Qi Liu

According to our database, Qi Liu authored at least 44 papers between 2008 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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

Nat. Comput. Sci., October, 2024

Delineating cell types with transcriptional kinetics.

Yicheng Gao, Qi Liu

Nat. Comput. Sci., September, 2024

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, Shanjin Wang, Chao Zhang, Qi Liu, He Zhang

Genom. Proteom. Bioinform., 2024

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

Nat. Mac. Intell., October, 2023

Semi-supervised heterogeneous graph contrastive learning for drug-target interaction prediction.

Kainan Yao, Xiaowen Wang, Wannian Li, Hongming Zhu, Yizhi Jiang, Yulong Li, Tongxuan Tian, Zhaoyi Yang, Qi Liu, Qin Liu

Comput. Biol. Medicine, September, 2023

Pan-Peptide Meta Learning for T-cell receptor-antigen binding recognition.

Yicheng Gao, Yuli Gao, Yuxiao Fan, Chengyu Zhu, Zhiting Wei, Chi Zhou, Guohui Chuai, Qinchang Chen, He Zhang, Qi Liu

Nat. Mac. Intell., March, 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, Qi Liu, De-Shuang Huang

Bioinform., January, 2023

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

Genom. Proteom. Bioinform., 2023

2022

DrSim: Similarity Learning for Transcriptional Phenotypic Drug Discovery.

Zhiting Wei, Sheng Zhu, Xiaohan Chen, Chen-Yu Zhu, Bin Duan, Qi Liu

Genom. Proteom. Bioinform., October, 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, De-Shuang Huang

PLoS Comput. Biol., 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, Ping Wang

Briefings Bioinform., 2022

PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein-protein interaction network.

Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Chen Tang, Xiaohan Chen, Yunjie Li, Qi Liu, Qin Liu

Briefings Bioinform., 2022

2021

FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery.

Shaoqi Chen, Dongyu Xue, Guohui Chuai, Qiang Yang, Qi Liu

Bioinform., 2021

Locating transcription factor binding sites by fully convolutional neural network.

Qinhu Zhang, Siguo Wang, Zhanheng Chen, Ying He, Qi Liu, De-Shuang Huang

Briefings Bioinform., 2021

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

Briefings Bioinform., 2021

2020

Data imbalance in CRISPR off-target prediction.

Yuli Gao, Guohui Chuai, Weichuan Yu, Shen Qu, Qi Liu

Briefings Bioinform., 2020

2019

Advanced Machine Learning Techniques for Bioinformatics.

Quan Zou, Qi Liu

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

<i>C³</i>: Consensus Cancer Driver Gene Caller.

Chen-Yu Zhu, Chi Zhou, Yun-Qin Chen, Ai-Zong Shen, Zong-Ming Guo, Zhao-Yi Yang, Xiangyun Ye, Shen Qu, Jia Wei, Qi Liu

Genom. Proteom. Bioinform., 2019

IMKPse: Identification of Protein Malonylation Sites by the Key Features Into General PseAAC.

Wenzheng Bao, Bin Yang, De-Shuang Huang, Dong Wang, Qi Liu, Yuehui Chen, Rong Bao

IEEE Access, 2019

MPdeep: Medical Procession with Deep Learning.

Qi Liu, Wenzheng Bao, Zhuo Wang

Proceedings of the Intelligent Computing Theories and Application, 2019

2018

Benchmarking CRISPR on-target sgRNA design.

Jifang Yan, Guohui Chuai, Chi Zhou, Chen-Yu Zhu, Jing Yang, Chao Zhang, Feng Gu, Han Xu, Jia Wei, Qi Liu

Briefings Bioinform., 2018

2015

When drug discovery meets web search: Learning to Rank for ligand-based virtual screening.

Wei Zhang, Lijuan Ji, Yanan Chen, Kailin Tang, Haiping Wang, Ruixin Zhu, Wei Jia, Zhiwei Cao, Qi Liu

J. Cheminformatics, 2015

2014

iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis.

Haoqi Sun, Haiping Wang, Ruixin Zhu, Kailin Tang, Qin Gong, Juan Cui, Zhiwei Cao, Qi Liu

Bioinform., 2014

Reconsideration of <i>in silico</i> siRNA design from a perspective of heterogeneous data integration: problems and solutions.

Qi Liu, Han Zhou, Ruixin Zhu, Ying Xu, Zhiwei Cao

Briefings Bioinform., 2014

2013

Transfer across Completely Different Feature Spaces via Spectral Embedding.

Xiaoxiao Shi, Qi Liu, Wei Fan, Philip S. Yu

IEEE Trans. Knowl. Data Eng., 2013

HIM-herbal ingredients in-vivo metabolism database.

Hong Kang, Kailin Tang, Qi Liu, Yi Sun, Qi Huang, Ruixin Zhu, Jun Gao, Duanfeng Zhang, Chenggang Huang, Zhiwei Cao

J. Cheminformatics, 2013

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, Yujia Chen, Qi Liu, Zhiwei Cao

Briefings Bioinform., 2013

2012

Dr.VIS: a database of human disease-related viral integration sites.

Xin Zhao, Qi Liu, Qingqing Cai, Yanyun Li, Congjian Xu, Yixue Li, Zuofeng Li, Xiaoyan Zhang

Nucleic Acids Res., 2012

Virtual Drug Screen Schema Based on Multiview Similarity Integration and Ranking Aggregation.

Hong Kang, Zhen Sheng, Ruixin Zhu, Qi Huang, Qi Liu, Zhiwei Cao

J. Chem. Inf. Model., 2012

Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis.

Tianlei Xu, Ruixin Zhu, Qi Liu, Zhi-Wei Cao

BMC Bioinform., 2012

Screening of selective histone deacetylase inhibitors by proteochemometric modeling.

Dingfeng Wu, Qi Huang, Yida Zhang, Qingchen Zhang, Qi Liu, Jun Gao, Zhi-Wei Cao, Ruixin Zhu

BMC 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

BMC Bioinform., 2012

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, Lin Liu, Jie Zhang, Chun Liang

Bioinform., 2012

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, Yuzong Chen, Yixue Li, Zhi-Wei Cao

Nucleic Acids Res., 2011

Multi-target QSAR Modelling in the Analysis and Design of HIV-HCV Co-Inhibitors : An In-silico Study.

Qi Liu, Han Zhou, Lin Liu, Xi Chen, Ruixin Zhu, Zhi-Wei Cao

BMC Bioinform., 2011

A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information.

Tianli Dai, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu

BMC Bioinform., 2011

An Integrative Approach for Genomic Island Prediction in Prokaryotic Genomes.

Han Wang, John Fazekas, Matthew Booth, Qi Liu, Dongsheng Che

Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

2010

Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study.

Qi Liu, Qian Xu, Vincent Wenchen Zheng, Hong Xue, Zhi-Wei Cao, Qiang Yang

BMC Bioinform., 2010

<i>In-silico </i>prediction of blood-secretory human proteins using a ranking algorithm.

Qi Liu, Juan Cui, Qiang Yang, Ying Xu

BMC Bioinform., 2010

Predictive Modeling with Heterogeneous Sources.

Xiaoxiao Shi, Qi Liu, Wei Fan, Qiang Yang, Philip S. Yu

Proceedings of the SIAM International Conference on Data Mining, 2010

Transfer Learning on Heterogenous Feature Spaces via Spectral Transformation.

Xiaoxiao Shi, Qi Liu, Wei Fan, Philip S. Yu, Ruixin Zhu

Proceedings of the ICDM 2010, 2010

2009

Analyses of domains and domain fusions in human proto-oncogenes.

Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, Ying Xu

BMC Bioinform., 2009

2008

RNACluster: An integrated tool for RNA secondary structure comparison and clustering.

Qi Liu, Victor Olman, Huiqing Liu, Xiuzi Ye, Shilun Qiu, Ying Xu

J. Comput. Chem., 2008

Computational prediction of human proteins that can be secreted into the bloodstream.

Juan Cui, Qi Liu, David Puett, Ying Xu

Bioinform., 2008