2024-07-17T15:21:35+08:002024-07-17|
Contact Information
Title
Visiting Lecturer
Office
(Office) N22-4031
Phone
(Office) +853 8822 4254
Email
chonkitchan@um.edu.mo
Consultation Hours

Tue, Thu 11:00 – 12:00

Teaching
Education
PhD The University of Melbourne, Australia, 2008
BE (1st Class Hons) The University of Melbourne, Australia, 2003
BCS The University of Melbourne, Australia, 2003
Position
2024/06 – Present Visiting Lecturer, Faculty of Health Sciences, University of Macau
2018/05 – 2024/03 Bioinformatics Manager, Australian Genome Research Facility, Australia
2015/01 – 2018/05 Senior Bioinformatics Researcher, The University of Western Australia, Australia
2011/02 – 2015/01 Senior Postdoctoral Researcher, The University of Queensland, Australia
2009/08 – 2011/02 Collaboration Data Manager and Bioinformatics Scientist, Monsanto Biotechnology Research Centre, China
2008/12 – 2009/08 Business Analyst, Objectiva, China
2008/10 – 2008/12 Software Development Engineer, Microsoft, China
Research Interests
My research focuses on advancing the field of bioinformatics through the development and application of cutting-edge AI and machine learning algorithms. In the area of bioinformatics, I apply sophisticated computational techniques to the analysis of next-generation sequencing (NGS) data, including both short and long reads.

 

I am particularly interested in developing robust bioinformatics pipelines for a variety of applications, such as variant calling, genome assembly, metagenomics, genotyping by sequencing and methylation sequencing analysis. These pipelines leverage the latest algorithmic innovations to extract meaningful biological insights from complex sequencing datasets.

 

In addition, I am engaged in the creation of specialized bioinformatics databases to facilitate data storage, organization, and retrieval. These databases serve as valuable resources for the broader research community, enabling collaborative work and accelerating scientific discoveries.

 

Overall, my research aims to harness the power of AI and machine learning to drive transformative advancements in the field of bioinformatics, with the ultimate goal of unlocking new possibilities in life sciences research and biotechnology.
Representative Publications
JOURNAL PUBLICATIONS

  1. Huerlimann R, Cowley JA, Wade NM, Wang Y, Kasinadhuni N, Chan C-KK, et al. Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence. G3 Genes|Genomes|Genetics. 2022;12. doi:10.1093/G3JOURNAL/JKAC034.
  2. Schliebs O, Chan CKK, Bayer PE, Petereit J, Singh A, Hassani-Pak K, Batley J, Edwards D (2021). Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies. Agronomy 2021, Vol. 11, Page 2587, 11(12), 2587. https://doi.org/10.3390/AGRONOMY11122587
  3. Scheben A, Verpaalen B, Lawley CT, Chan CKK, Bayer PE, Batley J, et al. CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. Plant Journal. 2019;98:142–52. doi:10.1111/tpj.14194.
  4. Chan CKK, Rosic N, Lorenc MT, Visendi P, Lin M, Kaniewska P, et al. A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference. Functional & Integrative 2019;19:363–71. doi:10.1007/s10142-018-0647-3.
  5. Bayer PE, Golicz AA, Tirnaz S, Chan CKK, Edwards D, Batley J. Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. Plant Biotechnology Journal. 2019;17:789–800. doi:10.1111/pbi.13015.
  6. Scheben A., Chan CKK, Mansueto L., Mauleon R., Larmande P, Alexandrov N., Wing RA, McNally KL, Quesneville H. Edwards D., Progress in single-access information systems for wheat and rice crop improvement, Briefings in Bioinformatics, Volume 20, Issue 2, March 2019, Pages 565–571, https://doi.org/10.1093/bib/bby016
  7. Hurgobin B, Golicz AA, Bayer PE, Chan CKK, et al. Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnology Journal. 2018;16(7):1265–1274. doi:10.1111/pbi.12867.
  8. Yuan Y, Bayer PE, Scheben A; Chan CKK and Edwards D: BioNanoAnalyst: A visualisation tool to assess genome assembly quality using BioNano data. BMC Bioinformatics. 2017;18 1:323. doi:10.1186/s12859-017-1735-4.
  9. Bayer PE, Hurgobin B, Golicz A, Chan CKK, Yuan Y, Lee HT, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King G, Batley J, Edwards D: Assembly and comparison of two closely related Brassica napus genomes. Plant Biotechnology Journal. 2017; doi:10.1111/pbi.12742.
  10. Montenegro JDM, Golicz AA, Bayer PE, Hurgobin B, Lee HT, Chan CKK, Visendi P, Lai K, Doležel J, Batley J, Edwards D: The pan-genome of modern hexaploid bread wheat.  The Plant Journal. 2017, doi:10.1111/tpj.13515
  11. Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CKK, Severn-Ellis A, McCombie WR, Parkin IAP et al: The pan-genome of an agronomically important crop plant Brassica oleracea. Nature Communications 2016, 7:13390.
  12. Kaniewska P, Chan CKK, Kline D, Ling EYS, Rosic N, Edwards D, Hoegh-Guldberg O, Dove S: Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change. PLoS ONE 2015, 10(10):e0139223.
  13. Bayer P, Ruperao P, Mason A, Stiller J, Chan CKK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P et al: High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 2015:1-9.
  14. Rosic N, Kaniewska P, Chan CKK, Ling E, Edwards D, Dove S, Hoegh-Guldberg O: Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 2014, 15(1):1052.
  15. Rosic N, Ling EYS, Chan CKK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O: Unfolding the secrets of coral-algal symbiosis. ISME Journal
  16. Ruperao P, Chan CKK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J et al: A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 2014, 12(6):778-786.
  17. Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CKK et al: Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 2014, doi: 10.1111/pbi.12240.
  18. Chan CKK, Halgamuge SK: A New Generalized Growth Threshold for Dynamic SOM for Comparing Average Mutual Information and Oligonucleotide Frequency as a Species Signature. International Journal of Bio-Science and Bio-Technology (IJBSBT), Vol. 1, No. 1, Dec 2009, Pg 1~10
  19. Chan CKK, Hsu AL, Halgamuge SK, Tang S-L: Binning sequences using very sparse labels within a metagenome. BMC Bioinformatics 2008, 9(215): doi:10.1186/1471-2105-1189-1215.
  20. Chan CKK, Hsu AL, Tang S-L, Halgamuge SK: Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing. Journal of Biomedicine and Biotechnology 2008, vol. 2008, Article ID 513701:10 pages. doi:10.1155/2008/513701.

BOOK CHAPTER PUBLICATION

  1. Yuan, Y., Scheben, A., Chan, CKK, Edwards, D. (2017). Databases for Wheat Genomics and Crop Improvement. In Methods in molecular biology (Clifton, N.J.) (Vol. 1679, pp. 277–291). https://doi.org/10.1007/978-1-4939-7337-8_18
  2. Ghosh S, Chan CKK: Analysis of RNA-Seq Data Using TopHat and Cufflinks. In: Plant Bioinformatics: Methods and Protocols. Edited by Edwards D. New York, NY: Springer New York; 2016: 339-361.
  3. Tseng C-H, Chan CKK, Hsu AL, Halgamuge SK, Tang S-L: Binning Metagenomic Sequences Using Seeded GSOM. In: Handbook of Molecular Microbial Ecology I. John Wiley & Sons, Inc.; 2011: 369-378
Awards
2011 UQ Research Start-Up Fund, The University of Queensland, Australia
2005 Travel Fellowship award, BIOINFO 2005 conference, Korea
2005 Universitas 21 Research Higher Degree Mobility Scholarship, The University of Melbourne, Australia
2004 – 2008 Melbourne Research Scholarship, The University of Melbourne, Australia
Grants
2014 QCIF Infrastructure Grant:
Chickpea Genome Browsing System
2013 QCIF Infrastructure Grant:
Australian wheat data collection system
2011 – 2012 UQ Early Research Grant:
Computational analysis of second-generation sequencing to identify presence/absence variation in the genome of Brassica oleracea