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Patrick Aloy

Patrick Aloy

Institut de Recerca Biomèdica

Life & Medical Sciences

Dr Patrick Aloy is an ICREA Research Professor and Principal Investigator of the Structural Systems Biology lab at the IRB. He has a BSc in Biochemistry and a MSc in Biotechnology from the Univ. Autònoma de Barcelona, Spain, and spent six years as postdoctoral researcher and staff scientist at the European Molecular Biology Laboratory, Heidelberg, Germany. For twenty years, Dr Aloy has been developing and implementing new technologies and algorithms, applying state-of-the-art methods to specific problems and bridging the gap between theoretical models and experiments in different disciplines. In the last years, he has pioneered system-scale analyses of macromolecular assemblies and networks using high-resolution three-dimensional structures, which has become a new discipline in structure prediction. Dr Aloy has over 120 publications in first-rate journals, with over 14,500 citations and remarkable press coverage, illustrating the scientific and social impact of the work.

Research interests

The main goal of his lab is to combine molecular, cell and computational biology to unveil the basic wiring architecture and dynamics of physio-pathological pathways to increase our understanding of how biological systems change from the healthy state to disease. In the last years he has been developing resources to process, harmonize and integrate bioactivity data on small molecules, providing compound bioactivity descriptors that push the similarity principle beyond chemical properties. Currently, the main research line in the lab is to collect heterogeneous datasets and develop novel methodologies to integrate different layers of regulation to unveil disease signatures. Moreover, they are convinced that artificial intelligence (AI) will transform drug discovery, as it is reshaping other areas of science and technology, and biological signatures are the key to guide the (semi) automated design of chemical compounds to globally revert disease states, beyond individual targets.

Selected publications

– Meldal BHM, Pons C, Perfetto L, Del-Toro N, Wong E, Aloy P, Hermjakob H, Orchard S & Porras P 2021, ‘Analysing the yeast complexome-the Complex Portal rising to the challenge‘, Nucleic Acids Research, 49, 6, 3156 – 3167.

– Parts L, Batte A, Lopes M, Yuen MW, Laver M, San Luis B-J, Yue J-X, Pons C, Eray E, Aloy P, Liti G & van Leeuwen J 2021, ‘Natural variants suppress mutations in hundreds of essential genes‘, Molecular Systems Biology, 17, 5, e10138.

– Costanzo M, Hou J, Messier V, Nelson J, Rahman M, VanderSluis B, Wang W, Pons C, Ross C, Usaj M, San Luis B-J, Shuteriqi E, Koch EN, Aloy P, Myers CL, Boone C & Andrews B 2021, ‘Environmental robustness of the global yeast genetic interaction network‘, Science, 372, 6542, 589 – +.

– Bertoni M, Duran-Frigola M, Badia-i-Mompel P, Pauls E, Orozco-Ruiz M, Guitart-Pla O, Alcalde V, Diaz VM, Berenguer-Llergo A, Brun-Heath I, Villegas N, Garcia de Herreros A & Aloy P 2021, ‘Bioactivity descriptors for uncharacterized chemical compounds‘, Nature Communications, 12, 1, 3932.

– Pauls E, Bayod S, Mateo L, Alcalde V, Juan-Blanco T, Sanchez-Soto M, Saido TC, Saito T, Berrenguer-Llergo A, Attolini CS-O, Gay M, de Oliveira E, Duran-Frigola M & Aloy P 2021, ‘Identification and drug-induced reversion of molecular signatures of Alzheimer’s disease onset and progression in App(NL-G-F), App(NL-F), and 3xTg-AD mouse models‘, Genome Medicine, 13, 1, 168.

– Fehér C, Pastor-Ibáñez R, Leal L, Plana M, Arnnedo M, van den Ham H-J, Andeweg AC, Gruters RA, Díez-Fuertes F, Alcamí J, Aloy P &  García F 2021, ‘ Association of transcriptomics signatures of inflammatory response with viral control after dendritic cell-based therapeutic vaccination in HIV-1 infected individuals‘. Vaccines, 19, 799.

ICREA Memoir 2021