Publications

50 latest publications

[1]

Li, X., Kim, W., Arif, M., Gao, C., Hober, A., Kotol, D. ... Mardinoglu, A. (2021). Discovery of Functional Alternatively Spliced PKM Transcripts in Human Cancers. Cancers, 13(2).

[2]

Turkez, H., Cacciatore, I., Marinelli, L., Fornasari, E., Aslan, M. E., Cadirci, K. ... Mardinoglu, A. (2021). Glycyl-L-Prolyl-L-Glutamate Pseudotripeptides for Treatment of Alzheimer's Disease. Biomolecules, 11(1).

[3]

Gummesson, A., Björnson, E., Fagerberg, L., Zhong, W., Abdellah, T., Edfors, F. ... Bergström, G. (2021). Longitudinal plasma protein profiling of newly diagnosed type 2 diabetes. EBioMedicine, 63.

[4]

Harzandi, A., Lee, S., Bidkhori, G., Saha, S., Hendry, B. M., Mardinoglu, A. ... Sharpe, C. C. (2021). Acute kidney injury leading to CKD is associated with a persistence of metabolic dysfunction and hypertriglyceridemia. iScience, 24(2).

[5]

Asplund Samuelsson, J. (2021). Adaptations and constraints associated with autotrophy in microbial metabolism (Doctoral thesis , KTH Royal Institute of Technology, TRITA-CBH-FOU 2021:11). Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-292437.

[6]

Arif, M., Zhang, C., Li, X., Güngör, C., Çakmak, B., Arslantürk, M. ... Mardinoglu, A. (2021). iNetModels 2.0 : an interactive visualization and database of multi-omics data. Nucleic Acids Research.

[7]

Arif, M., Klevstig, M., Benfeitas, R., Doran, S., Turkez, H., Uhlén, M. ... Boren, J. (2021). Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction. eLIFE, 10.

[8]

Karlsson, M. J., Svedman, F. C., Abdellah, T., Kotol, D., Hoiom, V., Fagerberg, L. ... Maddalo, G. (2021). Inflammation and Apolipoproteins Are Potential Biomarkers for Stratification of Cutaneous Melanoma Patients for Immunotherapy and Targeted Therapy. Cancer Research, 81(9), 2545-2555.

[9]

Månberg, A., Remnestål, J., Olofsson, J., Uhlén, M., Nilsson, P. & Lewandowski, S. (2021). Altered perivascular fibroblast activity precedes ALS disease onset. Nature Medicine, 27(4).

[10]

Bosley, J. R., Björnson, E., Zhang, C., Turkez, H., Nielsen, J., Uhlén, M. ... Mardinoglu, A. (2021). Informing Pharmacokinetic Models With Physiological Data : Oral Population Modeling of L-Serine in Humans. Frontiers in Pharmacology, 12.

[11]

Zhang, C., Wei, Y., Mardinoglu, A. & Zhang, P. (2021). Editorial : Application of Systems Biology in Molecular Characterization and Diagnosis of Cancer. Frontiers in Molecular Biosciences, 8.

[12]

Huang, J., Lin, L., Dong, Z., Yang, L., Zheng, T., Gu, W. ... Luo, Y. (2021). A porcine brain-wide RNA editing landscape. Communications Biology, 4(1).

[13]

Lam, S., Doran, S., Yüksel, H. H., Altay, Ö., Turkez, H., Nielsen, J. ... Mardinoglu, A. (2021). Addressing the heterogeneity in liver diseases using biological networks. Briefings in Bioinformatics, 22(2), 1751-1766.

[14]

Lee, S., Arefaine, B., Witherden, E., Begum, N., Harzandi, A., Zamalloa, A. ... Patel, V. C. (2021). In-depth shotgun metagenomic analysis of the gut microbiome identifies striking variations in microbial community structure based on severity and stage of cirrhosis. Journal of Hepatology, 75, S222-S223.

[15]

Karlsson, M., Zhang, C., Mear, L., Zhong, W., Digre, A., Katona, B. ... Lindskog, C. (2021). A single-cell type transcriptomics map of human tissues. Science Advances, 7(31).

[16]

Rossi, R., Falzarano, M. S., Osman, H., Armaroli, A., Scotton, C., Mantuano, P. ... Ferlini, A. (2021). Circadian Genes as Exploratory Biomarkers in DMD : Results From Both the mdx Mouse Model and Patients. Frontiers in Physiology, 12.

[17]

Adori, C., Daraio, T., Kuiper, R., Barde, S., Horvathova, L., Yoshitake, T. ... Hokfelt, T. (2021). Disorganization and degeneration of liver sympathetic innervations in nonalcoholic fatty liver disease revealed by 3D imaging. Science Advances, 7(30).

[18]

Wang, H., Robinson, J. L., Kocabas, P., Gustafsson, J., Anton, M., Cholley, P.-E. ... Nielsen, J. (2021). Genome-scale metabolic network reconstruction of model animals as a platform for translational research. Proceedings of the National Academy of Sciences of the United States of America, 118(30).

[19]

Yang, Y., Li, X., Yang, Y., Shoaie, S., Zhang, C., Ji, B. & Wei, Y. (2021). Advances in the Relationships Between Cow's Milk Protein Allergy and Gut Microbiota in Infants. Frontiers in Microbiology, 12.

[20]

Danielsson, H., Tebani, A., Zhong, W., Fagerberg, L., Brusselaers, N., Hård, A.-L. ... Hellström, A. (2021). Blood protein profiles related to preterm birth and retinopathy of prematurity. Pediatric Research.

[21]

Shabestary, K., Hernandez, H. P., Miao, R., Ljungqvist, E. E., Hallman, O., Sporre, E. ... Hudson, E. P. (2021). Cycling between growth and production phases increases cyanobacteria bioproduction of lactate. Metabolic engineering, 68, 131-141.

[22]

Zeybel, M., Altay, Ö., Arif, M., Li, X., Yang, H., Fredolini, C. ... Mardinoglu, A. (2021). Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients. Molecular Systems Biology, 17(10).

[23]

Yang, H., Mayneris-Perxachs, J., Boque, N., del Bas, J. M., Arola, L., Yuan, M. ... Caimari, A. (2021). Combined Metabolic Activators Decrease Liver Steatosis by Activating Mitochondrial Metabolism in Hamsters Fed with a High-Fat Diet. BIOMEDICINES, 9(10).

[24]

Abdellah, T., Jotanovic, J., Hekmati, N., Sivertsson, Å., Gudjonsson, O., Engstrom, B. E. ... Ponten, F. (2021). Annotation of pituitary neuroendocrine tumors with genome-wide expression analysis. Acta neuropathologica communications, 9(1).

[25]

Iglesias, M. J., Kruse, L. D., Sanchez-Rivera, L., Enge, L., Dusart, P., Hong, M.-G. ... Butler, L. M. (2021). Identification of Endothelial Proteins in Plasma Associated With Cardiovascular Risk Factors. Arteriosclerosis, Thrombosis and Vascular Biology, 41(12), 2990-3004.

[26]

Andersson, L., Cinato, M., Mardani, I., Miljanovic, A., Arif, M., Koh, A. ... Levin, M. C. (2021). Glucosylceramide synthase deficiency in the heart compromises beta 1-adrenergic receptor trafficking. European Heart Journal, 42(43), 4481-+.

[27]

Karlsson, M., Sjostedt, E., Oksvold, P., Sivertsson, Å., Huang, J., Alvez, M. B. ... Uhlén, M. (2022). Genome-wide annotation of protein-coding genes in pig. BMC Biology, 20(1).

[28]

Yang, H., Arif, M., Yuan, M., Li, X., Shong, K. E., Turkez, H. ... Mardinoglu, A. (2021). A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic liver disease. iScience, 24(11).

[29]

Smati, S., Polizzi, A., Fougerat, A., Ellero-Simatos, S., Blum, Y., Lippi, Y. ... Guillou, H. (2022). Integrative study of diet-induced mouse models of NAFLD identifies PPARα as a sexually dimorphic drug target. Gut, 71(4), 807-821.

[30]

Grapotte, M., Forsberg, M., Oksvold, P., Sivertsson, Å., Sjöstedt, E., Uhlén, M. ... et al, (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications.

[31]

Nilsson, A. K., Abdellah, T., Malmodin, D., Pedersen, A., Hellgren, G., Lofqvist, C. ... Hellström, A. (2022). Longitudinal Serum Metabolomics in Extremely Premature Infants : Relationships With Gestational Age, Nutrition, and Morbidities. Frontiers in Neuroscience, 16.

[32]

Yildirim, S., Nalbantoglu, O. U., Bayraktar, A., Ercan, F. B., Gundogdu, A., Velioglu, H. A. ... Hanoglu, L. (2022). Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort. mSystems, 7(1).

[33]

Altay, Ö., Arif, M., Li, X., Yang, H., Aydın, M., Alkurt, G. ... Mardinoglu, A. (2021). Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19. Advanced Science, 8(17).

[34]

Basak, T., Hasan, T., Feray, B., Enes, A. M., Abdulgani, T., Ivana, C. ... Mardinoglu, A. (2022). Synthesis and in Vitro Toxicity Assessment of Different Nano-Calcium Phosphate Nanoparticles. Brazilian archives of biology and technology, 65.

[35]

Ghaffari, P., Shoaie, S. & Nielsen, L. K. (2022). Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions. Journal of Translational Medicine, 20(1).

[36]

Turkez, H., Arslan, M. E., Tatar, A., Ozdemir, O., Sonmez, E., Cadirci, K. ... Mardinoglu, A. (2022). Molecular Genetics and Cytotoxic Responses to Titanium Diboride and Zinc Borate Nanoparticles on Cultured Human Primary Alveolar Epithelial Cells. Materials, 15(7).

[37]

Karlsson, M. (2022). Mapping and annotating the mammalian body-wide protein-coding gene expression (Doctoral thesis , KTH Royal Institute of Technology, Stockholm, TRITA-CBH-FOU 2022:32). Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-312033.

[38]

Kotol, D. (2022). Multiplexed absolute quantification of blood plasma proteins using targeted proteomics (Doctoral thesis , KTH Royal Institute of Technology, TRITA-CBH-FOU 2022:33). Retrieved from http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-312258.

[39]

Edfors, F., Iglesias, M. J., Butler, L. M. & Odeberg, J. (2022). Proteomics in thrombosis research. RESEARCH AND PRACTICE IN THROMBOSIS AND HAEMOSTASIS, 6(3).

[40]

Nain-Perez, A., Fuchtbauer, A. F., Haversen, L., Lulla, A., Gao, C., Matic, J. ... Grotli, M. (2022). Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase. European Journal of Medicinal Chemistry, 234, 114270.

[41]

Liu, Z., Xu, J., Que, S., Geng, L., Zhou, L., Mardinoglu, A. & Zheng, S. (2022). Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation. JOURNAL OF CLINICAL AND TRANSLATIONAL HEPATOLOGY, 10(2), 363-373.

[42]

Malm, M., Kuo, C.-C., Moradi, M., Mebrahtu, A., Wistbacka, N., Razavi, R. ... Rockberg, J. (2022). Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins. Metabolic engineering, 72, 171-187.

[43]

Yunus, I. S., Anfelt, J., Sporre, E., Miao, R., Hudson, E. P. & Jones, P. R. (2022). Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria. Metabolic engineering, 72, 14-23.

[44]

Mikus, M. S., Uhlén, M., Nilsson, P., James, A. & et al., (2022). Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation. European Respiratory Journal, 59(2), 2100142.

[45]

Cacciatore, I., Turkez, H., Di Rienzo, A., Ciulla, M., Mardinoglu, A. & Di Stefano, A. (2021). Boron-based hybrids as novel scaffolds for the development of drugs with neuroprotective properties. RSC Medicinal Chemistry, 12(11), 1944-1949.

[46]

Mohammadi, E., Tahmoorespur, M., Benfeitas, R., Altay, O., Javadmanesh, A., Lam, S. ... Sekhavati, M. H. (2022). Improvement of the performance of anticancer peptides using a drug repositioning pipeline. Biotechnology Journal, 17(1), 2100417.

[47]

Chen, A., Mulder, J., Uhlén, M., Esteban, M. A., Li, Y., Liu, L. ... Wang, J. (2022). Spatiotemporal transcriptomic atlas of mouseorganogenesis using DNA nanoball-patterned arrays. Cell, 185(10), 1777-1792.e21.

[48]

Turkez, H., Arslan, M. E., Yilmaz, A., Doru, F., Caglar, O., Arslan, E. ... Mardinoglu, A. (2021). In vitro transcriptome response to propolis in differentiated SH-SY5Y neurons. Journal of food biochemistry, 45(12).

[49]

Lam, S., Arif, M., Song, X., Uhlén, M. & Mardinoglu, A. (2022). Machine Learning Analysis Reveals Biomarkers for the Detection of Neurological Diseases. Frontiers in Molecular Neuroscience, 15.

[50]

Li, X., Shong, K. E., Kim, W., Yuan, M., Yang, H., Sato, Y. ... Mardinoglu, A. (2022). Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach. EBioMedicine, 78, 103963.