崔菲菲——海南大学副教授、博士生导师工程与技术科学创新人物科技创新网

崔菲菲，博士，海南大学副教授，博/硕士生导师。2012年获得山东大学计算机专业硕士学位，2017年至2020年获得日本文部科学省博士奖学金资助于东京大学攻读博士学位，专业为生物信息学。主要研究领域为人工智能、生物信息学，研究内容包括但不限于机器学习（深度学习）、生物序列分类、基于人工智能的药物发现及多组学数据整合的疾病相关预测等。

主持国家级自然科学基金地区项目1项、国家级自然科学基金青年项目1项，海南省重点研发项目1项，四川省自然科学基金青年项目1项；中国博士后科学基金面上项目1项及博士后国际交流计划引进项目1项（已结题）。以第一作者或通讯作者在Briefings in Bioinformatics、Computational and Structural Biotechnology Journal、IEEE BIBM等高水平生物信息学SCI期刊或会议发表论文多篇。目前担任Electronics等SCI期刊客座编辑，多个SCI期刊审稿人；中国计算机学会(CCF)生物信息学专业委员会委员，中国国家自然科学基金委(NSFC)函评专家，吴文俊人工智能科学技术奖评审专家，机器学习与自然语言处理国际会议（MLNLP 2023）Organizing Committee Chair。

教育经历

东京大学, 生物信息学, 博士

山东大学, 计算机应用技术, 硕士

工作经历

2022-03至今，海南大学，计算机科学与技术学院，副教授

2020-04至2022-03，电子科技大学，基础与前沿研究院，博士后

主讲课程：

人工智能、机器学习、深度学习、模式识别、生物医学工程前沿、Python语言程序设计基础

招生信息：

Ø 欢迎对生物信息学感兴趣的同学与我联系（署名邮件必回复），报考我的硕士、博士研究生。

Ø 优先考虑具有计算机、数学、统计、生物、医学等相关背景的同学，其他跨专业学生只要努力踏实也非常欢迎。

Ø 本人与多所国内外科研院校保持良好合作关系，优秀者可推荐前往深造/访学。

针对在读本科生：

欢迎希望本科阶段获得科研训练并取得科研成果的本科同学联系我作为学业导师；

本课题组可以提供参与协助课题研究的机会，而且为每位学生提供独立的研究课题和单独指导，希望为努力的同学提供指引和帮助，争取发表第一作者的高水平科研成果；

但是如果只是想完成选学业导师的任务、自主努力性不高、单纯以本科文凭为目标的学生请不要联系我。

指导本科生发表第一作者SCI或CCF论文：

1. Yunyun Su, Xiuhao Fu, Leyi Wei, Zilong Zhang*, Quan Zou*, Feifei Cui*. PROTCROWN: A manually curated resource of protein corona data for unlocking the potential of protein-nanoparticle Interactions. Nano Letters. 2025. 25(5): 1739-17444.(中科院大类一区，影响因子9.6，自然指数期刊、TOP期刊, 第一作者苏云云同学为2019级本科生，已保研进本课题组)

2. Yunyun Su, Shiyu Yan, Chen Cao, Feifei Cui, Quan Zou*, Zilong Zhang*. Human-Spa: An Online Platform Based on Spatial Transcriptome Data for Diseases of Human Systems. In: 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM); 2023. pp. 293-298. (CCF-B会议，第一作者苏云云同学为2019级本科生，已保研进本课题组)

3. Yazi Li, Xiaoman Wei, Qinglin Yang, An Xiong, Xingfeng Li, Quan Zou, Feifei Cui*, Zilong Zhang*. msBERT-Promoter: a multi-scale ensemble predictor based on BERT pre-trained model for the two-stage prediction of DNA promoters and their strengths. BMC Biology 2024; 22(1):126. (中科院大类一区，TOP期刊，第一作者李亚子同学为2021级本科生，应用数学专业)

4. Cuilin Xiao, Zheyu Zhou, Jiayi She, Jinfen Yin, Feifei Cui, Zilong Zhang*. PEL-PVP: Application of plant vacuolar protein discriminator based on PEFT ESM-2 and bilayer LSTM in an unbalanced dataset. International Journal of Biological Macromolecules 2024; 277:134317. (中科院大类一区，影响因子7.7, TOP期刊, 第一作者肖萃林同学为2021级本科生，软件工程专业)

5. Zheyu Zhou, Cuilin Xiao, Jinfen Yin, Hao Duan, Chunling Liu, Feifei Cui, Zilong Zhang*. PSAC-6mA: 6mA Site Identifier Using Self-Attention Capsule Network based on Sequence-Positioning. Computers in Biology and Medicine. (中科院小类一区，TOP期刊，第一作者周喆誉同学为2022级本科生，软件工程专业)

6. Jingwei Lv, Aoyun Geng, Zhuoyu Pan, Leyi Wei, Quan Zou, Zilong Zhang, and Feifei Cui*. iBitter-GRE: A Novel Stacked Bitter Peptide Predictor with ESM-2 and Multi-View Features. Journal of Molecular Biology, 2025: p. 169005.(中科院大类二区，第一作者吕经纬同学为2022级本科生，软件工程专业)

7. Zihang Wang, Aoyun Geng, Junlin Xu, Yajie Meng, Zilong Zhang, Leyi Wei, Quan Zou, and Feifei Cui*. A comprehensive review of computational methods for predicting DNA N4-methylcytosine sites. International Journal of Biological Macromolecules, 2025: p. 148221. （TOP期刊、中科院大类二区，影响因子8.5，第一作者王子航为2023级本科生，计算机科学与技术专业）

8. Yuanhao Li, Aoyun Geng, Zheyu Zhou, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Quan Zou, Qingchen Zhang and Zilong Zhang *. AVP-HNCL: Innovative Contrastive Learning with a Queue-Based Negative Sampling Strategy for Dual-Phase Antiviral Peptide Prediction. Journal of Chemical Information and Modeling, 2025, 65(12): 5868-5886. (Top期刊、中科院大类二区，影响因子5.7，第一作者李袁昊为2022级本科生，生态学专业)

9. Jingwei Lv, Kexin Li, Yike Wang, Junlin Xu, Yajie Meng, Feifei Cui, Leyi Wei, Qingchen Zhang and Zilong Zhang*. ACP-EPC: an interpretable deep learning framework for anticancer peptide prediction utilizing pre-trained protein language model and multi-view feature extracting strategy. Molecular Diversity, 2025. (TOP期刊、中科院大类二区，影响因子4.5，第一作者吕经纬同学为2022级本科生，软件工程专业)

10. Yunyun Su#, Binlu Yang#, Aoyun Geng, Zilong Zhang and Feifei Cui*. RTCDB: A Multi-Omics Database Supporting Research and Discovery in Rare Tumor Oncology. 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). (CCF-B 推荐会议, 共同第一作者杨滨璐同学为2022级本科生，软件工程专业)

11. Ziyi Wang, Aoyun Geng, Hao Duan, Feifei Cui, Quan Zou*, Zilong Zhang*. A Comprehensive Review of Approaches for Spatial Domain Recognition of Spatial Transcriptomes. Briefings in Functional Genomics. ,2024,23(6): 702–712. (第一作者王梓懿同学为2021级本科生，软件工程专业)

指导本科生科研项目及竞赛

第二十六届中国机器人及人工智能大赛创新赛-人工智能创新赛专项赛道全国一等奖（成员：王紫涵、周喆誉、肖萃林，22级、21级本科生）

2024年中国高校计算机大赛移动应用创新赛一等奖（成员：尹锦芬、周喆誉、肖萃林、佘嘉怡、王紫涵，22级、21级本科生）

第二十六届中国机器人及人工智能大赛人工智能创新上海南省一等奖

基于癌症基因表达数据的自适应加权中智C-均值聚类算法研究（本科生大创项目，项目负责人：裘昊晔，2021级本科生）

基于Diffusion的高穿膜性环肽定向生成模型（本科生大创项目，项目负责人：周喆誉，2022级本科生）

海南大学2025年大学生“AI”赋能创新实践项目立项（校级创新实践项目，项目负责人：吕经纬，22级本科生）

研究方向：

生物信息学，人工智能，机器学习，深度学习，基于人工智能的药物发现，多组学生物数据分析与处理。

科研项目：

主持国家级自然科学基金地区项目1项、国家级自然科学基金青年项目1项，海南省重点研发项目1项，四川省自然科学基金青年项目1项；中国博士后科学基金面上项目1项及博士后国际交流计划引进项目1项（已结题）。

1. 国家自然科学基金面上项目，62572156，基于蛋白质预训练大模型和图注意力网络的阿尔茨海默病研究，50万，主持，在研。

2. 国家自然科学基金地区项目，62262015，基于深度学习及多组学数据整合的三阴性乳腺癌多层任务模式挖掘研究，35万，主持，在研。

3. 国家自然科学基金青年项目，62101100，基于多模态多任务深度学习的蛋白质-核酸相互作用的系统性预测， 30万元，主持，已结题。

4. 海南省重点研发项目，ZDYF2024GXJS018，基于多模态生物医学数据的罕见肿瘤个性化诊疗模式挖掘中关键技术研发与应用， 64万，主持，在研。

5. 科技成果转化项目，基于人工智能的精准医疗模式挖掘，100万元，主持，在研。

6. 科技成果转化项目，基于人工智能预训练大模型的启动子及多肽精准鉴别平台技术，100万元，主持，在研。

7. 科技成果转化项目，基于人工智能的RNA甲基化位点修饰位点预测平台技术，100万，主持，在研。

8. 海南大学高层次人才科研启动基金， 35万元，主持，在研。

9. 博士后国际交流计划引进项目, YJ20200042, 非编码RNA的挖掘、疾病关系预测及相关计算方法的研究，70万元, 主持，已结题。

10. 四川省自然科学基金青年科学基金项目，2022NSFSC0943，基于深度迁移学习的蛋白质-核酸相互作用预测研究，10万元，主持，已结题。

11. 中国博士后科学基金面上资助项目，2021M700694，基于多模态深度学习的蛋白质-RNA结合偏好预测，8万元，主持，已结题。

12. 国家自然科学基金重点项目，62131004，面向单细胞RNA测序数据的深度迁移模型与细胞通信网络研究，305万元，参与。

13. 国家自然科学基金面上项目，62172076，面向药物副作用识别的多视角稀疏模型研究，60万元，参与。

14. 国家自然科学基金面上项目，62172128，基于多源生物数据融合的代谢综合征相关的lncRNA识别方法研究，60万元，参与。

发明公开：

[1]张子龙, 杨超, 崔菲菲, 付修豪. 基于边感知图注意力与自监督的细胞通信推断方法及系统[P]. 海南省: CN122822079A, 2026-09-25.

[2]张子龙, 李新宇, 崔菲菲. 结构增强与协同注意力的蛋白质-RNA相互作用预测方法及系统[P]. 海南省: CN122762011A, 2026-09-15.

[3]崔菲菲, 贾艳娜, 张子龙. 融合多尺度特征与两阶段对比学习的circRNA与miRNA相互作用预测方法及系统[P]. 海南省: CN122493976A, 2026-07-31.

[4]张子龙, 李奕朗, 崔菲菲, 耿奥运. 基于扩散Transformer与自适应表征学习的单细胞类型注释方法及系统[P]. 海南省: CN122493981A, 2026-07-31.

[5]崔菲菲, 张卓越, 张子龙, 耿奥运. 基于双对比学习的空间转录组学空间域识别方法及系统[P]. 海南省: CN122392639A, 2026-07-14.

[6]崔菲菲, 文乾茂, 张子龙. 基于能量平衡动态引导和流匹配的信号肽生成方法及系统[P]. 海南省: CN122369590A, 2026-07-10.

[7]崔菲菲, 崔志豪, 张子龙, 耿奥运. 基于注意力图神经网络的蛋白质相互作用位点识别方法及系统[P]. 海南省: CN122337318A, 2026-07-03.

[8]张子龙, 原勇涛, 崔菲菲. 统一空间多组学数据潜在表示的生成方法及系统[P]. 海南省: CN122337323A, 2026-07-03.

[9]张子龙, 刘健, 崔菲菲, 耿奥运. 基于多源特征及特征融合的肽-蛋白相互作用预测方法及系统[P]. 海南省: CN122201407A, 2026-06-12.

[10]崔菲菲, 熊安, 张子龙. 基于双通道特征一致性与课程伪标签的跨域药物-靶点相互作用预测方法及系统[P]. 海南省: CN122201412A, 2026-06-12.

[11]崔菲菲, 吕经纬, 张子龙. 融合序列与结构信息的血脑屏障穿透肽预测方法及系统[P]. 海南省: CN121999881A, 2026-05-08.

[12]崔菲菲, 李奕朗, 张子龙, 耿奥运. 结合知识图谱的大语言模型分层式单细胞注释方法及系统[P]. 海南省: CN121811983A, 2026-04-07.

[13]崔菲菲, 林晓萌, 张子龙. 基于多图神经网络与交叉注意力机制的抗真菌肽识别方法及系统[P]. 海南省: CN121662144A, 2026-03-13.

[14]张子龙, 王金伟, 崔菲菲. 基于多图对比学习的图卷积网络在空间转录组中的空间域识别方法及系统[P]. 海南省: CN121662161A, 2026-03-13.

[15]崔菲菲, 耿奥运, 张子龙. 基于泰勒线性注意力图卷积的空间多组学结构域识别方法及系统[P]. 海南省: CN121542572A, 2026-02-17.

[16]崔菲菲, 宋冠颉, 张子龙, 耿奥运. 基于GCN与改进注意力网络的蛋白质溶解度预测方法及系统[P]. 海南省: CN121438957A, 2026-01-30.

[17]崔菲菲, 宋佳星, 张子龙, 耿奥运. 一种嗜酸蛋白的识别方法、装置及设备[P]. 海南省: CN121331284A, 2026-01-13.

[18]崔菲菲, 熊安, 张子龙. 基于基因本体引导和多模态注意力的药物-靶点亲和力预测方法及系统[P]. 海南省: CN121148461A, 2025-12-16.

[19]崔菲菲, 夏燕, 张子龙. 基于多任务预训练和多模态融合的分子性质预测方法及系统[P]. 海南省: CN121122472A, 2025-12-12.

[20]崔菲菲, 严子源, 张子龙, 耿奥运. 一种DNA结合蛋白的识别方法及系统[P]. 海南省: CN120954480A, 2025-11-14.

[21]崔菲菲, 王善月, 张子龙, 耿奥运. 一种B细胞表位预测方法、系统、设备及介质[P]. 海南省: CN120954493A, 2025-11-14.

[22]崔菲菲, 文乾茂, 张子龙. 一种预测靶肽分类和裂解位点的方法及系统[P]. 海南省: CN120932745A, 2025-11-11.

[23]张子龙, 李新宇, 崔菲菲. 基于特征融合的m5U修饰位点预测方法及装置[P]. 海南省: CN120853688A, 2025-10-28.

[24]张子龙, 贾艳娜, 崔菲菲. 基于计算机预测RNA-蛋白质相互作用的方法及系统[P]. 海南省: CN120833849A, 2025-10-24.

[25]崔菲菲, 夏燕, 张子龙. 基于多模态信息融合的DDI预测方法和装置[P]. 海南省: CN120748547A, 2025-10-03.

[26]崔菲菲, 耿奥运, 张子龙. 基于多模态融合的抗病毒肽识别方法及系统[P]. 海南省: CN120510913A, 2025-08-19.

[27]张子龙, 刘健, 崔菲菲. 基于对比学习和交叉注意力机制的神经肽鉴别方法及系统[P]. 海南省: CN120452541A, 2025-08-08.

[28]张子龙, 李袁昊, 耿奥运, 崔菲菲. 基于队列负采样策略及对比学习的抗病毒肽预测方法及系统[P]. 海南省: CN120432019A, 2025-08-05.

[29]崔菲菲, 闫朝睿, 张子龙. 基于蛋白质语言模型与多尺度卷积神经网络的Cas蛋白识别方法及系统[P]. 海南省: CN120072053A, 2025-05-30.

[30]崔菲菲, 吕经纬, 张子龙, 耿奥运. 基于特征融合及交叉注意力机制的抗癌肽预测方法及系统[P]. 海南省: CN120015123A, 2025-05-16.

[31]崔菲菲, 刘瑞祺, 张子龙. 基于蛋白质语言模型的IL-4诱导肽预测方法及系统[P]. 海南省: CN119920322A, 2025-05-02.

[32]崔菲菲, 高顺, 张子龙. 基于蛋白质语言模型的抗癌肽预测方法及系统[P]. 海南省: CN119864081A, 2025-04-22.

[33]崔菲菲, 吕经纬, 张子龙, 耿奥运. 基于多特征编码融合的苦味肽识别方法和装置[P]. 海南省: CN119807929A, 2025-04-11.

[34]崔菲菲, 高顺, 张子龙, 张清辰. 基于蛋白质语言模型的肽毒性预测方法及系统[P]. 海南省: CN119763676A, 2025-04-04.

[35]张子龙, 杨超, 付修豪, 崔菲菲. 基于图卷积和长短期记忆注意网络的细胞间相互作用重建方法及系统[P]. 海南省: CN119673277A, 2025-03-21.

[36]张子龙, 王金伟, 崔菲菲, 耿奥运, 罗振杰. 植物非组蛋白赖氨酸巴豆酰化位点识别方法及系统[P]. 海南省: CN119517159A, 2025-02-25.

[37]崔菲菲, 熊安, 夏燕, 张子龙. 基于深度学习的药物-靶点相互作用的预测方法及系统[P]. 海南省: CN119339783A, 2025-01-21.

[38]崔菲菲, 罗振杰, 耿奥运, 张子龙. 基于掩码机制可控长度的多肽序列生成方法及系统[P]. 海南省: CN119339809A, 2025-01-21.

[39]张子龙, 贾艳娜, 崔菲菲, 耿奥运, 付修豪. 基于RNAErnie预训练模型的RNA N4-乙酰胞苷修饰位点预测方法及系统[P]. 海南省: CN119252330A, 2025-01-03.

[40]崔菲菲, 袁嘉豪, 耿奥运, 张子龙. 基于特征选择和深度神经网络的2OM甲基化修饰位点识别方法及系统[P]. 海南省: CN119207585A, 2024-12-27.

[41]崔菲菲, 闫朝睿, 耿奥运, 张子龙. 基于高效特征编码和集成学习的促炎肽识别方法[P]. 海南省: CN118866103A, 2024-10-29.

[42]崔菲菲, 付修豪, 张子龙. 基于机器学习的蛋白冠上蛋白质相对丰度的预测方法及系统[P]. 海南省: CN118841080A, 2024-10-25.

[43]张子龙, 段昊, 崔菲菲. 基于图神经网络的空间转录组空间域识别方法及系统[P]. 海南省: CN118711665A, 2024-09-27.

[44]崔菲菲, 袁嘉豪, 张子龙, 李兴风, 张清辰. mRNA中的N4-乙酰胞嘧啶位点检测方法及相关装置[P]. 海南省: CN118314956A, 2024-07-09.

[45]张子龙, 耿奥运, 崔菲菲. 一种抗癌肽预测方法及相关装置[P]. 海南省: CN118314949A, 2024-07-09.

[46]张子龙, 李亚子, 崔菲菲. 一种DNA启动子及其强度的两阶段预测方法[P]. 海南省: CN118197434A, 2024-06-14.

[47]崔菲菲, 付修豪, 张子龙, 李兴风, 张清辰. 基于混合特征模型和提升模型集成的抗结核肽预测系统[P]. 海南省: CN116631516A, 2023-08-22.

[48]张子龙, 段昊, 崔菲菲, 李兴风, 张清辰. 基于机器学习的转移性乳腺癌转录组测序数据识别方法[P]. 海南省: CN116564409A, 2023-08-08.

发明授权：

[1]崔菲菲, 文乾茂, 张子龙. 基于能量平衡动态引导和流匹配的信号肽生成方法及系统[P]. 海南省: CN122369590B, 2026-08-14.

[2]崔菲菲, 袁嘉豪, 耿奥运, 张子龙. 基于特征选择和深度神经网络的2OM甲基化修饰位点识别方法及系统[P]. 海南省: CN119207585B, 2026-06-26.

[3]崔菲菲, 罗振杰, 耿奥运, 张子龙. 基于掩码机制可控长度的多肽序列生成方法及系统[P]. 海南省: CN119339809B, 2026-03-13.

[4]崔菲菲, 闫朝睿, 张子龙. 基于蛋白质语言模型与多尺度卷积神经网络的Cas蛋白识别方法及系统[P]. 海南省: CN120072053B, 2025-11-28.

[5]崔菲菲, 吕经纬, 张子龙, 耿奥运. 基于多特征编码融合的苦味肽识别方法和装置[P]. 海南省: CN119807929B, 2025-11-14.

[6]张子龙, 杨超, 付修豪, 崔菲菲. 基于图卷积和长短期记忆注意网络的细胞间相互作用重建方法及系统[P]. 海南省: CN119673277B, 2025-10-17.

[7]崔菲菲, 吕经纬, 张子龙, 耿奥运. 基于特征融合及交叉注意力机制的抗癌肽预测方法及系统[P]. 海南省: CN120015123B, 2025-10-17.

[8]崔菲菲, 高顺, 张子龙. 基于蛋白质语言模型的抗癌肽预测方法及系统[P]. 海南省: CN119864081B, 2025-10-03.

[9]张子龙, 贾艳娜, 崔菲菲, 耿奥运, 付修豪. 基于RNAErnie预训练模型的RNA N4-乙酰胞苷修饰位点预测方法及系统[P]. 海南省: CN119252330B, 2025-08-22.

[10]崔菲菲, 付修豪, 张子龙. 基于机器学习的蛋白冠上蛋白质相对丰度的预测方法及系统[P]. 海南省: CN118841080B, 2025-04-25.

[11]张子龙, 耿奥运, 崔菲菲. 一种抗癌肽预测方法及相关装置[P]. 海南省: CN118314949B, 2024-12-13.

[12]崔菲菲, 袁嘉豪, 张子龙, 李兴风, 张清辰. mRNA中的N4-乙酰胞嘧啶位点检测方法及相关装置[P]. 海南省: CN118314956B, 2024-11-08.

[13]张子龙, 李亚子, 崔菲菲. 一种DNA启动子及其强度的两阶段预测方法[P]. 海南省: CN118197434B, 2024-08-16.

[14]崔菲菲, 付修豪, 张子龙, 李兴风, 张清辰. 基于混合特征模型和提升模型集成的抗结核肽预测系统[P]. 海南省: CN116631516B, 2024-07-12.

发表论文：

1. Jingwei Lv, Qianyang Wu , Jian Liu , Binlu Yang , Yuanhao Li , Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, Xiulai Li*, Feifei Cui*. INB3P: A Multi-Modal and Interpretable Co-Attention Framework Integrating Property-Aware Explanations and Memory-Bank Contrastive Fusion for Blood–Brain Barrier Penetrating Peptide Discovery. Advance Science. 2026. （中科院大类一区、TOP期刊，影响因子14.1）

2. Aoyun Geng, Chunyan Cui, Yunyun Su, Zhenjie Luo, Feifei Cui, Zilong Zhang*. TLAGC: Taylor Linear Attention-Guided Graph Convolutions for Revealing Spatial Domains in Spatial Multi-Omics Data. Proceedings of the AAAI Conference on Artificial Intelligence, 40(25), 21269-21277. (CCF-A会议)

3. Qianyang Wu, Jingwei Lv, Zilong Zhang, Feifei Cui*. Generalizable Drug–Target Interaction Prediction via ESM-2 Representations and Progressive Contrastive Curriculum Learning. Proceedings of the AAAI Conference on Artificial Intelligence, 40(2), 1276-1284. (CCF-A会议)

4. Qianmao Wen, Xinyu Li, Jiaxing Song, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, and Feifei Cui*. Computational methods for signal peptide prediction: From statistical models to deep learning. Biotechnology Advances, 2026. 88: p. 108819. (中科院大类一区，TOP期刊，影响因子12.5分)

5. Yan Xia, Yazi Li, Shuting Jin, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang*, Xin Gao*, and Feifei Cui*. MFDL-DDI: An effective deep learning-based framework for predicting drug-drug interactions through multimodal information fusion. Pattern Recognition, 2026. 178: p. 113431. (中科院大类一区，TOP期刊，影响因子7.6分)

6. Yajie Meng, Zhuang Zhang, Xudong Shang, Xianfang Tang, Jincan Li, Zilong Zhang, Feifei Cui, Shuting Jin, Junlin Xu*, and Peng Wang*. FusionMVSA: Multi-View Fusion Strategy With Self-Attention for Enhancing Drug Recommendation. IEEE Journal of Biomedical and Health Informatics, 2026. 30(2): p. 1746. (中科院小类一区，TOP期刊，影响因子6.8分)

7. Xu Guo, Jianbo Qiao, Siqi Chen, Junru Jin, Ding Wang, Wenjia Gao, Feifei Cui, Zilong Zhang, Hua Shi, Zhongmin Yan, Leyi Wei*, and Xinbo Jiang*. ABT-DDI: A Graph Transformer Model with Atomic-Bond Structure Awareness for Drug–Drug Interaction Prediction. ACS Synthetic Biology, 2026. 15(1): p. 297. (中科院小类一区，影响因子3.9分)

8. Jiajing Wang, Aoyun Geng, Ziyuan Yan, Xiaomeng Lin, Yuanhao Li, Junlin Xu, Yajie Meng, Zilong Zhang, Leyi Wei, Quan Zou, and Feifei Cui*. FA-Amy: An amyloid protein prediction model based on protein pre-trained large models and an attention-fusion strategy. International Journal of Biological Macromolecules, 2026. 335: p. 149267. (中科院大类二区，TOP期刊，影响因子8.5分)

9. Ziyuan Yan, Aoyun Geng, Yazi Li, Jiajing Wang, Junlin Xu, Yajie Meng, Leyi Wei, Quan Zou, Zilong Zhang, and Feifei Cui*. CNNCaps-DBP: Leveraging protein language models with attention-augmented convolution for DNA-binding protein prediction. Neural Networks, 2026. 195: p. 108261. (中科院大类二区，TOP期刊，影响因子6.3分)

10. Yike Wang, Jingwei Lv, Yan Xia, Junlin Xu, Yajie Meng, Feifei Cui, Leyi Wei, Quan Zou, and Zilong Zhang*. A unified survey on drug-target interaction and binding affinity prediction: Models, representations, and challenges. Biotechnology Advances, 2026. 88: p. 108843. (中科院大类一区，TOP期刊，影响因子12.5分)

11. Junlin Xu, Cheng Guo, Yajie Meng, Shuting Jin, Changcheng Lu, Zilong Zhang, Feifei Cui, Xiangzheng Fu, Quan Zou, Tian Tian*, and Xiangxiang Zeng*. A deep adversarial network model for multi-task analysis of single-cell omics data. Briefings in Bioinformatics, 2026. 27(2): p. bbag016. (中科院小类一区，影响因子7.7分)

12. Jinjin Li, Xiaorui Kang, Chen Su, Hua Shi, Feifei Cui, Zilong Zhang, Changhang Lin*, and Leyi Wei*. Multitask Contrastive Learning with Attention Mechanisms for Neuropeptide Prediction Using ESM Representations. ACS Synthetic Biology, 2026.

13. Changhang Lin, Shuwen Xiong, Jinjin Li, Feifei Cui, Zilong Zhang, Hua Shi, and Leyi Wei*. PepGraphormer: an ESM-GAT hybrid deep learning framework for antimicrobial peptide prediction. Journal of Cheminformatics, 2026. 18(1): p. 15. (中科院大类二区，影响因子5.7分)

14. Guanjie Song, Zhenjie Luo, Aoyun Geng, Junlin Xu, Yajie Meng, Feifei Cui, Leyi Wei, Quan Zou, and Zilong Zhang*. Protein Solubility Prediction Using Fused Graph Convolutional Networks and Improved Attention Networks with AlphaFold3-Derived Features. Journal of Chemical Information and Modeling, 2026. 66(2): p. 894. (中科院大类二区，TOP期刊，影响因子5.3分)

15. Aoyun Geng, Chunyan Cui, Zhenjie Luo, Junlin Xu, Yajie Meng, Feifei Cui, Leyi Wei, Quan Zou, and Zilong Zhang*. Computational methods for spatial multi-omics integration. Biotechnology Advances, 2026. 87: p. 108807. (中科院大类一区，TOP期刊，影响因子12.5分)

16. Jinwei Wang, Zhenjie Luo, Aoyun Geng, Junlin Xu, Yajie Meng, Shankai Yan, Leyi Wei, Zilong Zhang, Qingchen Zhang, Quan Zou, and Feifei Cui. DeepNhKcr: Explainable Deep Learning Framework for the Prediction of Crotonylation Sites of Non-Histone Lysine in Plants Based on Pre-Trained Protein Language Model. IEEE Transactions on Computational Biology and Bioinformatics, 2026. 23(1): p. 326.

17. Jiahao Yuan, Shun Gao, Ziyuan Yan, Feifei Cui, Leyi Wei, Qingchen Zhang, Quan Zou, and Zilong Zhang*. DeepR2OM: Accurate Recognition for RNA 2′-O-Methylation Sites in Human Genome Using Deep Learning. IEEE Transactions on Computational Biology and Bioinformatics, 2026. 23(1): p. 419.

18. Shuwen Xiong, FeifeiCui, Zilong Zhang, Rao Zeng, Ran Su, and Leyi Wei*. A Multi-Modal Contrastive Learning Framework for Cyclic Peptide Permeability Prediction. IEEE Transactions on Computational Biology and Bioinformatics, 2026. 23(1): p. 362.

19. Zhenjie Luo, Aoyun Geng, Leyi Wei, Quan Zou, Feifei Cui* and Zilong Zhang*. CPL‐Diff: A Diffusion Model for De Novo Design of Functional Peptide Sequences with Fixed Length. Advanced Science, 2025: p. 2412926. （中科院大类一区，TOP期刊，影响因子14.3分）

20. Yunyun Su, Xiuhao Fu, Leyi Wei, Zilong Zhang*, Quan Zou*, Feifei Cui*. PROTCROWN: A manually curated resource of protein corona data for unlocking the potential of protein-nanoparticle Interactions. Nano Letters. 2025, 25(5): 1739-1744. (中科院大类一区，影响因子9.6，自然指数期刊、TOP期刊)

21. Zihang Wang, Aoyun Geng, Junlin Xu, Yajie Meng, Zilong Zhang, Leyi Wei, Quan Zou, and Feifei Cui*. A comprehensive review of computational methods for predicting DNA N4-methylcytosine sites. International Journal of Biological Macromolecules, 2025: p. 148221. （TOP期刊、中科院大类二区，影响因子8.5）

22. Aoyun Geng, Zhenjie Luo, Aohan Li, Zilong Zhang, Quan Zou, Leyi Wei, and Feifei Cui*. ACP-CLB: An Anticancer Peptide Prediction Model Based on Multichannel Discriminative Processing and Integration of Large Pretrained Protein Language Models. Journal of Chemical Information and Modeling, 2025.（中科院大类二区、TOP期刊，影响因子5.7）

23. Yunyun Su, Binlu Yang, Aoyun Geng, Zilong Zhang and Feifei Cui*. RTCDB: A Multi-Omics Database Supporting Research and Discovery in Rare Tumor Oncology. 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). (CCF-B 推荐会议)

24. Jingwei Lv, Aoyun Geng, Zhuoyu Pan, Leyi Wei, Quan Zou, Zilong Zhang, and Feifei Cui*. iBitter-GRE: A Novel Stacked Bitter Peptide Predictor with ESM-2 and Multi-View Features. Journal of Molecular Biology, 2025: p. 169005. （TOP期刊、中科院大类二区，影响因子4.74）

25. Xinyu Li, Zhenjie Luo, Jingwei Lv, Chao Yang, Shankai Yan, Junlin Xu, Yajie Meng,Leyi Wei, Zilong Zhang, Quan Zou, and Feifei Cui*. m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites. Journal of Chemical Information and Modeling, 2025, 65(15): 8079-8096. （中科院大类二区、TOP期刊，影响因子5.7）

26. Yan Xia, An Xiong, Zilong Zhang*, Quan Zou*, Feifei Cui*. A comprehensive review of deep learning-based approaches for drug-drug interaction prediction. Briefings in Functional Genomics, 2025.

27. Ronglin Lu, Jianbo Qiao, Kefei Li, Yanxi Zhao, Junru Jin, Feifei Cui, Zilong Zhang, Balachandran Manavalan, and Leyi Wei. ERNIE-ac4C: A novel deep learning model for effectively predicting N4-acetylcytidine sites. Journal of Molecular Biology, 2025: p. 168978.

28. Chaorui Yan, Zilong Zhang, Junlin Xu, Yajie Meng, Shankai Yan, Leiyi Wei, Quan Zou, Qingchen Zhang and Feifei Cui*. CasPro-ESM2: Accurate identification of Cas proteins integrating pre-trained protein language model and multi-scale convolutional neural network. International Journal of Biological Macromolecules, 2025. 308: p. 142309. (中科院大类一区，影响因子9.6，自然指数期刊、TOP期刊)

29. Ruiqi Liu, Shankai Yan, Zilong Zhang, Junlin Xu, Yajie Meng, Qingchen Zhang, Leiyi Wei, Quan Zou, and Feifei Cui*. PLM-IL4: Enhancing IL-4-inducing peptide prediction with protein language model. Computational Biology and Chemistry, 2025: p. 108448.

30. Chunyan Cui, Feifei Cui, Quan Zou, Zilong Zhang, and Linpei Jia. Progress and applications of single-cell RNA sequencing and spatial transcriptome technology in acute kidney injury research. Molecular Therapy Nucleic Acids, 2025. 36(3).

31. Ge Tian, Chenglin Yin, Jianbo Qiao, Ruheng Wang, Hua Shi, Feifei Cui, Zilong Zhang, Xinbo Jiang, and Leyi Wei. EDNTOM: An Ensemble Learning and Weight Mechanism-Based Nanopore Methylation Detection Tool. ACS omega, 2025.

32. Jiangbo Zhang, Yunhui Peng, Feifei Cui, Zilong Zhang, Shankai Yan, and Qingchen Zhang. RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA–protein binding sites prediction. BMC bioinformatics, 2025. 26(1): p. 176.

33. Changhang Lin, Shuwen Xiong, Feifei Cui, Zilong Zhang, Hua Shi, and Leyi Wei. Deep Learning in Antimicrobial Peptide Prediction. Journal of Chemical Information and Modeling, 2025.

34. Yajie Meng, Zhuang Zhang, Xudong Shang, Xianfang Tang, Jincan Li, Zilong Zhang, Feifei Cui, Shuting Jin, Junlin Xu, and Peng Wang. FusionMVSA: Multi-View Fusion Strategy with Self-Attention for Enhancing Drug Recommendation. IEEE Journal of Biomedical and Health Informatics, 2025. (中科院小类一区，TOP期刊，影响因子6.8分)

35. Shun Gao, Yanna Jia, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Qingchen Zhang, Quan Zou, and Zilong Zhang*. PLPTP: A Motif-based Interpretable Deep Learning Framework Based on Protein Language Models for Peptide Toxicity Prediction. Journal of Molecular Biology, 2025. 437(12): p. 169115.

36. Yuanhao Li, Aoyun Geng, Zheyu Zhou, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Quan Zou, Qingchen Zhang, and Zilong Zhang*. AVP-HNCL: Innovative Contrastive Learning with a Queue-Based Negative Sampling Strategy for Dual-Phase Antiviral Peptide Prediction. Journal of Chemical Information and Modeling, 2025.

37. Jian Liu, Aoyun Geng, Feifei Cui, Junlin Xu, Yajie Meng, Leyi Wei, Qingchen Zhang, Quan Zou, and Zilong Zhang*. NeuroCL: A Deep Learning Approach for Identifying Neuropeptides Based on Contrastive Learning. Analytical Biochemistry, 2025: p. 115920.

38. Na Li, Jianbo Qiao, Fei Gao, Yanling Wang, Hua Shi, Zilong Zhang, Feifei Cui, Lichao Zhang, and Leyi Wei. GICL: A Cross-Modal Drug Property Prediction Framework Based on Knowledge Enhancement of Large Language Models. Journal of Chemical Information and Modeling, 2025.

39. Chao Yang, Xiuhao Fu, Zhenjie Luo, Leyi Wei, Jingbing Li, Feifei Cui, Quan Zou, Qingchen Zhang, and Zilong Zhang*. GCNLA: Inferring Cell-Cell Interactions From Spatial Transcriptomics With Long Short-Term Memory and Graph Convolutional Networks. IEEE Journal of Biomedical and Health Informatics, 2025. (中科院小类一区，TOP期刊，影响因子6.8分)

40. Jianbo Qiao, Xu Guo, Junru Jin, Ding Wang, Kefei Li, Wenjia Gao, Feifei Cui, Zilong Zhang, Hua Shi, and Leyi Wei. Taco-DDI: accurate prediction of drug-drug interaction events using graph transformers and dynamic co-attention matrices. Neural Networks, 2025: p. 107655. (中科院大类二区，TOP期刊，影响因子6.3分)

41. Yajie Meng, Yi Wang, Xinrong Hu, Changcheng Lu, Xianfang Tang, Feifei Cui, Pan Zeng, Yuhua Yao, Jialiang Yang, and Junlin Xu. Adaptive debiasing learning for drug repositioning. Journal of Biomedical Informatics, 2025: p. 104843. (中科院大类二区，影响因子4.5分)

42. Jingwei Lv, Kexin Li, Yike Wang, Junlin Xu, Yajie Meng, Feifei Cui, Leyi Wei, Qingchen Zhang and Zilong Zhang*. ACP-EPC: an interpretable deep learning framework for anticancer peptide prediction utilizing pre-trained protein language model and multi-view feature extracting strategy. Molecular Diversity, 2025. (中科院大类二区，影响因子3.8分)

43. Jinjin Li, Shuwen Xiong, Hua Shi, Feifei Cui, Zilong Zhang, and Leyi Wei*. NeuroPred-AIMP: Multimodal Deep Learning for Neuropeptide Prediction via Protein Language Modeling and Temporal Convolutional Networks. Journal of Chemical Information and Modeling, 2025. 65(9): p. 4740. (中科院大类二区，TOP期刊，影响因子5.3分)

44. Junlei Yu, Wenjia Gao, Siqi Chen, Ronglin Lu, Jianbo Qiao, Junru Jin, Leyi Wei, Hua Shi, Zilong Zhang, Feifei Cui, Xinbo Jiang, and Zhongmin Yan*. MCAMEF-BERT: an efficient deep learning method for RNA N7-methylguanosine site prediction via multi-branch feature integration. Briefings in Bioinformatics, 2025. 26(5): p. bbaf447. (中科院小类一区，影响因子7.7分)

45. Qianmao Wen, Aoyun Geng, Junlin Xu, Yajie Meng, Leyi Wei, Zilong Zhang, Quan Zou, and Feifei Cui*. DeepMaT: Prediction of Target Peptide Classification and Cleavage Site by Combining Mamba2 and Multiple Attention Mechanisms. Journal of Chemical Information and Modeling, 2025. 65(19): p. 10011. (中科院大类二区，TOP期刊，影响因子5.3分)

46. Yajie Meng, Zhuang Zhang, Jincan Li, Xianfang Tang, Changcheng Lu, Zilong Zhang, Feifei Cui, Pan Zeng, Bo Li, and Junlin Xu*. ML-PLA: Enhancing Protein–Ligand Binding Affinity Prediction with Microenvironment and Long-Range Interaction-Aware Graph Neural Networks. Journal of Chemical Information and Modeling, 2025. 65(20): p. 10988. (中科院大类二区，TOP期刊，影响因子5.3分)

47. Zihang Wang, Aoyun Geng, Junlin Xu, Yajie Meng, Zilong Zhang, Leyi Wei, Quan Zou, and Feifei Cui*. A comprehensive review of computational methods for predicting DNA N4-methylcytosine sites. International Journal of Biological Macromolecules, 2025. 330: p. 148221. (中科院大类二区，TOP期刊，影响因子8.5分)

48. Pan Zeng, Ling You, Bofei Zhang, Yajie Meng, Xianfang Tang, Zilong Zhang, Feifei Cui, Jing Jiang, and Junlin Xu*. Enhanced drug recommendation model with graph contrastive based on singular value decomposition. Engineering Applications of Artificial Intelligence, 2025. 162: p. 112674. (中科院大类一区，TOP期刊，影响因子8分)

49. Yajie Meng, Yongkang Wang, Cheng Guo, Xianfang Tang, Zilong Zhang, Feifei Cui, Xiangzheng Fu, Quan Zou, Xu Lu*, and Junlin Xu*. ST-GCP: a graph convolutional network model with contrastive consistency and permutation for spatial transcriptomics. Briefings in Bioinformatics, 2025. 26(6): p. bbaf643. (中科院小类一区，影响因子7.7分)

50. Siying Yang, Ping-an He, Pan Zeng, Yajie Meng, Zilong Zhang, Feifei Cui, Yuhua Yao*, Jialiang Yang*, and Junlin Xu*. Predicting drug-target interactions based on multivariate information fusion and graph contrast learning. Journal of Biomedical Informatics, 2025. 172: p. 104960. (中科院大类二区，影响因子4.5分)

51. An Xiong, Zhenjie Luo, Yan Xia, Quan Zou, Leyi Wei, Zilong Zhang*, Tao Wang*, Lesong Wei*, and Feifei Cui*. An interpretable geometric graph neural network for enhancing the generalizability of drug–target interaction prediction. BMC Biology, 2025. 23(1): p. 350. (中科院大类二区，TOP期刊，影响因子4.5分)

52. Jiaxing Song, Aoyun Geng, Qianmao Wen, Junlin Xu, Yajie Meng, Feifei Cui, Quan Zou, Leyi Wei, and Zilong Zhang*. AcidProNet: Acidophilic Protein Classification via DCGAN-GP-Based Data Augmentation and Parameter-Shared Mixture-of-Experts Transformer. Journal of Chemical Information and Modeling, 2025. 65(24): p. 13145. (中科院大类二区，TOP期刊，影响因子5.3分)

53. Xiaomeng Lin, Ruiqi Liu, Aoyun Geng, Junlin Xu, Yajie Meng, Feifei Cui, Leyi Wei, Quan Zou, and Zilong Zhang*. AFP-GFuse: an antifungal peptide identification model with structural information fusion via multi-graph neural networks and cross-attention mechanism. Molecular Diversity, 2025. (中科院大类二区，影响因子3.8分)

54. Yunyun Su, Binlu Yang, Aoyun Geng, Yuxuan Chen, Zilong Zhang*, and Feifei Cui*. RTCDB: A Multi-Omics Database Supporting Research and Discovery in Rare Tumor Oncology. 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2025: p. 556. (CCF-B类会议）

55. Yazi Li, Xiaoman Wei, Qinglin Yang, An Xiong, Xingfeng Li, Quan Zou, Feifei Cui*, and Zilong Zhang*. msBERT-Promoter: a multi-scale ensemble predictor based on BERT pre-trained model for the two-stage prediction of DNA promoters and their strengths. BMC biology, 2024. 22(1): p. 126. (中科院大类一区，影响因子5.4，TOP期刊)

56. Yanna Jia, Zilong Zhang, Shankai Yan, Qingchen Zhang, Leyi Wei, and Feifei Cui*. Voting-ac4C: Pre-trained large RNA language model enhances RNA N4-acetylcytidine site prediction. International Journal of Biological Macromolecules, 2024. 282: p. 136940.

57. Hao Duan, Qingchen Zhang, Feifei Cui*, Quan Zou*, and Zilong Zhang*. MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks. PLOS Computational Biology, 2024. 20(9): p. e1012409. （生物信息学经典期刊，影响因子3.97）

58. Xiuhao Fu, Chao Yang, Yunyun Su, Chunling Liu, Haoye Qiu, Yanyan Yu, Gaoxing Su, Qingchen Zhang, Leyi Wei, and Feifei Cui*, Quan Zou* and Zilong Zhang*. Machine learning enables comprehensive prediction of the relative protein abundance of multiple proteins on the protein corona. Research, 2024. (中科院大类一区，影响因子8.5)

59. Chaorui Yan, Aoyun Geng, Zhuoyu Pan, Zilong Zhang, and Feifei Cui*. MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides. Briefings in Bioinformatics, 2024. 25(6): p. bbae505. (中科院小类一区，影响因子6.8，TOP期刊)

60. Jiahao Yuan, Ziyi Wang, Zhuoyu Pan, Aohan Li, Zilong Zhang, and Feifei Cui*. DPNN-ac4C: A Dual-Path Neural Network with self-attention mechanism for identification of N4‑acetylcytidine (ac4C) in mRNA. Bioinformatics, 2024: p. btae625. (生物信息学顶刊，影响因子4.4)

61. Xiuhao Fu, Xiaofeng Zang, Chunling Liu, Xingfeng Li, Qingchen Zhang, Zilong Zhang*, Quan Zou*, and Feifei Cui*. Hyb_SEnc: An Antituberculosis Peptide Predictor Based on a Hybrid Feature Vector and Stacked Ensemble Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2024. (CCF-B期刊，影响因子3.6)

62. Jiahao Yuan, Xingfeng Li, Zilong Zhang, Qingchen Zhang, Quan Zou, Feifei Cui*. RNASite: A one-stop tool website that integrates multiple RNA modification site databases and servers. in 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Lisbon, Portugal, 2024, pp. 2816-2820

63. Xiuhao Fu, Ye Yuan, Haoye Qiu, Haodong Suo, Yingying Song, Anqi Li, Yupeng Zhang, Cuilin Xiao, Yazi Li, Lijun Dou, Zilong Zhang* and Feifei Cui*. AGF-PPIS: a protein–protein interaction site predictor based on an attention mechanism and graph convolutional networks. Methods, 2024. 222: p. 142-151. (影响因子4.2)

64. Hao Duan, Yu Zhang, Haoye Qiu, Xiuhao Fu, Chunling Liu, Xiaofeng Zang, Anqi Xu, Ziyue Wu, Xingfeng Li, Qingchen Zhang, Zilong Zhang and Feifei Cui*. Machine learning-based prediction model for distant metastasis of breast cancer. Computers in Biology and Medicine. 2024. 169: 107943. (中科院小类一区，影响因子7.0，TOP期刊)

65. Yidi Sun, Zhuoyu Pan, Ziyi Wang, Haofei Wang, Leyi Wei, Feifei Cui*, Quan Zou*, and Zilong Zhang*. Single-cell transcriptome analysis reveals immune microenvironment changes and insights into the transition from DCIS to IDC with associated prognostic genes. Journal of Translational Medicine, 2024. 22(1): p. 894. (影响因子6.1，TOP期刊)

66. Chaorui Yan, Yanxu Zhu, Miao Chen, Kainan Yang, Feifei Cui*, Quan Zou*, and Zilong Zhang*. Integration tools for scRNA-seq data and spatial transcriptomics sequencing data. Briefings in Functional Genomics, 2024. 23(4): p. 295-302. (影响因子4.0)

67. Cuilin Xiao, Zheyu Zhou, Jiayi She, Jinfen Yin, Feifei Cui, and Zilong Zhang*. PEL-PVP: Application of plant vacuolar protein discriminator based on PEFT ESM-2 and bilayer LSTM in an unbalanced dataset. International Journal of Biological Macromolecules, 2024. 277: p. 134317. (中科院大类一区，影响因子7.7, TOP期刊)

68. Zheyu Zhou, Cuilin Xiao, Jinfen Yin, Jiayi She, Hao Duan, Chunling Liu, Xiuhao Fu, Feifei Cui, Qi Qi, and Zilong Zhang*. PSAC-6mA: 6mA site identifier using self-attention capsule network based on sequence-positioning. Computers in Biology and Medicine, 2024, 171:108129. (中科院小类一区，影响因子7.0，TOP期刊)

69. Yidi Sun, Lingling Kong, Jiayi Huang, Hongyan Deng, Xinling Bian, Xingfeng Li, Feifei Cui, Lijun Dou, Chen Cao, Quan Zou and Zilong Zhang*. A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data. Briefings in Functional Genomics, 2024: p. elae023. (影响因子4.0)

70. Chen Cao, Mengting Shao, Chunman Zuo, Devin Kwok, Lin Liu, Yuli Ge, Zilong Zhang, Feifei Cui, Mingshuai Chen, and Rui Fan. RAVAR: a curated repository for rare variant–trait associations. Nucleic Acids Research, 2024. 52(D1): p. D990-D997. (影响因子16.6，TOP期刊)

71. Ziyi Wang, Aoyun Geng, Hao Duan, Feifei Cui, Quan Zou, Zilong Zhang*. A comprehensive review of approaches for spatial domain recognition of spatial transcriptomes. Briefings in Functional Genomics, 2024.23(6): 702–712.

72. Ruiqi Liu, Xiuhao Fu, Shankai Yan, Zilong Zhang, and Feifei Cui*. AIPPT: Predicts anti-inflammatory peptides using the most characteristic subset of bases and sequences by stacking ensemble learning strategies. in 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Istanbul, Turkiye, 2023, pp. 23-29.

73. Yunyun Su, Shiyu Yan, Chen Cao, Feifei Cui, Quan Zou*, and Zilong Zhang*. Human-Spa: An Online Platform Based on Spatial Transcriptome Data for Diseases of Human Systems. in 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 5-8 Dec, 2023. 293-298. (CCF-B 推荐会议)

74. Zhibin Lv#, Feifei Cui#, Quan Zou*, Lichao Zhang*, Lei Xu*. Anticancer peptides prediction with deep representation learning features. Briefings in Bioinformatics. 2021, 22(5): 1-14. (IF=13.994，中科院一区Top 期刊)

75. Feifei Cui#, Shuang Li#, Zilong Zhang, Miaomiao Sui, Chen Cao, Abd El-Latif Hesham, Quan Zou*. DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins. Computational and Structural Biotechnology Journal. 2022, 20: 2020-2028. (IF=7.271，中科院二区)

76. Feifei Cui, Zilong Zhang, Quan Zou*. Sequence representation approaches for sequence-based protein prediction tasks that use deep learning. Briefings in Functional Genomics. 2021, 20(1): 61-73. (IF=4.241)

77. Feifei Cui, Zilong Zhang, Chen Cao, Quan Zou, Dong Chen*, Xi Su*. Protein-DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data. Proteomics. 2022, 3: e2100197. Doi: 10.1002/pmic.202100197. (IF=3.984)

78. Feifei Cui, Liang Cheng*, Quan Zou*. Briefings in functional genomics special section editorial: analysis of integrated multiple omics data. Briefings in Functional Genomics. 2021, 20(4): p. 196-197. (IF=4.241)

79. Feifei Cui, Quan Zou*. Biocomputing and Synthetic Biology in Cells: Cells Special Issue. Cells. 2020, 9(11): 2459. (IF=4.326)

80. Feifei Cui, Quan Zou*, Qin Ma, Leyi Wei, Jijun Tang and Dariusz Mrozek. IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence Analysis. IEEE Access. 2021, 9: 33110-33119. (IF=3.367)

81. Feifei Cui, Murong Zhou, Quan Zou*. Computational biology and chemistry Special section editorial: Computational analyses for miRNA. Computational Biology and Chemistry. 2021, 91:107448. (IF=2.877)

82. Zilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang, and Quan Zou. Critical downstream analysis steps for single-cell RNA sequencing data. Briefings in Bioinformatics, 2021. 22(5): p. bbab105.

83. Zilong Zhang, Feifei Cui, Chunyu Wang, Lingling Zhao, and Quan Zou. Goals and approaches for each processing step for single-cell RNA sequencing data. Briefings in Bioinformatics, 2021. 22(4): p. bbaa314.

84. Zilong Zhang, Feifei Cui, Wei Su, Lijun Dou, Anqi Xu, Chen Cao, and Quan Zou. webSCST: an interactive web application for single-cell RNA-sequencing data and spatial transcriptomic data integration. Bioinformatics, 2022. 38(13): p. 3488-3489.

85. Zilong Zhang, Feifei Cui, Murong Zhou, Song Wu, Quan Zou, and Bo Gao. Single-cell RNA Sequencing Analysis Identifies Key Genes in Brain Metastasis from Lung Adenocarcinoma. Current Gene Therapy, 2021. 21(4): 338-348.

86. Zilong Zhang, Feifei Cui, Chen Cao, Qingsuo Wang, and Quan Zou. Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections. Computers in Biology and Medicine, 2022. 140: 105092.

87. Chen Cao, Jianhua Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, and Quan Zou. webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. Nucleic Acids Research, 2021: p. gkab957.

88. Kunsen Lin, Youcai Zhao, Jia-Hong Kuo, Hao Deng, Feifei Cui, Zilong Zhang, Meilan Zhang, Chunlong Zhao, Xiaofeng Gao, and Tao Zhou. Toward smarter management and recovery of municipal solid waste: A critical review on deep learning approaches. Journal of Cleaner Production, 2022. 346: p. 130943.

89. Kunsen Lin, Youcai Zhao, Lina Wang, Wenjie Shi, Feifei Cui, and Tao Zhou. MSWNet: A visual deep machine learning method adopting transfer learning based upon ResNet 50 for municipal solid waste sorting. Frontiers of Environmental Science & Engineering, 2023. 17(6): p. 77.

以人工智能技术破译“生命密码”

——记海南大学副教授、博士生导师崔菲菲

2023-12-28

千万年来，人类与各种疾病的博弈，从来都不仅是物质的角力，更是精神的对垒。对于绝大多数人而言，地位、权力、财富、荣誉都是生活中增添幸福感的“0”，虽然可以扩大位数却毫无意义，而健康才是“1”，为所有美好赋予意义的同时，也可能顷刻间覆灭一切。正因为如此，从古至今有许多学者接续奔走在人类健康事业的大道上，为驱逐疾病献智献策。学界先后诞生出多种解开“生命密码”的方式，其种类又随着近年来人工智能、测序技术等科技的革命性发展而节节攀升：基因组学、蛋白质组学、表观组学、转录组学……不胜枚举。而为了更好地整合浩如烟海的多组学信息，生物信息学在生命科学研究领域的重要意义日益凸显。2020年于日本东京大学获得生物信息学博士学位的青年学者崔菲菲恰好是此领域内一名坚定奋发的“追梦人”，她手执智能时代催生的“智慧医疗”技术利器，立志为完善疾病预测体系、创新癌症等重大疾病诊疗模式贡献己力。

回望崔菲菲的人生旅程，“科研梦”对她而言有一个由模糊到逐渐清晰的过程。本硕时期的计算机背景虽然给了崔菲菲扎实的学术功底，但却并未带给她一张对未来清晰明确的人生蓝图。于是，毕业之际，校园招聘会提供的稳定工作机遇轻易地吸引了她的注意。但在“一眼望到底”的人生轨道上前行一段路途之后，她却第一次感到自己在逐渐“脱力”，“我想改变当时的生活状况，那份工作非常好但激发不了我的兴趣，我渴望进入实验室，渴望将人生的航船驶向学术的海域”。这时，日本文部科学省提供的博士奖学金恰巧为她提供了走进梦想的机遇。“我非常珍惜这次重回校园的机会，所以即便跨专业也没有关系，我会拼尽全力。”崔菲菲是这么说的，也是这么做的。千余个脚踏实地、埋首书海的日夜为证，她将自己接触到的人工智能技术在生物学领域的应用手段一股脑带回了电子科技大学基础与前沿研究院，从而开启了自己的博士后研究生涯。

崔菲菲在博士后阶段更加深入地探究了生物序列分析领域的奥秘。对藏在基因序列中的生命信息及生物学的“中心法则”，她都有了进一步的认知与理解。据她介绍，基因序列通过转录与翻译合成特定生物学功能的蛋白质，从而实现从基因序列到蛋白结构并最终到生物学功能的精准预测，因此生物序列信息的有效利用对于生物医药领域的发展至关重要，不仅对研发疾病的靶向治疗大有助益，还有望将人类对生物学机制的认知边界推向更远方。其间，她所申请的国家自然科学基金青年项目“基于多模态多任务深度学习的蛋白质-核酸相互作用的系统性预测”顺利获得立项，这进一步坚定了她扎根领域的信心与决心。带着这份坚定与开启新征程的勇气，她于2022年正式入职海南大学。

海南这片位于我国最南端的土地虽在教育层面起步较晚，但在崔菲菲眼中却呈现一派蓬勃朝气，就如同它终年宜居的气候一般，利于成长、永葆生机。此外，2018年4月，习近平总书记在庆祝海南建省办经济特区30周年大会上的重要讲话更为竭力建设海南的学者们打了一剂强心针，“要支持海南大学创建世界一流学科”的号召既鼓舞了士气，也同时赋予了海南大学新的重大历史使命，使得崔菲菲深感重任在肩。于是，即便来此仅有短短一年时间，她也顺利申请到了国家自然科学基金地区项目，基于人工智能和多组学数据的研究手段，在攻治三阴性乳腺癌的研究中发光发热。

崔菲菲十分重视对学生的培养，“我的个人经历和过去我的导师对我的培养模式奠定了我的人才理念：过去的专业不重要，只要学生具备主观能动性和对科研的热爱之心，我都十分欢迎”。如今她的团队和课堂上已是人才济济，有望青出于蓝，但她仍在致力于帮助生物信息学行业人才永续。

来源：科学中国人 2023年11期