Ciulla, A. Mardinoglu, and A. Di Stefano
RSC Med Chem 12, no. 11 (Nov 17 2021): 1944-49.

161) Combined Metabolic Activators Therapy Ameliorates Liver Fat in Nonalcoholic Fatty Liver Disease Patients
Zeybel, M., O. Altay, M. Arif, X. Li, H. Yang, C. Fredolini, M. Akyildiz, B. Saglam, M. G. Gonenli, D. Ural, W. Kim, J. M. Schwenk, C. Zhang, S. Shoaie, J. Nielsen, M. Uhlen, J. Boren, and A. Mardinoglu
Mol Syst Biol 17, no. 10 (Oct 2021): e10459.

160) Revealing the Molecular Mechanisms of Alzheimer’s Disease Based on Network Analysis
Bayraktar, A., S. Lam, O. Altay, X. Li, M. Yuan, C. Zhang, M. Arif, H. Turkez, M. Uhlen, S. Shoaie, and A. Mardinoglu
Int J Mol Sci 22, no. 21 (Oct 26 2021).

159) The Assessment of Selected Mirna Profile in Familial Mediterranean Fever
Kahraman, C. Y., M. E. Egin, A. Tatar, H. Turkez, and A. Mardinoglu
Biomed Res Int 2021 (2021): 6495700.

158) Systems Biology Approaches to Decipher the Underlying Molecular Mechanisms of Glioblastoma Multiforme
Kaynar, A., O. Altay, X. Li, C. Zhang, H. Turkez, M. Uhlen, S. Shoaie, and A. Mardinoglu
Int J Mol Sci 22, no. 24 (Dec 8 2021).

157) Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer’s and Parkinson’s Diseases
Lam, S., N. Hartmann, R. Benfeitas, C. Zhang, M. Arif, H. Turkez, M. Uhlen, C. Englert, R. Knight, and A. Mardinoglu
Biomedicines 9, no. 10 (Sep 24 2021).

156) Therapeutic Potential of Ferulic Acid in Alzheimer’s Disease
Turkez, H., M. E. Arslan, J. N. Barboza, C. Y. Kahraman, D. P. de Sousa, and A. Mardinoglu
Curr Drug Deliv (Dec 28 2021).

155) In Vitro Transcriptome Response to Propolis in Differentiated Sh-Sy5y Neurons
Turkez, H., M. E. Arslan, A. Yilmaz, F. Doru, O. Caglar, E. Arslan, A. Tatar, A. Hacimuftuoglu, A. M. Abd El-Aty, and A. Mardinoglu
J Food Biochem 45, no. 12 (Dec 2021): e13990.

154) Next Generation Plasma Proteome Profiling of Covid-19 Patients with Mild to Moderate Symptoms
Zhong, W., O. Altay, M. Arif, F. Edfors, L. Doganay, A. Mardinoglu, M. Uhlen, and L. Fagerberg
EBioMedicine 74 (Dec 2021): 103723.

153) A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic fatty liver disease
Yang H, Arif M, Yuan M, Li X, Shong K, Türkez H, Nielsen J, Uhlén M, Borén J, Zhang C, Mardinoglu A.
iScience. 103222.

152) Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet
Yang H, Mayneris-Perxachs J, Boqué N, del Bas JM, Arola L, Yuan M, Turkez H, Uhlen M, Boren J, Zhang C, Mardinoglu A, Caimari, A.
Biomedicines, 9(10), 1440

151) Combined Metabolic Activators Improve Cognitive Functions without Altering Motor Scores in Parkinson’s Disease
Yulug, Burak, Ozlem Altay, Xiangyu Li, Lutfu Hanoglu, Seyda Cankaya, Simon Lam, Hong Yang, Ebru Coskun, Ezgi İdil, Rahim Nogaylar, Ahmet Hacımuftuoglu, Muhammad. Arif, Saeed Shoaie, Cheng Zhang, Jens Nielsen, Hasan Turkez, Jan Borén, Mathias Uhlén, and Adil Mardinoglu.
medRxiv

150) Combined Metabolic Activators Improves Cognitive Functions in Alzheimer’s Disease
Yulug, Burak, Ozlem Altay, Xiangyu Li, Lutfu Hanoglu, Seyda Cankaya, Simon Lam, Hong Yang, Ebru Coskun, Ezgi İdil, Rahim Nogaylar, Cemil Bayram, Ismail Bolat, Sena Oner, Ozlem Ozdemir Tozlu, Mehmet Enes Arslan, Ahmet Hacımuftuoglu, Serkan Yildirim, Muhammad. Arif, Saeed Shoaie, Cheng Zhang, Jens Nielsen, Hasan Turkez, Jan Borén, Mathias Uhlén, and Adil Mardinoglu.
Preprint

149) Systems biology based drug repositioning for development of cancer therapy
Turanli, B., O. Altay, J. Boren, H. Turkez, J. Nielsen, M. Uhlen, K. Y. Arga, and A. Mardinoglu
Semin Cancer Biol, 68: 47-58.

148) A single-cell type transcriptomics map of human tissues
Karlsson, M., C. Zhang, L. Mear, W. Zhong, A. Digre, B. Katona, E. Sjostedt, L. Butler, J. Odeberg, P. Dusart, F. Edfors, P. Oksvold, K. von Feilitzen, M. Zwahlen, M. Arif, O. Altay, X. Li, M. Ozcan, A. Mardinoglu, L. Fagerberg, J. Mulder, Y. Luo, F. Ponten, M. Uhlen, and C. Lindskog
Sci Adv, 7.

147) Acute kidney injury leading to CKD is associated with a persistence of metabolic dysfunction and hypertriglyceridemia
Harzandi, A., S. Lee, G. Bidkhori, S. Saha, B. M. Hendry, A. Mardinoglu, S. Shoaie, and C. C. Sharpe
iScience, 24: 102046.

146) Addressing the heterogeneity in liver diseases using biological networks
Lam, S., S. Doran, H. H. Yuksel, O. Altay, H. Turkez, J. Nielsen, J. Boren, M. Uhlen, and A. Mardinoglu
Brief Bioinform, 22: 1751-66.

145) Anticancer effects of novel NSAIDs derivatives on cultured human glioblastoma cells
Ozdemir, O., L. Marinelli, I. Cacciatore, M. Ciulla, B. Emsen, A. Di Stefano, A. Mardinoglu, and H. Turkez
Z Naturforsch C J Biosci, 76: 329-35.

144) Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19
Altay, O., M. Arif, X. Li, H. Yang, M. Aydin, G. Alkurt, W. Kim, D. Akyol, C. Zhang, G. Dinler-Doganay, H. Turkez, S. Shoaie, J. Nielsen, J. Boren, O. Olmuscelik, L. Doganay, M. Uhlen, and A. Mardinoglu
Adv Sci (Weinh), 8: e2101222.

143) Discovery of Functional Alternatively Spliced PKM Transcripts in Human Cancers
Li, X., W. Kim, M. Arif, C. Gao, A. Hober, D. Kotol, L. Strandberg, B. Forsstrom, A. Sivertsson, P. Oksvold, H. Turkez, M. Grotli, Y. Sato, H. Kume, S. Ogawa, J. Boren, J. Nielsen, M. Uhlen, C. Zhang, and A. Mardinoglu
Cancers (Basel), 13.

142) Editorial: Application of Systems Biology in Molecular Characterization and Diagnosis of Cancer
Zhang, C., Y. Wei, A. Mardinoglu, and P. Zhang
Front Mol Biosci, 8: 668146.

141) Glucosylceramide synthase deficiency in the heart compromises beta1-adrenergic receptor trafficking
Andersson, L., M. Cinato, I. Mardani, A. Miljanovic, M. Arif, A. Koh, M. Lindbom, M. Laudette, E. Bollano, E. Omerovic, M. Klevstig, M. Henricsson, P. Fogelstrand, K. Sward, M. Ekstrand, M. Levin, J. Wikstrom, S. Doran, T. Hyotylainen, L. Sinisalu, M. Oresic, A. Tivesten, M. Adiels, M. O. Bergo, R. Proia, A. Mardinoglu, A. Jeppsson, J. Boren, and M. C. Levin
Eur Heart J.

140) Glycyl-L-Prolyl-L-Glutamate Pseudotripeptides for Treatment of Alzheimer’s Disease
Turkez, H., I. Cacciatore, L. Marinelli, E. Fornasari, M. E. Aslan, K. Cadirci, C. Y. Kahraman, O. Caglar, A. Tatar, G. Di Biase, A. Hacimuftuoglu, A. Di Stefano, and A. Mardinoglu
Biomolecules, 11.

139) In vitro neuroprotective effects of farnesene sesquiterpene on alzheimer’s disease model of differentiated neuroblastoma cell line
Arslan, M. E., H. Turkez, and A. Mardinoglu
Int J Neurosci, 131: 745-54.

138) iNetModels 2.0: an interactive visualization and database of multi-omics data
Arif, M., C. Zhang, X. Li, C. Gungor, B. Cakmak, M. Arslanturk, A. Tebani, B. Ozcan, O. Subas, W. Zhou, B. Piening, H. Turkez, L. Fagerberg, N. Price, L. Hood, M. Snyder, J. Nielsen, M. Uhlen, and A. Mardinoglu
Nucleic Acids Res, 49: W271-W76.

137) Informing Pharmacokinetic Models With Physiological Data: Oral Population Modeling of L-Serine in Humans
Bosley, J. R., E. Bjornson, C. Zhang, H. Turkez, J. Nielsen, M. Uhlen, J. Boren, and A. Mardinoglu
Front Pharmacol, 12: 643179.

136) Integrative study of diet-induced mouse models of NAFLD identifies PPARalpha as a sexually dimorphic drug target
Smati, S., A. Polizzi, A. Fougerat, S. Ellero-Simatos, Y. Blum, Y. Lippi, M. Regnier, A. Laroyenne, M. Huillet, M. Arif, C. Zhang, F. Lasserre, A. Marrot, T. Al Saati, J. Wan, C. Sommer, C. Naylies, A. Batut, C. Lukowicz, T. Fougeray, B. Tramunt, P. Dubot, L. Smith, J. Bertrand-Michel, N. Hennuyer, J. P. Pradere, B. Staels, R. Burcelin, F. Lenfant, J. F. Arnal, T. Levade, L. Gamet-Payrastre, S. Lagarrigue, N. Loiseau, S. Lotersztajn, C. Postic, W. Wahli, C. Bureau, M. Guillaume, A. Mardinoglu, A. Montagner, P. Gourdy, and H. Guillou
Gut, gutjnl-2020-323323.

135) Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction
Arif, M., M. Klevstig, R. Benfeitas, S. Doran, H. Turkez, M. Uhlen, M. Clausen, J. Wikstrom, D. Etal, C. Zhang, M. Levin, A. Mardinoglu, and J. Boren
Elife, 10.

134) Lysine demethylase LSD1 delivered via small extracellular vesicles promotes gastric cancer cell stemness
Zhao, L. J., Y. Y. Li, Y. T. Zhang, Q. Q. Fan, H. M. Ren, C. Zhang, A. Mardinoglu, W. C. Chen, J. R. Pang, D. D. Shen, J. W. Wang, L. F. Zhao, J. Y. Zhang, Z. Y. Wang, Y. C. Zheng, and H. M. Liu
EMBO Rep, 22: e50922.

133) Molecular pathways behind acquired obesity: Adipose tissue and skeletal muscle multiomics in monozygotic twin pairs discordant for BMI
van der Kolk, B. W., S. Saari, A. Lovric, M. Arif, M. Alvarez, A. Ko, Z. Miao, N. Sahebekhtiari, M. Muniandy, S. Heinonen, A. Oghabian, R. Jokinen, S. Jukarainen, A. Hakkarainen, J. Lundbom, J. Kuula, P. H. Groop, T. Tukiainen, N. Lundbom, A. Rissanen, J. Kaprio, E. G. Williams, N. Zamboni, A. Mardinoglu, P. Pajukanta, and K. H. Pietilainen
Cell Rep Med, 2: 100226.

132) Multi-omics approaches for revealing the complexity of cardiovascular disease
Doran, S., M. Arif, S. Lam, A. Bayraktar, H. Turkez, M. Uhlen, J. Boren, and A. Mardinoglu
Brief Bioinform, 22.

131) Potential Anticancer Effect of Carvacrol Codrugs on Human Glioblastoma Cells
Yazici, A., L. Marinelli, I. Cacciatore, B. Emsen, P. Eusepi, G. Di Biase, A. Di Stefano, A. Mardinoglu, and H. Turkez
Curr Drug Deliv, 18: 350-56.

130) Promising potential of boron compounds against Glioblastoma: In Vitro antioxidant, anti-inflammatory and anticancer studies
Turkez, H., M. E. Arslan, A. Tatar, and A. Mardinoglu
Neurochem Int, 149: 105137.

129) Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling
Altay, O., C. Zhang, H. Turkez, J. Nielsen, M. Uhlen, and A. Mardinoglu
Metabolites, 11.

128) Safety and Efficacy Assessments to Take Antioxidants in Glioblastoma Therapy: From In Vitro Experiences to Animal and Clinical Studies
Turkez, H., O. O. Tozlu, M. E. Arslan, and A. Mardinoglu
Neurochem Int, 150: 105168.

127) Safety Assessments of Nickel Boride Nanoparticles on the Human Pulmonary Alveolar Cells by Using Cell Viability and Gene Expression Analyses
Turkez, H., M. E. Arslan, E. Sonmez, A. Tatar, F. Geyikoglu, M. Acikyildiz, and A. Mardinoglu
Biol Trace Elem Res, 199: 2602-11.

126) Seroprevalence of coronavirus disease 2019 (COVID-19) among health care workers from three pandemic hospitals of Turkey
Alkurt, G., A. Murt, Z. Aydin, O. Tatli, N. B. Agaoglu, A. Irvem, M. Aydin, R. Karaali, M. Gunes, B. Yesilyurt, H. Turkez, A. Mardinoglu, M. Doganay, F. Basinoglu, N. Seyahi, G. Dinler Doganay, and H. L. Doganay
PLoS One, 16: e0247865.

125) Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
Mahdessian, D., A. J. Cesnik, C. Gnann, F. Danielsson, L. Stenstrom, M. Arif, C. Zhang, T. Le, F. Johansson, R. Shutten, A. Backstrom, U. Axelsson, P. Thul, N. H. Cho, O. Carja, M. Uhlen, A. Mardinoglu, C. Stadler, C. Lindskog, B. Ayoglu, M. D. Leonetti, F. Ponten, D. P. Sullivan, and E. Lundberg
Nature, 590: 649-54.

124) Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning
Li, X., W. Kim, K. Juszczak, M. Arif, Y. Sato, H. Kume, S. Ogawa, H. Turkez, J. Boren, J. Nielsen, M. Uhlen, C. Zhang, and A. Mardinoglu
iScience, 24: 102722.

123) Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s disease
Rosario, D., G. Bidkhori, S. Lee, J. Bedarf, F. Hildebrand, E. Le Chatelier, M. Uhlen, S. D. Ehrlich, G. Proctor, U. Wullner, A. Mardinoglu, and S. Shoaie
Cell Rep, 34: 108807.

122) Targeted Gene Candidates for Treatment and Early Diagnosis of Age-Related Macular Degeneration
Cinici, E., O. Caglar, M. E. Arslan, N. Dilekmen, B. Utlu, A. Mardinoglu, and H. Turkez
Biomed Res Int, 2021: 6620900.

121) A Resilient Health System in Response to Coronavirus Disease 2019: Experiences of Turkey
Keskinkilic, B., I. Shaikh, A. Tekin, P. Ursu, A. Mardinoglu, and E. A. Mese
Front Public Health, 8: 577021.

120) A systems biology approach for studying neurodegenerative diseases
Lam, S., A. Bayraktar, C. Zhang, H. Turkez, J. Nielsen, J. Boren, S. Shoaie, M. Uhlen, and A. Mardinoglu
Drug Discov Today, 25: 1146-59.

119) Adipose tissue morphology, imaging and metabolomics predicting cardiometabolic risk and family history of type 2 diabetes in non-obese men
Rawshani, A., B. Eliasson, A. Rawshani, J. Henninger, A. Mardinoglu, A. Carlsson, M. Sohlin, M. Ljungberg, A. Hammarstedt, A. Rosengren, and U. Smith
Sci Rep, 10: 9973.

118) An adipocyte-specific defect in oxidative phosphorylation increases systemic energy expenditure and protects against diet-induced obesity in mouse models
Choi, M. J., S. B. Jung, S. E. Lee, S. G. Kang, J. H. Lee, M. J. Ryu, H. K. Chung, J. Y. Chang, Y. K. Kim, H. J. Hong, H. Kim, H. J. Kim, C. H. Lee, A. Mardinoglu, H. S. Yi, and M. Shong
Diabetologia, 63: 837-52.

117) An atlas of human metabolism
Robinson, J. L., P. Kocabas, H. Wang, P. E. Cholley, D. Cook, A. Nilsson, M. Anton, R. Ferreira, I. Domenzain, V. Billa, A. Limeta, A. Hedin, J. Gustafsson, E. J. Kerkhoven, L. T. Svensson, B. O. Palsson, A. Mardinoglu, L. Hansson, M. Uhlen, and J. Nielsen
Sci Signal, 13.

116) An atlas of the protein-coding genes in the human, pig, and mouse brain
Sjostedt, E., W. Zhong, L. Fagerberg, M. Karlsson, N. Mitsios, C. Adori, P. Oksvold, F. Edfors, A. Limiszewska, F. Hikmet, J. Huang, Y. Du, L. Lin, Z. Dong, L. Yang, X. Liu, H. Jiang, X. Xu, J. Wang, H. Yang, L. Bolund, A. Mardinoglu, C. Zhang, K. von Feilitzen, C. Lindskog, F. Ponten, Y. Luo, T. Hokfelt, M. Uhlen, and J. Mulder
Science, 367.

115) Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning
Mohammadi, E., R. Benfeitas, H. Turkez, J. Boren, J. Nielsen, M. Uhlen, and A. Mardinoglu
Cancers (Basel), 12.

114) Boosting Natural Killer Cell-Mediated Targeting of Sarcoma Through DM-1 and NKG2D
Sayitoglu, E. C., A. M. Georgoudaki, M. Chrobok, D. Ozkazanc, B. J. Josey, M. Arif, K. Kusser, M. Hartman, T. M. Chinn, R. Potens, C. Pamukcu, R. Krueger, C. Zhang, A. Mardinoglu, E. Alici, H. T. Temple, T. Sutlu, and A. D. Duru
Front Immunol, 11: 40.

113) Classification of clear cell renal cell carcinoma based on PKM alternative splicing
Li, X., B. Turanli, K. Juszczak, W. Kim, M. Arif, Y. Sato, S. Ogawa, H. Turkez, J. Nielsen, J. Boren, M. Uhlen, C. Zhang, and A. Mardinoglu
Heliyon, 6: e03440.

112) Current Status of COVID-19 Therapies and Drug Repositioning Applications
Altay, O., E. Mohammadi, S. Lam, H. Turkez, J. Boren, J. Nielsen, M. Uhlen, and A. Mardinoglu
iScience, 23: 101303.

111) Drug Repositioning for P-Glycoprotein Mediated Co-Expression Networks in Colorectal Cancer
Beklen, H., G. Gulfidan, K. Y. Arga, A. Mardinoglu, and B. Turanli
Front Oncol, 10: 1273.

110) Editorial: Redox Homeostasis and Cancer
Sinha, M., A. Mardinoglu, J. Ghose, and K. Singh
Oxid Med Cell Longev, 2020: 5487381.

109) Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development
Larsson, I., M. Uhlen, C. Zhang, and A. Mardinoglu
Front Genet, 11: 381.

108) Histidyl-Proline Diketopiperazine Isomers as Multipotent Anti-Alzheimer Drug Candidates
Turkez, H., I. Cacciatore, M. E. Arslan, E. Fornasari, L. Marinelli, A. Di Stefano, and A. Mardinoglu
Biomolecules, 10.

107) Improvement in the Current Therapies for Hepatocellular Carcinoma Using a Systems Medicine Approach
Ozcan, M., O. Altay, S. Lam, H. Turkez, Y. Aksoy, J. Nielsen, M. Uhlen, J. Boren, and A. Mardinoglu
Adv Biosyst, 4: e2000030.

106) Integration of molecular profiles in a longitudinal wellness profiling cohort
Tebani, A., A. Gummesson, W. Zhong, I. S. Koistinen, T. Lakshmikanth, L. M. Olsson, F. Boulund, M. Neiman, H. Stenlund, C. Hellstrom, M. J. Karlsson, M. Arif, T. Dodig-Crnkovic, A. Mardinoglu, S. Lee, C. Zhang, Y. Chen, A. Olin, J. Mikes, H. Danielsson, K. von Feilitzen, P. A. Jansson, O. Angeras, M. Huss, S. Kjellqvist, J. Odeberg, F. Edfors, V. Tremaroli, B. Forsstrom, J. M. Schwenk, P. Nilsson, T. Moritz, F. Backhed, L. Engstrand, P. Brodin, G. Bergstrom, M. Uhlen, and L. Fagerberg
Nat Commun, 11: 4487.

105) Low Shear Stress Increases Recombinant Protein Production and High Shear Stress Increases Apoptosis in Human Cells
Zhan, C., G. Bidkhori, H. Schwarz, M. Malm, A. Mebrahtu, R. Field, C. Sellick, D. Hatton, P. Varley, A. Mardinoglu, J. Rockberg, and V. Chotteau
iScience, 23: 101653.

104) MEMOTE for standardized genome-scale metabolic model testing
Lieven, C., M. E. Beber, B. G. Olivier, F. T. Bergmann, M. Ataman, P. Babaei, J. A. Bartell, L. M. Blank, S. Chauhan, K. Correia, C. Diener, A. Drager, B. E. Ebert, J. N. Edirisinghe, J. P. Faria, A. M. Feist, G. Fengos, R. M. T. Fleming, B. Garcia-Jimenez, V. Hatzimanikatis, W. van Helvoirt, C. S. Henry, H. Hermjakob, M. J. Herrgard, A. Kaafarani, H. U. Kim, Z. King, S. Klamt, E. Klipp, J. J. Koehorst, M. Konig, M. Lakshmanan, D. Y. Lee, S. Y. Lee, S. Lee, N. E. Lewis, F. Liu, H. Ma, D. Machado, R. Mahadevan, P. Maia, A. Mardinoglu, G. L. Medlock, J. M. Monk, J. Nielsen, L. K. Nielsen, J. Nogales, I. Nookaew, B. O. Palsson, J. A. Papin, K. R. Patil, M. Poolman, N. D. Price, O. Resendis-Antonio, A. Richelle, I. Rocha, B. J. Sanchez, P. J. Schaap, R. S. Malik Sheriff, S. Shoaie, N. Sonnenschein, B. Teusink, P. Vilaca, J. O. Vik, J. A. H. Wodke, J. C. Xavier, Q. Yuan, M. Zakhartsev, and C. Zhang
Nat Biotechnol, 38: 272-76.

103) Neuroprotective effects of boron nitride nanoparticles in the experimental Parkinson’s disease model against MPP+ induced apoptosis
Kucukdogru, R., H. Turkez, M. E. Arslan, O. O. Tozlu, E. Sonmez, A. Mardinoglu, I. Cacciatore, and A. Di Stefano
Metab Brain Dis, 35: 947-57.

102) Novel anti-Alzheimer phenol-lipoyl hybrids: Synthesis, physico-chemical characterization, and biological evaluation
Pagoni, A., L. Marinelli, A. Di Stefano, M. Ciulla, H. Turkez, A. Mardinoglu, S. Vassiliou, and I. Cacciatore
Eur J Med Chem, 186: 111880.

101) Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Lieven, C., M. E. Beber, B. G. Olivier, F. T. Bergmann, M. Ataman, P. Babaei, J. A. Bartell, L. M. Blank, S. Chauhan, K. Correia, C. Diener, A. Drager, B. E. Ebert, J. N. Edirisinghe, J. P. Faria, A. M. Feist, G. Fengos, R. M. T. Fleming, B. Garcia-Jimenez, V. Hatzimanikatis, W. van Helvoirt, C. S. Henry, H. Hermjakob, M. J. Herrgard, A. Kaafarani, H. U. Kim, Z. King, S. Klamt, E. Klipp, J. J. Koehorst, M. Konig, M. Lakshmanan, D. Y. Lee, S. Y. Lee, S. Lee, N. E. Lewis, F. Liu, H. Ma, D. Machado, R. Mahadevan, P. Maia, A. Mardinoglu, G. L. Medlock, J. M. Monk, J. Nielsen, L. K. Nielsen, J. Nogales, I. Nookaew, B. O. Palsson, J. A. Papin, K. R. Patil, M. Poolman, N. D. Price, O. Resendis-Antonio, A. Richelle, I. Rocha, B. J. Sanchez, P. J. Schaap, R. S. M. Sheriff, S. Shoaie, N. Sonnenschein, B. Teusink, P. Vilaca, J. O. Vik, J. A. H. Wodke, J. C. Xavier, Q. Yuan, M. Zakhartsev, and C. Zhang
Nat Biotechnol, 38: 504.

100) Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women
Chapman, M. A., M. Arif, E. B. Emanuelsson, S. M. Reitzner, M. E. Lindholm, A. Mardinoglu, and C. J. Sundberg
Cell Rep, 31: 107808.

99) Systems Biology Approaches to Understand the Host-Microbiome Interactions in Neurodegenerative Diseases
Rosario, D., J. Boren, M. Uhlen, G. Proctor, D. Aarsland, A. Mardinoglu, and S. Shoaie
Front Neurosci, 14: 716.

98) The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease
Zhang, C., E. Bjornson, M. Arif, A. Tebani, A. Lovric, R. Benfeitas, M. Ozcan, K. Juszczak, W. Kim, J. T. Kim, G. Bidkhori, M. Stahlman, P. O. Bergh, M. Adiels, H. Turkez, M. R. Taskinen, J. Bosley, H. U. Marschall, J. Nielsen, M. Uhlen, J. Boren, and A. Mardinoglu
Mol Syst Biol, 16: e9495.

97) The in vitro cytotoxic, genotoxic, and oxidative damage potentials of the oral artificial sweetener aspartame on cultured human blood cells
Cadirci, K., O. Ozdemir Tozlu, H. Turkez, and A. Mardinoglu
Turk J Med Sci, 50: 448-54.

96) A genome-wide transcriptomic analysis of protein-coding genes in human blood cells
Uhlen, M., M. J. Karlsson, W. Zhong, A. Tebani, C. Pou, J. Mikes, T. Lakshmikanth, B. Forsstrom, F. Edfors, J. Odeberg, A. Mardinoglu, C. Zhang, K. von Feilitzen, J. Mulder, E. Sjostedt, A. Hober, P. Oksvold, M. Zwahlen, F. Ponten, C. Lindskog, A. Sivertsson, L. Fagerberg, and P. Brodin
Science, 366.

95) Cardiac expression of the microsomal triglyceride transport protein protects the heart function during ischemia
Klevstig, M., M. Arif, M. Mannila, S. Svedlund, I. Mardani, M. Stahlman, L. Andersson, M. Lindbom, A. Miljanovic, A. Franco-Cereceda, P. Eriksson, A. Jeppsson, L. M. Gan, M. Levin, A. Mardinoglu, E. Ehrenborg, and J. Boren
J Mol Cell Cardiol, 137: 1-8.

94) The human secretome
Uhlen, M., M. J. Karlsson, A. Hober, A. S. Svensson, J. Scheffel, D. Kotol, W. Zhong, A. Tebani, L. Strandberg, F. Edfors, E. Sjostedt, J. Mulder, A. Mardinoglu, A. Berling, S. Ekblad, M. Dannemeyer, S. Kanje, J. Rockberg, M. Lundqvist, M. Malm, A. L. Volk, P. Nilsson, A. Manberg, T. Dodig-Crnkovic, E. Pin, M. Zwahlen, P. Oksvold, K. von Feilitzen, R. S. Haussler, M. G. Hong, C. Lindskog, F. Ponten, B. Katona, J. Vuu, E. Lindstrom, J. Nielsen, J. Robinson, B. Ayoglu, D. Mahdessian, D. Sullivan, P. Thul, F. Danielsson, C. Stadler, E. Lundberg, G. Bergstrom, A. Gummesson, B. G. Voldborg, H. Tegel, S. Hober, B. Forsstrom, J. M. Schwenk, L. Fagerberg, and A. Sivertsson
Sci Signal, 12.

93) Systems biology perspective for studying the gut microbiota in human physiology and liver diseases
Altay, O., J. Nielsen, M. Uhlen, J. Boren, and A. Mardinoglu
EBioMedicine, 49: 364-73.

92) The Potential Use of Metabolic Cofactors in Treatment of NAFLD
Mardinoglu, A., D. Ural, M. Zeybel, H. H. Yuksel, M. Uhlen, and J. Boren
Nutrients, 11.

91) Multi-Omic Data Interpretation to Repurpose Subtype Specific Drug Candidates for Breast Cancer
Turanli, B., K. Karagoz, G. Bidkhori, R. Sinha, M. L. Gatza, M. Uhlen, A. Mardinoglu, and K. Y. Arga
Front Genet, 10: 420.

90) Mature Human White Adipocytes Cultured under Membranes Maintain Identity, Function, and Can Transdifferentiate into Brown-like Adipocytes
Harms, M. J., Q. Li, S. Lee, C. Zhang, B. Kull, S. Hallen, A. Thorell, I. Alexandersson, C. E. Hagberg, X. R. Peng, A. Mardinoglu, K. L. Spalding, and J. Boucher
Cell Rep, 27: 213-25 e5.

89) Discovery of therapeutic agents for prostate cancer using genome-scale metabolic modeling and drug repositioning
Turanli, B., C. Zhang, W. Kim, R. Benfeitas, M. Uhlen, K. Y. Arga, and A. Mardinoglu
EBioMedicine, 42: 386-96.

88) Expression of PD-L1 and PD-1 in Chemoradiotherapy-Naive Esophageal and Gastric Adenocarcinoma: Relationship With Mismatch Repair Status and Survival
Svensson, M. C., D. Borg, C. Zhang, C. Hedner, B. Nodin, M. Uhlen, A. Mardinoglu, K. Leandersson, and K. Jirstrom
Front Oncol, 9: 136.

87) Pyruvate kinase L/R is a regulator of lipid metabolism and mitochondrial function
Liu, Z., C. Zhang, S. Lee, W. Kim, M. Klevstig, A. M. Harzandi, N. Sikanic, M. Arif, M. Stahlman, J. Nielsen, M. Uhlen, J. Boren, and A. Mardinoglu
Metab Eng, 52: 263-72.

86) Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis
Benfeitas, R., G. Bidkhori, B. Mukhopadhyay, M. Klevstig, M. Arif, C. Zhang, S. Lee, R. Cinar, J. Nielsen, M. Uhlen, J. Boren, G. Kunos, and A. Mardinoglu
EBioMedicine, 40: 471-87.

85) Discovery of KIRREL as a biomarker for prognostic stratification of patients with thin melanoma
Lundgren, S., H. Fagerstrom-Vahman, C. Zhang, L. Ben-Dror, A. Mardinoglu, M. Uhlen, B. Nodin, and K. Jirstrom
Biomark Res, 7: 1.

84) Elucidating the Reprograming of Colorectal Cancer Metabolism Using Genome-Scale Metabolic Modeling
Zhang, C., M. Aldrees, M. Arif, X. Li, A. Mardinoglu, and M. A. Aziz
Front Oncol, 9: 681.

83) LIPG-promoted lipid storage mediates adaptation to oxidative stress in breast cancer
Cadenas, C., S. Vosbeck, K. Edlund, K. Grgas, K. Madjar, B. Hellwig, A. Adawy, A. Glotzbach, J. D. Stewart, M. S. Lesjak, D. Franckenstein, M. Claus, H. Hayen, A. Schriewer, K. Gianmoena, S. Thaler, M. Schmidt, P. Micke, F. Ponten, A. Mardinoglu, C. Zhang, H. U. Kafferlein, C. Watzl, S. Frank, J. Rahnenfuhrer, R. Marchan, and J. G. Hengstler
Int J Cancer, 145: 901-15.

82) Plasma Proteomics Analysis Reveals Dysregulation of Complement Proteins and Inflammation in Acquired Obesity-A Study on Rare BMI-Discordant Monozygotic Twin Pairs
Sahebekhtiari, N., M. Saraswat, S. Joenvaara, R. Jokinen, A. Lovric, S. Kaye, A. Mardinoglu, A. Rissanen, J. Kaprio, R. Renkonen, and K. H. Pietilainen
Proteomics Clin Appl, 13: e1800173.

81) Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes
Bidkhori, G., R. Benfeitas, M. Klevstig, C. Zhang, J. Nielsen, M. Uhlen, J. Boren, and A. Mardinoglu
Proc Natl Acad Sci U S A, 115: E11874-E83.

80) Vimentin deficiency in macrophages induces increased oxidative stress and vascular inflammation but attenuates atherosclerosis in mice
Haversen, L., J. P. Sundelin, A. Mardinoglu, M. Rutberg, M. Stahlman, U. Wilhelmsson, L. M. Hulten, M. Pekny, P. Fogelstrand, J. F. Bentzon, M. Levin, and J. Boren
Sci Rep, 8: 16973.

79) A Network-Based Cancer Drug Discovery: From Integrated Multi-Omics Approaches to Precision Medicine
Turanli, B., K. Karagoz, G. Gulfidan, R. Sinha, A. Mardinoglu, and K. Y. Arga
Curr Pharm Des, 24: 3778-90.

78) Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome
Lovric, A., M. Graner, E. Bjornson, M. Arif, R. Benfeitas, K. Nyman, M. Stahlman, M. O. Pentikainen, J. Lundbom, A. Hakkarainen, R. Siren, M. S. Nieminen, N. Lundbom, K. Lauerma, M. R. Taskinen, A. Mardinoglu, and J. Boren
Sci Rep, 8: 14200.

77) Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia
Danielsson, F., E. Fasterius, D. Sullivan, L. Hases, K. Sanli, C. Zhang, A. Mardinoglu, C. Al-Khalili, M. Huss, M. Uhlen, C. Williams, and E. Lundberg
Oncotarget, 9: 19730-44.

76) Identification of Discriminating Metabolic Pathways and Metabolites in Human PBMCs Stimulated by Various Pathogenic Agents
Zhang, X., A. Mardinoglu, L. A. B. Joosten, J. A. Kuivenhoven, Y. Li, M. G. Netea, and A. K. Groen
Front Physiol, 9: 139.

75) ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling
Zhang, C., G. Bidkhori, R. Benfeitas, S. Lee, M. Arif, M. Uhlen, and A. Mardinoglu
Front Physiol, 9: 1355.

74) Meta-Analysis of Adiponectin as a Biomarker for the Detection of Metabolic Syndrome
Liu, Z., S. Liang, S. Que, L. Zhou, S. Zheng, and A. Mardinoglu
Front Physiol, 9: 1238.

73) Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma
Bidkhori, G., R. Benfeitas, E. Elmas, M. N. Kararoudi, M. Arif, M. Uhlen, J. Nielsen, and A. Mardinoglu
Front Physiol, 9: 916.

72) Drug Repositioning for Effective Prostate Cancer Treatment
Turanli, B., M. Grotli, J. Boren, J. Nielsen, M. Uhlen, K. Y. Arga, and A. Mardinoglu
Front Physiol, 9: 500.

71) Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling
Rosario, D., R. Benfeitas, G. Bidkhori, C. Zhang, M. Uhlen, S. Shoaie, and A. Mardinoglu
Front Physiol, 9: 775.

70) Systems biology in hepatology: approaches and applications
Mardinoglu, A., J. Boren, U. Smith, M. Uhlen, and J. Nielsen
Nat Rev Gastroenterol Hepatol, 15: 365-77.

69) Combined ASRGL1 and p53 immunohistochemistry as an independent predictor of survival in endometrioid endometrial carcinoma
Huvila, J., T. D. Laajala, P. H. Edqvist, A. Mardinoglu, L. Talve, F. Ponten, S. Grenman, O. Carpen, T. Aittokallio, and A. Auranen
Gynecol Oncol, 149: 173-80.

68) Associations of PD-1 and PD-L1 expression with mismatch repair status and prognosis in chemoradiotherapy-naïve esophageal and gastric adenocarcinoma.
Svensson M, Borg D, Zhang C, Hedner C, Nodin B, Uhlen M, Mardinoglu A, Leandersson K, Jirstrom K.
Journal of Clinical Oncology, no. 4_suppl 9-9.

67) An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans
Mardinoglu, A., H. Wu, E. Bjornson, C. Zhang, A. Hakkarainen, S. M. Rasanen, S. Lee, R. M. Mancina, M. Bergentall, K. H. Pietilainen, S. Soderlund, N. Matikainen, M. Stahlman, P. O. Bergh, M. Adiels, B. D. Piening, M. Graner, N. Lundbom, K. J. Williams, S. Romeo, J. Nielsen, M. Snyder, M. Uhlen, G. Bergstrom, R. Perkins, H. U. Marschall, F. Backhed, M. R. Taskinen, and J. Boren
Cell Metab, 27: 559-71 e5.

66) Broad Views of Non-alcoholic Fatty Liver Disease
Mardinoglu, A., M. Uhlen, and J. Boren
Cell Syst, 6(1):7-9.

65) Integrative Personal Omics Profiles during Periods of Weight Gain and Loss
Piening, B. D., W. Zhou, K. Contrepois, H. Rost, G. J. Gu Urban, T. Mishra, B. M. Hanson, E. J. Bautista, S. Leopold, C. Y. Yeh, D. Spakowicz, I. Banerjee, C. Chen, K. Kukurba, D. Perelman, C. Craig, E. Colbert, D. Salins, S. Rego, S. Lee, C. Zhang, J. Wheeler, M. R. Sailani, L. Liang, C. Abbott, M. Gerstein, A. Mardinoglu, U. Smith, D. L. Rubin, S. Pitteri, E. Sodergren, T. L. McLaughlin, G. M. Weinstock, and M. P. Snyder
Cell Syst, 6: 157-70 e8.

64) Dose-response analysis revealed closer relationship between obesity and perioperative outcomes in patients after liver transplantation
Liu, Z., A. Mardinoglu, and S. Que
Aliment Pharmacol Ther, 47: 310-12.

63) Elevated Plasma Levels of 3-Hydroxyisobutyric Acid Are Associated With Incident Type 2 Diabetes
Mardinoglu, A., S. Gogg, L. A. Lotta, A. Stancakova, A. Nerstedt, J. Boren, M. Bluher, E. Ferrannini, C. Langenberg, N. J. Wareham, M. Laakso, and U. Smith
EBioMedicine, 27: 151-55.

62) 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., L. B. Dror, A. Mardinoglu, J. Elebro, M. Heby, S. E. Olofsson, B. Nodin, J. Eberhard, W. Gallagher, M. Uhlen, and K. Jirstrom
Oncotarget, 9: 6188-200.

61) TCSBN: a database of tissue and cancer specific biological networks
Lee, S., C. Zhang, M. Arif, Z. Liu, R. Benfeitas, G. Bidkhori, S. Deshmukh, M. Al Shobky, A. Lovric, J. Boren, J. Nielsen, M. Uhlen, and A. Mardinoglu
Nucleic Acids Res, 46: D595-D600.

60) High Cell Density Perfusion Culture has a Maintained Exoproteome and Metabolome
Zamani, L., M. Lundqvist, Y. Zhang, M. Aberg, F. Edfors, G. Bidkhori, A. Lindahl, A. Mie, A. Mardinoglu, R. Field, R. Turner, J. Rockberg, and V. Chotteau
Biotechnol J, 13: e1800036.

59) The effect of the TM6SF2 E167K variant on liver steatosis and fibrosis in patients with chronic hepatitis C: a meta-analysis
Liu, Z., S. Que, L. Zhou, S. Zheng, S. Romeo, A. Mardinoglu, and L. Valenti
Sci Rep, 7: 9273.

58) 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.
Molecular systems biology. 13(8):938.

57) 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
Science, 357(6352):eaan2507

56) Rediscussion on linearity between fibrosis stages and mortality risk in nonalcoholic fatty liver disease patients
Liu, Z., S. Que, and A. Mardinoglu
Hepatology, 66: 1357-58.

55) Selection of complementary foods based on optimal nutritional values
Sen P, Mardinogulu A, Nielsen J.
Sci Rep, 7(1):5413

54) Plasma Mannose Levels Are Associated with Incident Type 2 Diabetes and Cardiovascular Disease
Mardinoglu A, Stančáková A, Lotta LA, Kuusisto J, Boren J, Blueher M, Wareham NJ, Ferrannini E, Groop PH, Laakso M, Langenberg C.
Cell metabolism. 26(2):281-3.

53) Improving the economics of NASH/NAFLD treatment through the use of systems biology
Bosley, J., C. Boren, S. Lee, M. Grotli, J. Nielsen, M. Uhlen, J. Boren, and A. Mardinoglu
Drug Discov Today, 22: 1532-38.

52) New Challenges to Study Heterogeneity in Cancer Redox Metabolism
Benfeitas, R., M. Uhlen, J. Nielsen, and A. Mardinoglu
Front Cell Dev Biol, 5: 65.

51) A subcellular map of the human proteome
Thul, P. J., L. Akesson, M. Wiking, D. Mahdessian, A. Geladaki, H. Ait Blal, T. Alm, A. Asplund, L. Bjork, L. M. Breckels, A. Backstrom, F. Danielsson, L. Fagerberg, J. Fall, L. Gatto, C. Gnann, S. Hober, M. Hjelmare, F. Johansson, S. Lee, C. Lindskog, J. Mulder, C. M. Mulvey, P. Nilsson, P. Oksvold, J. Rockberg, R. Schutten, J. M. Schwenk, A. Sivertsson, E. Sjostedt, M. Skogs, C. Stadler, D. P. Sullivan, H. Tegel, C. Winsnes, C. Zhang, M. Zwahlen, A. Mardinoglu, F. Ponten, K. von Feilitzen, K. S. Lilley, M. Uhlen, and E. Lundberg
Science, 356(6340):eaal3321.

50) AUP1 (Ancient Ubiquitous Protein 1): A Molecular Link Between Hepatic Lipid Mobilization and VLDL Secretion
Mardinoglu, A., and J. Boren
Arterioscler Thromb Vasc Biol, 37: 609-10.

49) 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.
Mol Syst Biol, 13(3):916.

48) Predicting growth of the healthy infant using a genome scale metabolic model
Nilsson, A., A. Mardinoglu, and J. Nielsen
NPJ Syst Biol Appl, 3: 3.

47) Principles of Systems Biology, No. 21
Cao J, Packer J, Waterston R, Trapnell C, Shendure J, Rajaram S, Wu LF, Altschuler SJ, Liang J, O’Brien LE, Eizenberg-Magar I.
Cell Systems. 5(3):158-60.

46) Mitochondria-related transcriptional signature is downregulated in adipocytes in obesity: a study of young healthy MZ twins
Heinonen, S., M. Muniandy, J. Buzkova, A. Mardinoglu, A. Rodriguez, G. Fruhbeck, A. Hakkarainen, J. Lundbom, N. Lundbom, J. Kaprio, A. Rissanen, and K. H. Pietilainen
Diabetologia, 60(1):169-181.

45) Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus
Casey, J. R., A. Mardinoglu, J. Nielsen, and D. M. Karl
mSystems, 1.

44) ARAP2 promotes GLUT1-mediated basal glucose uptake through regulation of sphingolipid metabolism
Chaudhari, A., L. Haversen, R. Mobini, L. Andersson, M. Stahlman, E. Lu, M. Rutberg, P. Fogelstrand, K. Ekroos, A. Mardinoglu, M. Levin, R. Perkins, and J. Boren
Biochim Biophys Acta, 1861(11):1643-1651.

43) Liver: Phenotypic and genetic variance: a systems approach to the liver
Mardinoglu, A., and M. Uhlen
Nat Rev Gastroenterol Hepatol, 13(8):439-40.

42) Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance
Lee, S., C. Zhang, M. Kilicarslan, B. D. Piening, E. Bjornson, B. M. Hallstrom, A. K. Groen, E. Ferrannini, M. Laakso, M. Snyder, M. Bluher, M. Uhlen, J. Nielsen, U. Smith, M. J. Serlie, J. Boren, and A. Mardinoglu
Cell Metab, 24: 172-84.

41) Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis
Lee, S., A. Mardinoglu, C. Zhang, D. Lee, and J. Nielsen
Nucleic Acids Res, 44: 5529-39.

40) Investigating the Combinatory Effects of Biological Networks on Gene Co-expression
Zhang, C., S. Lee, A. Mardinoglu, and Q. Hua
Front Physiol, 7: 160.

39) Transcriptomics resources of human tissues and organs
Uhlen, M., B. M. Hallstrom, C. Lindskog, A. Mardinoglu, F. Ponten, and J. Nielsen
Mol Syst Biol, 12: 862.

38) Confounding Effects of Metformin on the Human Gut Microbiome in Type 2 Diabetes
Mardinoglu, A., J. Boren, and U. Smith
Cell Metab, 23(1):10-2.

37) Editorial: The Impact of Systems Medicine on Human Health and Disease
Mardinoglu, A., and J. Nielsen
Front Physiol, 7: 552.

36) 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, I. E., A. Mardinoglu, S. Shoaie, T. H. Soliman, and J. Nielsen
Mol Biosyst, 12: 1496-506.

35) Personalized Cardiovascular Disease Prediction and Treatment-A Review of Existing Strategies and Novel Systems Medicine Tools
Bjornson, E., J. Boren, and A. Mardinoglu
Front Physiol, 7: 2.

34) 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 reports. 13(9):2014-26.

33) The gut microbiota modulates host amino acid and glutathione metabolism in mice
Mardinoglu, A., S. Shoaie, M. Bergentall, P. Ghaffari, C. Zhang, E. Larsson, F. Backhed, and J. Nielsen
Mol Syst Biol, 11: 834.

32) New paradigms for metabolic modeling of human cells
Mardinoglu, A., and J. Nielsen
Curr Opin Biotechnol, 34: 91-7.

31) Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Shoaie, S., P. Ghaffari, P. Kovatcheva-Datchary, A. Mardinoglu, P. Sen, E. Pujos-Guillot, T. de Wouters, C. Juste, S. Rizkalla, J. Chilloux, L. Hoyles, J. K. Nicholson, M. ICRO-Obes Consortium, J. Dore, M. E. Dumas, K. Clement, F. Backhed, and J. Nielsen
Cell Metab, 22: 320-31.

30) The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling
Lindskog, C., J. Linne, L. Fagerberg, B. M. Hallstrom, C. J. Sundberg, M. Lindholm, M. Huss, C. Kampf, H. Choi, D. A. Liem, P. Ping, L. Varemo, A. Mardinoglu, J. Nielsen, E. Larsson, F. Ponten, and M. Uhlen
BMC Genomics, 16: 475.

29) Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes
Varemo, L., C. Scheele, C. Broholm, A. Mardinoglu, C. Kampf, A. Asplund, I. Nookaew, M. Uhlen, B. K. Pedersen, and J. Nielsen
Cell Rep, 11: 921-33.

28) Logical transformation of genome-scale metabolic models for gene level applications and analysis
Zhang, C., B. Ji, A. Mardinoglu, J. Nielsen, and Q. Hua
Bioinformatics, 31: 2324-31.

27) Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
Ghaffari, P., A. Mardinoglu, A. Asplund, S. Shoaie, C. Kampf, M. Uhlen, and J. Nielsen
Sci Rep, 5: 8183.

26) 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.
Science, 347(6220):1260419.

25) Cancer Metabolism: A Modeling Perspective
Ghaffari, P., A. Mardinoglu, and J. Nielsen
Front Physiol, 6: 382.

24) Kinetic Studies to Elucidate Impaired Metabolism of Triglyceride-rich Lipoproteins in Humans
Adiels, M., A. Mardinoglu, M. R. Taskinen, and J. Boren
Front Physiol, 6: 342.

23) Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue
Mardinoglu, A., J. T. Heiker, D. Gartner, E. Bjornson, M. R. Schon, G. Flehmig, N. Kloting, K. Krohn, M. Fasshauer, M. Stumvoll, J. Nielsen, and M. Bluher
Sci Rep, 5: 14841.

22) Modelling the effect of SPION size in a stent assisted magnetic drug targeting system with interparticle interactions
Mardinoglu, A., and P. J. Cregg
ScientificWorldJournal, 2015: 618658.

21) Proteomics. Tissue-based map of the human proteome
Uhlen, M., L. Fagerberg, B. M. Hallstrom, C. Lindskog, P. Oksvold, A. Mardinoglu, A. Sivertsson, C. Kampf, E. Sjostedt, A. Asplund, I. Olsson, K. Edlund, E. Lundberg, S. Navani, C. A. Szigyarto, J. Odeberg, D. Djureinovic, J. O. Takanen, S. Hober, T. Alm, P. H. Edqvist, H. Berling, H. Tegel, J. Mulder, J. Rockberg, P. Nilsson, J. M. Schwenk, M. Hamsten, K. von Feilitzen, M. Forsberg, L. Persson, F. Johansson, M. Zwahlen, G. von Heijne, J. Nielsen, and F. Ponten
Science, 347: 1260419.

20) Toxicogenomics directory of chemically exposed human hepatocytes
Grinberg, M., R. M. Stober, K. Edlund, E. Rempel, P. Godoy, R. Reif, A. Widera, K. Madjar, W. Schmidt-Heck, R. Marchan, A. Sachinidis, D. Spitkovsky, J. Hescheler, H. Carmo, M. D. Arbo, B. van de Water, S. Wink, M. Vinken, V. Rogiers, S. Escher, B. Hardy, D. Mitic, G. Myatt, T. Waldmann, A. Mardinoglu, G. Damm, D. Seehofer, A. Nussler, T. S. Weiss, A. Oberemm, A. Lampen, M. M. Schaap, M. Luijten, H. van Steeg, W. E. Thasler, J. C. Kleinjans, R. H. Stierum, M. Leist, J. Rahnenfuhrer, and J. G. Hengstler
Arch Toxicol, 88: 2261-87.

19) Defining the human adipose tissue proteome to reveal metabolic alterations in obesity
Mardinoglu, A., C. Kampf, A. Asplund, L. Fagerberg, B. M. Hallstrom, K. Edlund, M. Bluher, F. Ponten, M. Uhlen, and J. Nielsen
J Proteome Res, 13: 5106-19.

18) Defining the human gallbladder proteome by transcriptomics and affinity proteomics
Kampf, C., A. Mardinoglu, L. Fagerberg, B. M. Hallstrom, A. Danielsson, J. Nielsen, F. Ponten, and M. Uhlen
Proteomics, 14: 2498-507.

17) The human liver-specific proteome defined by transcriptomics and antibody-based profiling
Kampf, C., A. Mardinoglu, L. Fagerberg, B. M. Hallstrom, K. Edlund, E. Lundberg, F. Ponten, J. Nielsen, and M. Uhlen
FASEB J, 28: 2901-14.

16) Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling
Agren, R., A. Mardinoglu, A. Asplund, C. Kampf, M. Uhlen, and J. Nielsen
Mol Syst Biol, 10: 721.

15) Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics
Fagerberg, L., B. M. Hallstrom, P. Oksvold, C. Kampf, D. Djureinovic, J. Odeberg, M. Habuka, S. Tahmasebpoor, A. Danielsson, K. Edlund, A. Asplund, E. Sjostedt, E. Lundberg, C. A. Szigyarto, M. Skogs, J. O. Takanen, H. Berling, H. Tegel, J. Mulder, P. Nilsson, J. M. Schwenk, C. Lindskog, F. Danielsson, A. Mardinoglu, A. Sivertsson, K. von Feilitzen, M. Forsberg, M. Zwahlen, I. Olsson, S. Navani, M. Huss, J. Nielsen, F. Ponten, and M. Uhlen
Mol Cell Proteomics, 13: 397-406.

14) Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease
Mardinoglu, A., R. Agren, C. Kampf, A. Asplund, M. Uhlen, and J. Nielsen
Nat Commun, 5: 3083.

13) Genome‐scale modeling of human metabolism–a systems biology approach
Mardinoglu A, Gatto F, Nielsen J.
Biotechnology journal. 8(9):985-96.

12) Understanding the interactions between bacteria in the human gut through metabolic modeling
Shoaie, S., F. Karlsson, A. Mardinoglu, I. Nookaew, S. Bordel, and J. Nielsen
Sci Rep, 3: 2532.

11) Integration of clinical data with a genome‐scale metabolic model of the human adipocyte
Mardinoglu A, Agren R, Kampf C, Asplund A, Nookaew I, Jacobson P, Walley AJ, Froguel P, Carlsson LM, Uhlen M, Nielsen J.
Mol Syst Biol (2013)9:649

10) Genome-scale modeling of human metabolism – a systems biology approach
Mardinoglu, A., F. Gatto, and J. Nielsen
Biotechnol J, 8: 985-96.

9) Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
Agren, R., S. Bordel, A. Mardinoglu, N. Pornputtapong, I. Nookaew, and J. Nielsen
PLoS Comput Biol, 8: e1002518.

8) Systems medicine and metabolic modelling
Mardinoglu, A., and J. Nielsen
J Intern Med, 271: 142-54.

7) Inclusion of interactions in mathematical modelling of implant assisted magnetic drug targeting
Cregg PJ, Murphy K, Mardinoglu A.
Applied Mathematical Modelling. 36(1):1-34.

6) Development of artificial neuronal networks for molecular communication
Balasubramaniam S, Boyle NT, Della-Chiesa A, Walsh F, Mardinoglu A, Botvich D, Prina-Mello A.
Nano Communication Networks. 2(2-3):150-60.

5) Artificial backbone neuronal network for nano scale sensors
F. Walsh, N.T. Boyle, A. Mardinoglu, A. Della Chiesa, D. Botvich, A. Prina-Mello, S. Balasubramaniam
2011 IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS) (pp. 449-454). IEEE.

4) Theoretical modelling of physiologically stretched vessel in magnetisable stent assisted magnetic drug targetingapplication
Mardinoglu A, Cregg PJ, Murphy K, Curtin M, Prina-Mello A.
Journal of Magnetism and Magnetic Materials. 323(3-4):324-9.

3) Many particle magnetic dipole–dipole and hydrodynamic interactions in magnetizable stent assisted magnetic drug targeting
Cregg PJ, Murphy K, Mardinoglu A, Prina-Mello A.
Journal of Magnetism and Magnetic Materials. 322(15):2087-94.

2) Inclusion of magnetic dipole–dipole and hydrodynamic interactions in implant-assisted magnetic drug targeting
Cregg PJ, Murphy K, Mardinoglu A.
Journal of Magnetism and Magnetic Materials. 321(23):3893-8.

1) Calculation of nanoparticle capture efficiency in magnetic drug targeting
Cregg PJ, Murphy K, Mardinoglu A.
Journal of Magnetism and Magnetic Materials 320, no. 23: 3272-3275.

PHD THESIS

Mathematical Modelling of Implant Assisted Magnetic Drug Targeting
A Mardinoglu
Waterford Institute of Technology