Publications

Organism-Specific rRNA Capture System for Application in Next-Generation Sequencing

Li, S. K., Zhou, J. W., Yim, A. K. Y., Leung, A. K. Y., Tsui, S. K. W., Chan, T. F., & Lau, T. C. K. (2013). Organism-Specific rRNA Capture System for Application in Next-Generation Sequencing. PloS one, 8(9), e74286. Abstract RNA-sequencing is a powerful tool in studying RNomics. However, the highly abundance of ribosomal […]

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Genomic Organization and Promoter Cloning of the Human X11α Gene APBA1

Chai, K. H., McLoughlin, D. M., Chan, T. F., Chan, H. Y. E., & Lau, K. F. (2012). Genomic Organization and Promoter Cloning of the Human X11α Gene APBA1. DNA and cell biology, 31(5), 651-659. Abstract X11α is a brain specific multi-modular protein that interacts with the Alzheimer’s disease amyloid precursor protein (APP). Aggregation of […]

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Transcriptional profiling of angiogenesis activities of calycosin in zebrafish

Li, S., Lou, S., Lei, B. U. W., Chan, T. F., Kwan, Y. W., Chan, S. W., … & Lee, S. M. Y. (2011). Transcriptional profiling of angiogenesis activities of calycosin in zebrafish. Molecular BioSystems, 7(11), 3112-3121. Abstract Angiogenesis plays an important role in a wide range of physiological processes and many diseases are associated […]

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ViralFusionSeq: Accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution

Li, J. W., Wan, R., Yu, C. S., Wong, N., & Chan, T. F. (2013). ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics, 29(5), 649-651. Abstract Summary: Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery […]

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Discovering protein-DNA binding sequence patterns using association rule mining.

Leung, K.-S., Wong, K.-C., Chan, T.-M., Wong, M.-H., Lee, K.-H., Lau, C.-K., et al. (2010). Discovering protein-DNA binding sequence patterns using association rule mining. Nucleic acids research, 38(19), 6324-37. doi: 10.1093/nar/gkq500. Abstract Extraction of meaningful information from large experimental data sets is a key element in bioinformatics research. One of the challenges is to identify […]

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Data mining on DNA sequences of hepatitis B virus.

Leung, K.-S., Lee, K. H., Wang, J.-F., Ng, E. Y. T., Chan, H. L. Y., Tsui, S. K. W., et al. (2009). Data mining on DNA sequences of hepatitis B virus. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 8(2), 428-40. Published by the IEEE CS, CI, and EMB Societies & the ACM. […]

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Discovering approximate-associated sequence patterns for protein-DNA interactions.

Leung, K.-S., Wong, K.-C., Chan, T.-M., Wong, M.-H., Lee, K.-H., Lau, C.-K., et al. (2010). Discovering protein-DNA binding sequence patterns using association rule mining. Nucleic acids research, 38(19), 6324-37. doi:10.1093/nar/gkq500. Abstract Motivation: The bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) are fundamental protein-DNA interactions in transcriptional regulation. Extensive efforts have been […]

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ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping

Lou, S.-K., Ni, B., Lo, L.-Y., Tsui, S. K.-W., Chan, T.-F., & Leung, K.-S. (2011). ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. Bioinformatics (Oxford, England), 27(3), 421-2. doi: 10.1093/bioinformatics/btq656.   Abstract: Summary: Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can […]

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An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database)

Lou, S.-K., Wong, K.-L., Li, M., But, P. P.-H., Tsui, S. K.-W., & Shaw, P.-C. (2010). An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database). BMC genomics, 11(1), 402. doi: 10.1186/1471-2164-11-402. Abstract Background Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials […]

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Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length.

Lou, S.-K., Li, J.-W., Qin, H., Yim, A., Lo, L.-Y., Ni, B., et al. (2011). Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length.BMC Bioinformatics, 12(Suppl 5), S2. doi: 10.1186/1471-2105-12-S5-S2. Abstract Background RNA sequencing (RNA-seq) measures gene expression levels and permits splicing analysis. Many existing […]

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