Publications

✝: corresponding authors; ⚹: co-first author
  1. Umair Ahsan, Qian Liu ⚹, Li Fang, Kai Wang. NanoCaller for accurate detection of SNPs and indels from long-read sequencing by deep neural networks. Genome Biology 2021; 22:261.
  2. Daniela Georgieva, Qian Liu ⚹, Kai Wang, Dieter Egli. Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing. Nucleic Acids Research 2020; gkaa517.
  3. Qian Liu , Li Fang, Guoliang Yu, Depeng Wang, Chuan-Le Xiao, Kai Wang. Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. Nat. Commun 2019; 10 (1), 1-11.
  4. Qian Liu , Peng Zhang, Depeng Wang, Weihong Gu, Kai Wang. Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing. Genome Medicine 2017; 9(1):65.
✝: corresponding authors; ⚹: co-first author
  1. Daniela Georgieva, Qian Liu ⚹, Kai Wang, Dieter Egli. Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing. Nucleic Acids Research 2020; gkaa517.
  2. Qian Liu , Li Fang, Guoliang Yu, Depeng Wang, Chuan-Le Xiao, Kai Wang. Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. Nat. Commun 2019; 10 (1), 1-11.
  3. Qian Liu , Daniela C. Georgieva, Dietrich M. Egli, Kai Wang. NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data. BMC genomics 2019; 20 (1), 31-42.
✝: corresponding authors; ⚹: co-first author
  1. MU Ahsan, Q Liu, JE Perdomo, L Fang, K Wang. A survey of algorithms for the detection of genomic structural variants from long-read sequencing data. Nature Methods 2023; 20: 1143–1158.
  2. L Fang, Q Liu ✝⚹, AM Monteys, P Gonzalez-Alegre, BL Davidson, K Wang. DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing. Genome Biology 2022; 23(1): 1-27.
  3. Qian Liu , Yao Tong, Kai Wang. Genome-wide detection of short tandem repeat expansions by long-read sequencing. BMC Bioinformatics 2020; 21:542
  4. Zeng, Mei-yun Zhang, Xue-jing Wang, Zheng-mao Hu, Jin-chen Li, Nan Li, Jun-ling Wang, Fan Liang, Qi Yang, Qian Liu , Li Fang, Jun-wei Hao, Fu-dong Shi, Xue-bing Ding, Jun-fang Teng, Xiao-meng Yin, Hong Jiang, Wei-ping Liao, Jing-yu Liu, Kai Wang, Kun Xia, Bei-sha Tang. Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy. J Med Genet. 2019; 56 (4), 265-270.
  5. Qian Liu , Lingling Shi, Kai Wang. Ethnicity-Specific Reference Genome Assembly by Long-Read Sequencing. J Mol Genet Med 2018; 12(4), 385.
  6. Atlas Khan, Qian Liu , Kai Wang. iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental disorders in personal genomes. BMC bioinformatics 2018; 19(17), 501.
  7. Xinhua Fu, Jingjing Li, Yu Tian, Weipeng Quan, Shu Zhang, Qian Liu , Fan Liang, Xinlei Zhu, Liangsheng Zhang, Depeng Wang, Jiang Hu. Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome. GigaScience 2017; 6(12):1–7.
  8. Qian Liu , Peng Zhang, Depeng Wang, Weihong Gu, Kai Wang. Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing. Genome Medicine 2017; 9(1):65.
✝: corresponding authors; ⚹: co-first author
  1. Qian Liu , Yu Hu, Andres Stucky, Li Fang, Jiang F. Zhong, Kai Wang. LongGF: computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing. BMC Genomics 2020; 21:793
  2. Atlas Khan, Qian Liu ⚹, Yunjing Zeng, Andres Stucky, Parish P. Sedghizadeh, Daniel Adelpour, Xi Zhang, Kai Wang, Jiang F. Zhong. Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA-seq and VirTect. Mol Oncol. 2019; 13 (4), 829-839.
  3. Renhua Song, Qian Liu , Jinyan Li: Connecting rules from paired miRNA and mRNA expression data sets of HCV patients to detect both inverse and positive regulatory relationships. BMC Genomics 2015; 16(Suppl 2):S11.
  4. Renhua Song, Qian Liu , Gyorgy Hutvagner, Hung Nguyen, Kotagiri Ramamohanarao, Limsoon Wong, Jinyan Li: Rule discovery and distance separation to detect reliable miRNA biomarkers for the diagnosis of lung squamous cell carcinoma. BMC Genomics 2014; 15(Suppl 9):S16.
✝: corresponding authors; ⚹: co-first author
  1. H Derbel, Z Zhao, Q Liu ✝. Accurate prediction of functional effect of single amino acid variants with deep learning. Computational and Structural Biotechnology Journal 2023; 21: 5776-5784.
  2. H Derbel, CJ Giacoletto, R Benjamin, G Chen, MR Schiller, Q Liu ✝. Accurate prediction of transcriptional activity of single missense variants in HIV Tat with deep learning. International Journal of Molecular Sciences 2023; 24(7): 6138.
  3. Qian Liu , Jing Ren, Jiangning Song, Jinyan Li. Co-occurring atomic contacts for the characterization of protein binding hot spots. PLoS ONE 2016; 10(12): e0144486.
  4. Jing Ren, Qian Liu , John Ellis and Jinyan Li: Prediction of conformational B cell epitopes from positive and unlabeled samples. BMC Bioinformatics 2015; 16(Suppl 18): S12.
  5. Qian Liu , Zhenhua Li, Jinyan Li: Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts. BMC Bioinformatics 2014; Suppl 12, S15.
  6. Jing Ren, Qian Liu , John Ellis, Jinyan Li: Tertiary structure-based prediction for conformational B-cell epitopes through B factors. Bioinformatics 2014; 30(12): i264–i273.
  7. Qian Liu , Steven C. H. Hoi, Chee-Keong Kwoh, Limsoon Wong, Jinyan Li: Integrating water exclusion theory into β contacts to predict binding free energy changes and binding hot spots. BMC bioinformatics 2014; 15(1), 57.
  8. Qian Liu , Yi-Ping Phoebe Chen, Jinyan Li: k-partite cliques of protein interactions: A novel subgraph topology for functional coherence analysis on PPI networks. Journal of Theoretical Biology 2014; 340, 146–154.
  9. Qian Liu , Chee-Keong Kwoh, Jinyan Li: Binding affinity prediction for protein-ligand complexes based on β contacts and B factor. Journal of Chemical Information and Modeling 2013; 53(11), 3076–3085.
  10. Zhenhua Li, Ying He, Qian Liu , Liang Zhao, Limsoon Wong, CK Kwoh, H Nguyen, Jinyan Li: Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. BMC Bioinformatics 2013; 14(16), 1–15.
  11. Qian Liu , Chee-Keong Kwoh, Steven C. H. Hoi: β atomic contacts: Identifying critical specific contacts in protein binding interfaces. PLOS ONE 2013; 8(4), e59737.
  12. Qian Liu , Limsoon Wong, Jinyan Li: Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2012; 1824(12):1457–1467.
  13. Qian Liu , Steven C. H. Hoi, Su T. T. Chinh, Zhenhua Li, Chee-Keong Kwoh, Limsoon Wong and Jinyan Li: Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: Do mutations of H1N1 from 1918 to 2009 affect much on this binding? Bioinformatics 2011; 27(18):2529–2536.
  14. Qian Liu , Jinyan Li: Protein binding hot spots and the residue-residue pairing preference: A water exclusion perspective. BMC Bioinformatics 2010; 11:244.
  15. Qian Liu , Jinyan Li: Propensity vectors of low-ASA residue pairs in the distinction of protein interactions. Proteins: Structure, Function and Bioinformatics 2009; 78(3):589–602.
  16. Jinyan Li, Qian Liu : Double water exclusion: A hypothesis refining the O-ring theory for the hot spots at protein interfaces. Bioinformatics 2009; 25(6):743–750.
  17. Qian Liu , Jinyan Li. Protein Binding Interfaces and Their Binding Hot Spot Prediction: A Survey. Bioinformatics for Diagnosis. Prognosis and Treatment of Complex Diseases, 79–106, 2013.
  18. Qian Liu , Yi-Ping Phoebe Chen, Jinyan Li: High functional coherence in k-partite protein cliques of protein interaction networks. in Bioinformatics and Biomedicine, 2009. BIBM'09. IEEE International Conference on. 2009; 111–117.
✝: corresponding authors; ⚹: co-first author
  1. Qian Liu , Shameek Ghosh, Jinyan Li, Limsoon Wong, Kotagiri Ramamohanarao. Discovering pan-correlation patterns from time course data sets by efficient mining algorithms. Computing 2018; 100(4):421–437.
  2. Qian Liu , Renhua Song and Jinyan Li: Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets. BMC Genomics 2015; 16(Suppl 12):S4.
  3. Zhiguo Gong, Qian Liu : Improving Keyword Based Web Image Search with Visual Feature Distribution and Term Expansion. Knowledge and Information Systems 2009; 21(1):113–132.
  4. Qian Liu , Jinyan Li, Limsoon Wong, Kotagiri Ramamohanarao: Efficient mining of pan-correlation patterns from time course data. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)2016; 10086 LNAI pp. 234–249.
  5. Jinyan Li, Qian Liu , Tao Zeng: Negative correlations in collaboration: concepts and algorithms. in Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining 2010; 463–472.
  6. Z Gong, J Zhang, Qian Liu : Automatic hidden Web database classification. in Knowledge Discovery in Databases: PKDD 2007; 454–461.
  7. Z Gong, Qian Liu , J Zhang: Web image retrieval refinement by visual contents. in Advances in Web-Age Information Management 2006; 134–145.
  8. Z Gong, Qian Liu , J Zhang: Automatic image annotation by mining the Web. in Data warehousing and knowledge discovery 2006; 449–458.
  9. Z Gong, J Zhang, Qian Liu : Hidden-Web database exploration. in Intelligent Systems Design and Applications, 2006. ISDA'06. Sixth International Conference on. 2006; 838–843.