Ye Yuan

Optimized Multiple Circular Sequence Alignment for Cyclic Peptide Motif Discovery

The paper optimizes multiple circular sequence alignment for cyclic peptides, achieving faster performance while maintaining alignment quality.

Benchmarking confidence estimation and rescoring for cyclic peptide-protein complex predictions

This study benchmarks confidence estimation and rescoring methods for cyclic peptide-protein complex predictions, finding that pose ranking is the main limitation and that structural features improve confidence-based selection.

Democratizing Agentic Access to Bioinformatics and Biopharmaceutical Databases and Analyses with BioMCP-TS

BioMCP-TS provides an open-source server enabling AI agents to access and analyze biomedical databases and run analyses without complex dependencies.

Sequestration of clock proteins into repressive nuclear condensates orchestrates circadian gene repression

The paper investigates how spatial organization of clock proteins and chromatin regulates circadian gene repression in Drosophila.

An intron-based timer for circadian rhythms

The paper identifies an intron in the Drosophila timeless gene that acts as an RNA-based timer regulating circadian period length through nuclear retention of mRNA.

Clock-dependent chromatin accessibility rhythms regulate circadian transcription

This study shows that chromatin accessibility oscillates with the circadian cycle in Drosophila clock neurons, with distinct motifs associated with dusk and dawn accessibility, and that Period protein is essential for these rhythms.

A one-step CRISPR-based strategy for endogenous gene tagging in Drosophila melanogaster

This paper describes a one-step CRISPR-based method for endogenous gene tagging in Drosophila melanogaster, enabling efficient screening and characterization of engineered lines without a visible eye marker.

Clock proteins regulate spatiotemporal organization of clock genes to control circadian rhythms

This study shows clock proteins form dynamic nuclear foci that organize clock genes at the nuclear envelope to control circadian rhythms.