Ziyan Zhuang

CYPForge: Auditable Preparation of Cytochrome P450 Molecular Dynamics Systems

Zhuang ZY, Zhao QY, Shao YRS, Zhao GR*, Li Y*, Zhang DC*
ChemRxiv (Preprint), 2026 Preprint
TL;DR: An automated, auditable pipeline that transforms raw PDB/SDF inputs into simulation-ready CYP450 MD systems with gated quality control at every stage.
Paper  |  Code

Spinetoram resistance in Tuta absoluta: selection, inheritance, biochemical mechanism and fitness cost

Xie JG, Rukiya T, Liu N, Zhuang ZY, Liu XN*, Song Y*.
Pesticide Biochemistry and Physiology, 2025 JCR Q1
TL;DR: Dissected the inheritance mode, biochemical mechanism, and fitness trade-offs of spinetoram resistance in the invasive tomato leafminer.
Paper

Molecular insights on the function of CYP380C12 in Aphis gossypii Glover (Hemiptera: Aphididae): in silico and RNAi analyses

Zhang LJ, Zhuang ZY (Co-first), Xie JG, Kong WT, Li TT, Wang SF, Liu XN*.
Journal of Economic Entomology, 2025 JCR Q1
TL;DR: Combined homology modeling, molecular docking, and RNAi knockdown to reveal CYP380C12's role in cotton aphid detoxification.
Paper

Functional analysis of lactase phlorizin hydrolase in insect-plant coevolution based on deglycosylation

Li Y, Kong WT, Li TT, Zhang LJ, Zhuang ZY, Liu N*, Liu XN*.
Journal of Agricultural and Food Chemistry, Cover Paper, 2025 JCR Q1
TL;DR: Showed that insect lactase phlorizin hydrolase mediates plant-insect coevolution by deglycosylating plant secondary metabolites to release defensive aglycones.
Paper

Exploring the role of CYP6AB328 in spinetoram resistance and growth and development of Phthorimaea absoluta

Xie JG, Wang SY, Zhuang ZY, Wang XH, Lin MH, Liu XN*.
Pesticide Biochemistry and Physiology, 2025 JCR Q1
TL;DR: Showed that CYP6AB328 plays a dual role in both spinetoram detoxification and normal growth and development in the tomato leafminer.
Paper

Functional Investigation of CYP304F1 in Tuta absoluta (Lepidopteran: Gelechiidae) by RNA Interference

Xie JG, Ali A, Li Y, Zhuang ZY, Liu XN*.
Journal of Economic Entomology, 2024 JCR Q1
TL;DR: RNAi-mediated silencing established CYP304F1's functional importance in the tomato leafminer's xenobiotic response and normal physiology.
Paper

Zhuangzhou (庄周): Autonomous Scientific Agent for Enzyme Design & Metabolic Engineering

Ziyan Zhuang & Qianyu Zhao
GitHub

An autonomous scientific intelligence platform that integrates a cross-disciplinary knowledge graph, a multi-agent reasoning system, and hierarchical scientific skills (protein design, molecular simulation, metabolic network analysis) into a closed Think→Act→Observe→Review→Re-decide loop. It enables cross-scale intelligent bioengineering — from catalytic mechanism reasoning and enzyme active-site design to whole-cell metabolic network optimization.

AutoGraphRAG: Automated Multimodal Knowledge Graph Construction Pipeline

Ziyan Zhuang
GitHub

A production-ready, end-to-end pipeline that transforms academic PDF documents (including figures and diagrams) into a queryable knowledge graph with GraphRAG. It leverages Vision Language Models (VLMs) to extract and describe figures, and organizes each execution as an isolated run with logs, prompts, and outputs for reproducibility.

ProXplorer: A Protein Sequence Analysis Toolbox

Ziyan Zhuang
GitHub

A MATLAB-based toolbox developed for comprehensive protein sequence analysis. Key features include Smith-Waterman alignment, motif discovery, and neighbor-joining phylogenetic analysis. It provides integrated visualization to streamline the workflow from raw sequence to structural insights.

Morphogen-DAU-Model

Ziyan Zhuang & Zifan Zhao
GitHub

A mathematical model focusing on Diffusion-Adsorption-Uptake (DAU) mechanisms. This project facilitates the efficient application of predictive values obtained from wet lab experiments to control morphogen distribution patterns.

BOGDA: Pest Resistance Evolution Models

Ziyan Zhuang, Qi-ao Sheng, et al.
GitHub

A Deep Learning framework utilizing Temporal Convolutional Networks (TCN) and Attention mechanisms to predict pest resistance evolution, bridging mathematical models with biological pest control strategies.

Ancient Ginkgo Leaf Collection Volunteer Program (Zhejiang University)

September 2025

Volunteered for Zhejiang University's China Temple Ancient Ginkgo Leaf Collection Initiative, performing standardized sampling of ancient ginkgo trees. Specimen data has been archived in the Zhejiang University Herbarium and incorporated into the GinkgoDB comprehensive ginkgo database, providing important specimens and data for ancient ginkgo germplasm conservation and genetic lineage research.

AI for Bioengineering Summer School (Shanghai Jiao Tong University)

August 2025

Participated in the summer school at the Institute of Natural Sciences, Shanghai Jiao Tong University, focusing on the application of artificial intelligence in bioengineering. Learned cutting-edge techniques including AI-driven protein design and computational biology workflows.

Quantitative Biology Summer School (Peking University)

July 2024

Participated in the summer school at the Center for Life Science (CLS), Peking University, exploring quantitative methods in biological research, including mathematical modeling of biological systems and data-driven experimental design.

Wildlife Monitoring Field Practice (Northern Tianshan Mountains)

June 2024
Ziyan Zhuang, Zifan Zhao, et al.

Participated in field research in the Northern Tianshan Mountains, using infrared camera technology to record and analyze the behavior and distribution of local wild animals. The visual above shows representative footage captured during the internship.