Publications

I’m currently building this website, and this Publications page is temporarily incomplete. You can find my full list of publications on Google Scholar.

You can also find my articles on my Google Scholar profile.

Journal Articles

Revealing 1, 3-diphenylpropane’s coagulation toxicity via infomaxnet-based network toxicology and molecular simulations

Published in Ecotoxicology and Environmental Safety, 2025

This study proposes a network toxicology analysis framework—InfomaxNet, which successfully addresses the challenge of lacking prior biological knowledge by analyzing complex biological networks using only network topology. Using the deep learning model MolTrans to predict SD-1 targets, InfomaxNet identified the critical proteins AKT2 and F9.

Recommended citation: Pan Y, Cai H, Ran Y, Qiu H, Huang Z, Wu D, Zhang W, Zhang N, Cheng L, Long J, Gao S, Qiu X, Li G, Xian B. Revealing 1, 3-diphenylpropane coagulation toxicity via infomaxnet-based network toxicology and molecular simulations. Ecotoxicology and Environmental Safety. 2025 Sep 15;303:118834.
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ElixirSeeker: A Machine Learning Framework Utilizing Fusion Molecular Fingerprints for the Discovery of Lifespan‐Extending Compounds

Published in Aging Cell, 2025

This project spanned from my first year (2022) to my third year (2025) of undergraduate study. I applied machine learning techniques to model anti-aging compound databases and conducted experimental validation using Caenorhabditis elegans. I am grateful for the guidance of Professor Hao Li (also affiliated with UCSF) and Professor Bo Xian at the Center for Aging Research.

Recommended citation: Yan Pan; Hongxia Cai; Fang Ye; Wentao Xu; Zhihang Huang; Jingyuan Zhu; Yiwen Gong; Yutong Li; Anastasia Ngozi Ezemaduka; Shan Gao; Shunqi Liu; Guojun Li; Hao Li; Jing Yang; Junyu Ning; Bo Xian. ElixirSeeker: A Machine Learning Framework Utilizing Fusion Molecular Fingerprints for the Discovery of Lifespan‐Extending Compounds. Aging Cell 2025, e70116 .
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Reduction of DNA Topoisomerase Top2 reprograms the epigenetic landscape and extends health and life span across species

Published in Aging Cell / elife preprint, 2025

I was honored to collaborate with Professor Jing Yang, Professor Hao Li, and Dr. Man Zhu on this publication. I contributed experimental data related to omics analysis in the context of aging.

Recommended citation: Zhu M, Ma M, Luo L, Li F, Zheng J, Pan Y, Yang L, Xiao Y, Wang Z, Xian B, Zheng Y, Li H, Yang J. Reduction of DNA Topoisomerase Top2 Reprograms the Epigenetic Landscape and Extends Health and Life Span Across Species. Aging Cell. 2025 Jun;24(6):e70010.
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L-Theanine Extends the Lifespan of Caenorhabditis elegans by Reducing the End Products of Advanced Glycosylation

Published in Foods, 2025

L-theanine was identified as a candidate compound through ElixirSeeker screening. Consistent with the model’s prediction, it was found to extend the lifespan of C. elegans. The initial lifespan assays were conducted by myself.

Recommended citation: Huang, Zhihang, Haiming Jing, Yan Pan, Hongxia Cai, Wenjing Zhang, Jingyuan Zhu, Nan Zhang, Dan Wu, Wentao Xu, Hexiang Qiu, and et al. 2025. "L-Theanine Extends the Lifespan of Caenorhabditis elegans by Reducing the End Products of Advanced Glycosylation" Foods 14, no. 2: 221. https://doi.org/10.3390/foods14020221
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Circular RNA CDR1as/ciRS-7–a novel biomarker in solid tumors

Published in Frontiers in Oncology, 2024

In this project, I had the privilege of contributing to the Gene Therapy Center at Sichuan Provincial Peoples Hospital, under the guidance of Professor Yu Zhou. I provided reference protocols for several machine learning approaches.

Recommended citation: Zhang Y, Xiong C, Jiang Z, Wang X, Ji J, Pan Y, Yu T, Wang Z, Zhu L, Yue Y, Li Q, Wang H, Zhu S, Zhou Y. Circular RNA CDR1as/ciRS-7- a novel biomarker in solid tumors. Front Oncol. 2024 Nov 29;14:1468363
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The joint toxicity effect of glyphosate and cadmium in a concentration-dependent manner on nematode Caenorhabditis elegans

Published in Ecotoxicology and Environmental Safety, 2024

This was my first experience working on an RNA-seq analysis project. In this study, I was responsible for all bioinformatics analyses, working in collaboration with Zhihang Huang, who conducted the wet-lab experiments. We were fortunate to identify a novel Cd²⁺-responsive gene using the GENIE3 algorithm based on random forest. Additionally, we applied computer vision techniques to preliminarily assess the activity states of C. elegans under different conditions. This publication also marks the first paper from our C. elegans lab at the Center for Aging Research.

Recommended citation: Zhihang H, Ezemaduka AN, Hongxia C, Yan P, Yiwen G, Nan Z, Xinrui L, Shan G, Guojun L, Jing Y, Bo X. The joint toxicity effect of glyphosate and cadmium in a concentration-dependent manner on nematode Caenorhabditis elegans. Ecotoxicol Environ Saf. 2024 Oct 15;285:117081.
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Optimization of polyethylene terephthalate biodegradation using a self-assembled multi-enzyme cascade strategy

Published in Journal of Hazardous Materials, 2024

This is my first academic publication. After participating in the International Genetically Engineered Machine (iGEM) Competition 2023, I had the privilege of joining a protein engineering laboratory, where I became involved in the rational design of PETase under the guidance of Professor Juan Feng and Professor Lixia Tang. I developed a high-throughput pipeline for virtual mutagenesis and molecular docking, combined with molecular dynamics simulations, which effectively enhanced the enzymatic activity of PETase. I must say, I’ve also developed a strong passion for synthetic biology.

Recommended citation: Aer L, Jiang Q, Zhong L, Si Q, Liu X, Pan Y, Feng J, Zeng H, Tang L. Optimization of polyethylene terephthalate biodegradation using a self-assembled multi-enzyme cascade strategy. J Hazard Mater. 2024 Sep 5;476:134887.
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WormCNN-Assisted Establishment and Analysis of Glycation Stress Models in C. elegans: Insights into Disease and Healthy Aging

Published in International Journal of Molecular Sciences, 2024

The WormCNN project originated from challenges I encountered during C. elegans lifespan assays (2022–present). In practice, human observers can often visually distinguish worms that appear biologically older or younger than others. This led me to explore whether a computer vision model could be trained to replicate this capability—enabling earlier and more objective assessments of worm health status (e.g., premature aging or youthfulness). Since 2025, I have been continuing to develop and enhance WormCNN to expand its functionality and accuracy.

Recommended citation: Yan Pan; Zhihang Huang; Hongxia Cai; Zhiru Li; Jingyuan Zhu; Dan Wu; Wentao Xu; Hexiang Qiu; Nan Zhang; Guojun Li; Shan Gao; Bo Xian. WormCNN-Assisted Establishment and Analysis of Glycation Stress Models in _C. elegans_: Insights into Disease and Healthy Aging. International Journal of Molecular Sciences 2024, 25, 9675 .
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