Aloy, Patrick

A reference map of the human binary protein interactome

Luck, K., Kim, D.-K., Lambourne, L., Spirohn, K., Begg, B. E., Bian, W., Brignall, R., Cafarelli, T., Campos-Laborie, F. J., Charloteaux, B., et al. (2020) · Nature

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

Cited by 1,197

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Yang, X., Coulombe-Huntington, J., Kang, S., Sheynkman, G. M., Hao, T., Richardson, A., Sun, S., Yang, F., Shen, Y. A., Murray, R. R., et al. (2016) · Cell

RNA Research and SplicingBioinformatics and Genomic Networks

Cited by 583

Interactome3D: adding structural details to protein networks

Mosca, R., Céol, A., & Aloy, P. (2013) · Nature Methods

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 479

Structure-Based Assembly of Protein Complexes in Yeast

Aloy, P., Böttcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A.-C., Bork, P., Superti-Furga, G., Serrano, L., et al. (2004) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 383

The binary protein-protein interaction landscape of Escherichia coli

Rajagopala, S. V., Sikorski, P., Kumar, A., Mosca, R., Vlasblom, J., Arnold, R., Franca-Koh, J., Pakala, S. B., Phanse, S., Ceol, A., et al. (2014) · Nature Biotechnology

Bioinformatics and Genomic NetworksBacterial Genetics and Biotechnology

Cited by 233

A framework for exhaustively mapping functional missense variants

Weile, J., Sun, S., Cote, A. G., Knapp, J., Verby, M., Mellor, J. C., Wu, Y., Pons, C., Wong, C., van Lieshout, N., et al. (2017) · Molecular Systems Biology

Genomics and Rare DiseasesCRISPR and Genetic Engineering

Cited by 187

Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker

Duran-Frigola, M., Pauls, E., Guitart-Pla, O., Bertoni, M., Alcalde, V., Amat, D., Juan-Blanco, T., & Aloy, P. (2020) · Nature Biotechnology

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 126

Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans

Copley, R. R., Aloy, P., Russell, R. B., & Telford, M. J. (2004) · Evolution & Development

Genomics and Phylogenetic StudiesInvertebrate Taxonomy and Ecology

Cited by 108

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline

Hennrich, M. L., Romanov, N., Horn, P., Jaeger, S., Eckstein, V., Steeples, V., Ye, F., Ding, X., Poisa-Beiro, L., Lai, M. C., et al. (2018) · Nature Communications

Hematopoietic Stem Cell TransplantationGenetics, Aging, and Longevity in Model Organisms

Cited by 101

Bioactivity descriptors for uncharacterized chemical compounds

Bertoni, M., Duran-Frigola, M., Badia-i-Mompel, P., Pauls, E., Orozco-Ruiz, M., Guitart-Pla, O., Alcalde, V., Diaz, V. M., Berenguer-Llergo, A., Brun-Heath, I., et al. (2021) · Nature Communications

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 92

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

Douglass, E. F., Allaway, R. J., Szalai, B., Wang, W., Tian, T., Fernández-Torras, A., Realubit, R., Karan, C., Zheng, S., Pessia, A., et al. (2022) · Cell Reports Medicine

Computational Drug Discovery MethodsGene expression and cancer classification

Cited by 68

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque

Fernández-Torras, A., Duran-Frigola, M., Bertoni, M., Locatelli, M., & Aloy, P. (2022) · Nature Communications

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 59

Assessing the Applicability of Template-Based Protein Docking in the Twilight Zone

Negroni, J., Mosca, R., & Aloy, P. (2014) · Structure

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 35

Truncating variant burden in high-functioning autism and pleiotropic effects of LRP1 across psychiatric phenotypes

Torrico, B., Shaw, A. D., Mosca, R., Vivó-Luque, N., Hervás, A., Fernàndez-Castillo, N., Aloy, P., Bayés, M., Fullerton, J. M., Cormand, B., et al. (2019) · Journal of Psychiatry and Neuroscience

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 34

Comprehensive detection and characterization of human druggable pockets through novel binding site descriptors

Comajuncosa-Creus, A., Jorba, G., Barril, X., & Aloy, P. (2024) · Nature Communications

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 32

Formatting biological big data for modern machine learning in drug discovery

Duran‐Frigola, M., Fernández‐Torras, A., Bertoni, M., & Aloy, P. (2019) · WIREs Computational Molecular Science

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 25