Structural Bioinformatics and Network Biology
Patrick Aloy
ICREA Research Professor
Lab members
Martino Bertoni, PhD
Nicolas Soler, PhD
Adrià Fernández-Torras, MSc
Our projects
Modern molecular and cell biology no longer focus on single macromolecules but now look into complexes, pathways or even entire organism interactomes. The field of systems biology is now mainly centred on unravelling these relationships and trying to use the information they contain to boost novel biomedical applications. Accordingly, the main goal of my laboratory is to combine computational and structural biology with interaction discovery experiments to unveil the basic wiring architecture of physio-pathological pathways. Our contribution to Structural Systems Biology (a term that we coined -Aloy & Russell, Nat Rev Mol Cell Biol 2006- and has now more that 140,000 exact matches in Google) related to human disease is indeed having important bearings in the discovery of new drug targets and biomarkers (e.g. Mateo et al. Genome Med 2018, 2020), optimization of preclinical models and understanding how biological networks change from the healthy state to disease (e.g. Mosca et al. Nat Methods 2013, 2015). Additionally, in the last years, we have incorporated a complementary research line on systems pharmacology, so that the group can now tackle complex diseases from the drugs´ perspective, providing compound bioactivity descriptors that push the similarity principle beyond chemical properties, reaching various ambits of biology (e.g. Duran-Frigola et al. Nat Commun 2016, Nat Biotechnol 2020). Overall, we are actively pursuing three interrelated research lines devoted to reveal the molecular bases of how cell networks operate in healthy and pathological states, suggesting network medicine (global) approaches to tackle complex disorders, and blending biology and chemistry to enable systems pharmacology.
Last publications
Bertoni M et al. Bioactivity descriptors for uncharacterized compounds. bioRxiv, 2020, DOI: https://doi.org/10.1101/2020.07.21.214197
van Leeuwen J et al. Systematic analysis of bypass suppression of essential genes. Mol Syst Biol, 2020, 16(9):e9828, DOI: 10.15252/msb.20209828
Mateo L et al. Personalized cancer therapy prioritization based on driver alteration co-occurrence patterns. Genome Med, 2020, 12(1):78, DOI: 10.1186/s13073-020-00774-x
Duran-Frigola M et al. Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs, J Chem Inf Model, 2020, DOI: https://doi.org/10.1021/acs.jcim.0c00420
Duran-Frigola M et al. Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. Nature Biotechnology, 2020, 38(9):1087-1096, DOI: https://doi.org/10.1038/s41587-020-0502-7
Patrick Aloy
ICREA Research Professor
Lab members
Martino Bertoni, PhD
Nicolas Soler, PhD
Adrià Fernández-Torras, MSc
Our projects
Modern molecular and cell biology no longer focus on single macromolecules but now look into complexes, pathways or even entire organism interactomes. The field of systems biology is now mainly centred on unravelling these relationships and trying to use the information they contain to boost novel biomedical applications. Accordingly, the main goal of my laboratory is to combine computational and structural biology with interaction discovery experiments to unveil the basic wiring architecture of physio-pathological pathways. Our contribution to Structural Systems Biology (a term that we coined -Aloy & Russell, Nat Rev Mol Cell Biol 2006- and has now more that 140,000 exact matches in Google) related to human disease is indeed having important bearings in the discovery of new drug targets and biomarkers (e.g. Mateo et al. Genome Med 2018, 2020), optimization of preclinical models and understanding how biological networks change from the healthy state to disease (e.g. Mosca et al. Nat Methods 2013, 2015). Additionally, in the last years, we have incorporated a complementary research line on systems pharmacology, so that the group can now tackle complex diseases from the drugs´ perspective, providing compound bioactivity descriptors that push the similarity principle beyond chemical properties, reaching various ambits of biology (e.g. Duran-Frigola et al. Nat Commun 2016, Nat Biotechnol 2020). Overall, we are actively pursuing three interrelated research lines devoted to reveal the molecular bases of how cell networks operate in healthy and pathological states, suggesting network medicine (global) approaches to tackle complex disorders, and blending biology and chemistry to enable systems pharmacology.
Last Publications
Bertoni M et al. Bioactivity descriptors for uncharacterized compounds. bioRxiv, 2020, DOI: https://doi.org/10.1101/2020.07.21.214197
van Leeuwen J et al. Systematic analysis of bypass suppression of essential genes. Mol Syst Biol, 2020, 16(9):e9828, DOI: 10.15252/msb.20209828
Mateo L et al. Personalized cancer therapy prioritization based on driver alteration co-occurrence patterns. Genome Med, 2020, 12(1):78, DOI: 10.1186/s13073-020-00774-x
Duran-Frigola M et al. Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs, J Chem Inf Model, 2020, DOI: https://doi.org/10.1021/acs.jcim.0c00420
Duran-Frigola M et al. Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. Nature Biotechnology, 2020, 38(9):1087-1096, DOI: https://doi.org/10.1038/s41587-020-0502-7