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Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery

GWAS hits (44 UK Biobank traits) and GTEx v8 cis-eQTLs (38 tissues) differ systematically: eQTLs cluster near transcription start sites of weakly constrained genes; GWAS hits favour constrained, multifunctional genes.

Generation of Vascularized Brain Organoids to Study Neurovascular Interactions

Fusing stem cell-derived vessel organoids with cerebral organoids yields brain organoids containing vascular networks, BBB-like features and responsive microglia, with more neural progenitors than unfused controls.

Learning inverse folding from millions of predicted structures

Adding 12 million AlphaFold2-predicted structures to training lifts native sequence recovery on held-out backbones to 51.6%, versus 42.2% for the best experimental-only model; likelihoods score mutation effects zero-shot.

Mapping genomic loci prioritises genes and implicates synaptic biology in schizophrenia

A genome-wide association study of 69,369 schizophrenia cases and 236,642 controls identifies 270 risk loci, prioritizes 130 genes, and links common and rare risk variants to neuronal synaptic biology.

DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks

Combining an ESM-1b encoder with a conditional random field decoder, DeepTMHMM classifies alpha-helical and beta-barrel transmembrane proteins and their topology, outperforming most compared tools, including on signal-peptide cleavage sites.

Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia

Exomes of 24,248 schizophrenia cases and 97,322 controls implicate ultra-rare damaging variants in 10 genes, including GRIN2A and GRIA3, with odds ratios of 3 to 50.

A comprehensive series of temporal transcription factors in the fly visual system

Drosophila larval optic lobe single-cell RNA-seq and pseudotime analysis define a near-complete medulla neuroblast temporal transcription factor series, with Eyeless and Dichaete acting as regulatory hubs.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

Improved prediction of protein-protein interactions using AlphaFold2

AlphaFold2, fed concatenated chains with optimized organism-paired alignments and pDockQ-ranked seeds, gives acceptable models for 63% of heterodimers; the same predicted DockQ score flags interacting pairs.

FinnGen: Unique genetic insights from combining isolated population and national health register data

Finnish-enriched low-frequency variants, often coding, underlie many GWAS signals across 1,932 register endpoints in 218,792 Finns; a 15-disease meta-analysis with Estonian and UK biobanks adds 30 unreported associations.

Generating publication ready visualizations for Single Cell transcriptomics using SCpubr

An R package that restyles the standard Seurat single-cell plots with fixed defaults, keeps the whole embedding visible when panels are split, and adds bar and bee swarm options.

Targeting Stem-loop 1 of the SARS-CoV-2 5'UTR to suppress viral translation and Nsp1 evasion

SARS-CoV-2 5' UTR stem-loop 1 (SL1) lets reporters escape Nsp1 translational shutdown. LNA antisense oligos against SL1 restore Nsp1 suppression and reduce infected Vero E6 cells.

De novo mass spectrometry peptide sequencing with a transformer model

Casanovo, a transformer encoder-decoder, translates unbinned tandem mass spectrum peaks into peptide sequences, beating DeepNovo and PointNovo on peptide-level precision across nine held-out species while running faster than both.

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

In 5,959 Finns with genotypes and stool metagenomes, GWAS found 583 independent SNP-taxon associations; dairy intake modified LCT effects on Bifidobacterium, and ABO-linked Faecalicatena lactaris tracked secretor status.

Squidpy: a scalable framework for spatial omics analysis

Squidpy extends Scanpy/AnnData with spatial neighbor graphs and a lazy-loading image container, enabling spatial statistics, ligand-receptor tests, image features, and ~10-fold faster neighborhood enrichment than Giotto.

Microbiome differential abundance methods produce disturbingly different results across 38 datasets

In 38 two-group 16S rRNA datasets, 14 differential abundance tools disagreed sharply; ALDEx2 and ANCOM-II were conservative and consistent, while edgeR and LEfSe inflated false positives.

conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics

conST learns embeddings from gene expression, spatial neighbors, and histology via three-level contrastive learning, reaching adjusted Rand index 0.65 on spatialLIBD slice 151673, with GNNExplainer-based explanations.

Cryo-EM Structures of Amyloid-β 42 Filaments from Human Brain

Cryo-EM shows brain-derived Aβ42 filaments adopt two related S-shaped protofilament folds: Type I dominates sporadic Alzheimer's, Type II familial Alzheimer's, other disorders and App^NL-F knock-in mice.

Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers

Greedy minimum set cover over FracMinHash k-mer sketches selects a small set of reference genomes explaining a metagenome, supporting species-level taxonomic profiling and choice of genomes for read mapping.

ProteinBERT: A universal deep-learning model of protein sequence and function

A ~16M-parameter protein language model, pretrained on ~106M UniRef90 proteins by denoising sequences and Gene Ontology annotations, rivals larger TAPE models using linear-cost global attention.