Discover, rate, and discuss biology preprints.

The paper introduces a method to perform set operations on k-mers using compacted representations, achieving efficient memory usage and high throughput.

The paper develops a workflow combining XGBoost rank aggregation and SVM-RFECV to identify compact, interpretable biomarker panels from small-sample microarray datasets.

FusedFCR identifies marker genes associated with developmental transitions in time-course scRNA-seq data by combining lasso and fusion penalties for interpretable gene selection.

This study evaluates IUPAC consensus references for improving variant detection in challenging genomic regions using a stratified benchmarking framework called BurdenBench.

The paper introduces a matrix framework to map directional entropy transfer in proteins by incorporating continuous distance-dependent weighting into the Kirchhoff matrix, applied to KRAS to identify allosteric communication pathways.

The paper identifies dysregulated pathways and candidate driver genes in skeletal muscle from individuals with type 2 diabetes using co-expression networks and single-nucleus RNA-seq data.

The paper introduces arteMIS, a framework for optimizing molecular network parameters in metabolomics, showing improved network quality over default settings.

RIFT-VAE improves RNA inverse folding by combining grammar-conditioned pretraining with latent-space optimization, achieving high structural recovery on benchmark datasets.

IsoAtlas provides an interactive database for visualizing and interpreting transcript isoforms using long-read RNA-seq data from humans and mice.

The paper evaluates LLM-generated phenotype-genotype associations using external validation, finding 74.19% match genomic knowledge bases with varying support levels.

The paper presents a pipeline for longitudinal plant disease phenotyping using time-series imaging, enabling objective quantification of disease progression in wheat rusts.

LongOmicsTraj provides a topology-based framework to represent and query longitudinal omics trajectories, identifying corticosteroid response genes with temporal patterns across treatment groups.

The paper shows that standard gene centrality measures miss cross-module connectors and introduces EDVS, a partition-free centrality measure that recovers these genes without functional annotations.

MeSyTo provides an ontology-driven framework for harmonizing metadata across toxicological omics to improve reproducibility and data integration.

This study evaluates Atera, a spatial transcriptomics platform, showing its ability to resolve clonal cancer evolution and immune response in situ using DCIS samples.

EnSEMBLE reduces redundant gene sets to enhancer-corroborated pathways by integrating enhancer RNA data with pathway enrichment analysis, improving biological relevance and reducing false positives.

NACraft generates high-confidence nucleic-acid aptamers for diverse protein targets using a programmatic framework with structure-model feedback, outperforming existing methods in several evaluations.

EpiTune is a B-cell epitope prediction model that fine-tunes a protein language model to predict linear and conformational epitopes from antigen sequences with high accuracy.

CaMeRe predicts patient-specific clinical responses to drug combinations by integrating causal representation learning and meta-learning, showing robust performance across multiple datasets and cancer types.

The paper introduces a simulator called antigen-prime to model influenza virus evolution and benchmarks methods for variant assignment and growth rate estimation.