Guidelines for Gene and Genome Assembly Nomenclature.

The rapid increase in the number of reference-quality genome assemblies presents significant new opportunities for genomic research. However, the absence of standardized naming conventions for genome assemblies and annotations across datasets creates substantial challenges. Inconsistent naming hinders the identification of correct assemblies, complicates the integration of bioinformatics pipelines, and makes it difficult to link assemblies across multiple resources.

Data reuse in agricultural genomics research: challenges and recommendations.

The scientific community has long benefited from the opportunities provided by data reuse. Recognizing the need to identify the challenges and bottlenecks to reuse in the agricultural research community and propose solutions for them, the data reuse working group was started within the AgBioData consortium framework. Here, we identify the limitations of data standards, metadata deficiencies, data interoperability, data ownership, data availability, user skill level, resource availability, and equity issues, with a specific focus on agricultural genomics research.

R2DT: A COMPREHENSIVE PLATFORM FOR VISUALISING RNA SECONDARY STRUCTURE.

RNA secondary (2D) structure visualisation is an essential tool for understanding RNA function. R2DT is a software package designed to visualise RNA 2D structures in consistent, recognisable, and reproducible layouts. The latest release, R2DT 2.

Lineage-specific patterns in the Moraceae family allow identification of convergent P450 enzymes involved in furanocoumarin biosynthesis.

Specialized metabolites are molecules involved in plants' interaction with their environment. Elucidating their biosynthetic pathways is a challenging but rewarding task, leading to societal applications and ecological insights. Furanocoumarins emerged multiple times in Angiosperms, raising the question of how different enzymes evolved into catalyzing identical reactions.

Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq.

Background: Bioinformatics is fundamental to biomedical sciences, but its mastery presents a steep learning curve for bench biologists and clinicians. Learning to code while analyzing data is difficult. The curve may be flattened by separating these two aspects and providing intermediate steps for budding bioinformaticians.

Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets.

The PRIDE database is the largest public data repository of mass spectrometry-based proteomics data and currently stores more than 40,000 data sets covering a wide range of organisms, experimental techniques, and biological conditions. During the past few years, PRIDE has seen a significant increase in the amount of submitted data-independent acquisition (DIA) proteomics data sets. This provides an excellent opportunity for large-scale data reanalysis and reuse.

Alleviating batch effects in cell type deconvolution with SCCAF-D.

Cell type deconvolution methods can impute cell proportions from bulk transcriptomics data, revealing changes in disease progression or organ development. But benchmarking studies often use simulated bulk data from the same source as the reference, which limits its application scenarios. This study examines batch effects in deconvolution and introduces SCCAF-D, a computational workflow that ensures a Pearson Correlation Coefficient above 0.

The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training.

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.

Ensembl 2025.

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.

New developments for the Quest for Orthologs benchmark service.

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

DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology.

Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data handling and processing, optimization, evaluation, and model interpretability. The recommendations help to ensure that key details are reported transparently by providing a structured set of questions.

Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers.

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.

CATH v4.4: major expansion of CATH by experimental and predicted structural data.

CATH (https://www.cathdb.info) is a structural classification database that assigns domains to the structures in the Protein Data Bank (PDB) and AlphaFold Protein Structure Database (AFDB) and adds layers of biological information, including homology and functional annotation.

InterPro: the protein sequence classification resource in 2025.

InterPro (https://www.ebi.ac.

GENCODE 2025: reference gene annotation for human and mouse.

GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result.

Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes.

The Complex Portal (www.ebi.ac.

The Pfam protein families database: embracing AI/ML.

The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure and function analysis (https://www.ebi.ac.

The international nucleotide sequence database collaboration (INSDC): enhancing global participation.

The members of the International Nucleotide Sequence Database Collaboration (INSDC; https://insdc.org) have built systems to collect, archive and disseminate sequence data for more than four decades. The three collaborating organizations, the National Library of Medicine, National Center for Biotechnology Information (NLM-NCBI) in the United States, Research Organization of Information and Systems, National Institute of Genetics (ROIS-NIG) in Japan; and the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) formalized their relationship through the adoption of an arrangement which documents their commitment to free and open access to genomic sequences.

The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity.

The NHGRI-EBI GWAS Catalog serves as a vital resource for the genetic research community, providing access to the most comprehensive database of human GWAS results. Currently, it contains close to 7 000 publications for >15 000 traits, from which more than 625 000 lead associations have been curated. Additionally, 85 000 full genome-wide summary statistics datasets-containing association data for all variants in the analysis-are available for downstream analyses such as meta-analysis, fine-mapping, Mendelian randomisation or development of polygenic risk scores.

Rfam 15: RNA families database in 2025.

The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes.