Opportunities and considerations for using artificial intelligence in bioinformatics education.

Artificial intelligence (AI) tools and techniques are undoubtedly being used in bioinformatics education, reflecting broader trends in education. However, many instructors and learners may be unaware of the full scope of potential uses for these tools within bioinformatics education, as well as effective practices for using them. Building on discussions held at the 6th Global Bioinformatics Education Summit, this perspective article provides insights about ways that AI might be used to generate or adapt instructional content, provide personalized help for learners, and automate assessment and grading.

Constructing and Using Cell Type Populations of the Human Reference Atlas.

The human body contains ~27-36 trillion cells of up to 10,000 cell types (CTs) within a volume of ~62-120 liters (males) and 52-89 liters (females). The Human Reference Atlas (HRA) v2.3 provides a quantitative 3D framework of CTs across 73 reference organs and 1,283 3D anatomical structures (ASs).

SBMLtoOdin and menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences.

Summary: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often restricted to experts in programming and mathematics. This is due to the need to implement entire models and solvers from the mathematical notation models are normally presented as.

Updates to the CASP Infrastructure in 2024.

CASP (critical assessment of structure prediction) conducts community experiments to determine the state of the art in calculating macromolecular structures. The CASP data management system is continually evolving to address the changing needs of the experiments. For CASP16, we expanded the infrastructure to enable data handling of newly introduced categories and fully support pilot categories introduced in CASP15.

metagRoot: a comprehensive database of protein families associated with plant root microbiomes.

The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences.

Mining Alzheimer's Interactomes, Macromolecular Complexes and Pathways for Drug Discovery.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that leads to dementia. Many cases are diagnosed annually and there is no currently available cure. Understanding the underlying disease biology of AD through the study of molecular networks, particularly by mapping clinical variants to tissue-specific interactomes and regulatory macromolecular assemblies, offers a promising avenue to elucidate altered disease pathways.

The International Health Cohorts Consortium (IHCC) advances population health research and genomic discovery.

Established in 2018 to push beyond the constraints of individual health and population cohorts, the IHCC is a community of cohorts advancing global science and health. We summarize the collective resources of 69 member cohorts, representing over 34 million people.

Group-based phylogenetic models on 3-sunlet networks.

Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa has a reticulate event. In molecular phylogenetics, substitution models can model the process of evolution at the genetic level, and the case of three taxa with a reticulate event can be modeled using a substitution model on a semi-directed graph called a 3-sunlet.

HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.

Background: Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as recent or non-recent within a window of several months, and cannot assess the cumulative impact of an intervention.

Results: We developed a Random Forest Regression model, HIV-phyloTSI, which combines measures of within-host diversity and divergence to generate continuous TSI estimates directly from viral deep-sequencing data, with no need for additional variables.

Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variantsh.

Streptococcus pneumoniae (pneumococcus) is a genetically diverse opportunistic bacterial pathogen that expresses two phase-variable loci encoding restriction-modification systems. Comparisons of two genetically-distinct pairs of epigenetically-distinct variants, each distinguished by a stabilised arrangement of one of these phase-variable loci, found the consequent changes in genome-wide DNA methylation patterns were associated with differential expression of mobile genetic elements (MGEs). This relationship was hypothesised to be mediated through changes in xenogenic silencing (XS) or nucleoid organisation.

A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages.

Resolving the microbiome of the Atlantic salmon Salmo salar gut is challenged by a low microbial diversity often dominated by one or two species of bacteria, and high levels of host contamination in sequencing data. Nevertheless, existing metabarcoding and metagenomic studies consistently resolve a putative beneficial Mycoplasma species as the most abundant organism in gut samples. The remaining microbiome is heavily influenced by factors such as developmental stage and water salinity.

A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens.

High-resolution posture tracking of C. elegans has applications in genetics, neuroscience, and drug screening. While classic methods can reliably track isolated worms on uniform backgrounds, they fail when worms overlap, coil, or move in complex environments.

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Typhi.

Background: Typhoid fever results from systemic infection with serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial resistant (AMR) Typhi lineages have emerged and become established in many parts of the world.

How to measure bacterial genome plasticity? A novel index helps gather insights on pathogens.

Genome plasticity can be defined as the capacity of a bacterial population to swiftly gain or lose genes. The time factor plays a fundamental role in the evolutionary success of microbes, particularly when considering pathogens and their tendency to gain antimicrobial resistance factors under the pressure of the extensive use of antibiotics. Multiple metrics have been proposed to provide insights into the gene content repertoire, yet they overlook the temporal component, which has a critical role in determining the adaptation and survival of a bacterial strain.

Diagnostic and therapeutic impact of miR-142, miR-146a, and miR-155 on cutaneous T-cell lymphoma.

Mycosis fungoides (MF) is the most common form of cutaneous T-cell lymphoma (CTCL). The diagnosis of early-stage MF can be very challenging due to shared clinical and histopathological features with benign inflammatory dermatoses. Moreover, a lack of understanding of the aetiopathology is having a negative impact on efficient diagnosis and therapy.

The Cell Ontology in the age of single-cell omics.

Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks for data integration and annotation. The Cell Ontology (CL) has emerged as a pivotal resource for achieving FAIR (Findable, Accessible, Interoperable, and Reusable) data principles by providing standardized, species-agnostic terms for canonical cell types-forming a core component of a wide range of platforms and tools.

Empowering bioinformatics communities with Nextflow and nf-core.

Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2).

Unlocking the African bioeconomy and strengthening biodiversity conservation through genomics and bioinformatics.

The African BioGenome Project (AfricaBP) is a Pan-African initiative aimed at improving food systems and biodiversity conservation through genomics while ensuring equitable data sharing and benefits. The Open Institute is the knowledge exchange platform of the AfricaBP, which aims to bridge local knowledge gaps in biodiversity genomics and bioinformatics and enable infrastructural developments. In 2024, the AfricaBP Open Institute advanced this mission by organizing 31 workshops that attracted more than 3500 registered attendees across 50 African countries, provided training to 401 African researchers in genomics, bioinformatics, molecular biology, sample collections and biobanking, and ethical considerations, across all five African geographical regions involving 40 African and non-African organizations.

A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space.

During gastrulation, mouse epiblast cells form the three germ layers that establish the body plan and initiate organogenesis. While single-cell atlases have advanced our understanding of lineage diversification, spatial aspects of differentiation remain poorly defined. Here, we applied spatial transcriptomics to mouse embryos at embryonic (E) E7.

EnsembleFlex: Protein structure ensemble analysis made easy.

Proteins exhibit conformational dynamics that underpin function and inform drug design. EnsembleFlex is a computational suite to extract, quantify, and visualize conformational heterogeneity from experimentally determined structure ensembles, thereby enabling both computational and experimental scientists to gain actionable insights into protein dynamics, ligand interactions, and drug-design applications. It performs dual-scale flexibility analysis (backbone and side-chain) via optimized superposition, dimension reduction (principal-component analysis [PCA] and uniform manifold approximation and projection [UMAP]), clustering, automated binding-site frequency mapping, and conserved water detection.

Single-cell transcriptomics identifies chondrocyte differentiation dynamics in vivo and in vitro.

Developing in vitro chondrocytes that replicate in vivo development would benefit musculoskeletal disease modeling and regenerative medicine. Although current methodologies have made progress, challenges such as off-target differentiation can result in heterogeneous cell states. Furthermore, the lack of comparison with human embryonic tissue precludes detailed evaluation of in vitro cells.

First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity.

Understanding how environmental and ecological factors shape variability in soil-associated microbial communities is a complex problem, particularly on islands, which contain a wide range of diverse and unique geology, fauna, and flora. The island of Crete features sharp altitudinal gradients, diverse landscapes, and distinct ecological zones shaped by its complex geological history making it an ideal natural laboratory for studying how environmental variation influences soil microbial communities. In this study, we characterized the soil microbial communities across Crete's ecozones and identify environmental factors associated with their diversity and composition.

Complex genetic variation in nearly complete human genomes.

Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (median continuity of 130 Mb), closing 92% of all previous assembly gaps and reaching telomere-to-telomere status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8 and AMY1/AMY2, and fully resolve 1,852 complex structural variants.