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Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer

A Local Interaction Score (LIS), computed from AlphaFold-Multimer predicted aligned error, separates curated fly and human protein interactions from controls better than ipTM, recovering small or flexible interfaces.

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

An epigenetic barrier sets the timing of human neuronal maturation

Chromatin regulators including EZH2, EHMT1/2, and DOT1L establish an epigenetic barrier in human neural progenitors that poises maturation genes and sets the protracted pace of cortical neuron maturation.

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

A molecularly defined and spatially resolved cell atlas of the whole mouse brain

MERFISH profiling of >1,100 genes in ~8 million cells spanning the whole mouse brain, integrated with scRNA-seq, maps >5,000 clusters into the Allen Common Coordinate Framework.

ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction

ProteinGym unifies over 250 deep mutational scans and ~65k clinical variants to benchmark over 70 models in zero-shot and supervised settings; TranceptEVE ranks best overall.

A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

Rare-variant depletion in 1kb windows of 76,156 gnomAD genomes, versus feature-adjusted mutation expectations, marks regulatory elements and outperforms seven alternative scores at flagging functional non-coding variants.

Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment

SigProfilerAssignment refits known substitution, doublet, indel and copy-number mutational signatures to single samples and probabilistically to individual mutations, outperforming four refitting tools on 2,700 synthetic genomes.

Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development

A 489,686-cell scRNA-seq atlas of 62 zebrafish stages (3.3–120 hpf) identifies 90 multi-tissue gene programs and markers for pericyte subtypes, intestinal smooth muscle layers, and best4+ enterocytes.

CellSAM: A Foundation Model for Cell Segmentation

Bounding boxes from a transformer detector let the Segment Anything Model segment cells automatically; one generalist model beats generalist Cellpose and matches inter-annotator agreement across mammalian, yeast and bacterial images.

An encyclopedia of enhancer-gene regulatory interactions in the human genome

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides

Autoencoder design plus a roughly 24-hour cell-free screen tested 500 candidates over five rounds, finding 30 functional AMPs; six were broad-spectrum with no resistance emerging in E. coli.

Genome-wide Association Identifies Novel Etiological Insights Associated with Parkinsons Disease in African and African Admixed Populations

Intronic GBA1 variant rs3115534-G, common in African and African admixed ancestry but rare elsewhere, raises Parkinson's disease risk (OR 1.58) and lowers onset age.

Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications

Over half of 614 commercial antibodies for 65 human neuroscience proteins failed a knockout-controlled assay, yet most targets had a well-performing antibody; recombinants performed best.

SaProt: Protein Language Modeling with Structure-aware Vocabulary

Pairing each residue with its Foldseek 3D-structure token and pre-training an ESM-2-sized model on about 40 million AlphaFold2 structures beat ESM-2 and structure-based baselines on variant-effect and function tasks.

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities

CollecTRI-derived signed regulons, spanning 1,183 transcription factors (TFs) and 45,856 TF-gene links, outperform DoRothEA, ChEA3, RegNetwork and Pathway Commons at identifying perturbed TFs in KnockTF data.

Fast and robust metagenomic sequence comparison through sparse chaining with skani

skani estimates average nucleotide identity (ANI) from sparse FracMinHash k-mer chains, staying robust to incomplete, fragmented metagenome-assembled genomes while running over 20 times faster than FastANI.

Clustering predicted structures at the scale of the known protein universe

A Foldseek-based linear-time structural clustering groups 52 million AlphaFold DB representatives into 2.27 million non-singleton clusters; 31% lack known structural or domain annotation.

Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans

Theta-burst transcranial ultrasound lowered GABA+ in the posterior cingulate but not dorsal anterior cingulate cortex in 24 adults, while raising resting-state connectivity of both targets.