Wen-Yu Chung (鐘文鈺)

Assistant Professor

Dept. Computer Science and Information Engineering

National Kaohsiung University of Science and Technology

Email: wychung@nkust.edu.tw, Phone: 886-7-3814526-15822


Research interests

Bioinformatics and Computational Biology, Network Biology, Machine Learning, Data Science, Graph Neural Network



Assistant professor, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan — 2012-Present

Post-doctoral position, University of Texas at Dallas, Dallas, USA — 2010-2012

Post-doctoral position, Cold Spring Harbor Laboratory, New York, USA — 2009-2010



The Pennsylvania State University, State College, PA, USA — PhD in Computer Science and Engineering, 2009

National Tsing-Hua University, Hsinchu, Taiwan — MS in Computer Science, 2002

National Tsing-Hua University, Hsinchu, Taiwan — BS in Computer Science, 2000


Journal Publication

1.   Wong R, Chang WL, Chung WY, Vasilakos AV, “Biomolecular and quantum algorithms for dominating set problem in arbitrary networks,” Scientific Reports, 2023, 13, 4205. doi: 10.1038/s41598-023-30600-4.

2.   Hsu YT, Wu CC, Wang CC, Chung WY, Sheu CC, Yang YH, Cheng MY, Lai RS, Leung SY, Lin CC, Wei YF, Lin CH, Lin SH, Hsu JY, Huang WC, Tseng CC, Lai YF, Cheng MH, Chen HC, Yang CJ, Su CH, Wang CJ, Hsu SC, Hung CH, Lee CL, Huang MS, Huang SK, “BTEX exposure and its body burden pose differential risks for asthma and its phenotypic clusters, “ Allergy, 2023. doi: 10.1111/all.15683.

3.   Lim LM, Chung WY, Hwang DY, Yu CC, Ke HL, Liang PI, Lin TW, Cheng SM, Huang AM, Whole-exome sequencing identified mutational profiles of urothelial carcinoma post kidney transplantation,” Journal of Translational Medicine, vol. 20, no. 1, p. 324, Jul. 2022, doi: 10.1186/s12967-022-03522-4.

4.   Wu CC, Wang CC, Chung WY, Sheu CC, Yang YH, Cheng MY, Lai RS, Leung SY, Lin CC, Wei YF, Lin CH, Lin SH, Hsu JY, Huang WC, Tseng CC, Lai YF, Cheng MH, Chen HC, Yang CJ, Hsu SC, Su CH, Wang CJ, Liu HJ, Chen HL, Hsu YT, Hung CH, Lee CL, Huang MS, Huang SK, “Environmental risks and sphingolipid signatures in adult asthma and its phenotypic clusters: a multicentre study,” Thorax, 2022 Jun 16:thoraxjnl-2021-218396. doi: 10.1136/thoraxjnl-2021-218396.

5.   Chang WL, Chung WY, Hsiao CY, Wong R, Chen JC, Feng M, Vasilakos AV, “Quantum Speedup for Inferring the Value of Each Bit of a Solution State in Unsorted Databases Using a Bio-Molecular Algorithm on IBM Quantum's Computers,” IEEE Trans Nanobioscience, 2022 Apr;21(2):286-293. doi: 10.1109/TNB.2021.3130811.

6.   Lee SW, Huang YC, Lin CY, Huang HY, Liu CW, Hsieh MT, Lee CL, Chung WY, Chung KF, Wang CH, Kuo HP, “Impact of Annual Exposure to Polycyclic Aromatic Hydrocarbons on Acute Exacerbation Frequency in Asthmatic Patients,” J Asthma Allergy, 2021 Jan 29;14:81-90. doi: 10.2147/JAA.S288052.

7.   Huang PY, Cheng WS, Chen JC, Chung WY, Chen YL, Lin KW, "A Distributed Method for Fast Mining Frequent Patterns From Big Data," in IEEE Access, vol. 9, pp. 135144-135159, 2021, doi: 10.1109/ACCESS.2021.3115514.

8.   Hsieh MT, Peng CY, Chung WY, Lai CH, Huang SK, Lee CL, “Simulating the spatiotemporal distribution of BTEX with an hourly grid-scale model,” Chemosphere, 2020 May;246:125722. doi: 10.1016/j.chemosphere.2019.125722.

9.   Liang CW, Chung WY, “Color feature extraction and selection for image retrieval,” in 2016 International Conference on Advanced Materials for Science and Engineering (ICAMSE), 2016, pp. 589-592, doi: 10.1109/ICAMSE.2016.7840207.

10.            Lee CL, Huang HC, Wang CC, Sheu CC, Wu CC, Leung SY, Lai RS, Lin CC, Wei YF, Lai IC, Jiang H, Chou WL, Chung WY, Huang MS, Huang SK, “A new grid-scale model simulating the spatiotemporal distribution of PM2.5-PAHs for exposure assessment," J Hazard Mater., 2016 Aug 15;314:286-294. doi: 10.1016/j.jhazmat.2016.04.047.

11.            Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ, “Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells,” Nucleic Acids Research, vol. 42, issue 5, pp. 3009–3016, 2014, doi: 10.1093/nar/gkt1306.

12.            Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B, “Epigenomic analysis of multilineage differentiation of human embryonic stem cells,” Cell, 2013 May 23;153(5):1134-48. doi: 10.1016/j.cell.2013.04.022.

13.            Chung WY, Schmitz RJ, Biorac T, Ye D, Dudas M, Meredith GD, Adams CC, Ecker JR, Zhang MQ, “Constructing Hepitypes: Phasing Local Genotype and DNA Methylation,” J Neurosci Neuroengng, vol. 2, no. 4, pp. 335–346, Aug. 2013, doi: 10.1166/jnsne.2013.1067.

14.            Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF,
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications,” Nat Biotechnol., 2010 Oct;28(10):1097-105. doi: 10.1038/nbt.1682.

15.            Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ, “Updates to the RMAP short-read mapping software,” Bioinformatics, 2009 Nov 1;25(21):2841-2. doi: 10.1093/bioinformatics/btp533.

16.            Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team, “Windshield splatter analysis with the Galaxy metagenomic pipeline,” Genome Res., 2009 Nov;19(11):2144-53. doi: 10.1101/gr.094508.109.

17.            Han X, Wu X, Chung WY, Li T, Nekrutenko A, Altman NS, Chen G, Ma H, "Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing,” Proc Natl Acad Sci, 2009 Aug 4;106(31):12741-6. doi: 10.1073/pnas.0902417106.

18.            Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A, “A first look at ARFome: dual-coding genes in mammalian genomes,” PLoS Comput Biol., 2007 May;3(5):e91. doi: 10.1371/journal.pcbi.0030091.

19.            Chung WY, Albert R, Albert I, Nekrutenko A, Makova KD, “Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network,” BMC Bioinformatics, 2006;7:46. doi: 10.1186/1471-2105-7-46.

20.            Zhang L, Lu HHS, Chung WY, Yang J, Li WH, “Patterns of Segmental Duplication in the Human Genome,” Molecular Biology and Evolution, vol. 22, issue 1, pp. 135–141, 2005, https://doi.org/10.1093/molbev/msh262

21.            Nekrutenko A, Chung WY, Li WH, An evolutionary approach reveals a high protein-coding capacity of the human genome,” Trends in Genetics, vol. 19, no. 6, pp. 306310, Jun. 2003, doi: 10.1016/S0168-9525(03)00114-8.

22.            Nekrutenko A, Chung WY, Li WH,, ETOPE: evolutionary test of predicted exons,” Nucleic Acids Research, vol. 31, no. 13, pp. 35643567, Jul. 2003, doi: 10.1093/nar/gkg597.