Our research focused on the application of algorithm to solve biology problems. We develop new computational tools to address a range of topics, including genome assembly, pathogen detection, phylogenetic, transcription factor binding sites finding, DNA motif prediction, and genomic sequence indexing. Currently, my research focus is on designing the pathogen chip, understanding the promoter/enhancer structure, and reconstructing the transcriptome. Below, we briefly describe the various projects.
- Understanding promoter and enhancer structures: It is well-known that enhancer will work with promoter to regulate the expression of genes. However, we still have little understanding of the mechanism. Using the exprimental data ChIP-seq and ChIA-PET, we aim to discover how the transcription factors on the promoters and the enhancers work together.
- Pathogen chip: Pathogen chip is a microarray which allows us to detect pathogen. We have developed the version 1 pathogen chip in 2007. Currently, we would like to enhance the chip so that we can covers more different pathogens while we can improve the sensitivity.
- Reconstructing the transcriptome: The aim of this project is to reconstruct the transcriptome uisng the RNA-seq data.
- Tennakoon C, Purbojati RW, Sung WK "BatMis: A fast algorithm for k-mismatch mapping." Bioinformatics 2012 Jun 10 Abstract
- Sung WK, Zheng H, Li S, Chen R, Liu X, Li Y, Lee NP, Lee WH, Ariyaratne PN, Tennakoon C, Mulawadi FH, Wong KF, Liu AM, Poon RT, Fan ST, Chan KL, Gong Z, Hu Y, Lin Z, Wang G, Zhang Q, Barber TD, Chou WC, Aggarwal A, Hao K, Zhou W, Zhang C, Hardwick J, Buser C, Xu J, Kan Z, Dai H, Mao M, Reinhard C, Wang J, Luk JM "Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma." Nat Genet 2012 ; 44(7) : 765-9 Epub 2012 May 27 Abstract
- Ariyaratne PN, Sung WK "PE-Assembler: de novo assembler using short paired-end reads." Bioinformatics 2011 Jan 15 ; 27(2) : 167-74 Epub 2010 Dec 12 Abstract
- Zhang Z, Chang CW, Goh WL, Sung WK, Cheung E "CENTDIST: discovery of co-associated factors by motif distribution." Nucleic Acids Res 2011 May 20 Abstract
- Lee CW, Koh CW, Chan YS, Aw PP, Loh KH, Han BL, Thien PL, Nai GY, Hibberd ML, Wong CW, Sung WK "Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays." Nucleic Acids Res 2010 Feb 25 Abstract
- Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK "ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing." Genome Biol 2010 Feb 25 ; 11(2) : R22 Epub 2010 Feb 25 Abstract
- Willy H, Song F, Aung Z, Ng SK, Sung WK "SLiM on DIet: Finding Short Linear Motifs on Domain Interaction Interfaces in PDB." Bioinformatics 2010 Feb 18 Abstract
- Narang V, Mittal A, Sung WK "Localized motif discovery in gene regulatory sequences." Bioinformatics 2010 May 1 ; 26(9) : 1152-9 Epub 2010 Mar 11 Abstract
- Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK "A signal-noise model for significance analysis of ChIP-seq with negative control." Bioinformatics 2010 May 1 ; 26(9) : 1199-204 Epub 2010 Apr 5 Abstract
- 6. Wing-Kai Hon, Kunihiko Sadakane, and Wing-Kin Sung. Breaking a Time-and-Space Barrier in Constructing Full-Text Indices. SIAM Journal on Computing. 38(6): 2162-2178, 2009. Abstract