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Land-use change undermines the stability of avian functional diversity

Across 1281 bird assemblages and 3696 species, land-use change lowers functional redundancy and resistance to simulated extinctions despite lower vulnerability, hitting frugivores and invertivores hardest.

Helixer--de novo Prediction of Primary Eukaryotic Gene Models Combining Deep Learning and a Hidden Markov Model

Helixer, a hybrid convolutional/bLSTM network with a hidden Markov model post-processor, predicts eukaryotic primary gene models from DNA alone, outscoring GenemarkES and AUGUSTUS on most species.

Long-term evaluation of the association between dominance, bib size, sex and age

Across eleven years and more than 1,800 sociable weavers, black bib size grew with age but did not predict dominance; age predicted dominance in males only.

Novel reporter of the PINK1-Parkin mitophagy pathway identifies its damage sensor in the import gate

A HaloTagged MFN2 reporter enabled CRISPRi screens showing diverse mitochondrial damage activates PINK1-Parkin via membrane potential loss, with TOM retaining PINK1 when TIM23 is blocked.

BoltzGen: Toward Universal Binder Design

An all-atom diffusion model unifying biomolecular structure prediction and sequence-structure generation designs experimentally validated nanobodies, mini-proteins, and linear or cyclic peptides across 26 diverse targets.

Genetic elements promote retention of extrachromosomal DNA in cancer cells

A genome-wide plasmid screen, Retain-seq, identifies thousands of CpG-rich promoter-like human elements that tether episomes to mitotic chromosomes, shape ecDNA structure, and lose function when methylated.

Deep generative modeling of temperature-dependent structural ensembles of proteins

aSAM, a latent diffusion model trained on molecular dynamics, generates heavy-atom protein ensembles; its temperature-conditioned variant aSAMt reproduces mdCATH thermal unfolding and extrapolates beyond training temperatures.

Targeting the canonical ER stress IRE1α/XBP1 pathway counteracts pancreatic cancer-induced skeletal muscle wasting

Muscle-specific XBP1 deletion or IRE1α inhibition with 4μ8C preserves muscle mass and strength in KPC pancreatic cachexia mice, curbing proteolysis, STAT3 signaling and fatty acid oxidation.

STPath: A Generative Foundation Model for Integrating Spatial Transcriptomics and Whole Slide Images

A masked-expression Transformer trained on 983 paired H&E and spatial transcriptomics slides predicts 38,984 genes from histology without fine-tuning, leading HEST-Bench and improving survival and mutation prediction.

PIEZO channels link mechanical forces to uterine contractions in parturition

Deleting Piezo1 and Piezo2 together in mice weakens uterine contractions and prolongs labor; uterine and sensory-neuron deletions act additively, and knockout uteri show reduced Gja1 (connexin43).

Targeting FSP1 triggers ferroptosis in lung cancer

Genetic deletion or pharmacological inhibition of ferroptosis suppressor protein 1 (FSP1) induces lipid peroxidation and restricts lung adenocarcinoma growth in vivo, establishing FSP1 as a therapeutic vulnerability.

A rapidly closing window for coral persistence under global warming

Eco-evolutionary simulations of 3,806 Great Barrier Reef reefs project coral cover falling to ∼14% by 2040 under every emission scenario; recovery afterwards needs warming below 2°C.

Modeling protein-small molecule conformational ensembles with PLACER

An atom-level graph neural network that denoises corrupted structures generates small-molecule and protein-ligand conformational ensembles, and its active-site pre-organization metric enriched for more active designed retroaldolases.

The Prevalence and Identification of Livestock Tick by Sex Ratio and Host in Tehran Province

In a 2019 survey of 1623 animals in 20 Tehran Province villages, 685 hard and 121 soft ticks were collected; females predominated (57.99%) and sheep yielded most ticks (60.04%).

Metalog: curated and harmonised contextual data for global metagenomics samples

Metalog manually curates and harmonises contextual metadata for 110,733 metagenomic samples from humans, animals, ocean water and other environments, linked to taxonomic profiles and SPIRE genomes.

Charting the landscape of cytoskeletal diversity in microbial eukaryotes

Ultrastructure expansion microscopy applied to 221 cultured planktonic eukaryotes maps diverse microtubule and centrin-based cytoskeletons, including dinoflagellate apical centrin rings and cryptophyte cortical centrin meshes.

Assessment of Nucleic Acid Structure Prediction in CASP16

Across 42 CASP16 nucleic acid targets, accuracy stayed tied to template availability; human experts (Vfold first) led servers and AlphaFold 3, though servers now improve on templates on average.

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

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

Bumble bees (Hymenoptera: Apidae) of Ecuador

Integrating 1,794 records from museum collections, literature, GBIF, and iNaturalist with COI DNA barcoding establishes a checklist of 15 Bombus species and their floral interaction networks across continental Ecuador.

Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development

Combining 99-gene smFISH across 48,225 cells with scRNA-seq of 26,009 cells maps 21 spatial expression domains and imputes 74,464 genes in early tetraploid wheat spikes.