Qing Ye

A Single-cell Spatiotemporal Atlas Encoding Age-dependent Evolution of the Ischemic Penumbra

This study creates a spatiotemporal transcriptomic atlas of the ischemic penumbra in young and aged mice, revealing age-dependent molecular changes and potential therapeutic targets.

TCR-FramePose: a local-frame representation for decomposing global docking and CDR3 loop geometry in TCR-pMHC recognition

This paper introduces TCR-FramePose, a geometric framework for analyzing TCR-pMHC recognition, showing it captures novel structural features beyond conventional descriptors.

A neuroendocrine principle: Pancreatic islets actively shape sympathetic innervation

The paper shows pancreatic islets actively shape sympathetic innervation, with Reg2 and Reg3β promoting nerve regeneration and islet function.

Literature-scaled immunological gene set annotation using AI-powered immune cell knowledge graph (ICKG)

The paper constructs an immune cell knowledge graph (ICKG) using AI to annotate immunological gene sets more accurately than existing methods.

Learning Structural Motif Representations For Efficient Protein Structure Search

This paper introduces DeepFold, a deep learning model that learns structural motif representations for efficient protein structure search, outperforming existing methods like FragBag.

Deciphering signaling specificity with interpretable deep neural networks

DeepSignal predicts kinase and SH2 domain substrate specificity using deep learning, outperforming existing methods and identifying cancer-related mutations and pathways.

Ex-STORM: Expansion Single Molecule Nanoscopy

This paper improves Expansion Microscopy to enable Ex-STORM, reducing fluorophore bleaching and preserving oxygen scavenging efficiency for better single molecule imaging.