LDA - a java-based linkage disequilibrium analyzer. - Keyue Ding; Kaixin Zhou; Fuchu He; Yan Shen (Bioinform., 2003)

SigFlux: A novel network feature to evaluate the importance of proteins in signal transduction networks. - Wei Liu; Dong Li 018; Jiyang Zhang 001; Yunping Zhu; Fuchu He (BMC Bioinform., 2006)

A nonparametric model for quality control of database search results in shotgun proteomics. - Jiyang Zhang 001; Jianqi Li; Xin Liu; Hongwei Xie; Yunping Zhu; Fuchu He (BMC Bioinform., 2008)

A novel parametric approach to mine gene regulatory relationship from microarray datasets. - Wanlin Liu; Dong Li 018; Qijun Liu; Yunping Zhu; Fuchu He (BMC Bioinform., 2010)

Computational identification of rare codons of Escherichia coli based on codon pairs preference. - Xianming Wu; Songfeng Wu; Dong Li 018; Jiyang Zhang 001; Lin Hou; Jie Ma; Wanlin Liu; Daming Ren; Yunping Zhu; Fuchu He (BMC Bioinform., 2010)

Using NMFAS to identify key biological pathways associated with human diseases. - Hao Guo 003; Yunping Zhu; Dong Li 018; Fuchu He; Qijun Liu (ISB, 2012)

Reconstruction of Signaling Network from Protein Interactions Based on Function Annotations. - Wei Liu; Dong Li 018; Yunping Zhu; Hongwei Xie; Fuchu He (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods. - Cheng Chang; Jiyang Zhang 001; Mingfei Han 001; Jie Ma; Wei Zhang; Songfeng Wu; Kehui Liu; Hongwei Xie; Fuchu He; Yunping Zhu (Bioinform., 2014)

Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources. - Zhongyang Liu; Feifei Guo; Jiangyong Gu; Yong Wang; Yang Li; Dan Wang; Liang Lu; Dong Li 018; Fuchu He (Bioinform., 2015)

ICM: a web server for integrated clustering of multi-dimensional biomedical data. - Song He; Haochen He; Wenjian Xu; Xin Huang 005; Shuai Jiang; Fei Li 004; Fuchu He; Xiaochen Bo (Nucleic Acids Res., 2016)

HisgAtlas 1.0: a human immunosuppression gene database. - Yuan Liu; Mengqi He; Dan Wang; Lihong Diao; Jinying Liu; Li Tang; Shuzhen Guo; Fuchu He; Dong Li 018 (Database J. Biol. Databases Curation, 2017)

AllerGAtlas 1.0: a human allergy-related genes database. - Jinying Liu; Yuan Liu; Dan Wang; Mengqi He; Lihong Diao; Zhongyang Liu; Yang Li; Li Tang; Fuchu He; Dong Li 018; Shuzhen Guo (Database J. Biol. Databases Curation, 2018)

PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data. - Cheng Chang; Kaikun Xu; Chaoping Guo; Jinxia Wang; Qi Yan; Jian Zhang; Fuchu He; Yunping Zhu (Bioinform., 2018)

PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis. - Cheng Chang; Mansheng Li; Chaoping Guo; Yuqing Ding; Kaikun Xu; Mingfei Han 001; Fuchu He; Yunping Zhu (Bioinform., 2019)

KeggExp: a web server for visual integration of KEGG pathways and expression profile data. - Xian Liu; Mingfei Han 001; Chen Zhao; Cheng Chang; Yunping Zhu; Changhui Ge; Ronghua Yin; Yiqun Zhan; Changyan Li; Miao Yu; Fuchu He; Xiaoming Yang (Bioinform., 2019)

iProX: an integrated proteome resource. - Jie Ma; Tao Chen 005; Songfeng Wu; Chunyuan Yang; Mingze Bai; Kunxian Shu; Kenli Li 001; Guoqing Zhang 006; Zhong Jin; Fuchu He; Henning Hermjakob; Yunping Zhu (Nucleic Acids Res., 2019)

iProX in 2021: connecting proteomics data sharing with big data. - Tao Chen 005; Jie Ma; Yi Liu; Zhiguang Chen 001; Nong Xiao 001; Yutong Lu; Yinjin Fu; Chunyuan Yang; Mansheng Li; Songfeng Wu; Xue Wang; Dongsheng Li; et al. (Nucleic Acids Res., 2022)

CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. - Zhongyang Liu; Jiale Liu; Xinyue Liu; Xun Wang; Qiaosheng Xie; Xinlei Zhang; Xiangya Kong; Mengqi He; Yuting Yang; Xinru Deng; Lele Yang; Yaning Qi; et al. (Nucleic Acids Res., 2022)

UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. - Xun Wang; Yang Li; Mengqi He; Xiangren Kong; Peng Jiang; Xi Liu; Lihong Diao; Xinlei Zhang; Honglei Li; Xinping Ling; Simin Xia; Zhongyang Liu; et al. (Nucleic Acids Res., 2022)

Exploration of Target Spaces in the Human Genome for Protein and Peptide Drugs. - Zhongyang Liu; Honglei Li; Zhaoyu Jin; Yang Li; Feifei Guo; Yangzhige He; Xinyue Liu; Yaning Qi; Liying Yuan; Fuchu He; Dong Li 018 (Genom. Proteom. Bioinform., 2022)

A Yeast BiFC-seq Method for Genome-wide Interactome Mapping. - Limin Shang; Yuehui Zhang; Yuchen Liu; Chaozhi Jin; Yanzhi Yuan; Chunyan Tian; Ming Ni; Xiaochen Bo; Li Zhang 097; Dong Li 018; Fuchu He; Jian Wang (Genom. Proteom. Bioinform., 2022)

Automating Exploratory Proteomics Research via Language Models. - Ning Ding 002; Shang Qu; Linhai Xie; Yifei Li; Zaoqu Liu; Kaiyan Zhang; Yibai Xiong; Yuxin Zuo; Zhangren Chen; Ermo Hua; Xingtai Lv; Youbang Sun; et al. (CoRR, 2024)

Introducing π-HelixNovo for practical large-scale de novo peptide sequencing. - Tingpeng Yang; Tianze Ling; Boyan Sun; Zhendong Liang; Fan Xu; Xiansong Huang; Linhai Xie; Yonghong He; Leyuan Li; Fuchu He; Yu Wang; Cheng Chang (Briefings Bioinform., 2024)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)

Automating Exploratory Multiomics Research via Language Models. - Shang Qu; Ning Ding 002; Linhai Xie; Yifei Li; Zaoqu Liu; Kaiyan Zhang; Yibai Xiong; Yuxin Zuo; Zhangren Chen; Ermo Hua; Xingtai Lv; Youbang Sun; et al. (CoRR, 2025)