Eva KF Chan

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Published Papers

2016

KalsbeekAMF, Chan EKF, Grogan J, Petersen DC, Jaratlerdsiri W, Gupta R, Lyons RJ, Haynes A, KenchJG, Stricker PD, HayesVM. cCrow J, Petersen DC, Louw M, , Harmeyer K, Vecchiarelli S, Lyons R, Bornman R, Hayes V. (2016) Mutational load of the mitochondrial genome predicts pathological features and biochemical recurrence in prostate cancer. Aging 8(11):2702-2712. doi:10.18632/aging.101044

McCrow J, Petersen DC, Louw M, Chan EKF, Harmeyer K, Vecchiarelli S, Lyons R, Bornman R, Hayes V. (2016) Spectrum of Mitochondrial Genomic Variation and Associated Clinical Presentation of Prostate Cancer in South African Men. The Prostate 76(4):349-58. doi:10.1002/pros.23126

2015

Chan EKF, Hardie RA, Petersen DC, Beeson K, Bornman MSR, Smith AB, Hayes VM. (2015) Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa. PLoS ONE 10(3): e0121223.  doi:10.1371/journal.pone.0121223

2014

Morris A, Heinze A, Chan EKF, Smith AB, Hayes VM. (2014) First Ancient Mitochondrial Genome from a Pre-Pastoralist Southern Africa. Genome Biology and Evolution6(10): 2647-2653. doi:10.1093/gbe/evu202

Porto-Neto LR, Reverter A, Prayaga KC, Chan EKF, Johnston DJ, Hawken RJ, Fordyce G, Garcia JF, Sonstegard TS, Bolormaa S, Goddard ME, Burrow HM, Henshall JM, Lehnert SA, Barendse W. (2014) The genetic architecture of climatic adaptation of tropical cattle. Plos One. 9(11): e113284. doi:10.1371/journal.pone.0113284

2012

Sandlin K, Prothro J, Heesacker A, Khalilian N, Okashah R, Xiang W, Bachlava E, Caldwell DG, Taylor CA, Seymour DK, White V, Chan E, Tolla G, White C, Safran D, Graham E, Knapp S, McGregor C. (2012) Comparative mapping in watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai]. Theoretical and Applied Genetics. 125 (8): 1603-1618. doi:10.1007/s00122-012-1938-z

Ainu Husna AMSS, Flatscher-Bader T, Lehnert SA, Reverter A, Chan EKF, Phillips NJ, McGowan M and D’Occhio MJ. (2012) Gene expression of GnRH, kisspeptin, neuropeptide Y and receptors for estrogen and leptin in the hypothalamus of suckled and weaned beef cows. Journal of Tropical Agriculture and Food Science. 40(2): 245-255.

2011

Chan EKF, Rowe HC, Corwin JA, Joseph B, Kliebenstein DJ. (2011) Combining genome wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana. PLoS Biology. 9(8): e1001125. doi: 10.1371/journal.pbio.1001125 

2010

Chan EKF, Rowe HC, Hansen BG, Kliebenstein DJ. (2010) The Complex Genetic Architecture of the Metabolome. PLoS Genetics 6(11): e1001198. doi: 10.1371/journal.pgen.1001198  [This publication appeared in Nature Research Highlights (2010) Genetics: Metabolic variation’s roots. Nature 468: 349.]

Chan EKF, Rowe HC, Kliebenstein DJ. (2010) Understanding the evolution of defense metabolites in Arabidopsis thaliana using genome-wide association mapping. Genetics 185: 991 – 1007. doi: 10.1534/genetics.109.108522

Rowe HC, Walley JW, Corwin J, Chan EK-F, Dehesh K, Kliebenstein DJ. (2010) Deficiencies in Jasmonate-Mediated Plant Defense Reveal Quantitative Variation in Botrytis cinerea Pathogenesis. PLoS Pathogens 6(4): e1000861. doi: 10.1371/journal.ppat.1000861 

Chan EKF, Nagaraj SH, Reverter A. (2010) The evolution of tropical adaptation: Comparing Taurine and Zebu cattle. Animal Genetics 41(5): 467 – 477. doi: 10.1111/j.1365-2052.2010.02053.x [preprint & SOM]

2009

Cowley MJ, Cotsapas CJ, Williams RBH, Chan EKF, Pulvers JN, Liu MY, Luo OJ, Nott DJ, Little PFR. (2009) Intra– and inter– individual genetic differences in gene expression. Mammalian Genome 20(5): 281–295. doi: 10.1007/s00335-009-9181-x [also available from Nature Preceedings]

Chan EKF and Reverter A. (2009) The combined effect of SNP-marker and phenotype attributes in genomewide association studies. Animal Genetics 40(2): 149-156. doi: 10.1111/j.1365-2052.2008.01816.x [preprint]

2008

Reverter A, Chan EKF. Combining partial correlation and an information theory approach to the reversed-engineering of gene co-expression networks. Bioinformatics 24(21):2491-2497. doi: 10.1093/bioinformatics/btn482  [The method presented in this paper was implemented into an R package R/PCIT by Nathan S Watson-Haigh.]

Meadows, JRS., Chan EKF, and Kijas, JW. (2008) Linkage Disequilibrium Compared Between Five Populations of Domestic Sheep. BMC Genetics 9:61. doi:10.1186/1471-2156-9-61

Reverter-Gomez A, Chan EKF, Lehnert S, Barris W, McWilliam S, Dalrymple B, Barendse W. (2008) Dissection of beef quality phenotypes using a Myogenin network-anchored systems biology approach. Australian Journal of Experimental Agriculture 48(8): 1053–1061. doi: 10.1071/EA08052

2007

Williams RBH*, Chan EKF*, Cowley MJ, Little PFR. (2007) The influence of genetic variation on gene expression. Genome Research 17: 1707-1716. doi: 10.1101/gr.6981507 (* equal first authors)

Nott DJ, Yu Z, Chan E, Cotsapas C, Cowley C, Pulvers J, Williams R and Little P. (2007) Hierarchical Bayes variable selection and microarray experiments. Journal of Multivariate Analysis 98 (4): 852-872. doi:10.1016/j.jmva.2006.10.001

2006

Williams RBH, Cotsapas CJ, Cowley MJ, Chan E, Nott CJ, Little PFR. (2006) Microarray normalisation and detection of linkage signal in genetical-genomics experiments. Nature Genetics 38: 855 - 856. doi:10.1038/ng0806-855

Cotsapas CJ, Williams RBH, Pulvers JN, Nott DJ, Chan EKF, Cowley MJ, Little PFR. (2006) Genetic dissection of gene regulation in multiple mouse tissues. Mammalian Genome 17 (6): 490-495. doi:10.1007/s00335-005-0186-9

2003

Cotsapas CJ, Chan E, Kirk M, Tanaka M, Little PFR. (2003) Genetic Variation and the Control of Transcription. Cold Spring Harbor Symposia on Quantitative Biology 68: 109 - 114. doi: 10.1007/s00335-005-0186-9

Patents

2014

Braun CJ III, Chan EKF, Garvey GS, Jones CM, Just BJ, Kniskern JM, Mein JR, Osborn TC, Van Poppel PMJA. Selection of Mature Fruit Color in Pepper Plants. World patent WO/2014/204815. 2014 December 24.

2011/2010

Caldwell D, Chan E, De Vries J, Joobeur T, King J, Reina A, Shetty N. Methods and Compositions for identifying Downy Mildew resistance in cucumber plants. World patent WO/2011/050,296. 2011 April 28; United States patent 12,910,478. 2010 October 22.

Theses

2007

Chan EKF. (2007) The influence of genetic variation in gene expression, PhD thesis, University of New South Wales. http://www.library.unsw.edu.au/~thesis/adt-NUN/public/adt-NUN20070823.122615

2002

Chan EKF. (2002) Genetic variation in gene expression, Honour thesis, University of New South Wales.