Rui Benfeitas, PhD

Translational Research, Precision Medicine, and Systems Biology

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I develop biomarker strategies for translational medicine and patient stratification, from early to late phase clinical research. My research focuses in employing systems medicine, network analysis and machine learning techniques for integration of high throughput data for disease characterization, 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 Head of Translational & Precision Medicine at Chiesi Pharma, working in respiratory disease with focus on chronic respiratory diseases such as interstitial lung disease, pulmonary hypertension, chronic obstructive pulmonary disease and bronchiectasis. I am also Scientific Advisor to met atlasMetabolic Atlas

News:

- 28/09/25 - I presented "Seralutinib targets fibrotic pathways in IPF: evidence from single-cell transcriptomics" (oral presentation, Abstract OA1201) at the ERS Congress 2025.

- 27/02/25 - Our study of the host plasma microenvironment in immunometabolically impaired HIV infection is now published at Advanced Science.

- 09/09/23 - I presented "An endothelial cell subtype is linked with altered Rho-kinase (ROCK)-associated pathways in PAH" (oral communication) at the ERS Congress 2023.

- 16/02/23 - Our network-based multi-omics integration revealing a metabolic at-risk profile within treated HIV-infection is now published at eLife.

- 07/07/22 - Our multi-omics personalized network analyses of central metabolism disruption associated with COVID-19 severity are now published at Cell Systems.

- 19/04/22 - Our multi-omics study of host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever virus is now published at eLife.

- 28/02/22 - 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

- 03/12/21 - Our meta-analysis of labeled and unlabeled Alzheimer's disease is now published at Scientific Data.

► More (click to expand):

- 28/09/21 - Our study of the proteomic behavior of SARS-CoV-2 and its severity is now published at Mol. Cel. Proteomics. See the press release.

- 24/09/21 - Our work in the analysis of transcriptomic data of Alzheimer's and Parkinson's disease highlighting age-related alterations is now published in Biomedicines.

- 10/09/21 - I hosted three open seminars in systems biology broadcasted online.
  - 06/09/21: Pedro Beltrao - "BiG Talks – Network based analysis of 1002 GWAS study defines a pleiotropy map of human cell biology" (youtube);
  - 10/09/21: Mihail Anton - "Metabolic Atlas: Genome-scale metabolic models for easy browsing and analysis" (youtube);
  - 10/09/21: Lars Juhl Jensen - "Network-based integration and visualization of large-scale data" (youtube);

- 06/08/21 - I organized and taught at the Elixir-Sweden Omics Integration and Systems Biology course.

- 22/07/21 - I organized and taught a short tutorial in omics integration and systems biology at the ISMB / ECCB 2021.

- 11/05/21 - Our work in CVD that was previously in biorxiv is now published in eLife. See also the highlight.

- 04/05/21 - We studied the lipidomic and metabolomic relationships displayed by HIV patients undergoing long-term retroviral treatment in a new preprint.

- 30/04/21 - New pre-print out for our work in metabolomic characterization in HIV of the COCOMO cohort.

- 02/03/21 - New pre-print out for our work in characterizing disrupted metabolism in host cells infected with SARS-CoV-2.