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.