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<!DOCTYPE HTML>
<html lang="en">
<head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>Wei Zhang</title>
<meta name="author" content="Wei Zhang">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="stylesheet.css">
<link rel="icon" type="image/png" href="images/Master-Ball.png">
</head>
<body>
<table style="width:100%;max-width:800px;border:0px;border-spacing:0px;border-collapse:separate;margin-right:auto;margin-left:auto;"><tbody>
<tr style="padding:0px">
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<table style="width:100%;border:0px;border-spacing:0px;border-collapse:separate;margin-right:auto;margin-left:auto;">
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<td style="padding:2.5%;width:70%;vertical-align:middle">
<p style="text-align:center">
<name>Wei Zhang</name>
</p>
<p> I am currently a research fellow at <a href="http://en.control.sdu.edu.cn/index.htm">the School of Control Science and Engineering</a>,
<a href="https://www.sdu.edu.cn/">Shandong University</a>.
I received my Bachelor's degree from the
<a href="https://www.uestc.edu.cn/">University of Electronic Science and Technology of China</a> in 2016. In 2022, I obtained my Ph.D. degree in control
science and engineering under the guidance of <a href="https://scholar.google.com/citations?user=ygzAmSAAAAAJ&hl=en">Prof. Yanda Li</a>
and <a href="https://scholar.google.com/citations?user=r0KzDh8AAAAJ&hl=en">Prof. Xiaowo Wang</a> from <a href="https://www.tsinghua.edu.cn/">Tsinghua University</a>.
My postdoctoral cooperation mentor is <a href="https://scholar.google.com/citations?user=zkBXb_kAAAAJ&hl=en">Prof. Zhiping Liu</a>.
</p>
<p style="text-align:center">
<a href="mailto:zw@sdu.edu.cn">Email</a>  / 
<a href="https://scholar.google.com/citations?hl=en&user=iVFuIA8AAAAJ">Google Scholar</a>  / 
<a href="https://github.com/Honchkrow">Github</a>
</p>
</td>
<td style="padding:2.5%;width:30%;max-width:40%">
<a href="images/Zhangwei.jpg"><img style="width:100%;max-width:100%" alt="profile photo" src="images/Zhangwei.jpg" class="hoverZoomLink"></a>
</td>
</tr>
</tbody>
</table>
<table style="width:100%;border:0px;border-spacing:0px;border-collapse:separate;margin-right:auto;margin-left:auto;">
<tbody>
<tr>
<td style="padding:20px;width:100%;vertical-align:middle">
<heading>Research Interests</heading>
<p>
My current research interests focus on the application of artificial intelligence in biomedical engineering. I am dedicated to leveraging artificial intelligence and machine learning
methods to uncover the mechanisms underlying disease onset and progression, as well as to develop algorithms and software for the early diagnosis of complex diseases. Specifically,
my research areas include:
<p>
(1) <strong>Understanding DNA language through LLMs; </strong>
</p>
<p>
(2) <strong>Integrating spatial omics data using graph neural networks and contrastive learning;</strong>
</p>
<p>
(3) <strong>Deciphering cancer mechanisms and enabling early detection with AI-driven approaches.</strong>
</p>
</td>
</tr>
</tbody>
</table>
<table style="width:100%;border:0px;border-spacing:0px;border-collapse:separate;margin-right:auto;margin-left:auto;">
<tbody>
<tr>
<td style="padding:20px;width:100%;vertical-align:middle">
<heading>Publications</heading>
<p>
# indicates the first author, * indicates the corresponding author.
</p>
</td>
</tr>
</tbody>
</table>
<table style="width:100%;border:0px;border-spacing:0px;border-collapse:separate;margin-right:auto;margin-left:auto;">
<tbody>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity</papertitle>
<br>
Zhang X<sup>#</sup>, <strong>Zhang W<sup>#</sup></strong>, Zhang J, Lyu X, Pan H, Jia T, Wang T, Wang X, Guo H
<br>
<em>Briefings in Bioinformatics</em>, 2025, IF=6.8 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Space: reconciling multiple spatial domain identification algorithms via consensus clustering</papertitle>
<br>
Zhang D<sup>#</sup>, Li W<sup>#</sup>, Sui X<sup>#</sup>, Yu N, Wang S, Liu Z, Wang X, Yuan Z*, Gao R*, <strong>Zhang W*</strong>
<br>
<em>Bioinformatics Advances</em>, 2025, IF=2.4 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Deconer: A comprehensive and systematic evaluation toolkit for reference-based cell type deconvolution algorithms using gene expression data</papertitle>
<br>
<strong>Zhang W<sup>#</sup></strong>, Zhang X<sup>#</sup>, Liu Q, Wei L, Qiao X, Gao R, Liu Z*, Wang X*
<br>
<em>Genomics, Proteomics & Bioinformatics</em>, 2025, IF=11.5 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>SpaGRA: Graph augmentation facilitates domain identification for spatially resolved transcriptomics</papertitle>
<br>
Sun X<sup>#</sup>, <strong>Zhang W<sup>#</sup></strong>, Li W, Yu N, Zhang D, Zou Q, Dong Q, Zhang X, Liu Z, Yuan Z*, Gao R*
<br>
<em>Journal of Genetics and Genomics</em>, 2025, IF=6.6 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>A Non-invasive Cell-free DNA Diagnosis Method for Hepatocellular Carcinoma Based on Deep Learning</papertitle>
<br>
XueYi Li, <strong>Zhang W*</strong>, Zhi-Ping Liu*
<br>
<em>Current Bioinformatics</em>, 2025, IF=2.4 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>stMMR: accurate and robust spatial domain identification from spatially resolved transcriptomics with multimodal feature representation</papertitle>
<br>
Zhang D<sup>#</sup>, Yu N<sup>#</sup>, Yuan Z<sup>#</sup>, Li W, Sun X, Zou Q, Li X, Liu Z, <strong>Zhang W*</strong>, Gao R*
<br>
<em>GigaScience</em>, 2024, IF=11.8 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Spall: accurate and robust unveiling cellular landscapes from spatially resolved transcriptomics data using a decomposition network</papertitle>
<br>
Jiang Z<sup>#</sup>, Huang W, Lam RH*, <strong>Zhang W*</strong>
<br>
<em>BMC Bioinformatics</em>, 2024, IF=2.9 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Deciphering spatial domains from spatially resolved transcriptomics through spatially regularized deep graph networks</papertitle>
<br>
Zhang D<sup>#</sup>, Yu N<sup>#</sup>, Sun X, Li H, Zhang W, Qiao X*, <strong>Zhang W*</strong>, Gao R*
<br>
<em>BMC Genomics</em>, 2024, IF=3.5 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Deep Learning in Biometric Recognition: Applications and Challenges</papertitle>
<br>
Jiang Z<sup>#</sup>, Li H<sup>#</sup>, Sui X<sup>#</sup>, Cai Y, Yu G, <strong>Zhang W*</strong>
<br>
<em>IEEE 2nd International Conference on Sensors, Electronics and Computer Engineering (ICSECE)</em>, 2024 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Weakly-supervised causal discovery based on fuzzy knowledge and complex data complementarity</papertitle>
<br>
Li W, <strong>Zhang W</strong>, Zhang Q, Zhang X, Wang X*
<br>
<em>IEEE Transactions on Fuzzy Systems</em>, 2024, IF=10.7 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Relating-Up: Advancing Graph Neural Networks through Inter-Graph Relationships</papertitle>
<br>
Zou Q, Yu N, <strong>Zhang W</strong>, Gao R*
<br>
<em>arXiv</em>, 2024 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Deep generative modeling and clustering of single cell Hi-C data</papertitle>
<br>
Liu Q<sup>#</sup>, Zeng W<sup>#</sup>, <strong>Zhang W</strong>, Wang S, Chen H, Jiang R*, Zhou M*, Zhang S*
<br>
<em>Briefings in Bioinformatics</em>, 2023, IF=9.5 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>stGCL: A versatile cross-modality fusion method based on multi-modal graph contrastive learning for spatial transcriptomics</papertitle>
<br>
Yu N<sup>#</sup>, Zhang D<sup>#</sup>, <strong>Zhang W<sup>#</sup></strong>, Liu Z, Qiao X, Wang C, Zhao M, Chao B, Li W*, De Marinis Y*, Gao R*
<br>
<em>bioRxiv</em>, 2023 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA</papertitle>
<br>
Zhang X, Jia X, Zhong B, Wei L, Li J, <strong>Zhang W</strong>, Fang H, Li Y, Lu Y, Wang X*
<br>
<em>Briefings in Bioinformatics</em>, 2022, IF=9.5 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>ARIC: accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data</papertitle>
<br>
<strong>Zhang W<sup>#</sup></strong>, Xu H<sup>#</sup>, Qiao R, Zhong B, Zhang X, Gu J, Zhang X, Wei L, Wang X*
<br>
<em>Briefings in Bioinformatics</em>, 2022, IF=13.9 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Genome-wide cell-free DNA methylation analyses improve accuracy of non-invasive diagnostic imaging for early-stage breast cancer</papertitle>
<br>
Liu J, Zhao H, Huang Y, Xu S, Zhou Y, <strong>Zhang W</strong>, Li J, Ming Y, Wang X, Zhao S, Li K, et al.
<br>
<em>Molecular Cancer</em>, 2021, IF=41.4 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data</papertitle>
<br>
<strong>Zhang W<sup>#</sup></strong>, Wei L, Huang J, Zhong B, Li J, Xu H, He S, Liu Y, Liu J, Lv H, Wang X*
<br>
<em>Bioinformatics</em>, 2021, IF=6.9 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>Dismir: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads</papertitle>
<br>
Li J, Wei L, Zhang X, <strong>Zhang W</strong>, Wang H, Zhong B, Xie Z, Lv H, Wang X<sup>*</sup>
<br>
<em>Briefings in Bioinformatics</em>, 2021, IF=13.9 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis</papertitle>
<br>
Wei Z<sup>#</sup>, <strong>Zhang W<sup>#</sup></strong>, Fang H, Li Y, Wang X<sup>*</sup>
<br>
<em>Bioinformatics</em>, 2018, IF=5.4 <br>
</td>
</tr>
<tr onmouseout="dualpixel_stop()" onmouseover="dualpixel_start()">
<td style="padding:20px;width:75%;vertical-align:middle">
<papertitle>HCSGD: an integrated database of human cellular senescence genes</papertitle>
<br>
Dong Q, Han H, Liu X, Wei L, <strong>Zhang W</strong>, Zhao Z, Zhang MQ, Wang X
<br>
<em>Journal of Genetics and Genomics</em>, 2017, IF=4.1 <br>
</td>
</tr>
</tbody>
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<table style="width:100%;border:0px;border-spacing:0px;border-collapse:separate;margin-right:auto;margin-left:auto;">
<tbody>
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<td style="padding:0px">
<br>
<p style="text-align:right;font-size:small;">
Template from <a href="https://jonbarron.info">Jon Barron</a>.
</p>
</td>
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</tbody>
</table>
</td>
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</body>
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