Ph.D., Nanyang Technological University, Singapore, 2008-2012

M.S., University of Macau, Macau, 2004-2007

B.S., Nankai University, Tianjin, China, 2000-2004


Research Area

Hidden Markov Models to analyze repeat elements in genome

Development of novel algorithms for long-read sequencing data


Research Summary


RepeatHMM is a novel computational tool to detect trinucleotide repeats and trinucleotide repeat disorders (TRD) from given long reads for a subject of interests. It is able to accurately estimate estimate expansion counts according to the evaluation performance on both simulation data and real data. It is user friendly and easy to install and use.


RepeatHMM takes long reads from a subject as input, and uses a novel unsymmetrical sequence alignment (UnsymSeqAlg) to map all reads to a specific gene of interest in a reference genome (hg38 here), and then, employs UnsymSeqAlg for optional error correction of repeat regions. After that, It uses a hidden Markov model (HMM) method to estimate the repeat count for each of long reads with higher coverage. Lastly, it will detect one or two peaks of expansion counts for the subject of interest.


RepeatHMM is evaluated on simulation data with in silico produced repeat counts and their simulation long reads, and also a real dataset of the ATXN3 gene for SCA3. The results demonstrate that our tool is able to accurately estimate expansion counts from long reads.





Journal papers
18. 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
17. Jing Ren, Qian Liu, John Ellis and Jinyan Li: Positive-unlabeled learning for the prediction of conformational B-cell epitopes. BMC Bioinformatics 2015; 16(Suppl 18): S12.
16. 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.
15. 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.
14. 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.
13. 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.
12. 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.
11. Qian Liu, Steven C. H. Hoi, Chee-Keong Kwoh, Limsoon Wong, Jinyan Li: Integrating water exclusion theory into $\beta$ contacts to predict binding free energy changes and binding hot spots. BMC bioinformatics 2014, 15(1), 57.
10. 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 $\beta$ contacts and B factor. Journal of Chemical Information and Modeling 2013, 53(11), 3076--3085.
8. 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.
7. Qian Liu, Chee-Keong Kwoh, Steven C. H. Hoi: $\beta$ atomic contacts: Identifying critical specific contacts in protein binding interfaces. PLOS ONE 2013, 8(4), e59737.
6. 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.
5. 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.
4. Qian Liu, Jinyan Li: Protein binding hot spots and the residue-residue pairing preference: A water exclusion perspective. BMC Bioinformatics 2010, 11:244.
3. 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.
2. 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.
1. Zhiguo Gong and Qian Liu: Improving Keyword Based Web Image Search with Visual Feature Distribution and Term Expansion. Knowledge and Information Systems 2009 21(1):113-132.

Conference papers
7. Qian Liu, Jinyan Li, Limsoon Wong, Kotagiri Ramamohanarao: Efficient mining of subspace pan-correlation patterns from time course data. Accepted by ADMA 2016.
6. 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.
5. 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.
4. Z Gong, J Zhang, Qian Liu: Automatic hidden Web database classification. in Knowledge Discovery in Databases: PKDD 2007, 454--461.
3. Z Gong, Qian Liu, J Zhang: Web image retrieval refinement by visual contents. in Advances in Web-Age Information Management. 2006, 134--145.
2. Z Gong, Qian Liu, J Zhang: Automatic image annotation by mining the Web. in Data warehousing and knowledge discovery. 2006: 449--458.
1. 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.