张宇辰，陕西西安人，于2022年12月在陕西师范大学获工学博士学位（硕博连读），同年进入西北农林科技大学信息工程学院工作，硕士生导师，于2021-2022年在加拿大University of Saskatchewan，生物医学工程系进行博士联合培养。在《Knowledge-Based Systems》、《Big Data Mining and Analytics》、《Briefings in Bioinformatics》、《Frontiers in Pharmacology》等期刊上发表研究性论文多篇，主持国家自然科学基金青年项目1项，陕西省科技计划青年项目1项，中央高校基本科研业务费项目2项，参与国家自然科学基金项目4项，省部级项目3项，撰写英文专著章节2章，授权专利2项。任中国自动化学会智能健康与生物信息专业委员会委员、CCF生物信息学“新未来”青年学者研讨会执行委员、陕西省生物信息学会首届会员、CCF会员、ACM会员、《PLOS Computational Biology》、《Frontiers in Pharmacology》、《Chinese Journal of Electronics》期刊审稿人，IEEE International Conference on Bioinformatics and Biomedicine (BIBM)、International Conference on Swarm Intelligence (ICSI)、International Conference on Data Mining and Big Data (DMBD)、International Conference on Intelligent Computing（ICIC）会议PC等。

ResearchGate: https://www.researchgate.net/profile/Yuchen-Zhang-51

Google Scholar: https://scholar.google.com.hk/citations?user=aXG0kK8AAAAJ&hl=zh-CN

     生物信息学、深度学习、智能计算等。

期刊论文：

[1]      Yuchen Zhang, Xiujuan Lei*, Yi Pan and Witold Pedrycz. Prediction of disease-associated circRNAs via circRNA–disease pair graph and weighted nuclear norm minimization. Knowledge-Based Systems, 2021, vol. 214, pp.106694. (SCI, 2021年中国科学院一区, Top, IF: 8.038)

[2]      Yuchen Zhang, Xiujuan Lei*, Yi Pan, Fang-Xiang Wu. Drug Repositioning with GraphSAGE and Clustering Constraints Based on Drug and Disease Networks. Frontiers in Pharmacology, 2022, vol. 13, pp. 872785（SCI, 2022年中国科学院二区, Top, IF: 5.810)

[3]      Yuchen Zhang, Xiujuan Lei*, Cai Dai, Fang-Xiang Wu, Yi Pan. Identify Potential CircRNA-Disesase Associations Through a Multi-Objective Evolutionary Algorithm. Information Sciences, 2023, vol.647, pp.119437. (SCI, 2023年中国科学院一区, Top, IF:8.100)

[4]      Yuchen Zhang, Xiujuan Lei*, Zengqiang Fang and Yi Pan*. CircRNA-disease associations prediction based on metapath2vec++ and matrix factorization. Big Data Mining and Analytics, 2020, vol. 3, no. 4, pp. 280-291. (SCI, 2023年中国科学院一区, CCF T2期刊, IF:13.60 )

[5]      Yi Pan*, Xiujaun Lei* and Yuchen Zhang. Association predictions of genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, radiomics, drug, symptoms, environment factor, and disease networks: a comprehensive approach. Medicinal Research Reviews, 2022, vol. 42, no. 1, pp. 441-461 (SCI, 2022年中国科学院一区 Top, IF：12.944) (该论文在2023年深圳市第三届优秀科技学术论文成果遴选中，获评优秀)

[6]      Xiujuan Lei, Thosini Bamunu Mudiyanselage, Yuchen Zhang, Chen Bian, Wei Lan, Ning Yu and Yi Pan*. A comprehensive survey on computational methods of non-coding RNA and disease association prediction. Briefings in Bioinformatics, 2021, vol. 22, no. 4, pp. bbaa350. (SCI, 2021年中国科学院二区, IF:11.622)

[7]      Chunyan Fan, Xiujuan Lei*, Jiaojiao Tie, Yuchen Zhang, Fang-Xiang Wu and Yi Pan. CircR2Disease v2.0: An Updated Web Server for Experimentally Supported CircRNA-Disease Associations and Its Application. Genomics Proteomics & Bioinformatics, 2022, 20(3): 435-445 (SCI, 2022年中国科学院二区, IF: 9.500)

[8]    Jianping Liu, Xiujuan Lei*, Yuchen Zhang, Yi Pan. The prediction of molecular toxicity based on BiGRU and GraphSAGE. Computers in Biology and Medicine. 2023, 153:106524 (SCI, 2023年中国科学院二区, IF: 7.700)

[9]   Xin Tang, Xiujuan Lei*, Yuchen Zhang. Prediction of Drug-Target Affinity Using Attention Neural Network. International Journal of Molecular Sciences. 2024, 25(10):5126 (SCI, 2024年中国科学院二区, IF: 5.6)

[10]  Zhengfeng Wang, Xiujuan Lei, Yuchen Zhang, Fang-Xiang Wu and Yi Pan. Recent Progress of Deep Learning Methods for RBP Binding Sites Prediction on circRNA, Current Bioinformatics,  online 31 July, 2024 (SCI, 2024年中国科学院三区, IF: 2.4)

[11] Mei Ma, Xiujuan Lei, Yuchen Zhang. A Review of Drug-related Associations Prediction Based on Artificial Intelligence Methods, Current Bioinformatics, 2024, 19(6): 530-550 (SCI, 2024年中国科学院三区, IF: 2.4)

会议论文：

[1]      Yuchen Zhang, Xiujaun Lei, Zhengfeng Wang and Yi Pan. 2024.  ICDFGF: Identification of potential circRNA-disease associations based  on feature graph factorization. In Proceedings of the 15th ACM  Conference on Bioinformatics, Computational Biology, and Health  Informatics (BCB’24), November 22-25, 2024, Shenzhen, China. ACM,  New York, NY, USA, 10 pages. https://doi.org/10.1145/3698587.3701365

[2]     Yeqiang Wang(指导本科生), Sharen Yun(指导本科生), Yuchen Zhang*, Xiujuan Lei*, Prediction of miRNA-Disease Associations Based on Hybrid Gated GNN and Multi-Data Integration, International Conference on Bioinformatics and Biomedicine (BIBM)，Lisbon, Portugal, December 3-6, 2024. (CCF B类会议)

[3]      Yuchen Zhang, Xiujuan Lei* and Shi. Cheng. PDG-PIO: Predicting Disease-genes Based on Pigeon-inspired Optimization. 2019 IEEE Congress on Evolutionary Computation (CEC), Jun. 2019, Wellington, New Zealand, pp. 3285-3291. (EI: 20193507373658)

[4]      Yuchen Zhang, Xiujuan Lei* and Ying Tan. Firefly clustering method for mining protein complexes. 2017 International Conference on Swarm Intelligence (ICSI), Aug. 2017, Fukuoka, Japan, Lecture Notes in Computer Science, vol. 10385, Springer, pp.601-610. (EI: 20173204020709)

[5]      Yuchen Zhang, Xiujuan Lei* and Ying Tan. Detecting Firefly Algorithm for Numerical Optimization. 2016 International Conference on Swarm Intelligence (ICSI), Jun. 2016, Bali, Indonesia, Lecture Notes in Computer Science, vol. 9712, Springer, pp. 200-210. (EI: 20170203229360)

[6]      Xiujuan Lei*, Yuchen Zhang, Fang-Xiang Wu and Aidong Zhang. Mining protein complexes based on topology potential from weighted dynamic PPI network. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Dec. 2016, Shenzhen, China, pp. 735-738. ( CCF B类会议, EI: 20170803377750)

[7]      Haiqiang Xiao, Xiujuan Lei*, Yuchen Zhang, Fang-Xiang Wu, Drug Combination Side Effect Prediction Based on Polypharmacy Network and GraphSAGE Algorithm. International Conference on Bioinformatics and Biomedicine (BIBM)，Lisbon, Portugal, December 3-6, 2024. (CCF B类会议)

专著章节：

[1]      Yuchen Zhang, Xiujuan Lei* and Ying Tan. Application of fireworks algorithm in bioinformatics, in 《Handbook of Research on Fireworks Algorithms and Swarm Intelligence》, book edited by Ying Tan, IGI Global, USA, Apr.2020, pp.233-262. (Invited Book Chapter), ISBN13: 978-1-79981-659-1.

[2]      Xiujuan. Lei*, Yuchen Zhang, Jie Zhao, Shi Cheng and Ying Tan. Firefly algorithm and its applications, in《Swarm Intelligence: Innovation, New Algorithms and Methods》, book edited by Ying Tan, IET, London, United Kingdom, Aug.2018, pp.221-250. (Invited Book Chapter), ISBN: 978-1-78561-629-7.

[3]      Yulian Ding, Fei Wang, Yuchen Zhang, Fangxiang Wu. Negative Sample Selection for miRNA-Disease Association Prediction Models, in《Machine Learning Methods for Multi-Omics Data Integration》, book edited by Alkhateeb, A., Rueda, L., Springer, Cham, Jul.2023, pp.75-90. (Invited Book Chapter), ISBN: 978-3-031-36501-0.

 授权专利：

      [1]       雷秀娟，方增强，张宇辰，基于梯度增强决策树预测环状RNA与疾病相关性的方法，发明专利，2022-08-16

  [1]      国家自然科学基金青年科学基金项目: 基于分子结构和图语言模型的靶向非编码RNA药物预测方法研究，2025.01-2027.12， 主持

  [2]      陕西省自然科学基础研究计划一般项目（青年项目）：基于多组学知识图Transformer与疾病非编码RNA的药物重定位预测方法研究，2024.01-2025.12，主持

  [3]      西北农林科技大学博士科研启动经费 ：基于图嵌入学习的药物重定位与组合药物发现研究，2023.03-2026.03，主持

  [4]      国家自然科学基金面上项目：基于计算方法的circRNA功能挖掘及其与复杂疾病的关系预测研究，2020.01-2023.12，参与

  [5]      国家自然科学基金面上项目：动态蛋白质网络复合物识别方法研究及其应用，2017.01-2020.12，参与

  [6]      国家自然科学基金青年科学基金项目：基于数据驱动的发展式头脑风暴优化算法研究，2019.01-2021.12，参与

  [7]      陕西师范大学，中央高校博士自由探索项目：基于生物网络分析的疾病基因与疾病circRNA预测方法研究，2018.10-2022.04，主持

• 2024届本科毕业生：张成杰、何芯蕊、徐慧婷

• 2024届张成杰论文《基于图注意力网络的药物相互作用预测方法研究》被评为“院级优秀毕业论文”。

• 
  

• 目前指导的本科生大创项目：

  《基于自然语言处理模型的药物靶点预测方法研究》（国家级）

  《基于知识图谱表征学习的miRNA-疾病关联关系预测方法研究》（省级）

• 
  

• 如有对深度学习、生物信息方向感兴趣的同学，欢迎邮件或QQ联系。

      科创主要方向:  药物发现研究

                             疾病标志物预测与平台开发

                             多组学数据分析等

      招生要求：

                      1. 学习态度端正，积极乐观，能主动交流沟通；

                      2. 对于科创项目具有热情，愿意积极主动探索，对失败具有耐心和勇气；

                      3. 对于深度学习编程十分感兴趣；

                      4. 数学和英语能力较好。

      支持：

                      1. 在深度学习/生物信息学科，从模型构建，方法设计、代码编写、论文撰写等方面给予学生一对一详细指导；

                      2. 指导和推荐各类科创项目或竞赛；

                      3. 对于在科创工作1年以上，取得一定科研成绩的本科同学，若取得我校推免资格，可优先录取；若想保送外校研究生，将协助推荐。

   [1]    The15th ACM  Conference on Bioinformatics, Computational Biology, and Health  Informatics (BCB’24), November 22-25, 2024, Shenzhen, China, 国际学术会议报告《ICDFGF: Identification of potential circRNA-disease associations based  on feature graph factorization》

   [2]    第三届中国智能健康与生物信息大会，福州，2024，学术报告《Identify Potential CircRNA-Disesase Associations Through a Multi-Objective Evolutionary Algorithm》

   [3]    第二届CCF生物信息“新未来”青年学者论坛，苏州，2023，学术报告《Drug Repositioning with GraphSAGE and Clustering Constraints Based on Drug and Disease Networks》

　　Zhang Yuchen, a native of Xi 'an, received his Ph.D. degree in engineering from Shaanxi Normal University in 2022. He is currently working at the College of Information Engineering, Northwest A&F University. He participated in the PhD co-training at the University of Saskatchewan, Canada, in 2021-2022. He has published many research papers in journals, presided over one project funded by the National Natural Science Foundation of China and one project funded by the Science and Technology Program of Shaanxi Province, 2 projects of Fundamental Research Funds for the Central Universities, participated in 4 projects of National Natural Science Foundation of China, and 3 projects of provincial and ministerial level. He has written 2 chapters of monographs and authorized 2 patents. He is a member of the Intelligent Health and Bioinformatics Committee of the Chinese Society of Automation, and an executive member of the CCF Bioinformatics "New Future" Young Scholars Seminar. He is also a reviewer for the journals Frontiers in Pharmacology, BMC Bioinformatics, and Chinese Journal of Electronics. He also served as a PC for IEEE International Conference on Bioinformatics and Biomedicine (BIBM), International Conference on Swarm Intelligence (ICSI), International Conference on Data Mining and Big Data (DMBD), and other conferences.

Google Scholar: https://scholar.google.com.hk/citations?user=aXG0kK8AAAAJ&hl=zh-CN

ResearchGate: https://www.researchgate.net/profile/Yuchen-Zhang-51