Computational prediction of human proteins that can be secreted into the bloodstream. - Juan Cui; Qi Liu 019; David Puett; Ying Xu 001 (Bioinform., 2008)

RNACluster: An integrated tool for RNA secondary structure comparison and clustering. - Qi Liu 019; Victor Olman; Huiqing Liu; Xiuzi Ye; Shilun Qiu; Ying Xu 001 (J. Comput. Chem., 2008)

Analyses of domains and domain fusions in human proto-oncogenes. - Qi Liu 019; Jinling Huang; Huiqing Liu; Ping Wan; Xiuzi Ye; Ying Xu 001 (BMC Bioinform., 2009)

Transfer Learning on Heterogenous Feature Spaces via Spectral Transformation. - Xiaoxiao Shi; Qi Liu 019; Wei Fan 001; Philip S. Yu; Ruixin Zhu (ICDM, 2010)

Predictive Modeling with Heterogeneous Sources. - Xiaoxiao Shi; Qi Liu 019; Wei Fan 001; Qiang Yang 001; Philip S. Yu (SDM, 2010)

In-silico prediction of blood-secretory human proteins using a ranking algorithm. - Qi Liu 019; Juan Cui; Qiang Yang 001; Ying Xu 001 (BMC Bioinform., 2010)

Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study. - Qi Liu 019; Qian Xu 005; Vincent Wenchen Zheng; Hong Xue 001; Zhi-Wei Cao; Qiang Yang 001 (BMC Bioinform., 2010)

An Integrative Approach for Genomic Island Prediction in Prokaryotic Genomes. - Han Wang; John Fazekas; Matthew Booth; Qi Liu 019; Dongsheng Che (ISBRA, 2011)

A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. - Tianli Dai; Qi Liu 019; Jun Gao; Zhiwei Cao; Ruixin Zhu (BMC Bioinform., 2011)

Multi-target QSAR Modelling in the Analysis and Design of HIV-HCV Co-Inhibitors : An In-silico Study. - Qi Liu 019; Han Zhou; Lin Liu 001; Xi Chen; Ruixin Zhu; Zhi-Wei Cao (BMC Bioinform., 2011)

HIT: linking herbal active ingredients to targets. - Hao Ye; Li Ye; Hong Kang; Duanfeng Zhang; Lin Tao; Kailin Tang; Xueping Liu; Ruixin Zhu; Qi Liu 019; Yuzong Chen 002; Yixue Li; Zhi-Wei Cao (Nucleic Acids Res., 2011)

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. - Pei Li; Guoli Ji; Min Dong; Emily Schmidt; Douglas Lenox; Liangliang Chen; Qi Liu 019; Lin Liu 001; Jie Zhang; Chun Liang (Bioinform., 2012)

Integrated QSAR study for inhibitors of hedgehog signal pathway against multiple cell lines: a collaborative filtering method. - Jun Gao; Dongsheng Che; Vincent Wenchen Zheng; Ruixin Zhu; Qi Liu 019 (BMC Bioinform., 2012)

Screening of selective histone deacetylase inhibitors by proteochemometric modeling. - Dingfeng Wu; Qi Huang; Yida Zhang; Qingchen Zhang; Qi Liu 019; Jun Gao; Zhi-Wei Cao; Ruixin Zhu (BMC Bioinform., 2012)

Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis. - Tianlei Xu; Ruixin Zhu; Qi Liu 019; Zhi-Wei Cao (BMC Bioinform., 2012)

Virtual Drug Screen Schema Based on Multiview Similarity Integration and Ranking Aggregation. - Hong Kang; Zhen Sheng; Ruixin Zhu; Qi Huang; Qi Liu 019; Zhiwei Cao (J. Chem. Inf. Model., 2012)

Dr.VIS: a database of human disease-related viral integration sites. - Xin Zhao; Qi Liu 019; Qingqing Cai; Yanyun Li; Congjian Xu; Yixue Li; Zuofeng Li; Xiaoyan Zhang (Nucleic Acids Res., 2012)

Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective. - Yi Sun; Ruixin Zhu; Hao Ye; Kailin Tang; Jing Zhao 003; Yujia Chen; Qi Liu 019; Zhiwei Cao (Briefings Bioinform., 2013)

HIM-herbal ingredients in-vivo metabolism database. - Hong Kang; Kailin Tang; Qi Liu 019; Yi Sun; Qi Huang; Ruixin Zhu; Jun Gao; Duanfeng Zhang; Chenggang Huang; Zhiwei Cao (J. Cheminformatics, 2013)

Transfer across Completely Different Feature Spaces via Spectral Embedding. - Xiaoxiao Shi; Qi Liu 019; Wei Fan 001; Philip S. Yu (IEEE Trans. Knowl. Data Eng., 2013)

Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration: problems and solutions. - Qi Liu 019; Han Zhou; Ruixin Zhu; Ying Xu 001; Zhiwei Cao (Briefings Bioinform., 2014)

iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis. - Haoqi Sun; Haiping Wang 001; Ruixin Zhu; Kailin Tang; Qin Gong; Juan Cui; Zhiwei Cao; Qi Liu 019 (Bioinform., 2014)

When drug discovery meets web search: Learning to Rank for ligand-based virtual screening. - Wei Zhang; Lijuan Ji; Yanan Chen; Kailin Tang; Haiping Wang 001; Ruixin Zhu; Wei Jia; Zhiwei Cao; Qi Liu 019 (J. Cheminformatics, 2015)

Benchmarking CRISPR on-target sgRNA design. - Jifang Yan; Guohui Chuai; Chi Zhou 003; Chen-Yu Zhu; Jing Yang; Chao Zhang; Feng Gu; Han Xu; Jia Wei; Qi Liu 019 (Briefings Bioinform., 2018)

MPdeep: Medical Procession with Deep Learning. - Qi Liu 019; Wenzheng Bao; Zhuo Wang (ICIC (2), 2019)

IMKPse: Identification of Protein Malonylation Sites by the Key Features Into General PseAAC. - Wenzheng Bao; Bin Yang 017; De-Shuang Huang; Dong Wang 021; Qi Liu 019; Yuehui Chen; Rong Bao (IEEE Access, 2019)

C3: Consensus Cancer Driver Gene Caller. - Chen-Yu Zhu; Chi Zhou 003; Yun-Qin Chen; Ai-Zong Shen; Zong-Ming Guo; Zhao-Yi Yang; Xiangyun Ye; Shen Qu; Jia Wei; Qi Liu 019 (Genom. Proteom. Bioinform., 2019)

Advanced Machine Learning Techniques for Bioinformatics. - Quan Zou 001; Qi Liu 019 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Data imbalance in CRISPR off-target prediction. - Yuli Gao; Guohui Chuai; Weichuan Yu; Shen Qu; Qi Liu 019 (Briefings Bioinform., 2020)

iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak. - Zhiting Wei; Yuli Gao; Fangliangzi Meng; Xin Chen; Yukang Gong; Chenyu Zhu; Bin Ju; Chao Zhang; Zhongmin Liu; Qi Liu 019 (Briefings Bioinform., 2021)

Locating transcription factor binding sites by fully convolutional neural network. - Qinhu Zhang; Siguo Wang; Zhanheng Chen; Ying He; Qi Liu 019; De-Shuang Huang (Briefings Bioinform., 2021)

FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery. - Shaoqi Chen; Dongyu Xue; Guohui Chuai; Qiang Yang 001; Qi Liu 019 (Bioinform., 2021)

PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein-protein interaction network. - Xiaowen Wang 003; Hongming Zhu; Yizhi Jiang; Yulong Li; Chen Tang; Xiaohan Chen; Yunjie Li; Qi Liu 019; Qin Liu 004 (Briefings Bioinform., 2022)

iCRISEE: an integrative analysis of CRISPR screen by reducing false positive hits. - Tengbo Zhang; Yaxu Li; Yanrong Yang; Linjun Weng; Zhiqiang Wu; Jiali Zhu; Jieling Qin; Qi Liu 019; Ping Wang (Briefings Bioinform., 2022)

Base-resolution prediction of transcription factor binding signals by a deep learning framework. - Qinhu Zhang; Ying He; Siguo Wang; Zhanheng Chen; Zhen-Hao Guo; Zhen Cui; Qi Liu 019; De-Shuang Huang (PLoS Comput. Biol., 2022)

DrSim: Similarity Learning for Transcriptional Phenotypic Drug Discovery. - Zhiting Wei; Sheng Zhu; Xiaohan Chen; Chen-Yu Zhu; Bin Duan; Qi Liu 019 (Genom. Proteom. Bioinform., 2022)

Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer. - Gongchen Zhang; Chenyu Zhu; Xiaohan Chen; Jifang Yan; Dongyu Xue; Zixuan Wei; Guohui Chuai; Qi Liu 019 (Genom. Proteom. Bioinform., 2023)

Computational prediction and characterization of cell-type-specific and shared binding sites. - Qinhu Zhang; Pengrui Teng; Siguo Wang; Ying He; Zhen Cui; Zhenghao Guo; Yixin Liu; Changan Yuan 001; Qi Liu 019; De-Shuang Huang (Bioinform., 2023)

Pan-Peptide Meta Learning for T-cell receptor-antigen binding recognition. - Yicheng Gao; Yuli Gao; Yuxiao Fan; Chengyu Zhu; Zhiting Wei; Chi Zhou 003; Guohui Chuai; Qinchang Chen; He Zhang; Qi Liu 019 (Nat. Mac. Intell., 2023)

Semi-supervised heterogeneous graph contrastive learning for drug-target interaction prediction. - Kainan Yao; Xiaowen Wang 003; Wannian Li; Hongming Zhu; Yizhi Jiang; Yulong Li; Tongxuan Tian; Zhaoyi Yang; Qi Liu 019; Qin Liu 004 (Comput. Biol. Medicine, 2023)

Reply to: The pitfalls of negative data bias for the T-cell epitope specificity challenge. - Yicheng Gao; Yuli Gao; Kejing Dong; Siqi Wu; Qi Liu 019 (Nat. Mac. Intell., 2023)

Predicting anticancer synergistic drug combinations based on multi-task learning. - Danyi Chen; Xiaowen Wang 003; Hongming Zhu; Yizhi Jiang; Yulong Li; Qi Liu 019; Qin Liu 004 (BMC Bioinform., 2023)

Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription. - Tianyi Ding; Shaliu Fu; Xiaoyu Zhang; Fan Yang; Jixing Zhang; Haowen Xu; Jiaqi Yang; Chaoqun Chen; Yibing Shi; Yiran Bai; Wannian Li; Xindi Chang; et al. (Genom. Proteom. Bioinform., 2024)

Delineating cell types with transcriptional kinetics. - Yicheng Gao; Qi Liu 019 (Nat. Comput. Sci., 2024)

Toward subtask-decomposition-based learning and benchmarking for predicting genetic perturbation outcomes and beyond. - Yicheng Gao; Zhiting Wei; Kejing Dong; Ke Chen; Jingya Yang; Guohui Chuai; Qi Liu 019 (Nat. Comput. Sci., 2024)

PrimeNet: rational design of Prime editing pegRNAs by deep learning. - Xichen Liao; Qi Liu 019; Guohui Chuai (Briefings Bioinform., 2025)

Fusing Micro- and Macro-Scale Information to Predict Anticancer Synergistic Drug Combinations. - Xiaowen Wang 003; Hongming Zhu; Qi Liu 019; Qin Liu 004 (IEEE J. Biomed. Health Informatics, 2025)