Publications KC

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Publications - Chon Kit Kenneth Chan

JOURNAL ARTICLES:

  1. Yuan Y, Bayer PE, Scheben A; Chan CKK and Edwards D. (2017) 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.
  2. Lim DKY, Schuhmann H, Thomas-Hall SR, Chan CKK, Wass TJ, Aguilera F, Adarme-Vega TC, Dal’Molin CGO, Thorpe GJ , Batley J, Edwards D, Schenk PM. (2017) RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 1 during nitrogen starvation reveals a 2 two-stage lipid accumulation mechanism Bioresource Technology. Bioresource Technology. 2017;  doi:http://dx.doi.org/10.1016/j.biortech.2017.06.003
  3. Bayer PE, Hurgobin B, Golicz A, Chan K, Yuan Y, Lee HT, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King G, Batley J, Edwards D. (2017) Assembly and comparison of two closely related Brassica napus genomes. Plant Biotechnol J. 2017;  doi:10.1111/pbi.12742 [doi].
  4. Montenegro JDM, Golicz AA, Bayer PE, Hurgobin B, Lee HT, Chan CKK, Visendi P, Lai K, Doležel J, Batley J, Edwards D. (2017) The pangenome of modern hexaploid bread wheat.  The Plant Journal. 2017:n/a-n/a. doi:10.1111/tpj.13515
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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
  16. 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.
  17. 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.
  18. 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. Yuan Y, Scheben A, Chan CKK and Edwards D. (2016) Databases for wheat genomics and crop improvement. Methods in Molecular Biology, Springer (USA)
  2. 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.
  3. 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.
  4. 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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