Discover, rate, and discuss biology preprints.

splicelogic converts transcript-set comparisons into interpretable splicing events, enabling downstream analysis of isoform changes in RNA-seq data.

This paper introduces simpleaf, a tool for efficient sub-gene-level quantification of probe-based single-cell data, showing improved speed and memory use compared to existing tools.

The paper derives a formula (Z-value) to predict contig length from read length, coverage, and genome properties, showing high accuracy and practical applications for assembler choice and experimental design.

The paper shows that plate design confounds donor variation in single-cell perturbation screens and demonstrates how improved analysis methods can change interpretations of recent studies.

Hybrax simplifies hybrid bioprocess modeling by providing a framework that automates model setup and data handling, enabling reproducible and reusable models.

Automahout autonomously tracks cells in time-lapse images using a self-tuning system that annotates, trains, and refines models without human input, achieving high TRA scores on public datasets.

This paper introduces Brieno, a self-supervised model for raw nanopore signals that improves read classification and methylation detection without reference genomes.

RadMultiBench evaluates pre-trained vision-language models on medical imaging tasks, showing performance gaps in report generation and classification across thoracic and breast imaging.

RoDPAA integrates multi-view microbiome data using dissimilarity-based principal angle analysis, recovering shared structure in IBD cohorts where log-ratio methods failed.

This paper introduces PDLMs, protein-DNA language models that jointly represent protein and DNA sequences to predict and engineer DNA recognition specificity.

LeadWeaver improves ECG diagnosis by modeling lead topology and uncertainty, outperforming methods that treat missing leads as zero-valued inputs.

UnDetect improves transcriptional prediction of unseen compounds by separating context from compound effects and integrating multi-view data.

This paper introduces a semiparametric method for joint mean-variability inference in longitudinal studies with missing data, demonstrating robustness and reliability through simulations and a real-world application.

QUANTA uses quantum annealing to improve species tree estimation from multi-locus data, achieving comparable accuracy to classical methods with significant speedup.

This paper develops a digital pathology workflow to quantify matrix remodeling in wounds using fractal analysis and derives an exploratory Histological Wound Index (HWI).

This paper introduces MODAE+, a multi-objective domain adaptation framework that improves drug response prediction across cancer cell lines and patient tumours by preserving biological structure and heterogeneity.

Protify benchmarks protein language models across tasks and evaluation settings, revealing task dependence and homology leakage in model performance.

The paper proposes a Latent Cell-State Model to reconstruct cellular trajectories by inferring hidden cell states and generating gene expression profiles at unobserved timepoints.

The paper compares transcriptomic profiles across kidney organoid, assembloid, and transplantation models to evaluate their maturity and suitability for research.

TRACE provides a framework for creating traceable biomedical resources, demonstrated with a single-cell glaucoma dataset, enabling reproducible analyses and resource reuse.