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TideCluster: clustering and classification of tandem repeats for comparative and pangenomic analysis

TideCluster is a pipeline for clustering and classifying tandem repeats across genomes, demonstrated on Arabidopsis and Solanum species.

Genomic signatures of local adaptation in marram grass highlight the importance of provenance in dune restoration

This study identifies genomic signatures of local adaptation in marram grass, showing that local provenance is important for dune restoration.

HomoeoGWAS enables experiment-wide homoeolog-group interaction mapping in allopolyploid crops

HomoeoGWAS identifies homoeolog-group interactions in allopolyploid crops by analyzing genotype encodings and controlling family-wise error across multiple species.

RCDome: A Multi-Database Human Gene Atlas of Regulated Cell Death

RCDome curates a human gene atlas of regulated cell death by integrating multiple databases and validating gene-RCD associations through literature and AI-assisted methods.

Polygenic Prediction of Depression Liability Reveals Broad Genetic Associations Across Development, Families, and Populations

This paper improves depression prediction by integrating psychiatric traits, showing stronger associations across development, families, and populations.

Overlapping enhancer activity robustly regulates rax expression during ocular development in zebrafish

This study identifies five novel ocular enhancers in zebrafish that regulate rax expression during eye development and shows their robustness to perturbations.

A cohesin acetylation complex that recognises nicked DNA

The paper predicts a cohesin acetylation complex in budding yeast that interacts with nicked DNA and confirms its function through experiments.

Distinct mechanical signatures of dairy and plant-based cheeses

The paper compares the mechanical properties of dairy and plant-based cheeses using various tests and consumer feedback, finding significant differences in texture and consumer preference.

A Continuum Fibre Network Model for the Anisotropic and Compressible Mechanics of Human Skin

This paper develops a Continuum Fibre Network model to simulate anisotropic and compressible mechanics of human skin using experimental data.

Choice of annotation data significantly impacts automated reconstruction of genome-scale metabolic networks

The paper shows that the source of annotation data significantly affects the quality of automatically reconstructed genome-scale metabolic models.

scPolyA enables efficient, interactive and agent-guided alternative polyadenylation analysis in single-cell and spatial transcriptomes

scPolyA provides a framework for analyzing alternative polyadenylation in single-cell and spatial transcriptomes, revealing APA patterns in cancer tissues.

IL4Ra Controls The Medullary Dwell Time Of Mature Thymocytes By Scheduling Their Release From The Thymus

This study shows that IL4Ra signaling in SP thymocytes prolongs their medullary dwell time, enhancing their maturation and functional capabilities.

Inference of cell division parameters in bacteria under transient growth conditions

The paper infers cell division parameters in E. coli under nonsteady growth conditions using single-cell size trajectories and time-resolved models.

The tiger shark, Galeocerdo cuvier (Peron & Lesueur, 1822), genome reveals genomic and epigenomic signatures of shark evolution and demographic history

The paper generates the first chromosome-scale genome and methylome for the tiger shark, revealing genomic and epigenomic features of shark evolution and population decline.

Evaluation effects can rival reported concordance gains in cross-cancer survival prediction

This paper evaluates how much improvement in cross-cancer survival prediction is due to model selection methods versus actual concordance gains, finding evaluation effects can be as significant as reported gains.

Unbiased lineage tracing across the adipose organ decouples developmental origin from anatomical and transcriptomic identities

This study uses CRISPR-mediated lineage tracing to show that adipose depot identity is shaped by anatomical niche rather than embryonic lineage.

Mutation and Recombination Rates in Free-Ranging Polar Bears

This study estimates mutation and recombination rates in polar bears using whole-genome sequencing, finding species-specific values that improve demographic inference for conservation.

SPARK: Physiology-informed inference of latent cardiac autonomic dynamics from RR intervals

SPARK infers latent cardiac autonomic dynamics from RR intervals, showing physiological information reduces solution variability and reveals distinct autonomic responses.

Positive relationships between interspecific association strength and elevational range overlap highlight the role of facilitation in community assembly

The paper examines how facilitation in mixed-species bird flocks influences elevational range overlap, finding positive correlations between association strength and range overlap.

Distinguishing evidence accumulation from choice confidence in neural signatures of perceptual decision making

This study investigates whether the centro-parietal positivity (CPP) reflects evidence accumulation or subjective confidence during perceptual decision-making, finding that CPP is an evidence accumulation signal, not confidence.