Rui Benfeitas, PhD

Multi-omics Integration and Systems Biology

Senior bioinformatician & Vice Training Coordinator

NBIS Scilifelab Stockholm University

My research focuses in employing systems biology, network analysis and machine learning techniques for integration of high throughput data for disease characterization, patient stratification, connecting risk factors with molecular features, and computational prediction of therapeutic targets. I develop new algorithms for subgroup identification and personalized medicine characterizations in cancer, metabolic and infectious diseases, by combining transcriptomic, proteomic, metabolomic, and epigenomic data.

I am involved in bioinformatics training as course leader and Vice-coordinator for Training. I coordinate about 20 courses per year, for national and international bioinformatic events driven by NBIS. I am also leader for the course in ScilifelabOmics Integration and Systems Biology, a course that we have taught several times in the past both nationally and internationally. I regularly contribute to other courses with ad-hoc lessons.

I contribute as Scientific Advisor to ScilifelabMetabolic Atlas, and am part of the elixirElixir Systems Biology Focus Group.


- 28/02/2022 - Several papers out in the last few months:
  - Metabolomic analysis of HIV individuals with metabolic syndrome [doi:](;   - Lipidomic analysis of HIV individuals with metabolic syndrome [doi:](;   - Metabolic reprograming in treated HIV subjects [doi:](

- 03/12/2021 - Our meta-analysis of labeled and unlabeled Alzheimer's disease is now published at Scientific Data.

- 28/09/2021 - Our study of the proteomic behavior of SARS-CoV-2 and its severity is now published at Mol. Cel. Proteomics. See the press release.

- 24/09/2021 - Our work in the analysis of transcriptomic data of Alzheimer's and Parkinson's disease highlighting age-related alterations is now published in Biomedicines.

- 10/09/2021 - I hosted three open seminars in systems biology broadcasted online.
  - 06/09/2021: Pedro Beltrao - "BiG Talks – Network based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology" (youtube);
  - 10/09/2021: Mihail Anton - "Metabolic Atlas: Genome-scale metabolic models for easy browsing and analysis" (youtube);
  - 10/09/2021: Lars Juhl Jensen - "Network-based integration and visualization of large-scale data" (youtube);

- 06/08/2021 - I organized and taught at the Elixir-Sweden Omics Integration and Systems Biology course.

► More (click to expand):

- 22/07/2021 - I organized and taught a short tutorial in omics integration and systems biology at the ISMB / ECCB 2021.

- 11/05/2021 - Our work in CVD that was previously in biorxiv is now published in eLife. See also the highlight.

- 04/05/2021 - We studied the lipidomic and metabolomic relationships displayed by HIV patients undergoing long-term retroviral treatment in a new preprint.

- 30/04/2021 - New pre-print out for our work in metabolomic characterization in HIV of the COCOMO cohort.

- 02/03/2021 - New pre-print out for our work in characterizing disrupted metabolism in host cells infected with SARS-CoV-2.

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