A5068329665- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Metabolomics and Mass Spectrometry Studies
- Advanced Proteomics Techniques and Applications
- Cutaneous Melanoma Detection and Management
- Microbial Natural Products and Biosynthesis
- Research Data Management Practices
- Sleep and Wakefulness Research
- Photoreceptor and optogenetics research
- Genomics and Phylogenetic Studies
- Semantic Web and Ontologies
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Neural dynamics and brain function
- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- Genetics, Bioinformatics, and Biomedical Research
- Genetics, Aging, and Longevity in Model Organisms
- Atmospheric and Environmental Gas Dynamics
- 14-3-3 protein interactions
- Diabetes and associated disorders
- Photosynthetic Processes and Mechanisms
- SARS-CoV-2 detection and testing
École Polytechnique Fédérale de Lausanne
2021-2023
European Bioinformatics Institute
2006-2013
Wellcome Trust
2006-2013
Centre National de la Recherche Scientifique
2008-2013
European Molecular Biology Laboratory
2013
Université Claude Bernard Lyon 1
2013
University of British Columbia
2011
SIB Swiss Institute of Bioinformatics
2009-2011
Institut de Biologie et Technologies
2008
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2008
IntAct is an open-source, open data molecular interaction database populated by either curated from the literature or direct depositions. Two levels of curation are now available within database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As September 2011, contains approximately 275 000 binary evidences over 5000 publications. The website has been improved to enhance search process in particular graphical display results. New download...
IntAct provides an open source database and toolkit for the storage, presentation analysis of protein interactions. The web interface both textual graphical representations interactions, allows exploring interaction networks in context GO annotations interacting proteins. A service direct computational access to retrieve XML format. currently contains approximately 2200 binary complex interactions imported from literature curated collaboration with Swiss-Prot team, making intensive use...
IntAct is an open source database and software suite for modeling, storing analyzing molecular interaction data.The data available in the originates entirely from published literature manually annotated by expert biologists to a high level of detail, including experimental methods, conditions interacting domains.The features over 126 000 binary interactions extracted 2100 scientific publications makes extensive use controlled vocabularies.The web site provides tools allowing users search,...
IntAct is an open-source, open data molecular interaction database and toolkit. Data abstracted from the literature or direct depositions by expert curators following a deep annotation model providing high level of detail. As September 2009, contains over 200.000 curated binary evidences. In response to growing volume user requests, now provides two-tiered view data. The search interface allows iteratively develop complex queries, exploiting detailed with hierarchical controlled...
Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided broad array of diverse formats, making access to this very difficult. The publication and wide implementation the Human Proteome Organisation Proteomics Standards Initiative Interactions (HUPO PSI-MI) format 2004 was major step towards establishment single, unified by which molecular interactions should be presented, but focused purely on protein-protein...
Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential alter biological function of expressed and even create new functions. has been suggested as explanation for discrepancy between number human functional complexity. Here, we carry out a detailed study alternatively spliced products annotated in ENCODE pilot project. We find alternative is frequent commonly suggested,...
Thalamoreticular circuitry plays a key role in arousal, attention, cognition, and sleep spindles, is linked to several brain disorders. A detailed computational model of mouse somatosensory thalamus thalamic reticular nucleus has been developed capture the properties over 14,000 neurons connected by 6 million synapses. The recreates biological connectivity these neurons, simulations reproduce multiple experimental findings different states. shows that inhibitory rebound produces...
Abstract Background Each major protein database uses its own conventions when assigning identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a challenge. This common problem attempting unify datasets have been annotated with from multiple data sources or querying providers one flavour of source another. Partial solutions for identifier mapping exist but they are limited specific species techniques and very small number databases. As...
SARS-CoV-2 started spreading toward the end of 2019 causing COVID-19, a disease that reached pandemic proportions among human population within months. The reasons for spectrum differences in severity across population, and particular why affects more severely aging those with specific preconditions are unclear. We developed machine learning models to mine 240,000 scientific articles openly accessible CORD-19 database, constructed knowledge graphs synthesize extracted information navigate...
The ever-increasing generation of, and corresponding interest in, molecular interaction data has lead to the establishment of a number high-quality databases which manually curate extracted from literature. In order effectively share curation load, ensure that is stored in accessible multiple sources, these have united form IMEx consortium. All also accept direct deposition authors prior publication, thus both assisting scientist preparing dataset for publication ensuring its subsequent...
The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies suitable level detail required when reporting a proteomics experiment (via Minimum Information About Experiment), provides extensible markup language (XML) formats dedicated controlled vocabularies (CVs) that must be combined generate standard compliant document. framework presented here tackles issue checking...
Protein affinity reagents (PARs), most commonly antibodies, are essential for protein characterization in basic research, biotechnology, and diagnostics as well the fastest growing class of therapeutics. Large numbers PARs available commercially; however, their quality is often uncertain. In addition, currently cover only a fraction human proteome, cost prohibitive proteome scale applications. This situation has triggered several initiatives involving large generation validation example...
Protein-protein interaction networks provide insights into the relationships between proteins of an organism thereby contributing to a better understanding cellular processes. Nevertheless, large-scale are available for only few model organisms. Thus, interologs useful systematic transfer protein However, no standard tool is so far that purpose.In this study, we present automated prediction developed all sequenced genomes in Integr8. We also have second method predict protein-protein...
In the absence of consolidated pipelines to archive biological data electronically, information dispersed in literature must be captured by manual annotation. Unfortunately, annotation is time consuming and coverage published interaction therefore far from complete. The use text-mining tools identify relevant publications assist initial extraction could help improve efficiency curation process and, as a consequence, database available literature. 2006 BioCreative competition was aimed at...
The complex biological processes that control cellular function are mediated by intricate networks of molecular interactions. Accumulating evidence indicates these interactions often interdependent, thus acting cooperatively. Cooperative prevalent in and indispensible for reliable robust cell regulation, as they underlie the conditional decision-making capability large regulatory complexes. Despite an increased focus on experimental elucidation details cooperative binding events, evidenced...
Modern data-driven science often consists of iterative cycles data discovery, acquisition, preparation, analysis, model building and validation leading to knowledge discovery as well dissemination at scale. The unique challenges simulating the whole rodent brain in Swiss EPFL Blue Brain Project (BBP) required a solution managing large-scale highly heterogeneous data, tracking their provenance ensure quality, reproducibility attribution throughout these cycles. Here, we describe Nexus (BBN),...
Abstract Motivation: The IntAct repository is one of the largest and most widely used databases for curation storage molecular interaction data. These datasets need to be analyzed by computational methods. Software packages in statistical environment R provide powerful tools conducting such analyses. Results: We introduce Rintact, a Bioconductor package that allows users transform PSI-MI XML2.5 data files from into graph objects. On these, they can use methods variety tasks: determining...
Abstract Thalamoreticular circuitry is known to play a key role in attention, cognition and the generation of sleep spindles, implicated numerous brain disorders, but cellular synaptic mechanisms remain intractable. Therefore, we developed first detailed computational model mouse thalamus thalamic reticular nucleus microcircuitry that captures morphological biophysical properties ∼14,000 neurons connected via ∼6M synapses, recreates biological gap junction connectivity. Simulations...