Qi Liu

46 papers A* 1A 1Journal 42Unranked 2
YearRankTypeTitle / Venue / Authors
2026 J jnl
ProTCR: a protein language model-driven framework for decoding TCR-antigen recognition toward precision immunotherapies.
Briefings Bioinform.
Minrui Xu, Manman Lu, Peng Liu, Siwen Zhang, Lanming Chen, Qi Liu, Yong Lin, Lu Xie
2025 J jnl
Fusing Micro- and Macro-Scale Information to Predict Anticancer Synergistic Drug Combinations.
IEEE J. Biomed. Health Informatics
Xiaowen Wang, Hongming Zhu, Qi Liu, Qin Liu
2025 J jnl
PrimeNet: rational design of Prime editing pegRNAs by deep learning.
Briefings Bioinform.
Xichen Liao, Qi Liu, Guohui Chuai
2024 J jnl
Delineating cell types with transcriptional kinetics.
Nat. Comput. Sci.
Yicheng Gao, Qi Liu
2024 J jnl
Inter3D: Capture of TAD Reorganization Endows Variant Patterns of Gene Transcription.
Genom. Proteom. Bioinform.
Tianyi Ding, Shaliu Fu, Xiaoyu Zhang, Fan Yang, Jixing Zhang, Haowen Xu, Jiaqi Yang, Chaoqun Chen, Yibing Shi, Yiran Bai, Wannian Li, Xindi Chang, Shanjin Wang, Chao Zhang, Qi Liu, He Zhang
2024 J jnl
Toward subtask-decomposition-based learning and benchmarking for predicting genetic perturbation outcomes and beyond.
Nat. Comput. Sci.
Yicheng Gao, Zhiting Wei, Kejing Dong, Ke Chen, Jingya Yang, Guohui Chuai, Qi Liu
2023 J jnl
Computational prediction and characterization of cell-type-specific and shared binding sites.
Bioinform.
Qinhu Zhang, Pengrui Teng, Siguo Wang, Ying He, Zhen Cui, Zhenghao Guo, Yixin Liu, Changan Yuan, Qi Liu, De-Shuang Huang
2023 J jnl
Pan-Peptide Meta Learning for T-cell receptor-antigen binding recognition.
Nat. Mac. Intell.
Yicheng Gao, Yuli Gao, Yuxiao Fan, Chengyu Zhu, Zhiting Wei, Chi Zhou, Guohui Chuai, Qinchang Chen, He Zhang, Qi Liu
2023 J jnl
Predicting anticancer synergistic drug combinations based on multi-task learning.
BMC Bioinform.
Danyi Chen, Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Qi Liu, Qin Liu
2023 J jnl
Reply to: The pitfalls of negative data bias for the T-cell epitope specificity challenge.
Nat. Mac. Intell.
Yicheng Gao, Yuli Gao, Kejing Dong, Siqi Wu, Qi Liu
2023 J jnl
Semi-supervised heterogeneous graph contrastive learning for drug-target interaction prediction.
Comput. Biol. Medicine
Kainan Yao, Xiaowen Wang, Wannian Li, Hongming Zhu, Yizhi Jiang, Yulong Li, Tongxuan Tian, Zhaoyi Yang, Qi Liu, Qin Liu
2023 J jnl
Systematic Exploration of Optimized Base Editing gRNA Design and Pleiotropic Effects with BExplorer.
Genom. Proteom. Bioinform.
Gongchen Zhang, Chenyu Zhu, Xiaohan Chen, Jifang Yan, Dongyu Xue, Zixuan Wei, Guohui Chuai, Qi Liu
2022 J jnl
Base-resolution prediction of transcription factor binding signals by a deep learning framework.
PLoS Comput. Biol.
Qinhu Zhang, Ying He, Siguo Wang, Zhanheng Chen, Zhen-Hao Guo, Zhen Cui, Qi Liu, De-Shuang Huang
2022 J jnl
DrSim: Similarity Learning for Transcriptional Phenotypic Drug Discovery.
Genom. Proteom. Bioinform.
Zhiting Wei, Sheng Zhu, Xiaohan Chen, Chen-Yu Zhu, Bin Duan, Qi Liu
2022 J jnl
PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein-protein interaction network.
Briefings Bioinform.
Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Chen Tang, Xiaohan Chen, Yunjie Li, Qi Liu, Qin Liu
2022 J jnl
iCRISEE: an integrative analysis of CRISPR screen by reducing false positive hits.
Briefings Bioinform.
Tengbo Zhang, Yaxu Li, Yanrong Yang, Linjun Weng, Zhiqiang Wu, Jiali Zhu, Jieling Qin, Qi Liu, Ping Wang
2021 J jnl
FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery.
Bioinform.
Shaoqi Chen, Dongyu Xue, Guohui Chuai, Qiang Yang, Qi Liu
2021 J jnl
Locating transcription factor binding sites by fully convolutional neural network.
Briefings Bioinform.
Qinhu Zhang, Siguo Wang, Zhanheng Chen, Ying He, Qi Liu, De-Shuang Huang
2021 J jnl
iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak.
Briefings Bioinform.
Zhiting Wei, Yuli Gao, Fangliangzi Meng, Xin Chen, Yukang Gong, Chenyu Zhu, Bin Ju, Chao Zhang, Zhongmin Liu, Qi Liu
2020 J jnl
Data imbalance in CRISPR off-target prediction.
Briefings Bioinform.
Yuli Gao, Guohui Chuai, Weichuan Yu, Shen Qu, Qi Liu
2019 J jnl
Advanced Machine Learning Techniques for Bioinformatics.
IEEE ACM Trans. Comput. Biol. Bioinform.
Quan Zou, Qi Liu
2019 J jnl
IMKPse: Identification of Protein Malonylation Sites by the Key Features Into General PseAAC.
IEEE Access
Wenzheng Bao, Bin Yang, De-Shuang Huang, Dong Wang, Qi Liu, Yuehui Chen, Rong Bao
2019 — conf
MPdeep: Medical Procession with Deep Learning.
ICIC (2)
Qi Liu, Wenzheng Bao, Zhuo Wang
2018 J jnl
Benchmarking CRISPR on-target sgRNA design.
Briefings Bioinform.
Jifang Yan, Guohui Chuai, Chi Zhou, Chen-Yu Zhu, Jing Yang, Chao Zhang, Feng Gu, Han Xu, Jia Wei, Qi Liu
2015 J jnl
When drug discovery meets web search: Learning to Rank for ligand-based virtual screening.
J. Cheminformatics
Wei Zhang, Lijuan Ji, Yanan Chen, Kailin Tang, Haiping Wang, Ruixin Zhu, Wei Jia, Zhiwei Cao, Qi Liu
2014 J jnl
Reconsideration of
Briefings Bioinform.
Qi Liu, Han Zhou, Ruixin Zhu, Ying Xu, Zhiwei Cao
2014 J jnl
iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis.
Bioinform.
Haoqi Sun, Haiping Wang, Ruixin Zhu, Kailin Tang, Qin Gong, Juan Cui, Zhiwei Cao, Qi Liu
2013 J jnl
HIM-herbal ingredients in-vivo metabolism database.
J. Cheminformatics
Hong Kang, Kailin Tang, Qi Liu, Yi Sun, Qi Huang, Ruixin Zhu, Jun Gao, Duanfeng Zhang, Chenggang Huang, Zhiwei Cao
2013 J jnl
Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective.
Briefings Bioinform.
Yi Sun, Ruixin Zhu, Hao Ye, Kailin Tang, Jing Zhao, Yujia Chen, Qi Liu, Zhiwei Cao
2013 J jnl
Transfer across Completely Different Feature Spaces via Spectral Embedding.
IEEE Trans. Knowl. Data Eng.
Xiaoxiao Shi, Qi Liu, Wei Fan, Philip S. Yu
2012 J jnl
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
Bioinform.
Pei Li, Guoli Ji, Min Dong, Emily Schmidt, Douglas Lenox, Liangliang Chen, Qi Liu, Lin Liu, Jie Zhang, Chun Liang
2012 J jnl
Dr.VIS: a database of human disease-related viral integration sites.
Nucleic Acids Res.
Xin Zhao, Qi Liu, Qingqing Cai, Yanyun Li, Congjian Xu, Yixue Li, Zuofeng Li, Xiaoyan Zhang
2012 J jnl
Integrated QSAR study for inhibitors of hedgehog signal pathway against multiple cell lines: a collaborative filtering method.
BMC Bioinform.
Jun Gao, Dongsheng Che, Vincent Wenchen Zheng, Ruixin Zhu, Qi Liu
2012 J jnl
Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis.
BMC Bioinform.
Tianlei Xu, Ruixin Zhu, Qi Liu, Zhi-Wei Cao
2012 J jnl
Screening of selective histone deacetylase inhibitors by proteochemometric modeling.
BMC Bioinform.
Dingfeng Wu, Qi Huang, Yida Zhang, Qingchen Zhang, Qi Liu, Jun Gao, Zhi-Wei Cao, Ruixin Zhu
2012 J jnl
Virtual Drug Screen Schema Based on Multiview Similarity Integration and Ranking Aggregation.
J. Chem. Inf. Model.
Hong Kang, Zhen Sheng, Ruixin Zhu, Qi Huang, Qi Liu, Zhiwei Cao
2011 J jnl
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information.
BMC Bioinform.
Tianli Dai, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu
2011 — conf
An Integrative Approach for Genomic Island Prediction in Prokaryotic Genomes.
ISBRA
Han Wang, John Fazekas, Matthew Booth, Qi Liu, Dongsheng Che
2011 J jnl
HIT: linking herbal active ingredients to targets.
Nucleic Acids Res.
Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Yuzong Chen, Yixue Li, Zhi-Wei Cao
2011 J jnl
Multi-target QSAR Modelling in the Analysis and Design of HIV-HCV Co-Inhibitors : An In-silico Study.
BMC Bioinform.
Qi Liu, Han Zhou, Lin Liu, Xi Chen, Ruixin Zhu, Zhi-Wei Cao
2010 J jnl
Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study.
BMC Bioinform.
Qi Liu, Qian Xu, Vincent Wenchen Zheng, Hong Xue, Zhi-Wei Cao, Qiang Yang
2010 A conf
Predictive Modeling with Heterogeneous Sources.
SDM
Xiaoxiao Shi, Qi Liu, Wei Fan, Qiang Yang, Philip S. Yu
2010 A* conf
Transfer Learning on Heterogenous Feature Spaces via Spectral Transformation.
ICDM
Xiaoxiao Shi, Qi Liu, Wei Fan, Philip S. Yu, Ruixin Zhu
2009 J jnl
Analyses of domains and domain fusions in human proto-oncogenes.
BMC Bioinform.
Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, Ying Xu
2008 J jnl
Computational prediction of human proteins that can be secreted into the bloodstream.
Bioinform.
Juan Cui, Qi Liu, David Puett, Ying Xu
2008 J jnl
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
J. Comput. Chem.
Qi Liu, Victor Olman, Huiqing Liu, Xiuzi Ye, Shilun Qiu, Ying Xu