Pre-prints

  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

Publications

  1. F. Mikaeloff, M. Gelpi, A. Escós, T. Wang, S. Gupta, A. Olofsson, S. Svensson Akusjärvi, S. Schuster, P. Naval, V. Sood, N. Nikouyan, A. D. Knudsen, B. Vestad, J. Høgh, J. R. Hov, T. Benfield, M. Trøseid, V. Pawar, M. Rucevic, R. Benfeitas, Á. Végvári, L. O’Mahony, R. Savai, N. K. Björkström, M. Lourda, J. P. de Magalhães, S. Weiss, A. Mardinoglu, M. K. Varshney, A. C. Karlsson, Y. A. Syed, S. D. Nielsen, U. Neogi. 2025. “Host Plasma Microenvironment in Immunometabolically Impaired HIV Infection Leads to Dysregulated Monocyte Function and Synaptic Transmission Ex Vivo.” Advanced Science 12(16):2416453. doi: 10.1002/advs.202416453
  2. F. Mikaeloff, M. Gelpi, R. Benfeitas, A. D. Knudsen, B. Vestad, J. Høgh, J. R. Hov, T. Benfield, D. D. Murray, C. G. Giske, A. Mardinoglu, M. Trøseid, S. D. Nielsen, U. Neogi. 2023. “Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection.” eLife 12:e82785. doi: 10.7554/eLife.82785
  3. A. T. Ambikan, H. Yang, S. Krishnan, S. Svensson Akusjärvi, S. Gupta, M. Lourda, M. Sperk, M. Arif, C. Zhang, H. Nordqvist, S. M. Ponnan, A. Sönnerborg, C. J. Treutiger, L. O’Mahony, A. Mardinoglu, R. Benfeitas, U. Neogi. 2022. “Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.” Cell Systems 13(8):665–681.e4. doi: 10.1016/j.cels.2022.06.006
  4. B. S. Song, J. S. Moon, J. Tian, H. Y. Lee, B. C. Sim, S. H. Kim, S. G. Kang, J. T. Kim, H. T. Nga, R. Benfeitas, Y. Kim, S. Park, R. R. Wolfe, H. S. Eun, M. Shong, S. Lee, I. Y. Kim, H. S. Yi. 2022. “Mitoribosomal defects aggravate liver cancer via aberrant glycolytic flux and T cell exhaustion.” J. Immunother. Cancer 10(5):e004337. doi: 10.1136/jitc-2021-004337
  5. U. Neogi, N. Elaldi, S. Appelberg, A. T. Ambikan, E. Kennedy, S. Dowall, B. K. Bagci, S. Gupta, J. E. Rodriguez, S. Svensson-Akusjärvi, V. M. Monteil, Á. Végvári, R. Benfeitas, A. C. Banerjea, F. Weber, R. Hewson, A. Mirazimi. 2022. “Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.” eLife 11:e76071. doi: 10.7554/eLife.76071
  6. 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 cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection” Nature Communications Biology
  7. 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
  8. 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: https://doi.org/10.18632/aging.203622
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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.
  27. 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
  28. 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
  29. 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

Conference abstracts

  1. R. Benfeitas, et al. 2025. “Seralutinib targets fibrotic pathways in IPF: Evidence from single-cell transcriptomics.” Oral presentation, ERS Congress 2025. Eur. Respir. J. 66(Suppl. 69):OA1201. abstract
  2. R. Benfeitas, F. Facchinetti, M. Govoni. 2023. “An endothelial cell subtype is linked with altered Rho-kinase (ROCK)-associated pathways in PAH.” Oral communication, ERS Congress 2023. abstract