Discover, rate, and verify biology preprints.

GPSNorm: Gaussian Process Spatial Normalization for Spatial Transcriptomics

GPSNorm fits slide, spatial technical and biological effects in one Bayesian negative binomial model, carrying normalization uncertainty into differential expression and lowering log-fold change error in simulations.

APICE-Py: An Open-Source MNE-Python Pipeline for Scalable EEG Preprocessing

A Python/MNE port of the APICE infant EEG preprocessing pipeline flags more artifacts than the MATLAB original but gives similar ERP measurement error in neonates and 5-month-olds.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

A sequence-encoded promoter proximal super pause stabilizes an offline RNA polymerase II state

A reconstituted, direct-RNA-sequencing transcription assay on 1,000 human promoter-proximal sequences identified a TFIIS-insensitive consensus super pause, whose cryo-EM structure shows a one-nucleotide sidetracked polymerase state.

Statistical tests for bivariate spatial association across multi-omics data with disjoint coordinates

Autocorrelation-aware bivariate Moran's I, bivariate Gaussian process tests and generalized additive models (R package sbivar) test cross-modality colocalisation on disjoint coordinates; many existing permutation tests inflate false positives.

Phylogeny informed international clone assignment with PhyloMLST

PhyloMLST, a Python command-line tool, groups MLST sequence types into clonal complexes and international clones, optionally using a phylogeny to remove spuriously chained 'straggly' assignments.

A platform for robust quantitative functional genomics reveals temporal fitness landscapes in African trypanosomes

DRiF-Seq, a sequencing-optimized RNAi platform with a posteriori noise estimation, quantifies clone-resolved fitness genome-wide in pleomorphic Trypanosoma brucei; over half of core genes carry fitness costs.

Circadian transcriptome in cultured cells depends on synchronisation method and differs from in vivo condition

Heat shock, dexamethasone and osmotic stress all entrain the clock of primary mouse chondrocytes but yield distinct rhythmic transcriptomes, overlapping only marginally with each other and in vivo cartilage.

Nuclear size and physical properties of the nucleoplasm are determined by colloid osmotic pressure at the nuclear envelope

Overexpressing mCherry-GST targeted to the nucleus or cytoplasm in fission yeast shifts the nuclear-to-cell volume ratio as a parameter-free colloid osmotic model predicts, retuning nucleoplasm diffusivity, condensates and heterochromatin.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Gene dosage imbalance disrupts systemic metabolism in the Dp16 Down syndrome mouse model

Dp16 mice, carrying 115 triplicated Hsa21 orthologs, show sex-shared insulin resistance, glucose intolerance and dyslipidemia, worsened by high-fat diet, with multi-tissue transcriptome and metabolome signatures.

IOBRpy enables agentic multi-omics decoding of anti-tumor immunity

Python toolkit chains RNA-seq quantification, six-method tumour microenvironment (TME) profiling, SpecHLA typing and TRUST4 repertoire analysis with AI agents; TME outputs match R implementations (Spearman 0.986 to ~1.0).

Neural-vocal phase coupling reveals structured timing in birdsong production

In three singing canaries, sliding-window cross-correlation with surrogate testing shows HVC multi-unit activity and song envelope couple at a few preferred lags (positive, near-zero, negative), correlated or anticorrelated.

338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders

From 338 beetle genomes, eight ancestral linkage groups were inferred; rearrangement rates vary widely, peaking in major radiations, and the X chromosome dates to Holometabola's ancestor.

Thousandfold Expansion Microscopy

A four-network sodium acrylate/dimethylacrylamide hydrogel, cast ionic-within-ionic without neutral re-embedding, reaches about 1000-fold linear expansion and resolves individual peptide residues on standard confocal microscopes.

LocusBlend: Flexible multi-index regional visualization of genomic association signals

LocusBlend blends linkage disequilibrium colors for up to three index variants in LocusZoom and LocusCompare plots, helping separate independent signals at complex Alzheimer's disease loci.

Evo 2's Perception of Single Nucleotide Substitutions in the Genes of Two Plant Model Organisms

Evo 2 7B assigns higher perplexity to plant gene alleles carrying randomly simulated single-nucleotide substitutions than to those observed in vivo, in Arabidopsis and rice; significant but small effect.

Rapid reconstitution and kinase-controlled regulation of algal pyrenoid condensates in engineered Nicotiana benthamiana

Knocking out Nicotiana benthamiana RBCS genes and complementing with algal RBCS2 enables rapid EPYC1 condensate formation, and the kinase KEY1 consolidates condensates to one per chloroplast.

Identification of Bone Morphogenetic Protein 7 as a Master Regulator of Gastric Cancer-Associated Cachexia

In a gastric cancer peritoneal dissemination mouse model, BMP7 knockdown in MKN45 cells attenuated cachexia, and BMP7 acted upstream of GDF11 and GDF15 expression.

Diversity at the Acinetobacter baumannii K locus: towards a comprehensive in silico database for prediction of capsular polysaccharide types

Survey of 46,185 A. baumannii assemblies and NCBI entries added 168 novel capsule loci, expanding the Kaptive typing database to 409 K loci with 1010 annotated protein clusters.