• Genomics
• Bioinformatics

Ken Sung specializes in bioinformatics and computational genomics, pioneering algorithms for large-scale genome analysis. With over 300 peer-reviewed publications, his seminal contributions include:

• Structural variant calling from high-throughput sequencing data (SV detection, virus integration)
• Chromatin interaction mapping via ChIA-PET analysis
• Mutation discovery pipelines linking genomic variants to disease phenotypes

As Director of JC STEM Laboratory of Computational Genomics, he bridges algorithmic innovation with clinical genomics, using in-house software to transform raw sequencing data into actionable biological insights.

Ken Sung received both the B.Sc. and the Ph.D. degree in the Department of Computer Science from the University of Hong Kong in 1993, 1998, respectively. He is a Global STEM professor in the Department of Chemical Pathology, Chinese University of Hong Kong. He is also the director of the JC STEM Lab of Computational Genomics. He has over 30 years of experience in Bioinformatics and Computational genomic research. Previously, he worked as a Professor in the Department of Computer Science, School of Computing, NUS and as a senior group leader in Genome Institute of Singapore. Ken has published over 300 research papers. These papers report original and improved (and sometimes optimal) solutions in bioinformatics and their applications in biomedical research. His current H-index is 77. He was elected an ISCB fellow in 2026. He was conferred the 2003 FIT paper award (Japan), the 2006 National Science Award (Singapore), and the 2008 Young Researcher Award (NUS) for his research contribution in bioinformatics and algorithm.

He published two books: “Algorithms in Bioinformatics: A Practical Introduction” (2009) and “Algorithms for Next-Generation Sequencing” (2017).

1. ISCB Fellow, International Society for Computational Biology (ISCB) (2026)
2. Young Researcher Award, National University of Singapore (2008)
3. DREAM2 Challenge, National Center for Data To Health, USA (2008)
4. National Science Award, Astar, Singapore (2006)
5. FIT Paper Award, Information Processing Society of Japan (IPSJ) (2003)

1. Darian JC, Kundu R, Rajaby R, Sung WK. Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly. Nature Methods. 2024;21(4):574-583. doi:10.1038/s41592-023-02141-1.
2. Rajaby R, Sung WK. SurVIndel2: Improving copy number variant calling from next-generation sequencing using hidden split reads. Nature Communications. 2024;15(1):10473-. doi:10.1038/s41467-024-53087-7.
3. Rajaby R, Liu DX, Au CH, Cheung YT, Lau AYT, Yang QY, Sung WK. INSurVeyor: Improving insertion calling from short read sequencing data. Nature Communications. 2023;14(1):3243-. doi:10.1038/s41467-023-38870-2.
4. Rajaby R, Zhou Y, Meng Y, Zeng X, Li G, Wu P, Sung WK. SurVirus: A repeat-aware virus integration caller. Nucleic Acids Research. 2021;49(6):E33-E33. doi:10.1093/nar/gkaa1237.
5. Liu DX, Rajaby R, Wei LL, Zhang L, Yang ZQ, Yang QY, Sung WK. Calling large indels in 1047 Arabidopsis with IndelEnsembler. Nucleic Acids Research. 2021;49(19):10879-10894. doi:10.1093/nar/gkab904.
6. Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E. An AR-ERG transcriptional signature defined by longrange chromatin interactomes in prostate cancer cells. Genome Research. 2019;29(2):223-235. doi:10.1101/gr.230243.117.
7. Sung WK. Algorithms for Next-Generation Sequencing. Boca Raton, FL: Chapman and Hall/CRC; 2017. (Book)
8. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148(1-2):84-98. doi:10.1016/j.cell.2011.12.014.
9. 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. Nature Genetics. 2012;44(7):765-769. doi:10.1038/ng.2295. (Letter)
10. Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK. BatMeth: Improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biology. 2012;13(10):R82-. doi:10.1186/gb-2012-13-10-r82.
11. Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed Y bin, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biology. 2010;11(2):R22-. doi:10.1186/gb-2010-11-2-r22.
12. Sung WK. Algorithms in Bioinformatics: A Practical Introduction. 1st ed. New York, NY: Chapman and Hall/CRC; 2009. doi:10.1201/9781420070347. (Book)
13. Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Ridwan A, Wong CH, Liu ET, Ruan Y. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nature Methods. 2005;2(2):105-111. doi:10.1038/nmeth733.
14. Hon WK, Sadakane K, Sung WK. Breaking a time-and-space barrier in constructing full-text indices. In: Proceedings of the 44th Annual IEEE Symposium on Foundations of Computer Science. IEEE; 2003:251-260. doi:10.1109/sfcs.2003.1238199. (Conference Paper)