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Book Chapter or Editorial
Qi Liu#, Editorial: Old Drugs Learn New Tricks: Advances and Applications for Drug Repurposing, Current Topics in Medicinal Chemistry,17(32),2017.
Yi Sun, Qi Liu#, Zhiwei Cao#, Network Based Deciphering of the Mechanism of TCM, in Data Analytics for Traditional Chinese Medicine Research, Springer-Verlag, 2014, XII, 248,P. 59.
Dongsheng Che, Qi Liu and Khaled Rasheed, Decision Tree and Ensemble Learning Algorithms with Their Applications in Bioinformatics, SoftwareTools and Algorithms forBiological Systems, Springer-Verlag, 2011, 696:191-9.
Select papers in the area of Bioinformatics
Danyi CHen et al, Qi Liu# and Qin Liu#, Predicting anticancer synergistic drug combinations based on multi-task learning, BMC Bioinformatics, 2023, Advance Acess.
Chen Tang et al., Qi Liu#, Personalized tumor combination therapy optimization using the single-cell transcriptome, Genome Medicine. Advance Access, 2023.
Qichang Chen et al., Qi Liu#, Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints, Nature Communications. Advance Access, 2023.
Yicheng Gao et al., Qi Liu#, Reply to: The pitfalls of negative data bias for the T-cell epitope specificity challenge, Nature Machine Intelligence. Advance Access, 2023.
Xiaowen Wang et al, Qi Liu#, Qin Liu#, A complete graph-based approach with multi-task learning for predicting synergistic drug combinations, Bioinformatics, Advance Access, 2023.
Yaokai Nan et al, Qi Liu#,Qin Liu#, Semi-supervised heterogeneous graph contrastive learning for drug-target interaction perdicition, Computers in Biology and Medicine, Advance Acess, 2023
Yicheng Gao et al., Qi Liu#, Pan-Peptide Meta Learning for T-Cell Receptor-Antigen Binding Recognition, Nature Machine Intelligence. Advance Access, 2023.
Qinhu Zhang et al., Qi Liu#, Deshuang Huang#, Computational prediction and characterization of cell-type-specific and shared binding sites, Bioinformatics. Advance Access, 2023.
Yanan Cao, Lingling Chen, Hua Chen, Yupeng Cun, Xiaofeng Dai, Hongli Du, Feng Gao, Fengbiao Guo, Yalong Guo, Pei Hao, Shunmin He, Shunping He, XiongLei He, Zheng Hu, Boon-Peng Hoh, Xin Jin, Qian Jiang, Qinghua Jiang, Asifullah Khan, Hong-Zhi Kong, Jinchen Li, Shuai Cheng Li, Ying Li, Qiang Lin, Jianquan Liu, Qi Liu, Jian Lu, Xuemei Lu, Shujin Luo, Qinghua Nie, Zilong Qiu, Tieliu Shi, Xiaofeng Song, Jianzhong Su, Sheng-ce Tao, Chaolong Wang, Chuan-Chao Wang, Guo-Dong Wang, Jiguang Wang, Qi WU, Shaoyuan Wu, Shuhua Xu, Yu Xue, Wenjun Yang, Zhaohui Yang, Kai Ye, Yuan-Nong Ye, Li Yu, Fangqing Zhao, Yiqiang Zhao, Weiwei Zhai, Dandan Zhang, Liye Zhang, Houfeng Zheng, Qi Zhou, Tianqi Zhu, Ya-ping Zhang, Was Wuhan the early epicenter of the COVID-19 pandemic? – A critique, National Science Review, nwac287, 2023.
Bang Wang et al, Qi Liu et al, Feng Gu#, CRISPR/Cas9-mediated mutagenesis at microhomologous regions of human mitochondrial genome, Science China-Life Sciences, Advance Access, 2022.
Shaoqi Chen et al, Qi Liu#, Privacy-preserving integration of multiple institutional data for single-cell type identification with scPrivacy, Science China-Life Sciences, Advance Access, 2022.
Gongchen Zhang et al., Qi Liu#, Systematic exploration of optimized base-editing gRNA design and pleiotropic effects with BExplorer, Genomics Proteomics & Bioinformatics. Advance Access, 2022.
Zhiting Wei et al.,Qi Liu#, DrSim: Similarity learning for transcriptional phenotypic drug discovery, Genomics Proteomics & Bioinformatics. Advance Access, 2022.
Qinchang Chen et al, Qi Liu#, Toward a molecular mechanism-based prediction of CRISPR-Cas9 targeting effects, Science Bulletin, Advance Access, 2022.
Dongyu Xue et al, Qi Liu#, X-MOL: large-scale pre-training for molecular understanding and diverse molecular analysis, Science Bulletin, Advance Access, 2022.
Gaoyang Li et al, Qi Liu#, A deep generative model for multi-view profiling of single cell RNA-seq and ATAC-seq data, Genome Biology, Advance Access, 2022.
Qinhu Zhang et al, Qi Liu#, Deshuang Huang#, Base-resulotion prediction of transcription factor binding signals by a deep learning framework, Plos Computational Biology, Advance Access, 2022.
Yukang Gong et al, Qi Liu#, DeepReac+: Deep active learning for quantitative modeling of organic chemical reactions, Chemical Science, Advance Access, 2021.
Xiaowen Wang, Qi Liu#, Qin Liu#, PRODeepSyn: integrating protein-protein interaction network with omics data to predict anticancer synergistic drug combinations, Briefings in Bioinformatics, Advance Access, 2021.
Tengbo Zhang et al, Qi Liu#, Ping Wang#, iCRISEE: an integrative analysis of CRISPR screen by reducing false positive hits, Briefings in Bioinformatics , Advance Access , 2021.
Xiangyong Li et al, Qi Liu#, Hao Ye#, Benchmark HLA genetyping and clarifying HLA impact on survival in tumor immunotherapy, Molecular Oncology, Advance Access, 2021.
Bin Duan et al, Qi Liu#, Integrating multiple references for single cell assignment, Nucleic Acids Research, Advance Access, 2021.
Biyu Zhanget al, Qi Liu#, The tumor therapy landscape of synthetic lethality, Nature Communications, Advance Access, 2021.
Qinghu Zhang et al, Qi Liu#, Deshuang Huang#, locating transcription factor biding sites by fully convolutional neural network, Briefings in Bioinformatics, Advance Access, 2021.
Mengshi Wu et al, Qi Liu, Eduardo Bejarano, Rosa Lozano-Duran, Plant DNA polymerases α and δ mediate replication of geminiviruses, Nature Communications, Advance Access, 2021.
Bin Duan et al, Qi Liu#, Learning for single cell assignment, Science Advances, Advance Access, 2020.
Jifang Yan et al, Qi Liu#, Benchmarking and integrating CRISPR off-target detection and prediction, Nucleic Acids Research, Advance Access , 2020.
Shaoqi Chen et al, Qi Liu#, FL-QSAR: a federated learning based QSAR prototype for collaborative drug discovery, Bioinformatics, Advance Access , 2020.
Zhiting Wei et al, Qi Liu#, iDMer: an integrative and Mechanism-driven response system for identifying compound interventions for sudden virus break, Briefings in Bioinformatics, Advance Access , 2020.
Zhanbing Zhang et al, Qi Liu#, Jing Yu#, ASNEO, Identificaiton of Personalized Alternative Splicing Based NEOantigens with RNA-seq, Aging, Advance Access, 2020.
Peng Zhang et al, Qi Liu et al, Zhiping Wen, Comprehensive identification of alternative back-splicing in human tissue transcriptomes, Nucleic Acids Research, Advance Access, 2020.
Yuyu Li et al, Qi Liu et al, Lu Xie, ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection, BMC Medical Genomics, Advance Access, 2020.
Chi Zhou et al, Qi Liu#, Systematically characterizing A-to-I RNA editing neoantigens in cancer, Frontiers in Oncology, Advance Access, 2020.
Bang Wang et al, Qi Liu et al, Feng Gu #. CRISPR/Cas9-mediated mutagenesis at microhomologous regions of human mitochondrial genome. SCIENCE CHINA Life Sciences, Advance Access, 2020.
Zhiting Wei et al, Qi Liu#, The landscape of tumor fusion neoantigens: a pan-cancer analysis, iScience, Advance Access , 2019.
Chi Zhou et al, Qi Liu#, pTuneos: prioritizing Tumor neoantigens from next-generation sequencing data, Genome Medicine, Advance Access , 2019.
Han Zhao et al, Qi Liu#, MetaMed: Linking microbiota functions with medicine therapeutics, mSystems, Advance Access , 2019.
Chi Zhou et al, Qi Liu#, Towards in silico identification of tumor neoantigens in immunotherapy, Trends in Molecular Medicine, Advance Access , 2019. (Featured Article!)
Bin Duan et al, Qi Liu#, Model based Understanding of Single Cell CRISPR screening, Nature Communications, Advance Access, 2019.
Yuli Gao et al, Qi Liu#, Data imbalance in CRISPR off-target prediction, Briefings in Bioinformatics, Advance Access , 2019.
Chenyu Zhu et al, Qi Liu#, C3: Consensus Cancer Driver Gene Caller, Genomics, Proteomics & Bioinformatics, Advance Access, 2019.
Dongyu Xue et al, Qi Liu#, Advances and challenges in deep generative models for de novo molecule generation, WIREs Computational Molecule Science , Advance Access, 2018.
Guohui Chuai et al, Qi Liu#, DeepCRISPR: optimized CRISPR guide RNA design by deep learning, Genome Biology, Advance Access , 2018.
Jingyang Gao et al, Qi Liu, Sheng Qu#, The change in the percent of android and gynoid fat mass correlated with increased testosterone after laparoscopic sleeve gastrectomy in Chinese obses men: a 6-month follow-up, Obesity Surgery, Advance Access, 2018.
Ke Chen et al, Qi Liu# , Towards in-silico prediction of the immune-checkpoint blockade response, Trends in Pharmacological Sciences, Advance Access , 2017.
Mengjun Tun et al, Qi Liu, et al , Feng Gu, A ‘new lease of life’: FnCpf1 possesses DNA cleavage activity for genome editing in human cells, Nucleic Acids Research , Advance Access , 2017.
Jifang Yan et al, Qi Liu#, Benchmarking CRISPR on-target sgRNA design, Briefings in Bioinformatics, Advance Access, 2017.
Jifang Yan, Tao Qi, Guohui Chuai, Ning Kang, Yuan He and Qi Liu# . MetaTopics: an integration tool to analyze microbial community profile by topic model, BMC Genomics , Advance Access, 2017.
Tingyi Wei etal, Qi Liu, Tao Duan and Jihong Kang, Folic acid supports pluripotency and reprogramming by regulating LIF-STAT3 and MAPK-ERK signaling, Stem Cells and Development, Advance Access, 2016.
Guohui Chuai, Jifang Yan et al, Qi Liu#, Deciphering relationship between microhomology and in-frame mutation occurence in human CRISPR-based gene knockout, Molecular Therapy-Nucleic Acids, Advance Access, 2016.
Bingqiang Liu et al, Qi Liu , Qing Ma, An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes, BMC Genomics , Advance Access, 2016.
Jian Ma et al, Qi Liu#, Han Xu# and X. Shirley Liu#, CRISPR-DO: A genome-wide CRISPR designer and optimizer for multiple species, Bioinformatics, Advance Access, 2016.
YH, YQC et al, Qi Liu# , Jenny Wei#, Ranking novel cancer driving synthetic lethal gene pairs, Oncotarget , Advance Access, 2016.
Guo-hui Chuai, Qi-Long Wang, Qi Liu# , In-silico meets in-vivo: towards computational CRISPR-based sgRNA design, Trends in Biotechnology , Advance Access, 2016.
Bingqiang Liu et al, Qi Liu , Qin Ma, Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses, Scientific Reports , doi:10.1038/srep23030.
SY, ZW, Qin Ma, Jenny Wei#, Qi Liu#, Identifying anti-cancer drug response related genes using an integrative analysis of transcriptomic and genomic variations with cell line-based drug perturbations ---- With implications for tumor samples, Oncotarget, 2016 Jan 25. doi: 10.18632/oncotarget.7012.
Yi Sun, Zhen Sheng, Chao Ma, Kailin Tang, Ruixin Zhu, Zhuanbin Wu, Ruling Shen, Jun Feng, Dingfeng Wu, Danyi Huang, Dandan Huang, Jian Fei#, Qi Liu#, Zhiwei Cao#, Combining genomic and network characteristics for extended capability in predicting synergistic drugs for cancer, Nature Communications, Advance Access, 2015.
Haiping Wang, Quanquan Gu,Jia Wei, Zhiwei Cao, Qi Liu#, Mining drug-disease relationships as a complement to medical genetics-based drug repositioning: Where a recommendation system meets GWAS, Clinical Pharmacology & Therapeutics, Advance Access, 2015.
WZ, LJ, KT, HP W, RX Z, WJ, ZW, Qi Liu#, When drug discovery meets web searching: learning to rank for ligand-based virtual screening, Journal of Cheminformatics, Advance Access, 2015.
HK, YZ et al, Qi Liu#, YY H#, ZW C#, Integrating Clinical Indexes into Four-Diagnostic Information Contribute to the Traditional Chinese Medicine (TCM) Syndrome Diagnosis of Chronic Hepatitis B, Scientific Reports, Advance Acess, 2015.
YS, Qi Liu#, Deciphering the Correlation between Breast Tumor Samples and Cell Lines by Integrating Copy Number Changes and Gene Expression Profiles, BioMed Research International , Advance Acess, 2015.
CZJ, HK, Qi Liu et al, Screening Ingredients from Herbs against Pregnane X Receptor in the Study of Inductive Herb-Drug Interactions: Combining Pharmacophore and Docking-Based Rank Aggregation, BioMed Research International, Advance Acess, 2015.
HY, Qi Liu and JW , Constructing of Drug Network based on Side Effects and its Application for Drug Repositioning, Plos one , 9(2):e87864, 2014.
Haoqi Sun, Haiping Wang, Ruixin Zhu, Kailin Tang, Qin Gong, Juan Cui, Zhiwei Cao, Qi Liu# , iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis, Bioinformatics, 2014 Mar 1;30(5):737-9 .
Yi Sun, Ruixin Zhu, Hao Ye, Jing Zhao, Yujia Chen, Qi Liu # and Zhiwei Cao#, Towards a bioinformatics analysis of anti-Alzheimer’s herbal medicines from a target network perspective, Briefings in Bioinformatics , May;14(3):327-43, 2013.
Hong Kang, Kailin Tang, Qi Liu , Yi Sun, Qi Huang, Ruixin Zhu, Jun Gao, Guoqing Zhang, Duanfeng Zhang, Chenggang Huang and Zhiwei Cao, HIM-Herbal Ingredients In-Vivo Metabolism Database, Journal of Cheminformatics, 5:28, 2013.
Chao Ma, Kailin Tang, Qi Liu , Ruixin Zhu, Zhiwei Cao, Calmodulin as a potential target by which berberine induce cell cycle arrest in human hepatoma Bel7402 cells, Chemical Biology & Drug Design , 81(6):775-83 , 2013.
Qi Liu , Han Zhou, Kui Zhang, Xiaoxiao Shi, Wei Fan, Philip Yu and Zhiwei Cao, In silico target-specific siRNA design based on domain transfer in heterogeneous data, Plos one , 7(12):e50697, 2012.
Hong Kang, Zhen Sheng, Ruixin Zhu, Qi Huang, Qi Liu# and Zhiwei Cao#, A virtual drug screen schema based on multi-view similarity integration and ranking aggregation, J. Chem. Inf. Model. 26;52(3):834-43, 2012.
Tianlei Xu, Ruixin Zhu, Qi Liu# and Zhiwei Cao#, Quantitatively Integrating Molecular Structure and Bioactivity Profile Evidence into Drug-Target Relationship Analysis, BMC Bioinformatics ,13:186, 2012.
Qi Liu , Han Zhou, Ruixin Zhu, Ying Xu and Zhiwei Cao, Reconsideration of in-silico siRNA design from a perspective of heterogeneous data integration: problems and solutions, Briefings in Bioinformatics , Advance Access, 2012.
Qi Liu , Han Zhou, Juan Cui, Zhiwei Cao and Ying Xu, Reconsideration of In-silico siRNA Design Based on Feature Selection: A Cross-platform Data Integration Perspective, Plos one , 7(5) :e37879 , 2012.
Jun Gao, Dongsheng Che, Vincent W. Zheng, Ruixin Zhu, Qi Liu#, Integrated QSAR study for inhibitors of Hedgehog Signal Pathway against multiple cell lines：a collaborative filtering method, BMC Bioinformatics , 13:186, 2012.
Jun Gao#, Qi Liu#, Hong Kang, Zhiwei Cao and Ruixin Zhu, Comparison of different ranking methods in protein-ligand binding sites prediction, Int. J. Mol. Sci ., 13(7):8752-61, 2012.
Jun Gao, Qi Huang, Dingfeng Wu, Qingchen Zhang, Yida Zhang, Tian Chen, Qi Liu , Ruixin Zhu, Zhiwei Cao and Yuan He, Study on human GPCR-inhibitor interactions by proteochemometric modeling, Gene , 2012, S0378-1119(12)01482-5.
Dingfeng Wu, Qi Huang, Yida Zhang, Qingchen Zhang, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu, Screening of selective histone deacetylase inhibitors by proteochemometric modeling, BMC Bioinformatics , 2012, 13:212.
Qi Huang, Haixiao Jin, Qi Liu , Qiong Wu, Hong Kang, Zhiwei Cao, Ruixin Zhu, Proteochemometric Modeling of the Bioactivity Spectra of HIV-1 Protease Inhibitors by Introducing Protein-Ligand Interaction Fingerprint, Plos one , 7(7):341698, 2012.
Qi Liu , Han Zhou, Lin Liu, Xi Chen, Ruixin Zhu and Zhiwei Cao, Multi-target QSAR Modelling in the Analysis and Design of HIV-HCV Co-Inhibitors An In-silico Study, BMC Bioinformatics, 2011 12:294.
Gao Jun, Zhu Ruixin Liu, Qi Liu# , Cao Zhiwei#, Petri Net based Metabolic Network Parameters Fitting with GPU Acceleration, Chin. J. Chem ., 2011, 29(9),1805-1810.
Zhu Ruixin, Wang Fei, Liu Qi# , Kang Tingguo#, Quantitative Structure-Activity Relationship of IOPY/ISPY Analogues as HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors, ACTA CHIMICA SINICA, Vol,69,2011, No.15,1731-1736.
Ruixin Zhu#, Qi Liu#, Jian Tang, Huiliang and Zhiwei Cao, Investigations on Inhibitors of Hedgehog Signal Pathway: A QSAR Study, Int. J. Mol. Sci. , 12, 3018-3033, 2011.
Tianli Dai, Qi Liu , Jun Gao, Zhiwei Cao, Ruixin Zhu, A New Protein-Ligand Binding Sites Prediction Method by integrating Sequence Conservation of Protein, BMC Bioinformatics , 12 Suppl 14,2011.
Shenzhen, Huangqi, Kanghong, Liu Qi , Zhiwei Cao, Ruixin Zhu, A new fingerprint of chemical compounds and its application for virtual drug screens, ACTA CHIMICA SINICA, Vol. 69, 2011, 1845-1850.
Huang Qi, Kang Hong, Duanfeng Zhang, Sheng, Zhen, Liu Qi , Ruixin Zhu, Cao Zhiwei, Comparison of Ligand-, Target Structure-, and Protein-Ligand Interaction Fingerprint-base Virtual Screening Methods, ACTA CHIMICA SINICA , 2011,69(5),515-522.
Chao Ma, Hong Kang, Qi, Liu , Ruixin Zhu, Zhiwei Cao, Insight into potential toxicity mechanisms of melamine: an in silico study, Toxicology, 2011, Volume 283, Issues 2-3, 96-100.
Sheng Zhen, Kong Hong, Dai Tianli, Liu Qi#, Zhu Ruixin#, Complementary study of structure features and gene profile features for chemical compounds, ACTA CHIMICA SINICA, 2010, 68(23),2395-2400.
Liu Qi , Che Dongsheng, Huang Qi, Cao Zhiwei , Zhu Ruixin, Multi-target QSAR Study in the Analysis and Design of HIV-1 Inhibitors, Chin. J. Chem . 1587-1592, 2010.
Qi Liu , Juan Cui, Qiang Yang and Ying Xu, In-silico prediction of blood-secretory human proteins using a ranking algorithm, BMC Bioinformatics , 11:250, 2010.
Qi Liu, Qian Xu, Wencheng Zhen, Hong Xue, ZhiWei Cao, Qiang Yang, Multi-task learning for cross-platform siRNA efficacy prediction, an in-silico study. BMC Bioinformatics, 11:181, 2010.
Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li and ZW Cao, HIT: linking herbal active ingredients to targets, Nucleic Acids Research . 2010, 1-5.
Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, Ying Xu, Analyses of Domains and Domain Fusions in Human Proto-Oncogenes, BMC Bioinformatics, 2009, 10:88.
Qi Liu ,Yin Zhang,Ying Xu, Xiuzi Ye, Fuzzy kernel clustering of RNA secondary structure ensemble using a novel similarity metric. Journal of Biomolecular Structure and Dynamics , 25(6):685-696, 2008. ( RNAsscc: software upon request )
Qi Liu , Yu Yang, Chun Chen, Jiajun Bu,Ying Zhang, Xiuzi Ye, RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure. BMC Bioinformatics , 9:176, 2008.
Qi Liu, V. Olman, Huiqing Liu, Xiuzi Ye, Shilun Qiu, Ying Xu, RNACluster : an integrated tool for RNA secondary structure comparison and clustering. Journal of Computational Chemistry, 26(9), 1517-1526, 2008.
Juan Cui, Qi Liu, David Puett, Ying Xu, Computational prediction of human proteins that can be secreted into the bloodstream, Bioinformatics, 24(20),2370-2375,2008.
Qi Liu , Ying Zhang, Mingyi Wang, Rongdong Yu and Xiuzi Ye, Progress of normalization methods for high-density oligonucleotide microarray data, Journal of Zhejiang University (Engineering Science) , 2008,42(9),1653-1660.
Qi Liu , Yin Zhang, Xiuzi Ye, Rongdong Yu, A Discrete Hopfield Neural Network based MIS finding algorithm for stems selecting and its application in RNA secondary structure prediction, Chinese Journal of Computers , 2008(1), 51-58.
Select papers in the area of Machine Learning
Xiaoxiao Shi, Qi Liu , Wei Fan, and Philip S. Yu, Transfer across Completely Different Feature Spaces via Spectral Embedding, IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 25, no. 4, pp. 906-918, 2011. ( Top Journal in Machine Learning Community )
Xiaoxiao Shi, Qi Liu , Wei Fan, Philip Yu, and Ruixin Zhu, Training Data Extraction from Completely Different Feature Spaces via Spectral Transformation, IEEE International Conference on Data Mining (ICDM 2010) , 1049-1054, 2010. ( Top Conference in Machine Learning Community )
Xiao Xiao shi, Qi Liu , Wei Fan,Qiang Yang, Philip S.Yu. Predictive Modeling with heterogeneous Sources, the 2010 SIAM International Conference on Data Mining (SDM’2010), 814-825, 2010. ( Top Conference in Machine Learning Community)
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