Yuanyuan Zhang

Distance-AF Multimer: A Multi-Step Approach for Protein Complex Structure Modeling with User-Defined Distance Constraints

Distance-AF Multimer improves protein complex structure prediction by incorporating user-defined residue distance constraints, achieving competitive or better performance than existing methods.

Neutrophils orchestrate pre-metastatic immunosuppressive bone marrow remodeling during prostate cancer metastasis

This study identifies IGF1R-dependent neutrophil reprogramming in the bone marrow microenvironment during prostate cancer metastasis and shows its therapeutic targeting potential.

ctDNA Release Heterogeneity in Luminal Breast Cancer Revealed by Single-Cell Multi-Omics Spatial Analysis

The paper identifies cellular and spatial determinants of ctDNA release in HR+/HER2- breast cancer using single-cell multi-omics spatial analysis, linking tumor states, mutations, and immune interactions to ctDNA release patterns.

Cell-Lens: Advancing LLM Reasoning at Single-Cell Resolution

Cell-Lens improves LLM reasoning on single-cell data by using a structured representation that captures more biological content than gene lists alone.

A tunable receptor separates root barrier formation from nutrient signaling through ligand-perception states

This study shows how the receptor SCHENGEN3 separates root barrier formation from nutrient signaling through distinct ligand-perception states in different plant species.

πDIA-CLIP: efficient identification of highly heterogeneous proteomics data via a generalized zero-shot framework

The paper introduces πDIA-CLIP, a zero-shot framework for DIA proteomics data analysis that improves protein identification and reduces false positives across diverse datasets.

Co-expression of IBDV VP2 and H9N2 HA by recombinant HVT induces high protection against both pathogens in chickens

Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta

CryoZeta improves cryo-EM structure modeling by integrating density features with sequence data using a diffusion-based deep learning model, achieving higher accuracy than existing methods.