1. C. Zhang, S. Lee, G. Bidkhori, R. Benfeitas, A. Lovric, S. Chen, M. Uhlen, J. Nielsen, A. Mardinoglu. 2019. “RMetD2: A Tool for Integration of Relative Transcriptomics Data into Genome-Scale Metabolic Models.” BioRxiv 663096


  1. F. Mikaeloff, S. Svensson-Akusjärvi, G. M. Ikomey, S. Krishnan, M. Sperk, S. Gupta, G. D. V. Magdaleno, A. Escós, E. Lyonga, M. C. Okomo, C. T. Tagne, H. Babu, C. L Lorson, A. Vegvari, A. C. Banerjea, J. Kele, L. E. Hanna, K. Singh, J. P. Magalhães, Rui Benfeitas, Ujjwal Neogi. 2022 “Trans Cohorts Metabolomic Modulation Following Long-Term Successful Therapy in HIV-Infection” Nature Communications Biology
  2. S. O. Villumsen, Rui Benfeitas, A. D. Knudsen, M. Gelpi, J. Høgh, M. T. Thomsen, D. Murray, H. Ullum, U. Neogi, S. D. Nielsen. 2021 “Integrative lipidomics and metabolomics for system-level understanding of the metabolic syndrome in long-term treated HIV-infected individuals.” Frontiers Immunology 12:732736doi: 10.3389/fimmu.2021.742736
  3. M. Gelpi, F. Mikaeloff, A. D. Knudsen, Rui Benfeitas, S. Krishnan, J. Høgh, D. D. Murray, H. Ullum, U. Neogi, S. D. Nielsen. 2021. “The central role of the glutamate metabolism in long-term antiretroviral treated HIV-infected individuals with metabolic syndrome” Aging 13(19): 22732. doi:
  4. H. Haytural, R. Benfeitas, S. Schedin-Weiss, E. Bereczki, M. Rezeli, R. D. Unwin, X. Wang, E. B. Dammer, E. C. B. Johnson, N. T. Seyfried, B. Winblad, B. M. Tijms, Pieter J. Visser, S. Frykman, L. O. Tjernberg. 2021 “Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis”. Sci. Data 8, 312. doi: 10.1038/s41597-021-01090-8
  5. E. Mohammadi, M. Tahmoorespur, R. Benfeitas, O. Altay, A. Javadmanesh, S. Lam, A. Mardinoglu, M. H. Sekhavati. 2021. “Improvement of the performance of anticancer peptides using a drug repositioning pipeline”. Biotech. Journal doi: 10.1002/biot.202100417
  6. S. Krishnan, H. Nordqvist, A. T. Ambikan, S. Gupta, M. Sperk, S. Svensson-Akusjärvi, F. Mikaeloff, R. Benfeitas, E. Saccon, S. M. Ponnan, J. E. Rodriguez, N. Nikouyan, A. Odeh, G. Ahlen, M. Asghar, M. Sällberg, J. Vesterbacka, P. Nowak, Á. Végvári, A. Sönnerborg, C. J. Treutiger, U. Neogi. 2021. “Metabolic perturbation associated with COVID-19 disease severity and SARS-CoV-2 replication”. Mol. Cel. Proteomics S1535-9476(21)00131-6 doi: 10.1016/j.mcpro.2021.100159
  7. S. Lam, N. Hartmann, R. Benfeitas, C. Zhang, M. Arif, H. Turkez, M. Uhlén, C. Englert, R. Knight, A. Mardinoglu. 2021. “Systems analysis reveals ageing-related perturbations in retinoids and sex hormones in Alzheimer’s and Parkinson’s disease”. Biomedicines 2021, 9(10), 1310. doi: 10.3390/biomedicines9101310
  8. M. Arif, M. Klevstig, R. Benfeitas, S. Doran, H. Turkez, M. Uhlén, M. Clausen, J. Wikström, D. Etal, C. Zhang, M. Levin, A. Mardinoglu, J. Boren. 2021. “Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction (highlighted in eLife) .” eLife 10.7554/eLife.66921
  9. N. Acevedo, R. Benfeitas, S. Katayama, S. Bruhn, A. Andersson, G. Wikberg, L. Lundeberg, J. M. Lindvall, D. Greco, J. Kere, C. Söderhäll, A. Scheynius. 2020. “Epigenetic Alterations in Skin Homing CD4+CLA+ T Cells of Atopic Dermatitis Patients.” Scientific Reports 10(1):18020. doi: 10.1038/s41598-020-74798-z
  10. S. Appelberg, S. Gupta, S. S. Akusjärvi, A. T. Ambikan, F. Mikaeloff, E. Saccon, Á. Végvári, R. Benfeitas, M. Sperk, M. Ståhlberg, S. Krishnan, K. Singh, J. M. Penninger, A. Mirazimi, U. Neogi. 2020. “Dysregulation in Akt/MTOR/HIF-1 Signaling Identified by Proteo-Transcriptomics of SARS-CoV-2 Infected Cells.” Emerging Microbes and Infections 9(1):1–36. doi: 10.1080/22221751.2020.1799723
  11. E. Mohammadi, R. Benfeitas, H. Turkez, J. Boren, J. Nielsen, M. Uhlen, A. Mardinoglu. 2020. “Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning.” Cancers. doi: 10.3390/cancers12092694
  12. C. Zhang, E. Bjornson, M. Arif, A. Tebani, A. Lovric, R. Benfeitas, M. Ozcan, K. Juszczak, W. Kim, J. T. Kim, G. Bidkhori, M. Ståhlman, P. Bergh, M. Adiels, H. Turkez, M. Taskinen, J. Bosley, H. Marschall, J. Nielsen, M. Uhlén, J. Borén, A. Mardinoglu. 2020. “The Acute Effect of Metabolic Cofactor Supplementation: A Potential Therapeutic Strategy against Non‐alcoholic Fatty Liver Disease.” Molecular Systems Biology 16(4). doi: 10.15252/msb.209495
  13. R. Benfeitas, G. Bidkhori, B. Mukhopadhyay, M. Klevstig, M. Arif, C. Zhang, S. Lee, R. Cinar, J. Nielsen, M. Uhlen, J. Boren, G. Kunos, A. Mardinoglu. 2019. “Characterization of Heterogeneous Redox Responses in Hepatocellular Carcinoma Patients Using Network Analysis.” EBioMedicine 40:471–87. doi: 10.1016/j.ebiom.2018.12.057
  14. B. Turanli, C. Zhang, W. Kim, R. Benfeitas, M. Uhlen, K. Y. Arga, A. Mardinoglu. 2019. “Discovery of Therapeutic Agents for Prostate Cancer Using Genome-Scale Metabolic Modeling and Drug Repositioning.” EBioMedicine 42:386–96. doi: 10.1016/j.ebiom.2019.03.009
  15. G. Bidkhori, R. Benfeitas, E. Elmas, M. N. Kararoudi, M. Arif, M. Uhlen, J. Nielsen, A. Mardinoglu. 2018. “Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma.” Frontiers in Physiology 9(JUL):916. doi: 10.3389/fphys.2018.00916
  16. G. Bidkhori, R. Benfeitas, M. Klevstig, C. Zhang, J. Nielsen, M. Uhlen, J. Boren, A. Mardinoglu. 2018. “Metabolic Network-Based Stratification of Hepatocellular Carcinoma Reveals Three Distinct Tumor Subtypes.” Proceedings of the National Academy of Sciences of the United States of America 115(50):E11874–83. doi: 10.1073/pnas.1807305115
  17. S. Lee, C. Zhang, M. Arif, Z. Liu, R. Benfeitas, G. Bidkhori, S. Deshmukh, M. Al Shobky, A. Lovric, J. Boren, J. Nielsen, M. Uhlen, A. Mardinoglu. 2018. “TCSBN: A Database of Tissue and Cancer Specific Biological Networks.” Nucleic Acids Research 46(D1):D595–600. doi: 10.1093/nar/gkx994
  18. A. Lovric, M. Granér, E. Bjornson, M. Arif, R. Benfeitas, K. Nyman, M. Ståhlman, M. O. Pentikäinen, J. Lundbom, A. Hakkarainen, R. Sirén, M. S. Nieminen, N. Lundbom, K. Lauerma, M. R. Taskinen, A. Mardinoglu, J. Boren. 2018. “Characterization of Different Fat Depots in NAFLD Using Inflammation-Associated Proteome, Lipidome and Metabolome.” Scientific Reports. doi: 10.1038/s41598-018-31865-w
  19. D. Rosario, R. Benfeitas, G. Bidkhori, C. Zhang, M. Uhlen, S. Shoaie, A. Mardinoglu. 2018. “Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling.” Frontiers in Physiology 9(JUN):775. doi: 10.3389/fphys.2018.00775
  20. C. Zhang, G. Bidkhori, R. Benfeitas, S. Lee, M. Arif, M. Uhlén, A. Mardinoglu. 2018. “ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.” Frontiers in Physiology. doi: 10.3389/fphys.2018.01355
  21. R. Benfeitas, M. Uhlen, J. Nielsen, A. Mardinoglu. 2017. “New Challenges to Study Heterogeneity in Cancer Redox Metabolism.” Frontiers in Cell and Developmental Biology 5(JUL):65.
  22. M. Uhlen, 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.-H. H. Edqvist, D. Djureinovic, P. Micke, C. Lindskog, A. Mardinoglu, F. Ponten. 2017. “A Pathology Atlas of the Human Cancer Transcriptome.” Science 357(6352):eaan2507. doi: 10.1126/science.aan2507
  23. J. Comas, R. Benfeitas, E. Vilaprinyo, A. Sorribas, F. Solsona, G. Farré, J. Berman, U. Zorrilla, T. Capell, G. Sandmann, C. Zhu, P. Christou, R. Alves. 2016. “Identification of Line-Specific Strategies for Improving Carotenoid Production in Synthetic Maize through Data-Driven Mathematical Modeling.” The Plant Journal : For Cell and Molecular Biology. doi: 10.1111/tpj.13210
  24. R. Benfeitas, G. Selvaggio, F. Antunes, P. M. B. M. Coelho, A. Salvador. 2014. “Hydrogen Peroxide Metabolism and Sensing in Human Erythrocytes: A Validated Kinetic Model and Reappraisal of the Role of Peroxiredoxin II.” Free Radical Biology & Medicine 74(1):35–49. doi: 10.1016/j.freeradbiomed.2014.06.007