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Lista de obras de Patrick Aloy

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

artículo científico publicado en 1997

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

artículo científico publicado en 2008

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

artículo científico publicado en 2013

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

artículo científico publicado el 21 de octubre de 2010

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

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 2014

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.

artículo científico publicado en 2002

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

artículo científico publicado en 1998

A framework for exhaustively mapping functional missense variants.

artículo científico publicado en 2017

A molecular interpretation of genetic interactions in yeast

artículo científico publicado en 2008

A network medicine approach to human disease

artículo científico publicado en 2009

A novel framework for the comparative analysis of biological networks

artículo científico publicado en 2012

A proteome-scale map of the human interactome network

artículo científico publicado en 2014

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.

artículo científico publicado en 2004

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

artículo científico publicado en 2016

Analysis of Chemical and Biological Features Yields Mechanistic Insights into Drug Side Effects ⬇️

artículo científico publicado el 18 de abril de 2013

Approved drug mimics of short peptide ligands from protein interaction motifs

artículo científico publicado en 2008

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.

artículo científico publicado en 2001

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

artículo científico publicado en 2020

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

artículo científico publicado en 2015

Cancer network activity associated with therapeutic response and synergism

artículo científico publicado en 2016

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

artículo científico publicado en 2018

Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases

artículo científico publicado en 2019

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

artículo científico publicado en 2014

Classification of protein disulphide-bridge topologies

artículo científico publicado en 2001

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

artículo científico publicado en 1998

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

artículo científico publicado en 2016

Contextual specificity in peptide-mediated protein interactions

artículo científico publicado en 2008

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

artículo científico publicado en 2022

Democratizing knowledge representation with BioCypher

Detecting similar binding pockets to enable systems polypharmacology

artículo científico publicado en 2017

Discovery and hypothesis generation through bioinformatics

artículo científico publicado en 2006

Drug repositioning beyond the low-hanging fruits

artículo científico publicado en 2017

Drug sensitivity in cancer cell lines is not tissue-specific

artículo científico publicado en 2015

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

artículo científico publicado en 2018

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

artículo científico publicado en 2009

Encircling the regions of the pharmacogenomic landscape that determine drug response

Encircling the regions of the pharmacogenomic landscape that determine drug response

artículo científico publicado en 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

artículo científico publicado en 2009

Exploring genetic suppression interactions on a global scale

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2012

Functional and structural analysis of C-terminal BRCA1 missense variants

artículo científico publicado en 2013

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

artículo científico publicado en 2021

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

artículo científico publicado en 2008

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

artículo científico publicado en 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

artículo científico publicado en 2022

InterPreTS: protein interaction prediction through tertiary structure.

artículo científico publicado en 2003

Interactome mapping suggests new mechanistic details underlying Alzheimer's disease

artículo científico publicado en 2011

Interactome3D: adding structural details to protein networks ⬇️

artículo científico publicado el 16 de diciembre de 2012

Interrogating protein interaction networks through structural biology

artículo científico publicado en 2002

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

artículo científico publicado en 2015

Modelling repressor proteins docking to DNA.

artículo científico publicado en 1998

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

artículo científico publicado en 2022

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

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

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

artículo científico publicado en 2011

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

artículo científico publicado en 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

artículo científico publicado en 2010

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

artículo científico publicado el 1 de enero de 2003

Protein complexes: structure prediction challenges for the 21st century

artículo científico publicado en 2005

Protein similarities beyond disulphide bridge topology

artículo científico publicado en 1998

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

artículo científico publicado en 2018

Proteome survey reveals modularity of the yeast cell machinery

artículo científico publicado en 2006

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

artículo científico publicado en 2020

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

artículo científico publicado en 2009

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

artículo científico publicado en 2016

Rationalizing Drug Response in Cancer Cell Lines

artículo científico publicado en 2018

Recycling side-effects into clinical markers for drug repositioning ⬇️

artículo científico publicado el 27 de enero de 2012

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

artículo científico publicado en 2000

Relation between amino acid composition and cellular location of proteins.

artículo científico publicado en 1997

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

artículo científico publicado en 2015

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

artículo científico publicado en 2010

Ribonucleotide reductases: divergent evolution of an ancient enzyme.

artículo científico publicado en 2002

Shaping the future of interactome networks

artículo científico publicado en 2007

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

artículo científico publicado en 2009

Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development ⬇️

artículo científico publicado el 23 de mayo de 2013

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

artículo científico publicado en 2005

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

artículo científico publicado en 2002

Structural systems biology: modelling protein interactions.

artículo científico publicado en 2006

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

artículo científico publicado en 2010

Structure-based assembly of protein complexes in yeast

artículo científico publicado en 2004

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

artículo científico publicado en 2005

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

artículo científico publicado en 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

artículo científico publicado en 2015

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

artículo científico publicado en 2004

Systems analysis of intracellular pH vulnerabilities for cancer therapy

artículo científico publicado en 2018

Taking the mystery out of biological networks.

artículo científico publicado en 2004

Target selection for complex structural genomics

artículo científico publicado en 2006

Targeting and tinkering with interaction networks

artículo científico publicado en 2008

Targeting and tinkering with interaction networks

artículo científico publicado en 2008

Ten thousand interactions for the molecular biologist

article

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

artículo científico publicado en 2014

The Relationship Between Sequence and Interaction Divergence in Proteins ⬇️

artículo científico publicado el 3 de octubre de 2003

The binary protein-protein interaction landscape of Escherichia coli

artículo científico publicado en 2014

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

artículo científico publicado en 2001

The proton-pump inhibitor lansoprazole enhances amyloid beta production

artículo científico publicado en 2013

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

artículo científico publicado en 2012

The third dimension for protein interactions and complexes.

artículo científico publicado en 2002

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

artículo científico publicado en 2018

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

artículo científico publicado el 12 de febrero de 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

artículo científico publicado en 2012

Towards a detailed atlas of protein–protein interactions ⬇️

artículo científico publicado el 26 de julio de 2013

Towards a molecular characterisation of pathological pathways.

artículo científico publicado en 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

artículo científico publicado en 2010

Understanding and predicting protein assemblies with 3D structures

artículo científico publicado en 2003

Unveiling the role of network and systems biology in drug discovery

artículo científico publicado en 2010

Using neighborhood cohesiveness to infer interactions between protein domains

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

dSysMap: exploring the edgetic role of disease mutations

artículo científico publicado en 2015

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