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Publications - Chon Kit Kenneth Chan

JOURNAL ARTICLES:

1. Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CKK, Severn-Ellis A, McCombie WR, Parkin IAP et al: The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications 2016, 7:13390.
2. Lee H, Golicz AA, Bayer PE, Jiao Y, Tang H, Paterson AH, Sablok G, Krishnaraj RR, Chan CK, Batley J et al: The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri). Plant Physiol 2016, 172(1):272-283.
3. Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan C-KK, Staňková H et al: An efficient approach to BAC based assembly of complex genomes. Plant Methods 2016, 12:2.
4. Kaniewska P, Chan C-KK, 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.
5. Bayer P, Ruperao P, Mason A, Stiller J, Chan C-KK, 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, 128(6):1039-1047.
6. Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan C-KK, Sablok G, Ralph PJ, Edwards D: Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany 2015, 66(5):1489-1498.
7. Rosic N, Kaniewska P, Chan C-K, 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.
8. Rosic N, Ling EYS, Chan C-KK, Lee HC, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O: Unfolding the secrets of coral-algal symbiosis. ISME J 2014.
9. Ruperao P, Chan C-KK, 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.
10. Lai K, Lorenc MT, Lee HC, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan C-KK 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.
11. Chan C-KK, 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
12. Chan C-KK, 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.
13. Chan C-KK, 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.
14. Guru SM, Fernando S, Halgamuge SK, Chan K: Intelligent fastening with A-BOLT Technology and Sensor Network. Assembly Automation 2004, 24(4):386-393.

BOOK CHAPER:

1. Ghosh S, Chan C-KK: 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.
2. Tseng C-H, Chan C-KK, Hsu AL, Halgamuge SK, Tang S-L: Binning Sequences Using Very Sparse Labels Within a Metagenome. In: Encyclopedia of Metagenomics. Edited by Nelson EK. New York, NY: Springer New York; 2013: 1-13.
3. Tseng C-H, Chan C-KK, 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.

CONFERENCE PAPERS:

1. Chan C.-KK, Halgamuge S.K.: Investigation of Average Mutual Information for Species Separation using GSOM. In: Future Generation Information Technology (FGIT 2009), pp. 42-49. Lecture Notes in Computer Science, Springer, Jeju Island, Korea (2009)
2. Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK: A method for evaluating quality of clustering DNA fragments encoded in different nucleotide frequencies. In: 2007 Frontiers in the convergence of bioscience and information technologies (FBIT 2007): 11-13 Oct 2007; Jeju Island, Korea; 2007: 60-63.
3. Reinhard J, Chan C-KK, Halgamuge SK, Tang S-L, Kruse R: Region Identification on a Trained Growing Self-Organizing Map for Sequence Separation between Different Phylogenetic Genomes In: BIOINFO 2005: 22-24 Sep 2005; Busan, Korea: KAIST PRESS; 2005: 124-129.
4. Chan K, Kansara N, Mirbagheri M, Guru SM, Halgamuge SK, Fernando S: Development of hybrid interface for intelligent sensor management. In: HIS03: Dec 14-17 2003; Melbourne, Australia: IOS Press; 2003: 820-829.
5. Chan K, Lam G, Guru SM, Halgamuge MN, Fernando S: Development of a SMARTBOLT prototype with energy model for clustered sensor systems. In: FSKD'02: Nov 18-22 2002; Singapore; 2002: 280-284.
6. Guru SM, Chan C-KK, Halgamuge SK: Advanced Networked Sensor System. In: Knowledge Commercialisation Australasia Forum & Fair of Ideas: 26-28 Mar 2003; Sydney; 2003: Poster Communication.

MONSANTO INTERNAL CONFERENCE POSTERS:

1. Chan C.-KK, He K., Lv L., Wu X., Sun J., Zhang R., Cao Y.: In-house rice genome browser. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
2. Sun J., Chan C-KK, Tao N., Blanchard M., Cao Y.: TE-Viewer: A visualization tool for examine molecular quality of transgenic events in our biotech plant testing pipeline. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
3. He K., Chan C-KK, Lv L., Sun J., Wu X., Zhang R., Cao Y.: Visualizing Genomic Data: a survey of publicly available genome browsers and recommendations for Monsanto implementation. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)
4. Zhang R., Lv L., Sun J., He K., Chan C-KK, Wu X., Cao Y.: GE-Atlas: A graphical visualization tool for viewing and mining gene expression patterns. In: TCM 2010, Jun 08-11, St. Louis, MO, USA (2010)

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