Rui Benfeitas, PhD

Multi-omics Integration and Systems Biology

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 disease characterizations combining transcriptomic, proteomic, metabolomic, and epigenomic data.

I am currently Translational & Precision Medicine lead at Chiesi Pharma and Scientific Advisor to met atlasMetabolic Atlas


- 28/02/2022 - Several papers out in the last few months:
  - Metabolomic analysis of HIV individuals with metabolic syndrome in Aging
  - Lipidomic analysis of HIV individuals with metabolic syndrome in Frontiers in Immunology
  - Metabolic reprograming in treated HIV subjects in Nature Communications Biology

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

► More (click to expand):

- 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.

- 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.