3,803 results match your criteria: "European Bioinformatics Institute[Affiliation]"

Since the COVID-19 pandemic, considerable advances have been made to improve epidemic preparedness by accelerating diagnostics, therapeutics, and vaccine development. However, we argue that it is crucial to make equivalent efforts in the field of outbreak analytics to help ensure reliable, evidence-based decision making. To explore the challenges and key priorities in the field of outbreak analytics, the Epiverse-TRACE initiative brought together a multidisciplinary group of experts, including field epidemiologists, data scientists, academics, and software engineers from public health institutions across multiple countries.

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Background: Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. However, the problem-solving potential of most, if not all, RV programs is still largely unexploited by experimental vaccinologists that impaired by somehow difficult interfaces, requiring bioinformatic skills.

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We profiled a large heterogenous cohort of matched diagnostic-relapse tumour tissue and paired plasma-derived cell free DNA (cfDNA) from patients with relapsed and progressive solid tumours of childhood. Tissue and cfDNA sequencing results were concordant, with a wider spectrum of mutant alleles and higher degree of intra-tumour heterogeneity captured by the latter, if sufficient circulating tumour-derived DNA (ctDNA) was present. Serial tumour sequencing identified putative drivers of relapse, with alterations in epigenetic drivers being a common feature.

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Quantifying conformational changes in the TCR:pMHC-I binding interface.

Front Immunol

December 2024

Koohy Lab, Medical Research Council Translational Immune Discovery Unit (MRC TIDU), Weatherall Institute of Molecular Medicine (WIMM), Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.

Background: T cells form one of the key pillars of adaptive immunity. Using their surface bound T cell antigen receptors (TCRs), these cells screen millions of antigens presented by major histocompatibility complex (MHC) or MHC-like molecules. In other protein families, the dynamics of protein-protein interactions have important implications for protein function.

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The CABANA project (Capacity Building for Bioinformatics in Latin America) was funded by the UK's Global Challenges Research Fund in 2017 with the aim to strengthen the bioinformatics capacity and extend its applications in Latin America focused on three challenge areas - communicable diseases, sustainable food production and protection of biodiversity. For 5 years, the project executed activities including data analysis workshops, train-the-trainer workshops, secondments, eLearning development, knowledge exchange meetings, and research projects in 10 countries. The project was successful in accomplishing all its goals with a major impact on the region.

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Introduction: The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped.

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Motivation: Developing competency in the broad area of bioinformatics is challenging globally, owing to the breadth of the field and the diversity of its audiences for education and training. Course design can be facilitated by the use of a competency framework-a set of competency requirements that define the knowledge, skills and attitudes needed by individuals in (or aspiring to be in) a particular profession or role. These competency requirements can help to define curricula as they can inform both the content and level to which competency needs to be developed.

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The Open Targets Platform (https://platform.opentargets.org) is a unique, open-source, publicly-available knowledge base providing data and tooling for systematic drug target identification, annotation, and prioritisation.

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Ensembl 2025.

Nucleic Acids Res

December 2024

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity.

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New developments for the Quest for Orthologs benchmark service.

NAR Genom Bioinform

December 2024

Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden.

The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation.

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Background: Mycobacterial culture is routinely performed to diagnose tuberculosis (TB) in Canada. Globally, meta-analyses suggest that up to 2% of positive cultures are falsely positive for due to laboratory cross-contamination. Five patients from distinct clinical institutions in Montréal were diagnosed with culture-positive TB as their clinical samples were processed in a centralized mycobacteria laboratory.

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π-HuB: the proteomic navigator of the human body.

Nature

December 2024

State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.

The human body contains trillions of cells, classified into specific cell types, with diverse morphologies and functions. In addition, cells of the same type can assume different states within an individual's body during their lifetime. Understanding the complexities of the proteome in the context of a human organism and its many potential states is a necessary requirement to understanding human biology, but these complexities can neither be predicted from the genome, nor have they been systematically measurable with available technologies.

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Motivation: High confidence structure prediction models have become available for nearly all protein sequences. More than 200 million AlphaFold2 models are now publicly available. We observe that there can be significant variability in the prediction confidence as judged by plDDT scores across a protein family.

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Genomic perspective on the bacillus causing paratyphoid B fever.

Nat Commun

December 2024

Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, F-75015, France.

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Motivation: Genome-wide association studies (GWAS) have been remarkably successful in identifying associations between genetic variants and imaging-derived phenotypes. To date, the main focus of these analyses has been on established, clinically-used imaging features. We sought to investigate if deep learning approaches can detect more nuanced patterns of image variability.

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Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0.

Curr Protoc

December 2024

National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.

Ever-increasing availability of experimental volumetric data (e.g., in .

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Validation requirements for AI-based intervention-evaluation in aging and longevity research and practice.

Ageing Res Rev

December 2024

Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. Electronic address:

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RNA-Puzzles Round V: blind predictions of 23 RNA structures.

Nat Methods

December 2024

GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.

Article Synopsis
  • - RNA-Puzzles is a collaborative project focused on improving the prediction of RNA three-dimensional structures, with predictions made by modeling groups before experimental structures are published.
  • - A significant set of predictions was made by 18 groups for 23 different RNA structures, including various elements like ribozymes and aptamers.
  • - The study highlights key challenges in RNA modeling, such as identifying helix pairs and ensuring proper stacking, and notes that some top-performing groups also excelled in a separate competition (CASP15).
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Target 2035 is a global initiative that seeks to identify a pharmacological modulator of most human proteins by the year 2035. As part of an ongoing series of annual updates of this initiative, we summarise here the efforts of the EUbOPEN project whose objectives and results are making a strong contribution to the goals of Target 2035. EUbOPEN is a public-private partnership with four pillars of activity: (1) chemogenomic library collections, (2) chemical probe discovery and technology development for hit-to-lead chemistry, (3) profiling of bioactive compounds in patient-derived disease assays, and (4) collection, storage and dissemination of project-wide data and reagents.

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Immune digital twins for complex human pathologies: applications, limitations, and challenges.

NPJ Syst Biol Appl

November 2024

Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, 47408, USA.

Digital twins represent a key technology for precision health. Medical digital twins consist of computational models that represent the health state of individual patients over time, enabling optimal therapeutics and forecasting patient prognosis. Many health conditions involve the immune system, so it is crucial to include its key features when designing medical digital twins.

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EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.

Nucleic Acids Res

November 2024

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SA, UK.

The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory, Europe's only intergovernmental life sciences organization. This overview summarizes the latest developments in services that EMBL-EBI data resources provide to scientific communities globally (https://www.

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PHI-base - the multi-species pathogen-host interaction database in 2025.

Nucleic Acids Res

November 2024

Protecting Crops and the Environment, Rothamsted Research, Harpenden AL5 2JQ, UK.

Article Synopsis
  • The Pathogen-Host Interactions Database (PHI-base) has been curating genes related to various pathogens since 2005, focusing on their roles in pathogenicity and interactions with different hosts, including humans and plants.
  • The latest update, version 4.17, shows significant growth with a 19% increase in genes and a 23% increase in interactions since the previous version.
  • The upcoming version 5.0 introduces a new curation workflow, unifies existing data, and enhances data-sharing capabilities, making it a more comprehensive resource for researchers, available at specific online portals.
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REDIportal: toward an integrated view of the A-to-I editing.

Nucleic Acids Res

November 2024

Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, via Orabona 4, 70125, Bari, Italy.

A-to-I RNA editing is the most common non-transient epitranscriptome modification. It plays several roles in human physiology and has been linked to several disorders. Large-scale deep transcriptome sequencing has fostered the characterization of A-to-I editing at the single nucleotide level and the development of dedicated computational resources.

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Proteogenomics integrates genomic and proteomic data to elucidate cellular processes by identifying variant peptides, including single amino acid variants (SAAVs). In this study, we assessed the capability of data-independent acquisition mass spectrometry (DIA-MS) to identify SAAV peptides in HeLa cells using various search engine pipelines. We developed a customised sequence database (DB) incorporating SAAV sequences from the HeLa genome and conducted searches using DIA-NN, Spectronaut, and Fragpipe-MSFragger.

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