P. Aloy

P. Aloy, J. Gómez-Verjan, I. González-Sánchez, 2016, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

Predicting protein-protein interaction specificity through the integration of three-dimensional structural information and the evolutionary record of protein domains.

P. Aloy, A. Panjkovich, 2010, Molecular bioSystems.

Uncovering new substrates for Aurora A kinase

Roland A. Pache, I. Vernos, P. Aloy, 2010, EMBO reports.

Integrating and formatting biomedical data in the Bioteque, a comprehensive repository of pre-calculated knowledge graph embeddings

P. Aloy, Miquel Duran-Frigola, Martino Bertoni, 2022 .

Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations.

Roland A. Pache, B. Séraphin, P. Aloy, 2010, Structure.

Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori *

P. Uetz, S. Wuchty, P. Aloy, 2018, Molecular & Cellular Proteomics.

The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium

R. Eils, H. Augustin, C. Plass, 2018, eLife.

Systematic analysis of bypass suppression of essential genes

C. Myers, P. Aloy, B. Andrews, 2020, Molecular systems biology.

Ribonucleotide Reductases: Divergent Evolution of an Ancient Enzyme

P. Aloy, F. Rodríguez-Trelles, E. Torrents, 2002, Journal of Molecular Evolution.

The Crystal Structure of the Inhibitor-complexed Carboxypeptidase D Domain II and the Modeling of Regulatory Carboxypeptidases*

P. Aloy, F. Avilés, V. Companys, 2001, The Journal of Biological Chemistry.

Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs

Victor R. Martinez, P. Aloy, Roi Blanco, 2020, J. Chem. Inf. Model..

Residues Coevolution Gui des the Systematic Identification of Alternative Functional Conformations in Proteins Graphical

P. Aloy, M. Orozco, Roberto Mosca, 2022 .

Analysing the yeast complexome—the Complex Portal rising to the challenge

P. Aloy, H. Hermjakob, S. Orchard, 2020, bioRxiv.

Increasing the precision of orthology-based complex prediction through network alignment

Roland A. Pache, P. Aloy, 2014, PeerJ.

Proteome data improves protein function prediction in the interactome of H. pylori

Sabine C. Mueller, S. Wuchty, P. Aloy, 2018 .

Novel Neuroprotective Multicomponent Therapy for Amyotrophic Lateral Sclerosis Designed by Networked Systems

P. Aloy, X. Navarro, Albert Pujol, 2016, PloS one.

Characterization of p38α signaling networks in cancer cells using quantitative proteomics and phosphoproteomics

P. Aloy, A. Nebreda, Adrià Fernández-Torras, 2022, bioRxiv.

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

P. Aloy, Miquel Duran-Frigola, Martino Bertoni, 2022, Nature Communications.

A proteome-scale map of the SARS-CoV-2–human contactome

Nora Marín-de la Rosa, Atina G. Coté, M. Calderwood, 2022, Nature Biotechnology.

Diverse natural variants suppress mutations in hundreds of essential genes

P. Aloy, Bryan-Joseph San Luis, L. Parts, 2020, bioRxiv.

Co-occurrence of essential gene dispensability and bypass suppressor mutations across species

P. Aloy, Carles Pons, Jolanda van Leeuwen, 2022, bioRxiv.

Global analysis of suppressor mutations that rescue human genetic defects

P. Aloy, Carles Pons, Jolanda van Leeuwen, 2022, bioRxiv.

Low Complexity Region

P. Aloy, J. Heringa, 2004, Definitions.

Global analysis of suppressor mutations that rescue human genetic defects

P. Aloy, Carles Pons, Jolanda van Leeuwen, 2022, bioRxiv.

Democratising Knowledge Representation with BioCypher

Benjamin M. Gyori, Charles Tapley Hoyt, Maximilian T. Strauss, 2022, 2212.13543.

Binary interactome models of inner- versus outer-complexome organisation

István A. Kovács, Atina G. Coté, Miles W. Mee, 2022, bioRxiv.

Environmental robustness of the global yeast genetic interaction network

Elizabeth N. Koch, C. Myers, P. Aloy, 2021, Science.

Towards Alzheimer's root cause: ECSIT as an integrating hub between oxidative stress, inflammation and mitochondrial dysfunction

P. Aloy, Andreas Zanzoni, M. Soler‐Lopez, 2012, BioEssays : news and reviews in molecular, cellular and developmental biology.

Target selection for complex structural genomics.

Patrick Aloy, Jerónimo Bravo, P. Aloy, 2006, Current opinion in structural biology.

Association of Transcriptomic Signatures of Inflammatory Response with Viral Control after Dendritic Cell-Based Therapeutic Vaccination in HIV-1 Infected Individuals

P. Aloy, M. Plana, M. Arnedo, 2021, Vaccines.

Structural Insights into the Target Specificity of Plant Invertase and Pectin Methylesterase Inhibitory Proteins

P. Aloy, K. Scheffzek, M. Hothorn, 2004, The Plant Cell Online.

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

P. Aloy, Miquel Duran-Frigola, Teresa Juan-Blanco, 2020, Nature Biotechnology.

Molecular characterization of chronic liver disease dynamics: From liver fibrosis to acute-on-chronic liver failure

P. Aloy, C. Fondevila, P. Sancho-Bru, 2022, JHEP reports : innovation in hepatology.

A reference map of the human binary protein interactome

Patrick Aloy, Gary D. Bader, Yang Wang, 2020, Nature.

Towards a detailed atlas of protein-protein interactions.

Tirso Pons, Alfonso Valencia, Arnaud Céol, 2013, Current opinion in structural biology.

Democratising Knowledge Representation with BioCypher

Benjamin M. Gyori, Charles Tapley Hoyt, Maximilian T. Strauss, 2022, 2212.13543.

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

Ashkan Golshani, Omar Wagih, John Parkinson, 2016, Cell reports.

Resource Conditional Epistatic Inter actionMaps Reveal Global Functional Rewiring ofGenome Integrity Pathways in Escherichia coli Graphical

A. Emili, James Vlasblom, G. Musso, 2016 .

Bioactivity descriptors for uncharacterized chemical compounds

P. Aloy, Miquel Duran-Frigola, A. G. de Herreros, 2021, Nature Communications.

Bioactivity descriptors for uncharacterized compounds

Patrick Aloy, Martino Bertoni, Oriol Guitart-Pla, 2020, bioRxiv.

Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence

P. Aloy, Amelie Stein, R. Medema, 2010, Nucleic acids research.

Functional and Structural Analysis of C-Terminal BRCA1 Missense Variants

P. Aloy, Roberto Mosca, C. Lázaro, 2013, PloS one.

Functional and Structural Analysis of C-Terminal BRCA 1 Missense Variants

P. Aloy, Roberto Mosca, C. Lázaro, 2013 .

Systematic identification of molecular links between core and candidate genes in breast cancer.

Guillermo Suñé, Patrick Aloy, Miquel Duran-Frigola, 2015, Journal of molecular biology.

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

P. Aloy, Miquel Duran-Frigola, Martino Bertoni, 2022, Nature Communications.

Identification and drug-induced reversion of molecular signatures of Alzheimer’s disease onset and progression in AppNL-G-F, AppNL-F, and 3xTg-AD mouse models

Camille Stephan-Otto Attolini, P. Aloy, Miquel Duran-Frigola, 2021, Genome medicine.

Connecting chemistry and biology through molecular descriptors.

P. Aloy, Miquel Duran-Frigola, Adrià Fernández-Torras, 2021, Current opinion in chemical biology.

Identification and drug-induced reversion of molecular signatures of Alzheimer’s disease onset and progression in AppNL-G-F, AppNL-F, and 3xTg-AD mouse models

Camille Stephan-Otto Attolini, P. Aloy, Miquel Duran-Frigola, 2021, Genome Medicine.

Encircling the regions of the pharmacogenomic landscape that determine drug response

P. Aloy, Miquel Duran-Frigola, Adrià Fernández-Torras, 2018, Genome Medicine.

Insights & Perspectives Towards Alzheimer's root cause: ECSIT as an integrating hub between oxidative stress, inflammation and mitochondrial dysfunction

P. Aloy, 2012 .

An inter‐species protein–protein interaction network across vast evolutionary distance

Albert-László Barabási, Yu Xia, David E Hill, 2016, Molecular systems biology.

Drug sensitivity in cancer cell lines is not tissue-specific

Patrick Aloy, Miquel Duran-Frigola, P. Aloy, 2015, Molecular Cancer.

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

Judith B. Zaugg, P. Bork, A. Gavin, 2018, Nature Communications.

Ten thousand interactions for the molecular biologist

Patrick Aloy, Robert B Russell, R. Russell, 2004, Nature Biotechnology.

Systematic Identification and Quantification of Substrate Specificity Determinants in Human Protein Kinases

P. Aloy, Roberto Mosca, Manuel A. Alonso-Tarajano, 2014 .

Personalized cancer therapy prioritization based on driver alteration co-occurrence patterns

Patrick Aloy, Lidia Mateo, Miquel Duran-Frigola, 2019, bioRxiv.

On the analysis of protein–protein interactions via knowledge‐based potentials for the prediction of protein–protein docking

Elisenda Feliu, Patrick Aloy, P. Aloy, 2011, Protein science : a publication of the Protein Society.

Revealing the molecular relationship between type 2 diabetes and the metabolic changes induced by a very-low-carbohydrate low-fat ketogenic diet

P. Aloy, Albert Pujol, J. Farrés, 2010, Nutrition & metabolism.

Natural variants suppress mutations in hundreds of essential genes

P. Aloy, Bryan-Joseph San Luis, L. Parts, 2021, Molecular systems biology.

Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage

Patrick Aloy, Francesco M. Mancuso, P. Aloy, 2015, Scientific Reports.

3did: a catalog of domain-based interactions of known three-dimensional structure

Arnaud Céol, Patrick Aloy, Roberto Mosca, 2013, Nucleic Acids Res..

Novel Peptide-Mediated Interactions Derived from High-Resolution 3-Dimensional Structures

Patrick Aloy, Amelie Stein, P. Aloy, 2010, PLoS Comput. Biol..

A reference map of the human binary protein interactome

Gary D Bader, István A. Kovács, Robert J. Weatheritt, 2020, Nature.

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

P. Aloy, J. Fullerton, M. Bayés, 2019, Journal of Psychiatry & Neuroscience.

Exploring genetic suppression interactions on a global scale

Mojca Mattiazzi Usaj, Atina G. Coté, A. Murray, 2016, Science.

DynBench3D, a Web-Resource to Dynamically Generate Benchmark Sets of Large Heteromeric Protein Complexes.

Martino Bertoni, Patrick Aloy, P. Aloy, 2018, Journal of molecular biology.

dSysMap: exploring the edgetic role of disease mutations

Jofre Tenorio-Laranga, Arnaud Céol, Patrick Aloy, 2015, Nature Methods.

Drug repositioning beyond the low-hanging fruits

Patrick Aloy, Lidia Mateo, Miquel Duran-Frigola, 2017 .

Understanding and predicting protein assemblies with 3 D structures

R. Russell, P. Aloy, 2014 .

Understanding and Predicting Protein Assemblies With 3D Structures

Robert B. Russell, Patrick Aloy, R. Russell, 2003, Comparative and functional genomics.

'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins

Baldomero Oliva, Francesc X. Avilés, Enrique Querol, 1997, Comput. Appl. Biosci..

Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions.

M. Madan Babu, Patrick Aloy, Roland A. Pache, 2009, BMC systems biology.

A molecular interpretation of genetic interactions in yeast

P. Aloy, Amelie Stein, 2008, FEBS letters.

Systems analysis of intracellular pH vulnerabilities for cancer therapy

E. Ruppin, R. Gillies, P. Aloy, 2018, Nature Communications.

Analysing the yeast complexome—the Complex Portal rising to the challenge

P. Aloy, H. Hermjakob, S. Orchard, 2021, Nucleic acids research.

Charting the molecular links between driver and susceptibility genes in colorectal cancer.

P. Aloy, M. Soler‐Lopez, Miquel Duran-Frigola, 2014, Biochemical and biophysical research communications.

Isolation of Human Colon Stem Cells Using Surface Expression of PTK7

P. Aloy, M. Selbach, P. Jung, 2015, Stem cell reports.

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

Patrick Aloy, Richard R Copley, Robert B Russell, 2004, Evolution & development.

Pooled‐matrix protein interaction screens using Barcode Fusion Genetics

David E Hill, Marc Vidal, Laurence Pelletier, 2016, Molecular systems biology.

The Proton-Pump Inhibitor Lansoprazole Enhances Amyloid Beta Production

Patrick Aloy, Montserrat Soler-López, Alberto Lleó, 2013, PloS one.

3did: interacting protein domains of known three-dimensional structure

Robert B. Russell, Patrick Aloy, Amelie Stein, 2004, Nucleic Acids Res..

Classification of protein disulphide-bridge topologies

M. Martí-Renom, P. Aloy, E. Querol, 2001, J. Comput. Aided Mol. Des..

Predictions without templates: New folds, secondary structure, and contacts in CASP5

Patrick Aloy, Robert B Russell, Alexander Stark, 2003, Proteins.

3did Update: domain–domain and peptide-mediated interactions of known 3D structure

Alejandro Panjkovich, Patrick Aloy, Amelie Stein, 2008, Nucleic Acids Res..

A classifier to predict viral control after antiretroviral treatment interruption in chronic HIV-1 infected patients.

P. Aloy, Felipe García, M. Plana, 2020, Journal of acquired immune deficiency syndromes.

Using neighborhood cohesiveness to infer interactions between protein domains

José María Carazo, Carlos Oscar Sánchez Sorzano, Patrick Aloy, 2015, Bioinform..

Breast Cancer Genes PSMC3IP and EPSTI1 Play a Role in Apoptosis Regulation

P. Aloy, M. Soler‐Lopez, Víctor Alcalde, 2015, PloS one.

M. Martí-Renom, P. Aloy, E. Querol, 1998, Journal of molecular biology.

3did: identification and classification of domain-based interactions of known three-dimensional structure

Arnaud Céol, Patrick Aloy, Amelie Stein, 2010, Nucleic Acids Res..

Systems analysis of intracellular pH vulnerabilities for cancer therapy

E. Ruppin, R. Gillies, P. Aloy, 2018, Nature Communications.

Global analysis of suppressor mutations that rescue human genetic defects

P. Aloy, Carles Pons, Jolanda van Leeuwen, 2023, bioRxiv.

BQsupports: systematic assessment of the support and novelty of new biomedical associations

P. Aloy, Martino Bertoni, Adrià Fernández-Torras, 2023, bioRxiv.

ISMB 2010 Organization

Roger L. Chang, S. Batzoglou, L. Cowen, 2010, Bioinformatics.

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

Judith B. Zaugg, P. Bork, A. Gavin, 2018, Nature Communications.

Expanding the Atlas of Functional Missense Variation for Human Genes

Atina G. Coté, R. Nussbaum, M. Vidal, 2017, bioRxiv.

InterPreTS: protein Interaction Prediction through Tertiary Structure

Robert B. Russell, Patrick Aloy, R. Russell, 2003, Bioinform..

Modelling repressor proteins docking to DNA

M J Sternberg, M. Sternberg, P. Aloy, 1998, Proteins.

Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs

Fergal P. Casey, Denis C. Shields, Patrick Aloy, 2008, J. Chem. Inf. Model..

Analysis of chemical and biological features yields mechanistic insights into drug side effects.

Patrick Aloy, Miquel Duran-Frigola, P. Aloy, 2013, Chemistry & biology.

IntSide: a web server for the chemical and biological examination of drug side effects

Patrick Aloy, Miquel Duran-Frigola, Teresa Juan-Blanco, 2014, Bioinform..

The EHEC-host interactome reveals novel targets for the translocated intimin receptor

Peter Uetz, Roman Häuser, Patrick Aloy, 2014, Scientific Reports.

Virological Outcome Measures During Analytical Treatment Interruptions in Chronic HIV-1-Infected Patients

P. Aloy, Felipe García, M. Plana, 2019, Open forum infectious diseases.

Comparative Analysis of the Sequences and Three-Dimensional Models of Human Procarboxypeptidases A1, A2 and B

P. Aloy, F. Avilés, V. Villegas, 1998, Biological chemistry.

Atina G. Coté, A. Meyer, A. Gingras, 2018, Science.

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

Juan Fernández-Recio, Patrick Aloy, Roberto Mosca, 2009, PLoS Comput. Biol..

Recycling side-effects into clinical markers for drug repositioning

P. Aloy, Miquel Duran-Frigola, 2012, Genome Medicine.

Eytan Ruppin, Xavier Barril, Gabriele Cruciani, 2017, PLoS Comput. Biol..

Helix–Coil Transition

P. Aloy, 2004 .

Pooled#matrix protein interaction screens using Barcode Fusion Genetics

Atina G. Coté, M. Vidal, Haiyuan Yu, 2016 .

NetAligner—a network alignment server to compare complexes, pathways and whole interactomes

Arnaud Céol, Patrick Aloy, Roland A. Pache, 2012, Nucleic Acids Res..

Unveiling the role of network and systems biology in drug discovery.

P. Aloy, Albert Pujol, Roberto Mosca, 2010, Trends in pharmacological sciences.

A network medicine approach to human disease

P. Aloy, Andreas Zanzoni, M. Soler‐Lopez, 2009, FEBS letters.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Gloria M. Sheynkman, Alyce A. Chen, Bridget E. Begg, 2016, Cell.

Personalized cancer therapy prioritization based on driver alteration co-occurrence patterns

P. Aloy, S. Chandarlapaty, P. Razavi, 2020, Genome Medicine.

Pooled‐matrix protein interaction screens using Barcode Fusion Genetics

Atina G. Coté, M. Vidal, Haiyuan Yu, 2016, Molecular systems biology.

Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions

Roland A. Pache, P. Aloy, M. Madan Babu, 2009, BMC Systems Biology.

The Role of Structural Disorder in the Rewiring of Protein Interactions through Evolution*

Roland A. Pache, P. Aloy, Roberto Mosca, 2012, Molecular & Cellular Proteomics.