代表性论文

Zhao H#, Lou S#, Li X#, Gao Y, Cao W, Gu H*, Zhang F*. BCRInsight: an antibody language model to decode biological signals from BCR sequences. Brief Bioinform. 2026 Mar 1;27(2):bbag154. (corresponding author)

Chen C#, Zhen Z#, Cui M#, Hu X#, Yu L#, Zhou F, Yu X, Yang D, Wu H, Cui Y, Li X, Cui X, Liang X, Gao Y, Liu Y, Yu Y, Huang Z*, Zhang F*. The core cellular network modulates immune phenotype switching in hepatitis B. Sci Bull (Beijing). 2025 Mar 15:S2095-9273(25)00289-0. (IF: 21.1, corresponding author)

Chen Y#, Zhao N#*, Xu L#, Jia X, Liu F, Huang J, Li X, Wang Y, Lai C, Shen Y, Wang F, Lv Y, Huang X, Zhang F*, Gu H*, Dai S*. Integrative multi-omics analysis reveals the LncRNA 60967.1-PLCD4-ATRA axis as a key regulator of colorectal cancer progression and immune response. Mol Cancer. 2025 Jun 6;24(1):164. (IF: 33.9, corresponding author)

Liu X#, Pang Y#, Shan J#, Wang Y, Zheng Y, Xue Y, Zhou X, Wang W, Sun Y, Yan X, Shi J, Wang X*, Gu H*, Zhang F*. Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies. Brief Bioinform. 2024 Jul 25;25(5):bbae440. (IF: 7.7, corresponding author)

Zhou F#*, Yu X#, Gan R#, Ren K, Chen C, Ren C, Cui M, Liu Y, Gao Y, Wang S, Yin M, Huang T, Huang Z*, Zhang Fan*. CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing. Nucleic Acids Res. 2023 Jul 5;51(W1):W93-W107. (IF: 14.9, corresponding author)

Ren K#, Zhou F#, Zhang F#*, Yin M#, Zhu Y#, Wang S#, Chen Y, Huang T, Wu Z, He J, Zhang A, Guo C, Huang Z*. Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs. Cell Res. 2024 Apr 4. doi: 10.1038/s41422-024-00952-1. Epub ahead of print. PMID: 38575718. (IF: 44.1, corresponding author)

Fan Zhang#, Rui Gan#, Ziqi Zhen#, Xiaoli Hu#, Xiang Li, Fengxia Zhou, Ying Liu, Chuangeng Chen, Shuangyu Xie, Bailing Zhang, Xiaoke Wu & Zhiwei Huang*. Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals. Sig Transduct Target Ther 5, 156 (2020)(IF: 38.12 cover story)

Fan Zhang, Zhiwei Huang*. Mechanistic Insights into the Versatile Class II CRISPR Toolbox. Trends in Biochemical Sciences. (IF: 13.807, invited review 2021)

Shengli Ma#*, Fan Zhang#, Fengxia Zhou#, Hui Li#, Wenyu Ge, Rui Gan, Huan Nie, Biao Li, Yindong Wang, Meng Wu, Duo Li, Dongmei Wang, Zheng Wang, Yuhong You & Zhiwei Huang* Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19. Sig Transduct Target Ther 6, 191 (2021)(IF: 38.12 co-first author)

Zhang, R.#, F. Zhang#, Z. Sun#, P. Liu, X. Zhang, Y. Ye, B. Cai, M. J. Walsh, X. Ren, X. Hao, W. Zhang* and J. Yu* (2019). "LINE-1 Retrotransposition Promotes the Development and Progression of Lung Squamous Cell Carcinoma by Disrupting the Tumor Suppressor Gene FGGY." Cancer Research: canres.0076.2019.（co-first author, IF: 12.701）

Zhang, F.#*, Zhao, S.#, Ren, C.#, Zhu, Y., Zhou, H., Lai, Y., Zhou, F., Jia, Y., Zheng, K. and Huang, Z*. (2018) CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions. Commun Biol, 1, 180. (IF: 6.268)

Fan Zhang*, Chunyan Ren, Kwun Kit Lau, Zihan Zheng, Geming Lu, Zhengzi Yi, Yongzhong Zhao, Fei Su, Shaojun Zhang, Bin Zhang, Eric A. Sobie, Weijia Zhang*, Martin J. Walsh*, A network medicine approach to build a comprehensive atlas for the prognosis of human cancer, BRIEFINGS IN BIOINFORMATICS, 2016.11, 17(6): 1044~1059.（IF: 9.5）

Ka Lung Cheung#, Fan Zhang#, Anbalagan Jaganathan#, Rajal Sharma, Qiang Zhang, Tsuyoshi Konuma, Tong Shen, June-Yong Lee, Chih-Hung Chen, Geming Liu, Weijia Zhang, Dan R. Littman, Martin J. Walsh, Huabao Xiong, & Ming-Ming Zhou* Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation, MOLECULAR CELL, 2017.3.16, 65(6): 1068~+（co-first author IF: 17.970）

Fan Zhang, Won-min Song, SiDe Li, Vashisht Ajay, Francesca Aguilo, Anindya Bagchi, James A. Wohlschlegel, Bin Zhang, Martin Walsh. The enhancer landscape involves a core noncoding RNA protein interaction network for C-MYC expression. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl).

Aguilo F*, Zhang F, Sancho A, Fidalgo M, Di Cecilia S, Vashisht A, Lee DF, Chen CH, Rengasamy M, Andino B, Jahouh F, Roman A, Krig SR, Wang R, Zhang W, Wohlschlegel JA, Wang J, Walsh MJ*. Coordination of m(6)A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming. Coordination of m(6)A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming, CELL STEM CELL, 2015.12.3, 17(6): 689~704.（IF: 24.633）

Guo H, Ahmed M, Zhang F, Yao CQ, Li S, Liang Y, Hua J, Soares F, Sun Y, Langstein J, Li Y, Poon C, Bailey SD, Desai K, Fei T, Li Q, Sendorek DH, Fraser M, Prensner JR, Pugh TJ, Pomerantz M, Bristow RG, Lupien M, Feng FY, Boutros PC, Freedman ML, Walsh MJ, He HH*. Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer, NATURE GENETICS, 2016.10, 48(10): 1142~1150.（IF: 38.330）

Rengasamy M, Zhang F, Vashisht A, Song WM, Aguilo F, Sun Y, Li S, Zhang W, Zhang B, Wohlschlegel JA, Walsh MJ*. The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer, NUCLEIC ACIDS RESEARCH, 2017.8.21, 45(19): 11106~11120.（IF: 16.971）

Di Cecilia S, Zhang F, Sancho A, Li S, Aguiló F, Sun Y, Rengasamy M, Zhang W, Del Vecchio L, Salvatore F, Walsh MJ*. RBM5-AS1 Is Critical for Self-Renewal of Colon Cancer Stem-like Cells., Cancer Res, 2016.10.1, 76(19): 5615~5627.（IF: 12.701）

Ren, X.#,Wen, W.#, Fan, X.#, Hou, W.#, Su, B.#, Cai, P.#, Li, J.#, Liu, Y.#, Tang, F. #, Zhang, F. #, Yang, Y.#, He, J. #, Ma, W. #, He, J. #, Wang, P. #, Cao, Q., Chen, F., Chen, Y., Cheng, X., Deng, G., Deng, X., Ding, W., Feng, Y., Gan, R., Guo, C., Guo, W., He, S., Jiang, C., Liang, J., Li, Y.-m., Lin, J., Ling, Y., Liu, H., Liu, J., Liu, N., Liu, S.-Q., Luo, M., Ma, Q., Song, Q., Sun, W., Wang, G., Wang, F., Wang, Y., Wen, X., Wu, Q., Xu, G., Xie, X., Xiong, X., Xing, X., Xu, H., Yin, C., Yu, D., Yu, K., Yuan, J., Zhang, B., Zhang, P., Zhang, T., Zhao, J., Zhao, P., Zhou, J., Zhou, W., Zhong, S., Zhong, X., Zhang, S., Zhu, L., Zhu, P., Zou, B., Zou, J., Zuo, Z., Bai, F., Huang, X., Zhou, P., Jiang, Q.*, Huang, Z. *, Bei, J.-X. *, Wei, L. *, Bian, X.-W. *, Liu, X. *, Cheng, T. *, Li, X. *, Zhao, P. *, Wang, F.-S. *, Wang, H. *, Su, B. *, Zhang, Z. *,Qu, K. *, Wang, X. *, Chen, J. *, Jin, R. *, Zhang, Z. *, COVID-19 immune features revealed by a large-scale single cell transcriptome atlas, Cell (2021)（co-first author，IF: 41.58）

专利

王宏志; 孙晓君; 张帆; 谷红仓；一种基于主题模型的DNA甲基化测序数据反卷积方法，2025-4-15，CN202510305223.7

谷红仓; 梁馨月; 张帆; 徐栋；一种基于液相探针的cfDNA-TCR文库的构建分析方法及其应用，2025-9-26，CN202510718302.0

谷红仓；李晗；张帆；李浩；基于血浆 rDNA 序列的甲基化信号癌症检测与溯源方法，2026-1-23，CN202511935818.7

承担项目

安徽省科技厅, 安徽省级科技创新攻坚计划项目子课题, 202523n10050006, 面向免疫治疗创新药物发 现的样本数据库和 AI 大模型的构建及应用, 2025-11 至 2028-10, 50万元, 在研, 主持

中国科学院, 中国科学院引才计划B类项目, NA, cfDNA组学数 据的解析与应 用研究, 2025-01 至 2027-12, 200万元, 在研, 主持

国家卫生健康委医药卫生科技发展研究中心, 国家科技重大专项, 2024ZD0520101, 结直肠癌及癌前病 变多组学图谱构建与诊断新技术研究, 2024-12 至 2028-11, 150万元, 在研, 参与

安徽省科技厅, 安徽省“JQ”项目, E4BDAGAH58B, 循环游离DNA（cfDNA）多组学大数据驱动的肿瘤早 筛及溯源技术研究, 2024-09 至 2027-08, 50万元, 在研, 主持

国家自然科学基金委员会, 联合基金项目, U21A20276, 新型基因编辑系统发现与机制研究, 2022-01- 01 至 2025-12-31, 266万元, 资助期满, 参与