Peer-reviewed articles and conference presentations, grouped by research theme. Select a theme to jump to its section. Within each theme, items are newest first; (conference presentation) and (preprint) are labelled as such.

Chronic respiratory disease2 presentations Immunometabolism, HIV & immune-mediated disease6 papers Viral infection & host–pathogen systems biology4 papers Cancer systems biology & metabolism8 papers Cardiometabolic & liver disease4 papers Neurodegeneration & ageing2 papers Computational methods, tools & modeling6 papers

Chronic respiratory disease

  • 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 (conference presentation)
  • 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 (conference presentation)

Immunometabolism, HIV & immune-mediated disease

  • 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
  • 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
  • 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
  • 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 12:732736 doi: 10.3389/fimmu.2021.742736
  • 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: 10.18632/aging.203622
  • 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

Viral infection & host–pathogen systems biology

  • 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
  • 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
  • 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
  • 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

Cancer systems biology & metabolism

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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.
  • 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

Cardiometabolic & liver disease

  • 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.” eLife 10.7554/eLife.66921 (highlighted in eLife)
  • 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
  • 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
  • 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

Neurodegeneration & ageing

  • 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
  • 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

Computational methods, tools & modeling

  • 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
  • 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 (preprint)
  • 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
  • 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
  • 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
  • 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