A5078192682- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- Computational Drug Discovery Methods
- Genetic Associations and Epidemiology
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Fungal and yeast genetics research
- Genomics and Chromatin Dynamics
- Protein Structure and Dynamics
- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- Advanced Proteomics Techniques and Applications
- Biomedical Text Mining and Ontologies
- SARS-CoV-2 and COVID-19 Research
- Science, Research, and Medicine
- COVID-19 Clinical Research Studies
- Cell Image Analysis Techniques
- interferon and immune responses
- Microtubule and mitosis dynamics
- Protein Kinase Regulation and GTPase Signaling
- Evolution and Genetic Dynamics
- Research Data Management Practices
European Bioinformatics Institute
2016-2025
Open Targets
2020-2025
Wellcome Trust
2014-2025
Wellcome Sanger Institute
2023
Spanish National Cancer Research Centre
2015
Centro Nacional de Biotecnología
2010-2012
Open Targets Genetics (https://genetics.opentargets.org) is an open-access integrative resource that aggregates human GWAS and functional genomics data including gene expression, protein abundance, chromatin interaction conformation from a wide range of cell types tissues to make robust connections between GWAS-associated loci, variants likely causal genes. This enables systematic identification prioritisation genes across all published trait-associated loci. In this paper, we describe the...
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification prioritisation for drug discovery based upon underlying evidence. It is publicly available the code open source. Since our last update two years ago, we have had 10 releases maintain continuously improve evidence target-disease relationships from 20 different data sources. In addition, integrated new key datasets, including...
The Open Targets Platform (https://platform.opentargets.org/) is an open source resource to systematically assist drug target identification and prioritisation using publicly available data. Since our last update, we have reimagined, redesigned, rebuilt the in order streamline data integration harmonisation, expand ways which users can explore data, improve user experience. gene-disease causal evidence has been enhanced expanded better capture disease causality across rare, common, somatic...
Abstract The current wealth of genomic variation data identified at nucleotide level presents the challenge understanding by which mechanisms amino acid affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in development disease. Physical interactions molecules are linking steps underlying most, if not all, Understanding that sequence has on a molecule’s is key step towards connecting mechanistic characterization...
Interacting proteins tend to have similar functions, influencing the same organismal traits. Interaction networks can be used expand list of candidate trait-associated genes from genome-wide association studies. Here, we performed network-based expansion for 1,002 human traits showing that this recovers known disease or drug targets. The similarity network scores identifies groups likely share an underlying genetic and biological process. We identified 73 pleiotropic gene modules linked...
Abstract The coordinated regulation of protein kinases is a rapid mechanism that integrates diverse cues and swiftly determines appropriate cellular responses. However, our understanding decision‐making has been limited by the small number simultaneously monitored phospho‐regulatory events. Here, we have estimated changes in activity 215 human 399 conditions derived from large compilation phosphopeptide quantifications. This atlas identifies commonly regulated as those are central signaling...
Abstract There are thousands of distinct disease entities and concepts, each which known by different sometimes contradictory names. The lack a unified system for managing these poses major challenge both machines humans that need to harmonize information better predict causes treatments disease. Mondo Disease Ontology is an open, community-driven ontology integrates key medical biomedical terminologies, supporting data integration improve diagnosis, treatment, translational research....
Many drug discovery projects are started but few progress fully through clinical trials to approval. Previous work has shown that human genetics support for the therapeutic hypothesis increases chance of trial progression. Here, we applied natural language processing classify free-text reasons 28,561 stopped before their endpoints were met. We then evaluated these classes in light underlying evidence and target properties. found more likely stop because a lack efficacy absence strong genetic...
Phosphoproteomic experiments are increasingly used to study the changes in signaling occurring across different conditions. It has been proposed that phosphorylation of kinase target sites can be infer when a activity is under regulation. However, these approaches have not yet benchmarked due lack appropriate benchmarking strategies.We curated phosphoproteomic and gold standard dataset containing total 184 kinase-condition pairs where regulation expected occur benchmark compare inference...
Abstract The European Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources public biomolecular data. Based at Wellcome Genome Campus in Hinxton, UK, EMBL-EBI six sites Laboratory (EMBL), Europe's only intergovernmental life sciences organisation. This overview summarises latest developments services provided by data resources to scientific communities globally. These aim ensure meet current and future needs these communities, accelerating...
Three cDNA clones isolated from Syrian hamster cells (p4F1, p2F1, and p2A9) contain sequences that are preferentially expressed in the G1 phase of cell cycle. The expression these was investigated human peripheral blood normal individuals patients with leukemia. p4F1 p2F1 is clearly dependent on cycle mononuclear stimulated to proliferate phytohemagglutinin; p2A9 cannot be detected lymphocytes but a cell-cycle-dependent manner diploid fibroblasts (WI-38). These genes also show different...
Abstract Summary: The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, investigate their possible interactions functional relationships in a taxonomic context. includes possibility starting from single sequences hence it can be used by non-expert users. Availability Implementation: web is freely available at http://csbg.cnb.csic.es/mtserver. It was tested main browsers. Adobe Flash Player required client side perform interactive...
Abstract Protein phosphorylation is the best characterized post-translational modification that regulates almost all cellular processes through diverse mechanisms such as changing protein conformations, interactions, and localization. While inventory for sites across different species has rapidly expanded, their functional role remains poorly investigated. Here, we combine 537,321 phosphosites from 40 eukaryotic to identify highly conserved hotspot regions within domain families. Mapping...
Epigenetic communication through histone and cytosine modifications is essential for gene regulation cell identity. Here, we propose a framework that based on chromatin model to get insight the function of epigenetic in ESCs. The network was inferred from genome-wide location data plus extensive manual annotation. Notably, found 5-hydroxymethylcytosine (5hmC) most-influential hub this network, connecting DNA demethylation nucleosome remodeling complexes key transcription factors...
Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge requires tailored analyses integrating different types molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt pheromone stimulation developed machine learning approach explore associations between metabolism signal transduction. Existing phosphoproteomics same...
The virus SARS-CoV-2 can exploit biological vulnerabilities (e.g. host proteins) in susceptible hosts that predispose to the development of severe COVID-19.To identify proteins may contribute risk COVID-19, we undertook proteome-wide genetic colocalisation tests, and polygenic (pan) cis-Mendelian randomisation analyses leveraging publicly available protein COVID-19 datasets.Our analytic approach identified several known targets ABO, OAS1), but also nominated new such as soluble Fas...
Abstract Motivation The Open Targets Platform (https://platform.opentargets.org) is a unique, comprehensive, open-source resource supporting systematic identification and prioritisation of targets for drug discovery. combines, harmonises integrates data from >20 diverse sources to provide target-disease associations, covering evidence derived genetic somatic mutations, known drugs, differential expression, animal models, pathways systems biology. An in-house target scoring framework...
Abstract Summary The lit-OTAR framework, developed through a collaboration between Europe PMC and Open Targets, leverages deep learning to revolutionise drug discovery by extracting evidence from scientific literature for target identification validation. This novel framework combines Named Entity Recognition (NER) identifying gene/protein (target), disease, organism, chemical/drug within texts, entity normalisation map these entities databases like Ensembl, Experimental Factor Ontology...