2022年天津市自然科学一等奖（杨建益、张瀚、胡刚)

主持在研项目：

--蛋白质组学数据处理与表示的人工智能方法研究，No.92470124，国家自然科学基金重大研究计划培育项目（负责人）

--基于可解释深度学习的复杂组学数据分析的关键方法研究，No.62373200，国家自然科学基金面上项目（负责人）

--国家社科基金重大项目：大数据背景下医患关系的分析与政策研究：18ZDA087（子课题负责人）

已结题项目：

--面向神经疾病的高通量异构组学数据集成分析的关键方法研究，No.61973174， 国家自然科学基金面上项目（负责人）

--面向功能与注释的蛋白质分类与识别的智能方法研究，21JCZDJC00140天津市自然基金重点项目（负责人）

--国家自然科学基金项目海外及港澳学者合作研究基金-碳水化合物活性酶家族分类与深度注释的生物信息工具研究和开发:31728013(中方负责人)

--智能计算平台子课题，NO.2018YFB0204304 国家重点研发计划项目，参与人

--天津市应用基础与前沿技术研究计划项目: 基于大肠埃希菌的染色体超螺旋折叠边界研究:15JCYBJC18900（负责人）

--国家自然科学基金项目: 基于本体的计算机病毒自适应建模方法研究 项目批准号:61004086        (负责人)

--教育部博士点基金: 复杂网络下基于语义建模的智能病毒防御技术研究,课题号200800551024(负责人)

--天津市自然科学基金: 基于保守混沌系统的密码新理论与新方法研究,项目号:07JCYBJC14700,   (负责人)

研究室开发重要软件、数据库、服务器最新地址：

scMHNN: https://github.com/zhanglabNKU/scMHNN

LR-GNN: https://github.com/zhanglabNKU/LR-GNN

MGEGFP: https://github.com/zhanglabNKU/MGEGFP

HDMC: https://github.com/zhanglabNKU/HDMC

VGAELDA: https://github.com/zhanglabNKU/VGAELDA

ATTCry: https://github.com/zhanglabNKU/ATTCry

GDASC: https://bioinfo.nankai.edu.cn/

DASC: https://github.com/zhanglabNKU/DASC

TDAN: https://github.com/zhanglabNKU/TDAN

dbCAN2: http://bcb.unl.edu/dbCAN2/

dbCAN-seq: http://bcb.unl.edu/dbCAN_seq/index.php

eCAMI: https://github.com/zhanglabNKU/eCAMI

pHMM-tree: http://bcb.unl.edu/pHMM-Tree/source/index.php

APIN: https://github.com/zhanglabNKU/APIN

近期论文：（*为通讯作者,#为并列第一作者）

1.Wei Li, Fan Yang, Fang Wang, Yu Rong, Linjing Liu, Bingzhe Wu, Han Zhang*, Jianhua Yao*, scPROTEIN: A Versatile Deep Graph Contrastive Learning Framework for Single-cell Proteomics Embedding , Nature Methods, DOI : 10.1038/s41592-024-02214-9.影响因子48

2. Xiongwen Quan, Guangyao Hou, Wenya Yin, Han Zhang*, A multi-modal and multi-stage fusion enhancement network for segmentation based on OCT and OCTA images, Information Fusion, 2024, PII: S1566-2535(24)00372-5, DOI: 10.1016/j.inffus.2024.102594.

3. Chuanze Kang, Han Zhang*, Yanbin Yin, A dual-modality complex-valued fusion method for predicting side effects of drug-drug interactions based on graph neural network, IEEE Journal of Biomedical and Health Informatics, 10.1109/JBHI.2024.3422673. SCI小类一区

4. Xiangxin Zhan, Yanbin Yin and Han Zhang∗, BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel  framework，Bioinformatics，doi: 10.1093/bioinformatics/btae127.

5. Mingjing Han, Han Zhang*, KAGNN: Graph neural network with kernel alignment for heterogeneous graph learning, Knowledge-Based Systems, 289 (2024) 111561, https://doi.org/10.1016/j.knosys.2024.111561.

6. Mingjing Han, Han Zhang*, Wei Li, Yanbin Yin. Semantic-guided graph neural network for heterogeneous graph embedding, Expert Systems with Applications, 2023, doi:10.1016/j.eswa.2023.120810. SCI一区top期刊

7. Wei Li, Bin Xiang, Fan Yang, Yu Rong, Yanbin Yin, Jianhua Yao∗,and Han Zhang*. scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data, Briefings in Bioinformatics, 2023, DOI: 10.1093/bib/bbad391. SCI小类一区top期刊

8. Qingqing Zhao, Han Zhang*, Mengyao He, Wei Li, Chuanze Kang, Mingjing Han, Graph pooling via Dual-view Multi-level Infomax, Knowledge-Based Systems, 260(2023)：1-15. doi.org/10.1016/j.knosys.2022.110089. SCI一区top期刊

9. Mengyao He, Qingqing Zhao, Han Zhang*，et al. Graph Representation Learning via Redundancy Reduction. Neurocomputing, 533, 161–177. doi:10.1016/j.neucom.2023.02.062.

10. Mingjing Han, Han Zhang*, Multiple Kernel Learning for Label Relation and Class Imbalance in Multi-label Learning, Information Sciences, 2022, 613:344-356. SCI一区top

11. Wanwan Huang, Han Zhang*, Zeyuan Li, Yanbin Yin, Mutual Information Estimation-Based Disentangled Representation Network for Medical Image Fusion, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 最佳学生论文奖（会场唯一），Best Student Paper.

12.Wanwan Huang, Han Zhang*, Huike Guo, Wei Li, Xiongwen Quan, Yuzhi Zhang. ADDNS: An Asymmetric Dual Deep Network with Sharing Mechanism for Medical Image Fusion of CT and MR-T2, Computers in Biology and Medicine. doi.org/10.1016/j.compbiomed.2023.107531. SCI小类一区

13.Minghe Li, Huike Guo, Keao Wang, Chuanze Kang, Yanbin Yin, Han Zhang*. AVBAE-MODFR: a novel deep learning framework of embedding and feature selection on multi-omics data for pan-cancer classification, Computers in Biology and Medicine. 177 (2024) 108614, doi.org/10.1016/j.compbiomed.2024.108614

14.Xiongwen Quan, Xingyuan Ou, Li Gao, Wenya Yin, Guangyao Hou, Han Zhang*. SCINet: A Segmentation and Classification Interaction CNN Method for Arteriosclerotic Retinopathy Grading. Interdisciplinary Sciences: Computational Life Sciences. 2024, DOI :10.1007/s12539-024-00650-x. SCI

15. Mingjing Han, Han Zhang*, Huan Wang, and Yanbin Yin, Hierarchical Semantic Augmentation Graph Neural Network for Drug-Disease Association Prediction, 2023 BIBM, regular paper, CCF B类会议

16. Xiongwen Quan, Xia Guo, Han Zhang*, Mingjing Han, Zeyuan Li, and Yanbin Yin, Unsupervised Feature Selection by Fusing Spectral Clustering and Locality Preserving Projection, 2023 BIBM, regular paper, CCF B类会议

17. Wanwan Huang, Han Zhang*, Yu Cheng, Xiongwen Quan, DRCM: A Disentangled Representation Network based on Coordinate and Multimodal attention for Medical Image Fusion, Frontiers in Physiology,2023, 14, doi:10.3389/fphys.2023.1241370, SCI二区top期刊

18. Mengyao He, Qingqing Zhao, Han Zhang*. Multi-sample dual-decoder graph autoencoder, Methods, 2023, 211,31-41, DOI:10.1016/j.ymeth.2023.02.002

19. Yuzhou Ma, Han Zhang*, Chen Jin, Chuanze Kang. Predicting lncRNA-protein interactions with bipartite graph embedding and deep graph neural networks, Frontiers in Genetics,2023, doi.org/10.3389/fgene.2023.1136672. SCI

20. Guan Hou#, Yuhao Jian#, Qingqing Zhao, Quan Xiongwen and Han Zhang*. Language Model based on Deep Learning Network for Biomedical Named Entity Recognition. The 21th Asia Pacific Bioinformatics Conference(APBC). CCF C类会议regular paper. 推荐至Methods. doi: 10.1016/j.ymeth.2024.04.013.

主要论文：

1. Han Zhang#, Tanner Yohe#, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter Busk, Ying Xu, Yanbin Yin. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Research, 2018, 46 (Web Server issue) :W95-W101. SCI一区top期刊，影响因子19.160 (2019 ESI 0.1% 热点，高被引，SCI引用1500次).

2. Le Huang, Han Zhang*, Peizhi Wu, Sarah Entwistle, Xueqiong Li, Tanner Yohe, Haidong Yi, Zhenglu Yang, Yanbin Yin*. dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Research, 2018, 46(Database-Issue): D516-D521. SCI一区top期刊，影响因子19.160，SCI引用194次

3. Yanbin Yin#, Han Zhang#, Victor Olman, Ying Xu. (2010) Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome. Proc Natl Acad Sci USA （PNAS）, 107(14): 6310-6315 (*equal contribution),《美国国家科学院院刊》

4. Chuanze Kang, Han Zhang*, Zhuo Liu, Shenwei Huang, Yanbin Yin. LR-GNN: a graph neural network based on link representation for predicting molecular associations. Briefings in Bioinformatics, 2021, doi.org/10.1093/bib/bbab513，SCI一区top期刊，影响因子13.994

5. Wei Li, Han Zhang*, et al. MGEGFP: a multi-view graph embedding method for gene function prediction based on adaptive estimation with GCN. Briefings in Bioinformatics 23(5), 2022. SCI一区top期刊，影响因子13.994

6. Wanwan Huang, Han Zhang*, Xiongwen Quan, Jia Wang. A Two-level Dynamic Adaptive Network for Medical Image Fusion, IEEE Transactions on Instrumentation & Measurement, 71, 2022, 5010917. SCI二区top

7. Jia Wang, Xiao Wang, Han Zhang*. Domain-aware Multi-modality Fusion Network for Generalized Zero-shot Learning. Neurocomputing, 488 (2022) 23–35. SCI二区top期刊

8. Xiao Wang, Jia Wang, Han Zhang*, Shenwei Huang, Yanbin Yin. HDMC: a novel deep learning based framework for removing batch effects in single-cell RNA-seq data. Bioinformatics, 2021，doi.org/10.1093/bioinformatics/btab821，2021年SCI小类一区top期刊

9. Haidong Yi, Ayush.raman, Han Zhang*, Genevera Allen,Zhandong Liu*. Detecting hidden batch factors through data adaptive adjustment for biological effects. Bioinformatics, 2018,34(7):1141-1147, 2021年SCI小类一区top期刊

10. Xiao Wang, Haidong Yi, Jia Wang, Zhandong Liu, Yanbin Yin, Han Zhang*. GDASC: A GPU parallel based web server for detecting hidden batch factors. Bioinformatics,2020, 36(14),4211–4213, 2021年SCI小类一区top期刊

11. Shi, Zhuangwei, Zhang, Han*, Jin, Chen, A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations, BMC Bioinformatics,2021, 22(1): 589:1-589:11. SCI

12. Chen Jin, Zhuangwei Shi, Han Zhang*, and Yanbin Yin, Predicting lncRNA protein interactions based on graph autoencoders and collaborative training. 2021 BIBM,regular paper. CCF B类会议

13. Chen Jin, Jianzhao Gao, Zhuangwei Shi, Han Zhang*. Attcry: attention-based neural network model for protein crystallization prediction. Neurocomputing, 2021, 463, 265-274.SCI二区top期刊

14. Wei Li, Han Zhang*, Qingqing Zhao, Jian Liu, and Yanbin Yin, Adversarial Dual-Channel Variational Graph Autoencoder for Synthetic Lethality Prediction in Human Cancers. 2021 BIBM, regular paper. CCF B类会议

15. Wei Li, Qingqing Zhao, Han Zhang*, Xiongwen Quan, Jing Xu, and Yanbin Yin,Bayesian Multi-scale Convolutional Neural Network for Motif Occupancy Identification, 2020 BIBM, regular paper. CCF B类会议

16. Luyang Huo, Han Zhang*,Xueting Huo,Xueqiong Li,Yanbin Yin*. pHMM-tree: Phylogeny of Profile Hidden Markov Models .Bioinformatics, 2017,33(7), 1093-1095, 2021年SCI小类一区top期刊

17. Jing Xu, Han Zhang*, Jinfang Zheng, Philippe Dovoedo, Yanbin Yin. eCAMI: simultaneous classification and motif identification for enzyme annotation. Bioinformatics,2020,36(7),2068–2075, 2021年SCI小类一区top期刊

18. Zhang Han, Huo Xueting, Guo Xia, Su Xin, Quan Xiongwen*, Jin Chen. A disease-related gene mining method based on weakly supervised learning model. BMC Bioinformatics,2019, 20-S(16): 589:1-589:11. SCI，影响因子2.213（CCF B类BIBM会议regular paper推荐）.

19. Wei Li , Yanbin Yin , Xiongwen Quan, Han Zhang*. Gene Expression Value Prediction Based on XGBoost Algorithm. Frontiers in Genetics, 2019, DOI: 10.3389/fgene.2019.01077.( SCI引用154次).

20. Xin Su, Jing Xu, Yanbin Yin, Xiongwen Quan, Han Zhang*. Antimicrobial Peptide Identification Using Multi-scale Convolutional Network. BMC Bioinformatics, 2019,20(1): 730. 

21. Le Huang, Bowen Yang, Haidong Yi, Amina Asif, Jiawei Wang, Trevor Lithgow, Han Zhang, Fayyaz ul Amir Afsar Minhas, Yanbin Yin*. AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses. Nucleic Acids Research, 49 (D1) , pp.D622-D629. SCI一区top期刊, 影响因子19.160.

22. Haidong Yi, Le Huang, Bowen Yang, Javi Gomez, Han Zhang, Yanbin Yin*. Acrfinder: genome mining anti-crispr operons in prokaryotes and their viruses. Nucleic Acids Research.2020, 48 (W1) , pp.W358-W365. SCI一区top期刊, 影响因子19.160.

23. Xizeng Mao, Han Zhang, Yanbin Yin, Ying Xu*. The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces. Nucleic Acids Research, 2012, 40(17):8210-8218. SCI一区top期刊, 影响因子19.160.

24. Qin Ma, Yanbin Yin, Mark A. Schell, Han Zhang, Guojun Li, Ying Xu*. Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions, Nucleic Acids Research, 2013, 41(11), 5594-5603. SCI一区top期刊, 影响因子19.16027.

25. Shuo Gao, Li Gao, Xiongwen Quan*, Han Zhang, Hang Bai, Chuanze Kang.Automatic arteriosclerotic retinopathy grading using four-channel with image merging. Computer Methods and Programs in Biomedicine, 2021, 208: 106274, doi.org/10.1016/j.cmpb.2021.106274

26. Hang Bai, Li Gao, Xiongwen Quan*, Han Zhang, Shuo Gao, Chuanze Kang, Jiaqiang Qi. OTNet: A CNN Method Based on Hierarchical Attention Maps for Grading Arteriosclerosis of Fundus Images with Small Samples. Interdisciplinary Sciences: Computational Life Sciences, 2021, doi.org/10.1007/s12539-021-00479-8，SCI二区

27. Xingyuan Ou; Li Gao; Xiongwen Quan*;Han Zhang; Jinglong Yang; Wei Li. BFENet: A Two-Stream Interaction CNN Method for Multi-Label Ophthalmic Diseases Classification with Bilateral Fundus Images, Computer Methods and Programs in Biomedicine,2022，SCI二区

28. 付垒朋, 张瀚*, 霍路阳.基于多类特征的智能恶意脚本检测算法[J] 《模式识别与人工智能》, 2015,28卷,12期(通讯作者) .

29. 张涛, 张瀚*, 付垒朋.基于模糊模式与决策树融合的脚本病毒检测算法[J] 《电子与信息学报》, 2014,V36(1): 108-113(通讯作者) ,EI.

30. Jicai HUANG, Han ZHANG; Bifurcations of periodic orbits in Three-well Duffing system with a phase shift. Journal of Systems Science and Complexity(2011) 24: 519-531.

31. 张瀚，王秀峰，李朝晖,刘大海，一种基于时空混沌的Hash函数构造，《物理学报》, Vol.54（9）:4006-4011，2005.9 (EI :05389375776,SCI: 960DD).

32. 张瀚，王秀峰，李朝晖,刘大海，一种基于混沌系统及Henon映射的快速图像加密算法,《计算机研究与发展》, Vol.42（12）：2137-2142，2005.12. (EI:06029638018)

      授权专利：OCT 和 OCTA 图像融合的视网膜血管图像分割方法 证书号202410642900.X