database / resource

The B-value calculator: expected diversity with background selection

The paper introduces Bvalcalc, a tool to calculate B-values, which quantify the effect of background selection on genetic diversity, and validates it using simulations and public data.

Characterisation of cis-regulatory elements and genome wide enhancer prediction in Heliconiini butterflies

This study characterizes cis-regulatory elements and predicts enhancers in Heliconiini butterflies using ATAC-seq and histone modification data, revealing temporal divergence and developing a CNN for enhancer prediction.

OpenAntigens: a structure-aware database for antigen construct design across the human cell-surface and secreted proteome

A static web database proposes 55 305 construct suggestions for 5328 human secreted and cell-surface proteins, using AlphaFold pLDDT and PAE, with ortholog, paralog and BLAST cross-reactivity context.

Survey of the human proteostasis network: the ubiquitin-proteasome system

The paper provides a comprehensive survey of the ubiquitin-proteasome system (UPS) and estimates its size and scope within the human proteostasis network.

Integrating stool chemistry measurements with metagenomics in adults reveals distinct gut health profiles

The paper integrates stool chemistry metrics with shotgun metagenomics in adults to identify distinct gut health profiles associated with microbial and inflammatory markers.

Histone modifications define distinct nucleosome positions in cell-free DNA

This paper identifies histone modification-associated nucleosome positions in cfDNA that correlate with tumor fraction and cancer state across multiple cancers.

Zea Lip: An atlas of glycerolipid profiles across leaf development in maize

UHPLC-MS/MS lipidomics of maize leaves (149 species, three genotypes, four growth stages, three leaf zones) shows genotype and leaf number explain most lipid variation.

Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression

Single-cell eQTL mapping in 5.4 million PBMCs from 1,925 individuals with matched WGS finds common-variant eQTLs for 83% and rare-variant signals for 47% of 21,404 genes.

Salmonid science on the move: Twenty years of research through the lens of early career researchers

This review analyzes 20 years of salmonid research through early-career researchers' contributions, identifying trends, gaps, and future directions in the field.

SAR11 Genome Atlas: a genome and gene catalog for functional profiling of the most abundant bacterial clade in the ocean

The paper introduces the SAR11 Genome Atlas, a resource integrating SAR11 genomes and functional data to support ecological and genomic analysis of oceanic bacteria.

Single-Nucleus Profiling Reveals Neuronal Metabolic Collapse During the Transition to Alzheimer's Disease Dementia

This study uses single-nucleus RNA-sequencing and multiome data to identify neuronal mitochondrial gene suppression as a driver of Alzheimer's dementia, revealing genetic and epigenetic mechanisms underlying cognitive resilience.

Integrating sequence-to-omics predictions and personal multi-omics for rare variant prioritization

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

Expanding the Repertoire of Associations Between Antibiotic Resistance Genes and Putative Mobile Genetic Element Carriers Using Metagenomic Long Reads

This study identifies new antibiotic resistance gene-mobile genetic element associations using metagenomic long reads from diverse environments.

Genomic and phenotypic adaptation tunes an endangered California plant to the fog that climate change and wind energy will reshape

This study identifies genomic adaptations in an endangered California plant to coastal fog, revealing candidate genes and potential impacts of wind farms on gene flow.

A novel lineage of Chilomastix mesnili in wild Moroccan Barbary macaques (Macaca sylvanus)

The paper identifies a novel Chilomastix lineage in wild Moroccan Barbary macaques using metagenomic sequencing, showing it is distinct from human-derived C. mesnili.

Widespread Presence of Catalytic RNAs in All Domains of Life

The paper identifies millions of self-cleaving ribozymes in humans and other species, revealing a much larger ribozyme-ome than previously thought and their potential roles in gene regulation and biotechnology.

According to a large citizen science dataset, UK farmland bird indicator species and other bird groups, are more likely to be found on farms with shoots than on otherwise similar farms

The paper analyzes a citizen science dataset to show that UK farmland bird species richness is higher on farms with gamebird shoots compared to similar farms without shoots.

'PhyTaxR', a set of phytoplankton taxonomic curation tools in R

PhyTaxR provides an R package for harmonizing phytoplankton taxonomic records by resolving inconsistencies and retaining uncertainty through automated and semi-automated workflows.

Thyra: Bridging Mass Spectrometry Imaging and SpatialData for Unified Multi-Modal Analysis

Thyra converts Mass Spectrometry Imaging data into the SpatialData format to improve interoperability and enable multi-modal spatial analysis.

Pervasive short hairpin folding in non-encapsidated RNA viruses

The paper identifies pervasive short hairpin RNA structures in non-encapsidated viruses and shows their association with structural constraints and evolutionary origins.

Phenologs at knowledge-graph scale: a mouse-to-slime-mold catalog of candidate genes for thousands of human diseases

The paper identifies 61,243 phenologs between human diseases and model organism phenotypes, using a hypergeometric method to rank candidate genes and validate their predictive power.

Xenograft supervision and joint methylation-fragment-end encoding define a reusable molecular scoring layer for cell-free tumor DNA

ctDNA-BERT scores individual bisulfite reads for cell-free DNA methylation analysis, achieving high accuracy in cancer staging without cohort-specific retraining.

Mixtures of stably coexisting species overyield

In generalized Lotka–Volterra communities, stable coexistence almost always requires overyielding; in four long-term biodiversity experiments, underyielding raised species-loss odds within two observations (pooled odds ratio 2.61).

Neuroline: an integrated modular pipeline for FAIR multimodal neurophysiology data processing

Neuroline integrates multimodal neurophysiology data into a standardized format, enabling FAIR data sharing and cross-modal analysis.

Genedex: Contextualizing gene signatures across Alzheimer's disease pathology, cell types, and brain regions

Genedex integrates gene signatures from Alzheimer's disease studies to contextualize gene expression across pathology, cell types, and brain regions, revealing new insights into disease mechanisms.

Integration of ATAC and RNA-sequencing identifies chromatin and transcriptomic signatures in classical and non-classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation

The paper integrates ATAC-seq and RNA-seq data from zebrafish osteoblasts to identify chromatin and transcriptomic signatures and mechanisms of entpd5a regulation.

ArthroVerse: mapping protein family diversity across arthropod-associated microbiomes

ArthroVerse compiles and annotates protein families from arthropod-associated microbiomes to explore functional diversity and host-microbe interactions.

Computational Design and Evaluation of De Novo Protein Minibinders Targeting Specific Sites of STAT3

The paper designs and evaluates de novo protein minibinders targeting specific STAT3 sites using AI and AlphaFold3, identifying high-confidence binders with novel sequences.

Global RNA-RNA interactome mapping in B. burgdorferi reveals base-pairing sRNAs that rewire gene expression across growth

The paper identifies sRNA candidates in B. burgdorferi and maps their regulatory interactions across growth phases, revealing a dynamic RNA-RNA interactome.

An evidence-governed agent harness for spatial transcriptomics prioritizes ICAM-1 as a target in lung fibrosis

DeepMAST, an AI system for spatial transcriptomics, identifies ICAM-1 as a therapeutic target in lung fibrosis through evidence-based analysis and validation.