Rui Benfeitas

Rui Benfeitas NBIS expert

Omics Integration, Systems Biology, Biological Network Analysis, Precision Medicine, RNAseq, Metabolism, Metabolic Modeling
phone +46 (0)760842583

Rui has a PhD in Systems Biology from the University of Coimbra, Portugal, and a biochemistry background. During his graduate studies he used kinetic models, parameter estimation from experimental time series to understand metabolism in human cells. He then pursued a postdoc in systems and precision medicine at KTH – Royal Institute of Technology where his main projects involved multi-omics integration in cancer and metabolic diseases including metabolomic, proteomic and particularly transcriptomic data (microarray and RNA-seq). He developed novel methods for biological network analysis, patient stratification and association between biological and clinical features, identification of potential therapeutic targets, and drug repositioning.

Rui joined NBIS short-term support during 2019 and is primarily involved in omics integration and systems biology projects.

Google Scholar profile

Selected publications

Benfeitas, R., Bidkhori, G., Mukhopadhyay, B., Klevstig, M., Arif, M., Zhang, C., Lee, S., Cinar, R., Nielsen, J., Uhlen, M., Boren, J., Kunos, G., and Mardinoglu, A. (2018) Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis. EBioMedicine.

Bidkhori, G., Benfeitas, R., Klevstig, M., Zhang, C., Nielsen, J., Uhlen, M., Boren, J., and Mardinoglu, A. (2018) Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes. Proc Natl Acad Sci U S A, 115, E11874–E11883.

Bidkhori, G., Benfeitas, R., Elmas, E., Kararoudi, M. N., Arif, M., Uhlen, M., Nielsen, J., and Mardinoglu, A. (2018) Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma. Front Physiol, 9, 916.

Zhang, C., Bidkhori, G., Benfeitas, R., Lee, S., Arif, M., Uhlen, M., and Mardinoglu, A. (2018) ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling. Front Physiol, 9, 1355.

Rosario, D., Benfeitas, R., Bidkhori, G., Zhang, C., Uhlen, M., Shoaie, S., and Mardinoglu, A. (2018) Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling. Front Physiol, 9, 775.

Lee, S., Zhang, C., Arif, M., Liu, Z., Benfeitas, R., Bidkhori, G., Deshmukh, S., Al Shobky, M., Lovric, A., Boren, J., Nielsen, J., Uhlen, M., and Mardinoglu, A. (2018) TCSBN: a database of tissue and cancer specific biological networks. Nucleic Acids Res, 46, D595–D600.

Lovric, A., Graner, M., Bjornson, E., Arif, M., Benfeitas, R., Nyman, K., Stahlman, M., Pentikainen, M. O., Lundbom, J., Hakkarainen, A., Siren, R., Nieminen, M. S., Lundbom, N., Lauerma, K., Taskinen, M. R., Mardinoglu, A., and Boren, J. (2018) Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome. Sci Rep, 8, 14200.

Uhlen, M., Zhang, C., Lee, S., Sjostedt, E., Fagerberg, L., Bidkhori, G., Benfeitas, R., Arif, M., Liu, Z., Edfors, F., Sanli, K., Feilitzen, K. von, Oksvold, P., Lundberg, E., Hober, S., Nilsson, P., Mattsson, J., Schwenk, J. M., Brunnstrom, H., Glimelius, B., Sjoblom, T., Edqvist, P. H., Djureinovic, D., Micke, P., Lindskog, C., Mardinoglu, A., and Ponten, F. (2017) A pathology atlas of the human cancer transcriptome. Science, 357.

Benfeitas, R., Uhlen, M., Nielsen, J., and Mardinoglu, A. (2017) New Challenges to Study Heterogeneity in Cancer Redox Metabolism. Front Cell Dev Biol, 5, 65.

Comas, J., Benfeitas, R., Vilaprinyo, E., Sorribas, A., Solsona, F., Farre, G., Berman, J., Zorrilla, U., Capell, T., Sandmann, G., Zhu, C., Christou, P., and Alves, R. (2016) Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modeling. Plant J, 87, 455–71.

Benfeitas, R., Selvaggio, G., Antunes, F., Coelho, P. M., and Salvador, A. (2014) Hydrogen peroxide metabolism and sensing in human erythrocytes: a validated kinetic model and reappraisal of the role of peroxiredoxin II. Free Radic Biol Med, 74, 35–49.