List of works by Patrick Aloy

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

scientific article

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

scientific article published on 25 October 2008

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

scientific article

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

scientific article published on October 21, 2010

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

scientific article

A Classifier to Predict Viral Control After Antiretroviral Treatment Interruption in Chronic HIV-1-Infected Patients

scientific article published on 01 April 2020

A PanorOmic view of personal cancer genomes

scientific article published on 27 April 2017

A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks

A chemo-centric view of human health and disease

scientific article

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

scientific article published on 18 January 2022

A complex prediction: three-dimensional model of the yeast exosome.

scientific article published on July 2002

A computational system for modelling flexible protein-protein and protein-DNA docking.

scientific article published in January 1998

A framework for exhaustively mapping functional missense variants.

scientific article published on 21 December 2017

A molecular interpretation of genetic interactions in yeast

scientific article published on 20 February 2008

A network medicine approach to human disease

scientific article published on 06 March 2009

A novel framework for the comparative analysis of biological networks

scientific article

A proteome-scale map of the human interactome network

scientific article

A reference map of the human binary protein interactome

scientific article published on 08 April 2020

A second-generation protein-protein interaction network of Helicobacter pylori

scientific journal article

A structural perspective on protein-protein interactions.

scientific article

An inter-species protein-protein interaction network across vast evolutionary distance

scientific article (publication date: 22 April 2016)

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

scientific article published in April 2013

Approved drug mimics of short peptide ligands from protein interaction motifs

scientific article

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

article

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

scientific article

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

scientific article published on 16 July 2020

Breast cancer genes PSMC3IP and EPSTI1 play a role in apoptosis regulation

scientific article

Cancer network activity associated with therapeutic response and synergism

scientific article published on 24 August 2016

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

scientific article published in Nature Communications

Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases

scientific article published on 27 March 2019

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

scientific article

Classification of protein disulphide-bridge topologies.

scientific article published in May 2001

Comparative analysis of the sequences and three-dimensional models of human procarboxypeptidases A1, A2 and B.

scientific article published on February 1998

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

scientific article

Contextual specificity in peptide-mediated protein interactions

scientific article

DYRK1A Overexpression Alters Cognition and Neural-Related Proteomic Pathways in the Hippocampus That Are Rescued by Green Tea Extract and/or Environmental Enrichment

scientific article published on 15 November 2019

Democratising Knowledge Representation with BioCypher

scientific article published on 27 December 2022

Democratizing knowledge representation with BioCypher

Detecting similar binding pockets to enable systems polypharmacology

scientific article published on 29 June 2017

Discovery and hypothesis generation through bioinformatics

scientific article published on 27 February 2006

Drug repositioning beyond the low-hanging fruits

scientific article (publication date: April 2017)

Drug sensitivity in cancer cell lines is not tissue-specific

scientific article

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

scientific article published on 22 September 2018

Dynamic interactions of proteins in complex networks: a more structured view.

scientific article published on 27 August 2009

Encircling the regions of the pharmacogenomic landscape that determine drug response

Encircling the regions of the pharmacogenomic landscape that determine drug response

scientific article published on 26 March 2019

Expanding the Atlas of Functional Missense Variation for Human Genes

article

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

scientific article

Exploring genetic suppression interactions on a global scale

scientific article

Exploring the OncoGenomic Landscape of cancer

scholarly article by Lidia Mateo published in August 2018

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

scientific article published on 18 May 2020

Formatting biological big data for modern machine learning in drug discovery

scientific article published on 28 December 2018

From protein interaction networks to novel therapeutic strategies

scientific article published on 09 May 2012

Functional and structural analysis of C-terminal BRCA1 missense variants

scientific article

Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

scholarly article by Estelle M.N. Laurent published in August 2020

Identification and drug-induced reversion of molecular signatures of Alzheimer's disease onset and progression in App<sup>NL-G-F</sup>, App<sup>NL-F</sup>, and 3xTg-AD mouse models

scientific article published on 26 October 2021

Incorporating high-throughput proteomics experiments into structural biology pipelines: Identification of the low-hanging fruits

scientific article published on 01 May 2008

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

scientific article published on 29 May 2014

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

article

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

scientific article published on 9 September 2022

InterPreTS: protein interaction prediction through tertiary structure.

scientific article

Interactome mapping suggests new mechanistic details underlying Alzheimer's disease

scientific article

Interactome3D: adding structural details to protein networks

scientific article published on 16 December 2012

Interrogating protein interaction networks through structural biology

scientific article

Isolation of Human Colon Stem Cells Using Surface Expression of PTK7.

scientific article published on 5 November 2015

Modelling repressor proteins docking to DNA.

scientific article published in December 1998

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

scientific article published on 04 April 2022

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

scientific article published on 22 May 2012

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

scientific article published on 18 March 2015

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

scientific article

Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures

scientific article

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

scientific article published on March 2011

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

scientific article published on 09 September 2020

Pooled-matrix protein interaction screens using Barcode Fusion Genetics

scientific journal article

Potential artefacts in protein-interaction networks

article

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

scientific article published on 23 February 2010

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

scientific article published on January 1, 2003

Protein complexes: structure prediction challenges for the 21st century

scientific article

Protein similarities beyond disulphide bridge topology

scientific article published on 01 December 1998

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

scientific article published in February 2018

Proteome survey reveals modularity of the yeast cell machinery

scientific article

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

scientific article published on 21 May 2020

Pushing structural information into the yeast interactome by high-throughput protein docking experiments

scientific article

Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer.

scientific article

Rationalizing Drug Response in Cancer Cell Lines.

scientific article

Recycling side-effects into clinical markers for drug repositioning

scientific article

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2.

scientific article published in January 2000

Relation between amino acid composition and cellular location of proteins.

scientific article

Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins

scientific article published on 25 November 2015

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

scientific article

Ribonucleotide reductases: divergent evolution of an ancient enzyme.

scientific article

Shaping the future of interactome networks

scientific article published on January 2007

Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations.

scientific article

Structural insights into the target specificity of plant invertase and pectin methylesterase inhibitory proteins

article

Structural similarity to bridge sequence space: finding new families on the bridges

scientific article published on May 2005

Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics.

scientific article

Structural systems biology: modelling protein interactions.

scientific article

Structural systems pharmacology: the role of 3D structures in next-generation drug development

scientific article published on May 2013

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

scientific article

Structure-based assembly of protein complexes in yeast

scientific article

Structure-based systems biology: a zoom lens for the cell.

scientific article

Systematic analysis of bypass suppression of essential genes

scientific article published on 01 September 2020

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

scientific article published in September 2010

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability

scientific article published on 01 February 2020

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

scientific article

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

scientific article

Systems analysis of intracellular pH vulnerabilities for cancer therapy

scientific article published in Nature Communications

Taking the mystery out of biological networks.

scientific article

Target selection for complex structural genomics

scientific article

Targeting and tinkering with interaction networks

scientific article

Targeting and tinkering with interaction networks.

scientific article published on 6 March 2008

Ten thousand interactions for the molecular biologist

article

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

scientific article

The Relationship Between Sequence and Interaction Divergence in Proteins ⬇️

scientific article published on October 3, 2003

The binary protein-protein interaction landscape of Escherichia coli

scientific article

The crystal structure of the inhibitor-complexed carboxypeptidase D domain II and the modeling of regulatory carboxypeptidases

scientific article

The proton-pump inhibitor lansoprazole enhances amyloid beta production

scientific article

The role of structural disorder in the rewiring of protein interactions through evolution.

scientific article published on 2 March 2012

The third dimension for protein interactions and complexes.

scientific article

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

scientific article

Three-dimensional modeling of protein interactions and complexes is going 'omics

scientific article published on 12 February 2011

Towards Alzheimer's root cause: ECSIT as an integrating hub between oxidative stress, inflammation and mitochondrial dysfunction. Hypothetical role of the adapter protein ECSIT in familial and sporadic Alzheimer's disease pathogenesis

scientific article published on 19 April 2012

Towards a detailed atlas of protein-protein interactions

scientific article published on 26 July 2013

Towards a molecular characterisation of pathological pathways.

scientific article published on 20 February 2008

Truncating Variant Burden in High Functioning Autism and Pleiotropic Effects of LRP1 Across Psychiatric Phenotypes

scholarly article published 28 September 2018

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

scientific article published on 01 September 2019

Uncovering new substrates for Aurora A kinase

scientific article published on 12 November 2010

Understanding and predicting protein assemblies with 3D structures

scientific article

Unveiling the role of network and systems biology in drug discovery

scientific article published on February 2010

Using neighborhood cohesiveness to infer interactions between protein domains

scientific article published on 2 April 2015

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

scientific article published on 03 November 2019

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

scientific article published on February 2016

Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships

scientific article

dSysMap: exploring the edgetic role of disease mutations

scientific article published in March 2015

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