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The paper introduces a permutation-free method to control family-wise error rate in differential expression analysis under gene correlation by adjusting the empirical-Bayes prior.

The Everything Bagel feature finder automates metabolomics data processing, achieving comparable or better performance than existing methods with significantly reduced computational time.

The paper introduces MASCOT, a multi-agent framework for molecular optimization, which improves anesthetic candidates with better safety and recovery properties.

The paper evaluates cryptic binding site detection methods by separating coverage from ranking, showing that ranking improvements can significantly enhance recovery.

The paper introduces DiscOperon, a tool for predicting operon structures in bacterial genomes, and applies it to Mycococcus xanthus, demonstrating its effectiveness across multiple species.

The paper analyzes protein-ligand interactions to show that ancient metabolites form a globally connected network across protein families, while non-ancient metabolites expand this network without disrupting its connectivity.

BoYueGRN infers directed gene regulatory networks from single-cell transcriptomes using synthetic structural causal models, achieving high directional accuracy on CRISPRi screens and disease-specific GRN dynamics.

The paper identifies recurrent signaling pathways in breast cancer using single-cell data and suggests drug combinations targeting these pathways.

This paper introduces GUIA, an interoperable research-agent network that enables collaboration between scientific agents across domains, demonstrating its utility in therapeutic target discovery, drug discovery, and spatial proteomics analysis.

This paper introduces DuetRNA, a dual-frame flow matching model for RNA co-design that improves sequence-structure generation by jointly modeling base-and-sugar frames.

ETAP-CLF uses ESM3 embeddings and transformer attention to classify proteins into binary categories, achieving high AUROC scores across different biological processes.

Cell-Hub provides a user-friendly interface for single-cell RNA sequencing analysis, integrating multiple tools to support all essential analysis steps without requiring programming expertise.

The paper introduces a reference-free scRNA-seq analysis method using k-mers, identifies elevated rRNA and mtRNA transcription during axolotl neurogenesis, and detects other RNA features in disease datasets.

This paper develops a Pan-Cancer Multi-Omic SuperLearner to map non-linear Survival Topologies of regulated cell death, improving risk prediction beyond linear models.

LevenMap is a new small RNA-sequencing alignment tool that outperforms existing aligners in mapping reads to non-coding RNA databases.

The paper develops GuideRefine to identify and remove multi-targeting and off-targeting sgRNAs from CRISPR-KO libraries, improving the accuracy of gene hit lists.

This paper introduces a normalization framework to decouple protocol and instrument effects in multicenter proteomics studies, demonstrating its application to the PME13 dataset.

The paper develops a computational framework using optimal transport to analyze macrophage state transitions in atherosclerosis, identifying origin-dependent plasticity mechanisms and shared regulatory circuits in inflammation and fibrosis.

ibSLS provides a platform for accessing multi-omics data and biospecimens from spaceflight research to support biomedical and disease studies.