Applied Bioinformatics Group - User contributions [en]

Publications DE

2015-08-11T04:21:40Z

Appbio: /* JOURNAL ARTICLES: */

==Publications - David Edwards==

===BOOKS:===

#[http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA). (2012)
#[http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA). (2009)
#[http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA). (2007)

===BOOK CHAPTERS:===

#Visendi P, Batley J and Edwards D. Next Generation Sequencing and Germplasm Resources. In Advances in Genomics of Plant Genetic resources. Volume 1. Genomics platforms, crop domestication and allele mining. Ed. Tuberosa R. Springer (USA) (accepted August 2012)
#Edwards D. (2013) Bioinformatics tools to assist breeding for climate change. In Genomics and breeding for climate resilient crops. Ed, Kole C. Springer (USA), pp 391-414
#Edwards D and Gupta PK. (2013) Sequence based DNA markers and genotyping for cereal genomics and breeding. In Cereal Genomics II. Eds. Gupta PK and Varshney, RK. Springer (USA) pp 57-76
#Edwards D and Wang X. (2012) Genome Sequencing Initiatives. In [http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 152-157
#Lorenc M, Boskovic Z, Stiller J, Duran C and Edwards D. (2012) Role of Bioinformatics as a Tool for Oilseed Brassica Species. In [http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 194-205
#Edwards D. (2011) Wheat Bioinformatics. In: [http://www.cplbookshop.com/contents/C63.htm The World Wheat Book II.] Eds. Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) pp 851-875
#Duran C, Boskovic Z, Batley J and Edwards D. (2011) Brassica Bioinformatics. In [http://www.scipub.net/agriculture/genetics-genomics-and-breeding-of-vegetable-brassicas.html Vegetable Brassicas] Ed. Sadowski J. Science Publishers, Inc., New Hampshire pp 406-418
#Edwards D, Hansen D and Stajich J. (2009) DNA Sequence Databases. In [http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 1-11
#Duran C, Edwards D and Batley J. (2009) Molecular Marker Discovery and Genetic map Visualisation. In [http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 165-189
#Imelfort M, Batley J, Grimmond S and Edwards D. (2009) Genome sequencing approaches and successes. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 345-358
#Batley J and Edwards D. (2009) Mining for Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: [http://www.springer.com/life+sciences/bioinformatics/book/978-1-58829-910-9 Bioinformatics for DNA Sequence Analysis.] Ed. Posada D. Methods in Molecular Biology, Humana Press (USA), pp 303-322
#Appleby N, Edwards D and Batley J. (2009) New technologies for ultra-high throughput genotyping in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press, (USA), pp 19-40
#Duran C, Edwards D and Batley J. (2009) Genetic maps and the use of synteny. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 41-56
#Edwards D and Batley J. (2008) Bioinformatics: Fundamentals and Applications in Plant Genetics, Mapping and Breeding. In: [http://aob.oxfordjournals.org/content/102/5/879.full Principles and Practices of Plant Genomics.] Eds. Kole C and Abbott AG. Science Publishers, Inc., (USA), pp 269-302
#Edwards D. (2007) Bioinformatics and plant genomics for staple crops improvement. In: [http://au.wiley.com/WileyCDA/WileyTitle/productCd-0813818354.html Breeding Major Food Staples.] Eds. Kang MS and Priyadarshan PM. Blackwell, pp 93-106
#Batley J, Jewell E and Edwards D. (2007) Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA), pp. 473-494
#Love CG and Edwards D. (2007) Accessing integrated Brassica genetic and genomic data using the BASC server. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA) (2007), pp. 229-244
#Edwards D, Salisbury PA, Burton WA, Hopkins CJ and Batley J. (2007) Indian Mustard, in [http://www.springer.com/series/7367 Genome Mapping and Molecular Breeding in Plants, Vol. 2.] Ed. Kole C. Springer NY, pp 179-210
#Edwards D, Forster JW, Chagné D and Batley J. (2007) What are SNPs? In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 41-52.
#Edwards D, Batley J, Cogan NOI, Forster JW and Chagné D. 2007. Single Nucleotide Polymorphism Discovery. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 53-76.
#Chagné D, Batley J, Edwards D, and Forster JW. (2007) Single Nucleotide Polymorphisms genotyping in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 77-94.
#Batley J and Edwards D. (2007) SNP applications in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 95-102.
#Spangenberg GC, Forster JW, Edwards D, John U, Mouradov A, Emmerling M, Batley J, Felitti S, Cogan NOI, Smith KF and Dobrowolski M. (2005) Future Directions in the Molecular Breeding of Forage and Turf. In: [http://www.wageningenacademic.com/molecular Molecular Breeding for Genetic Improvement of Forage Crops and Turf.] Ed. Humphreys MO. Wageningen Academic Publishers, pp 83-97.
#Spangenberg GC, Felitti SA, Shields K, Ramsperger M, Tian P, Ong EK, Singh D, Logan E and Edwards D. (2005) Gene Discovery and Microarray-Based Transcriptome Analysis of the Grass-Endophyte Association. In: [http://onlinelibrary.wiley.com/book/10.1002/9780470384916 Neotyphodium in Cool Season Grasses.] Eds. Roberts CA, West CP and Spiers DE. Blackwell, pp 103-140

===JOURNAL ARTICLES:===

# Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke L, Dempewolf H, De Pace C, Edwards D, Gepts P , Greenland A, Hall A, Henry R, Hori K, Howe G, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen H, Ogbonnaya F, Ortiz R, Paterson A, Tuberosa R, Valliyodan B, Varshney R, Yano M. (2015) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnology Journal (accepted August 2015)
# Gou L, Hattori J, Fedak G, Balcerzak M, Klassen D, Sharpe A, Visendi P, Edwards D, Tinker N, Wei Y, Chen G and Ouellet T. (2015) Development and validation of Thinopyrum elongatum expressed molecular markers specific for the long arm of chromosome 7E. Crop Science (accepted July 2015)
# Cai G, Yang Q, Yi B, Fan C, Zhang C, Edwards D, Batley J and Zhou Y. (2015) A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics 16, 409
# Pang W, Li X, Choi SR, Nguyen VD, Dhandapani V, Kim YY, Ramchiary N, Kim JG, Edwards D, Batley J, Na J, Kim HR, Lim YP. (2015) Mapping QTLs of resistance to head splitting in cabbage (Brassica oleracea L.var. capitata L). Molecular Breeding 35:126
# Patel DA, Zander M, Van de Wouw AP, Mason AS, Edwards D, Batley J. (2015) Population Diversity of Leptosphaeria maculans in Australia. International Journal of Biology 7 (3): 18-36
# Mohd-Yusoff NF, Ruperao P, Tomoyoshi NE, Edwards D, Gresshoff PM, Biswas B and Batley J. (2015) Scanning ethyl methanesulphonate effects on the whole genome of Lotus japonicus using second generation sequencing analysis. G3. 5 (4): 559-67
# Bayer PE, Ruperao P, Mason AS, Stiller J, Chan CKK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J, Edwards D. (2015) High resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 128 (6): 1039-1047.
# Mason M, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J. (2015) High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources (Accepted January 2015).
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan CKK, Sablok G, Ralph PJ, Edwards D. (2015) Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany. 66 (5):1489-98
# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13 (1):97-104.
# Rosic N, Kaniewska P, Chan K, Ling E, Edwards D, Dove D and Hoegh-Guldberg O. (2014) Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 15:1052.
# Shin SC, Ahn DH, Kim SJ, Pyo CW, Lee H, Kim MK, Lee J, Lee JE, H. Detrich III HW, Postlethwait JH, Edwards D, Lee SG, Lee JH, Park H. The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment. (2014) Genome Biology 15:468.
# Chalhoub B., Denoeud F., Liu S., Parkin I.A.P., Tang H., Wang X., Chiquet J., Belcram H., Tong C., Samans B., Corréa M., Da Silva C., Just J., Falentin C., Koh C.S., Le Clainche I., Bernard M., Bento P., Noel B., Labadie K., Alberti A., Charles M., Arnaud D., Guo H., Daviaud C., Alamery S., Jabbari K., Zhao M., Edger P.P., Chelaifa H., Tack D., Lassalle G., Mestiri I., Schnel N., Le Paslier M.-C., Fan G., Renault V., Bayer P.E., Golicz A.A., Manoli S., Lee T.-H., Thi V.H.D., Chalabi S., Hu Q., Fan C., Tollenaere R., Lu Y., Battail C., Shen J., Sidebottom C.H.D., Wang X., Canaguier A., Chauveau A., Bérard A., Deniot G., Guan M., Liu Z., Sun F., Lim Y.P., Lyons E., Town C.D., Bancroft I., Wang X., Meng J., Ma J., Pires J.C., King G.J., Brunel D., Delourme R., Renard M., Aury J.-M., Adams K.L., Batley J., Snowdon R.J., Tost J., Edwards D., Zhou Y., Hua W., Sharpe A.G., Paterson A.H., Guan C., Wincker P. (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. [http://www.sciencemag.org/content/345/6199/950.full Science 345:950-953.]
# Rosic N, Ling E, Chan K, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O, and Lee H. (2014) Unfolding the secrets of coral-algal symbiosis. The ISME Journal 9(4):844-56
# International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. [http://www.sciencemag.org/content/345/6194/1251788.abstract Science 345:1251788-1251788]
# Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., Jakobsen K.S., Wulff B.B.H., Steuernagel B., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. [http://www.sciencemag.org/content/345/6194/1250092.abstract Science 345:1250092-1250092]
# Pfeifer M., Kugler K.G., Sandve S.R., Zhan B., Rudi H., Hvidsten T.R., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. [http://www.sciencemag.org/content/345/6194/1250091.abstract Science 345:1250091-1250091]
# Parkin, I., Koh, C., Tang, H., Robinson, S., Kagale, S., Clarke, W., Town, C., Nixon, J., Krishnakumar, V., Bidwell, S., Denoeud, F., Belcram, H., Links, M., Just, J., Clarke, C., Bender, T., Huebert, T., Mason, A., Pires, J., Barker, G., Moore, J., Walley, P., Manoli, S., Batley, J., Edwards, D., Nelson, M., Wang, X., Paterson, A., King, G., Bancroft, I., Chalhoub, B. and Sharpe, A. (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. [http://genomebiology.com/2014/15/6/R77 Genome Biology 15, R77]
# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. [http://www.onlinelibrary.wiley.com/doi/10.1111/pbi.12240/abstract Plant Biotechnology Journal 13 (1), 97-104]
# Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M, Kumar P, Parkin I, Batley J, Luckett D, and Wratten N. (2014) Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101673 PLOS ONE. 9(7): e101673]
# Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, Zhao M, Ma J, Yu J, SH, Wang X, Wang J, Lu K, Fan Z, Bancroft I, Yang TJ, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee TH, Wang J, Jin H, Li Z, Li X, Zhang J, L Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. [http://www.nature.com/ncomms/2014/140523/ncomms4930/full/ncomms4930.html Nature Communications. 5. DOI: 10.1038/ncomms4930]
# Raman H, Dalton-Morgan J, Diffey S, Raman R, Alamery S, Edwards D and Batley, J. (2014) High-density SNP markers based map construction and genome-wide linkage analysis in Brassica napus. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12186/abstract Plant Biotechnology Journal. 12:851-860]
# Ruperao P, Chan KCK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J, Chitikineni A, Visendi P, Gaur PM, Millán T, Singh KB, Taran B, Wang J, Batley J, Doležel J, Varshney RK and Edwards D. (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12182/abstract Plant Biotechnology Journal. 12:778-786]
# Visendi P, Batley J, Edwards D. (2013) Next generation characterisation of cereal genomes for marker discovery. Biology 2: 1357-1377 [http://www.mdpi.com/2079-7737/2/4/1357/pdf Biology 2: 1357-1377]
# Golicz AA, Bayer PE, Martinez PA, Lai K, Lorenc MT, Alamery S, Hayward A, Tollenaere R, Long Y, Meng J, Batley J, Edwards D. (2013) Characterising diversity in the Brassica genomes. [http://www.actahort.org/books/1005/ Acta Horticulturae. 1005: 33-48]
# Deng P, Nie X, Wang L, Cui L, Liu P, Tong W, Biradar SS, Edwards D, Berkman P, Šimková H, Doležel J, Luo M, You F, Batley J, Fleury D, Appels R, Weining S. (2013) Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes. [http://link.springer.com/article/10.1007%2Fs11105-013-0669-x Plant Molecular Biology Reporter. 1-14]
# Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang WJ, Liang X , Kahl G, Edwards D, Varshney RK. (2013) Functional genomics to study stress responses in crop legumes: Progress and prospects. [http://www.publish.csiro.au/paper/FP13191.htm Functional Plant Biology. 40(12) 1221-1233]
# Zander M, Patel DA, Van de Wouw A, Lai K, Lorenc MY, Campbell E, Hayward A, Edwards D, Raman H and Batley J. (2013) Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. [http://link.springer.com/article/10.1007%2Fs10142-013-0324-5 Functional and Integrative Genomics. 13: 295–308]
# Raman H, Raman R, Kilian A, Detering F, Long Y, Edwards D, Parkin IAP, Sharpe AG, Nelson MN, Larkan N, Zou J, Meng J, Aslam MN, Batley J, Cowling WA, Lydiate D. (2013) A consensus map of rapeseed (Brassica napus L) based on diversity array technology markers: Applications in genetic dissection of qualitative and quantitative traits. [http://www.biomedcentral.com/1471-2164/14/277 BMC Genomics 14: 277]
# Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Tar'an B, Millan T, Zhang X, Rosen B, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Thudi M, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, SinghKB, Datta SK, Jackson SA, Wang J, Cook D. (2013) Draft genome sequence of kabuli chickpea (Cicer arietinum): genetic structure and breeding constraints for crop improvement. [http://www.nature.com/nbt/journal/v31/n3/full/nbt.2491.html Nature Biotechnology 31, 240–246]
# Duran C, Singhania R, Raman H, Batley J, Edwards D. Predicting polymorphic EST-SSRs in silico. (2013) [http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12078/abstract Molecular Ecology Resources 13 (3): 538-45]
# Berkman, P.J., Visendi, P., Lee, H.C., Stiller, J., Manoli, S., Lorenc, M.T., Lai, K., Batley, J., Fleury, D., Šimková, H., Kubaláková, M., Weining, S., Doležel, J. and Edwards, D. (2013) Dispersion and domestication shaped the genome of bread wheat. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12044/full Plant Biotechnology Journal 11 (5): 564-571]
# Kazakoff SH, Imelfort M, Edwards D, Koehorst J, Biswas B, Batley J, Scott PT, Gresshoff PM. (2012) Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0051687 PLOS ONE e51687]
# Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J,Luckett D, Wratten N, Dennis E. (2013) Genetic and physical mapping of flowering time loci in canola (Brassica napus L.) [http://link.springer.com/article/10.1007/s00122-012-1966-8 Theoretical and Applied Genetics 126 (1): 119-132]
# Edwards D, Batley J and Snowdon, R. (2013) Accessing complex crop genomes with next-generation sequencing. [http://link.springer.com/article/10.1007/s00122-012-1964-x Theoretical and Applied Genetics 126 (1): 1-11]
# Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, J. Berkman PJ, Lai K, Batley J and Edwards D. (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. [http://www.mdpi.com/2079-7737/1/2/370 Biology 1(2): 370-38]
# Edwards D, Henry RJ and Edwards KJ. (2012) Advances in DNA sequencing accelerating plant biotechnology. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00724.x/full Plant Biotechnology Journal. 10 (6): 621–622]
# Hayashi S, Reid D, Lorenc M, Stiller J, Edwards D, Gresshoff PM and Ferguson BJ. (2012) Transient Nod-factor dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00729.x/abstract Plant Biotechnology Journal. 8: 995–1010]
# Jiang Q, Yen SH, Stiller J, Edwards D, Scott PT and Gresshoff PM. (2012) Diversity Analysis of the Tree Legume Pongamia pinnata using PISSRs (Pongamia Inter-Simple Sequence Repeats). Journal of Plant Genome Sciences. 1 (3): 54–67
# Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D. (2012) Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00718.x/abstract Plant Biotechnology Journal. 10 (6): 743-749]
# Hayward A, Vighnesh G, Delay G, Samian MR, Manoli SM, Stiller J, McKenzie M, Edwards D and Batley J. (2012) Second Generation Sequencing for Gene Discovery in the Brassicaceae. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00719.x/abstract Plant Biotechnology Journal. 10 (6): 750-759]
# Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, McLanders J, Lorenc M, Manoli S, Stiller J, Raman R, Raman H, Edwards D and Batley J. (2012) Identification and characterisation of candidate Rlm4 blackleg resistance genes in Brassica napus using next generation sequencing. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00716.x/abstract Plant Biotechnology Journal. 10 (6): 709-715]
# Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A. (2012) Bread matters: A national initiative to profile the genetic diversity of Australian wheat. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00717.x/abstract Plant Biotechnology Journal. 10 (6): 703-708]
# Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S. (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. [http://www.amjbot.org/content/99/9/e369.short American Journal of Botany. 99 (9) e369-e371]
# Reid DE, Hayashi S, Lorenc M, Stiller J, Edwards D, Gresshoff PM, Ferguson BJ. (2012) Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00706.x/abstract Plant Biotechnology Journal. 10 (6): 680-689]
#Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D and Batley J. (2012) SNP discovery and applications in Brassica napus. Journal of Plant Biotechnology. 39: 1-12
#Raman R, Taylor B, Marcroft S, Stiller J, Eckermann P, Coombes N, Rehman A, Lindbeck K, Luckett D, Wratten N, Batley J, Edwards D, Wang X, Raman H. Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.) [http://www.springerlink.com/content/a1h7t6648087735w/abstract/ Theoretical and Applied Genetics 125: 405-415]
#Lai K, Lorenc MT and Edwards D. (2012) Genomic databases for crop improvement. [http://www.mdpi.com/2073-4395/2/1/62/ Agronomy 2: 67-73]
#Azam S, Thakur V, Pradeep R, Shah T, Jayashree B, BhanuPrakash A, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JDG and Varshney R. (2012) Coverage based consensus calling (CBCC) of short sequence reads and comparison of CBCC-results for the identification of SNPs in chickpea, a crop species without the reference genome. [http://www.amjbot.org/content/early/2012/01/31/ajb.1100419 American Journal of Botany 99 (2): 186-192]
#Hayward A, McLanders J, Campbell E, Edwards D and Batley J. (2012) Genomic advances will herald new insights into the Brassica:Leptosphaeria maculans pathosystem. [http://onlinelibrary.wiley.com/doi/10.1111/j.1438-8677.2011.00481.x/abstract Plant Biology 14 (1): 1-10]
#Berkman PJ, Lai K, Lorenc MT and Edwards D. Next generation sequencing applications for wheat crop improvement. (2012) [http://www.amjbot.org/content/99/2/365.short American Journal of Botany 99 (2): 365-371]
#Lee H, Lai K, Lorenc MT, Imelfort M, Duran C and Edwards D. (2012) Bioinformatics tools and databases for analysis of next generation sequence data. [http://bfg.oxfordjournals.org/content/early/2011/12/18/bfgp.elr037.abstract Briefings in Functional Genomics 11 (1), 12-24]
#Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J and Edwards D. (2012) WheatGenome.info: An integrated database and portal for wheat genome information. [http://pcp.oxfordjournals.org/content/early/2011/10/18/pcp.pcr141.short Plant and Cell Physiology 53(2): e2(1–7)]
#Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Pilar Hernandez P, and Edwards D. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. [http://www.springerlink.com/content/uk508r17832pkht8/ Theoretical and Applied Genetics 3: 423-432]
#Rosic N, Kaniewska P, Ling E, Edwards D, Dove S, Hoegh-Guldberg O. (2011) Transcriptomics of the Coral-Algal Symbiosis in Response to Environmental Stress. European Journal of Phycology 46, 97
#The Brassica rapa Genome Sequencing Project Consortium. (2011) The genome of the mesopolyploid crop species Brassica rapa. [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html Nature Genetics 43: 1035-1040]
#Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J and Edwards D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract Plant Biotechnology Journal 9 (7): 768-775]
#Mun JH, Kwon SJ, Seol YJ, Kim JA, Jin M, Kim JS, Lim MH, Lee SI, Hong JK, Park TH, Lee SC, Kim BJ, Seo MS, Baek S, Lee MJ, Shin JY, Hahn JH, Hwang YJ, Lim KB, Park JY, Lee J, Yang TJ, Yu HJ, Choi SR, Ramchiary N, Lim YP, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Parkin IAP, Batley J, Edwards D and Park BS. (2010) Sequence and structure of Brassica rapa chromosome A3. [http://genomebiology.com/2010/11/9/R94 Genome Biology 11: R94]
#Koo DH, Hong CP, Batley J, Chung YS, Edwards D, Bang JW, PhD; Hur Y and Lim YP. (2010) Rapid Divergence of Repetitive DNAs in Brassica Relatives. [http://dx.doi.org/10.1016/j.ygeno.2010.12.002 Genomics 97(3): 173-185 ]
#Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman P, Clark T, McKenzie M, Appleby N, Batley J, Basford K, and Edwards D. (2010) Future tools for association mapping in crop plants. [http://rparticle.web-p.cisti.nrc.ca/rparticle/AbstractTemplateServlet?calyLang=eng&journal=gen&volume=53&year=2010&issue=11&msno=g10-057 Genome 53: 1017-1023]
#Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. [http://www.plantmethods.com/content/6/1/19 Plant Methods 6:19]
#Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. [http://bioinformatics.oxfordjournals.org/content/26/2/273.short Bioinformatics 26 (2): 273-274]
#Edwards D and Batley J. (2010) Plant genome sequencing: applications for crop improvement. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00459.x/abstract Plant Biotechnology Journal 8: 2–9]
#Kaur S, Cogan N.O.I, Ye G, Baillie R.C, M. L. Hand M.L, Ling A.E., Mcgearey A.K., Kaur J, Hopkins C.J, Todorovic M, Mountford H, Edwards D, Batley J, Burton W, Salisbury P, Gororo N, Marcroft S, Kearney G, Smith K.F, Forster J.W, Spangenberg G.C. (2009) Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. [http://www.springerlink.com/content/lk759m559hl8quw2/ Theoretical and Applied Genetics 120 (1): 71-83]
#Imelfort M and Edwards D. (2009) De novo sequencing of plant genomes using second-generation technologies. [http://bib.oxfordjournals.org/content/10/6/609.abstract Briefings in Bioinformatics 10: 609-618]
#Batley J and Edwards D. (2009) Genome sequence data: management, storage, and visualization. [http://www.biotechniques.com/multimedia/archive/00044/BTN_A_000113134_O_44655a.pdf Biotechniques 46:333-336]
#Duran C, Appleby N, Vardy M, Imelfort M, Edwards D and Batley J. (2009) Single Nucleotide Polymorphism Discovery in Barley using AutoSNPdb. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00407.x/abstract Plant Biotechnology Journal 7 (4): 326 – 333]
#Imelfort M, Duran C, Batley J and Edwards D. (2009) Discovering genetic polymorphisms in next generation sequencing data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00406.x/abstract Plant Biotechnology Journal 7 (4): 312 – 317]
#Duran C, Appleby N,, Edwards D and Batley J. (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. [http://www.bentham.org/cbio/Samples/cbio%204-1/0003CBIO.pdf Current Bioinformatics 4: 16-27]
#Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J and Edwards D. (2009) AutoSNPdb: An Annotated Single Nucleotide Polymorphism Database for Crop Plants. [http://nar.oxfordjournals.org/content/37/suppl_1/D951.short Nucleic Acids Research 37: 951–953]
#Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ, Barker GC, Hand P, Lydiate DJ, Batley J, Edwards D, Koo DH, Bang JW, Park BS and Lim YP. (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. [http://www.springerlink.com/content/n6h2q013qn105667/ Theoretical and Applied Genetics 115 (6): 777-792]
#Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Batley J, Spangenberg G and Edwards D. (2007) A Comparative Map Viewer Integrating Genetic Maps for Brassica and Arabidopsis. [http://www.biomedcentral.com/1471-2229/7/40 BMC Plant Biology 7: 40]
#Hong CP, Piao ZY, Kang TW, Batley J, Yang TJ, Hur YK, Bhak J, Edwards D and Lim YP. (2007) Genomic distribution of Simple Sequence Repeats in Brassica rapa. [http://molcells.inforang.com/article_pdf/Ksmcb/23/Ksmcb23-3-10.pdf Molecules and Cells 23 (3): 349-356]
#Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Kaur S, Li X, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Walkiewicz M, Spangenberg GC and Edwards D. (2007) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Brassica napus expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01738.x/abstract Molecular Ecology Notes 7: 886–889.]
#Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X, Lim GAC, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Spangenberg GC, Edwards D and Batley J. (2007) Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01681.x/abstract Molecular Ecology Notes 7: 697-700]
#Ling AE, Kaur J, Burgess B, Hand M, Hopkins CJ, Li X, Love CG, Vardy M, Walkiwiecz M, Spangenberg G, Edwards D and Batley J. (2007) Characterisation of Simple Sequence Repeat markers derived in silico from Brassica rapa Bacterial Artificial Chromosome sequences and their application in Brassica napus. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01578.x/abstract Molecular Ecology Notes 7: 273-277]
#Erwin T, Jewell E, Love C, Lim G, Li X, Chapman R, Batley J, Stajich J, Mongin E, Stupka E, Ross B, Spangenberg G and Edwards D. (2007) BASC: an integrated bioinformatics system for Brassica research. [http://nar.oxfordjournals.org/content/35/suppl_1/D870.full Nucleic Acids Research 35: D870–D873]
#Donnison IS, Gay AP, Thomas H, Edwards KJ, Edwards D, James CL, Thomas AM, Ougham HJ. (2007) Modification of nitrogen remobilisation, grain fill and leaf senescence in maize (Zea mays L.) by transposon insertional mutagenesis. [http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2006.01928.x/abstract New Phytologist 173: 481-494]
#Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg G, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01488.x/abstract Molecular Ecology Notes 6: 1191-1194]
#Hong CP, Plaha P, Koo DH, Yang TJ, Choi SR, Lee YK, Uhm T, Bang JW, Edwards D, Bancroft I, Park BS, Lee J, and Lim YP. (2006) A Survey of the Brassica rapa Genome through BAC-End Sequence Analysis, and Comparative Analysis with Arabidopsis thaliana. [http://molcells.inforang.com/article_pdf/Ksmcb/22/Ksmcb22-3-8.pdf Molecules and Cells 22: 300-307]
#Philippar K, Büchsenschütz K, Edwards D, Löffler J, Lüthen H, Kranz E, Edwards KJ and Hedrich R. (2006) The auxin-induced K+ channel gene Zmk1 in maize functions in coleoptile growth and is required for embryo development. [http://www.springerlink.com/content/aj37695670l2h21g/ Plant Molecular Biology 61: 757-768]
#Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GAC, Li X, Batley J, Spangenberg GC and Edwards D. (2006) SSR Primer and SSR Taxonomy Tree: Biome SSR discovery. [http://nar.oxfordjournals.org/content/34/suppl_2/W656.abstract Nucleic Acids Research 34: W656–W659]
#Love C, Logan E, Erwin T, Spangenberg G and Edwards D. (2006) Analysis of the Brassica A and C Genomes and Comparison with the Genome of Arabidopsis thaliana. [http://www.actahort.org/books/706/706_9.htm Acta Horticulturae 706: 99-104]
#Love C, Logan E, Erwin T, Kaur J, Lim GAC, Hopkins C, Batley J, James N, May S, Spangenberg G and Edwards D. (2006) Integrating and interrogating diverse Brassica data within an EnsEMBL structured database. [http://www.actahort.org/books/706/706_7.htm Acta Horticulturae 706: 77-82]
#Hopkins C, Mogg R, Gororo N, Salisbury PA, Burton WA, Love C, Spangenberg GC, Edwards D and Batley J. (2006) An assessment of genetic diversity within and between Brassica napus and Brassica juncea lines from international germplasm collections. [http://www.actahort.org/books/706/706_11.htm Acta Horticulturae 706: 115-119]
#Keniry A, Hopkins CJ, Jewell E, Morrison B, Spangenberg GS, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Fragaria x ananassa expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2005.01215.x/abstract Molecular Ecology Notes 6: 319-322]
#Felitti S, Shields K, Ramsperger M, Tian P, Sawbridge T, Webster T, Logan E, Erwin T, Forster J, Edwards D and Spangenberg G. (2006) Transcriptome analysis of Neotyphodium and Epichloë grass endophytes. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WFV-4JJ2BVB-1&_user=10&_coverDate=07%2F31%2F2006&_rdoc=2&_fmt=high&_orig=browse&_origin=browse&_zone=rslt_list_item&_srch=doc-info%28%23toc%236804%232006%23999569992%23623142%23FLA%23display%23Volume%29&_cdi=6804&_sort=d&_docanchor=&_ct=6&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=946ca03d60d162de79d2b5c3c8079bdc&searchtype=a Fungal Genetics and Biology 43: 465-475]
#Sexton A, Cozijnsen A, Keniry A, Logan E, Love C, Batley J, Edwards D and Howlett B. (2006) Transcription profile of genes from three developmental stages of the plant pathogen Sclerotinia sclerotiorum. [http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2006.00212.x/abstract FEMS Microbiology Letters 258: 150-160]
#Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker GLA, Spangenberg GC and Edwards D. (2005) SNPServer: A Realtime SNP Discovery tool. [http://nar.oxfordjournals.org/content/33/suppl_1/D656.abstract Nucleic Acids Research 33: D656-D659]
#Mortimer J, Batley J, Love C, Logan E and Edwards D. (2005) Simple Sequence Repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. Journal of Plant Biotechnology 7: 17-25
#Love C, Robinson A, Lim G, Hopkins C, Batley J, Barker G, Spangenberg G and Edwards D. (2005) Brassica ASTRA: An Integrated Database for Brassica Genomic Research. [http://nar.oxfordjournals.org/content/33/suppl_2/W493.abstract Nucleic Acids Research 33: W493-W495]
#Robinson AJ, Love CG, Batley J, Barker G and Edwards D. (2004) Simple Sequence Repeat Marker Loci Discovery using SSR Primer. [http://bioinformatics.oxfordjournals.org/content/20/9/1475.abstract Bioinformatics 20: 1475-1476]
#Wilson ID, Barker GLA, Beswick RW, Shepherd SK, Lu C, Coghill JA, Edwards D, Owen P, Lyons R, Parker JS, Lenton JR, Holdsworth MJ, Shewry PR and Edwards KJ. (2004) A transcriptomics resource for wheat functional genomics. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2004.00096.x/abstract Plant Biotechnology Journal 2: 495-506]
#Edwards D and Batley J. (2004) Plant Bioinformatics: From Genome to Phenome. [http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2804%2900076-9 Trends in Biotechnology 22: 232-237]
#Love CG, Batley J, Lim G, Robinson AJ, Savage D, Singh D, Spangenberg GC, and Edwards D. (2004) New computational tools for Brassica genome research. [http://www.hindawi.com/journals/cfg/2004/160354.abs.html Comparative and Functional Genomics 5: 276-280]
#Love CG, Batley J and Edwards D. (2003) Applied Computational Tools for Crop Genome Research. Journal of Plant Biotechnology 5: 193-195
#Batley J, Barker G, O'Sullivan H, Edwards KJ and Edwards D. (2003) Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data. [http://www.plantphysiol.org/cgi/content/abstract/132/1/84 Plant Physiology 132: 84-91]
#Batley J, Mogg R, Edwards D, O’Sullivan H and Edwards KJ. (2003) A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. [http://www.springerlink.com/content/q142t023674pl328/ Molecular Breeding 11: 111-120]
#Barker G, Batley J, O'Sullivan H, Edwards KJ and Edwards D. (2003) Redundancy Based Detection of Sequence Polymorphisms in Expressed Sequence Tag Data using AutoSNP. [http://bioinformatics.oxfordjournals.org/content/19/3/421.abstract Bioinformatics 19: 421-422]
#Edwards D, Coghill J, Batley J, Holdsworth M and Edwards KJ. (2002) Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. [http://www.biotechniques.com/multimedia/archive/00011/02325rr04_11101a.pdf Biotechniques 32: 1090-1097]
#Edwards D, Stevenson D, Forsyth A, Hegarty M, Batley J, Holdsworth M and Edwards KJ. (2002) Identification of transposon-tagged maize genes displaying homology to arrayed cDNA clones using Mutator insertion display. Genome letters 1: 48-55
#Mogg R, Batley J, Hanley S, Edwards D, O’Sullivan H and Edwards KJ. (2002) Characterisation of the flanking regions of Zea Mays microsatellites reveals a large number of useful sequence polymorphisms. [http://www.ingentaconnect.com/content/asp/glet/2002/00000001/00000001/art00006 Theoretical and Applied Genetics 105: 532-543]
#O’ Sullivan D, Edwards D, Edwards KJ. Maize Genomics. [http://www.cabi.org/AgBioTechNet/ AgBiotechNet (2000) 2]
#Hanley S, Edwards D, Stevenson D, Haines S, Hegarty M, Schuch W, Edwards KJ. Identification of transposon tagged genes by the random sequencing of Mutator-tagged DNA fragments from Zea mays. [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313x.2000.00830.x/abstract Plant Journal (2000) 23 (4):557-566]
#Edwards D, Murray JAH, Smith AG. (1998) Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. [http://www.plantphysiol.org/cgi/content/abstract/117/3/1015 Plant Physiology 117 (3): 1015-1022]
#Edwards KJ, Thompson H, Edwards D, DeSaizeu A, Sparks C, Thompson JA, Greenland AJ, Eyers M and Schuch W. (1992) Construction and Characterisation of a Yeast Artificial Chromosome Library Containing 3 Haploid Maize Genome Equivalents. [http://www.springerlink.com/content/t44p88j375vr2522/ Plant Molecular Biology 19: (2) 299-308]

===CONFERENCE PAPERS: ===

#Batley J, Edwards D, Spangenberg G, Burgess BR, Burton W, Erwin T, Hand M, Hopkins C, Howlett B, Jewell E, Kaur J, Keniry A, Li X, Love CG, Marcroft S, Mountford H, Salisbury P and Walkiewicz M. (2005) Development of molecular markers for implementation in Australian Brassica Improvement. In: 14th Australian Research Assembly on Brassicas. of a conference, Port Lincoln 2005. Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 65-69
#Edwards D, Batley J, Spangenberg G, Burgess BR, Erwin T, Hand M, Hopkins C, Jewell E, Keniry A, Li X, Love CG, Mountford H and Walkiewicz M. (2005) The Multinational Brassica Genome Project. In: 14th Australian Research Assembly on Brassicas. Port Lincoln 2005, Proceedings Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 70-72
#Batley J and Edwards D. (2004) Molecular Tools for Plant Biology. In: Proceedings of Vision for Practical Use of Biotechnology. The Korean Society of Plant Biotechnology. Korea pp 19-24
#Batley J, Vecchies A, Mogg R, Bond J, Cogan N, Hopkins C, Gororo N, Marcroft S, Forster J, Spangenberg G and Edwards D. (2003) A study of genetic diversity among Brassica napus and Brassica juncea germplasm collections using Simple Sequence Repeat (SSR) markers. Thirteen Biennial Australian Research Assembly on Brassicas. Proceedings of a conference, Tamworth, New South Wales. pp 84-86
#Edwards D. (2003) Applied Computational Tools for Crop Genome Research. In: Proceedings of Development of Core Biotechnology for Next Generation. The Korean Society of Plant Biotechnology. Korea 33-34

===OTHER PUBLICATIONS:===

#Li X, Jewell E, Erwin TA, Lim GAC, Love CG, Batley J, Spangenberg GC and Edwards D. (2007) Brassica Bacterial Artificial Chromosome (BAC) and Gene Annotator. Cruciferae Newsletter 27
#Ling A, Hopkins C, Burton W, Hand M, Kaur S, McGearey A, Kaur J, Love C, Salisbury P, Todorovic M, Vardy M, Walkiewicz M, Spangenberg G, Edwards D and Batley J. (2007) Development of Molecular Markers for Implementation in the Australian National Brassica Improvement Program. Cruciferae Newsletter 27
#Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Spangenberg GC and Edwards D. (2007) CMap: A Comparative Mapping Tool for Brassica. Cruciferae Newsletter 27
#Erwin TA, Jewell E, Love CG, Xi Li, Lim GAC, Chapman R, Spangenberg G, and Edwards D. (2007) Brassica BASC: An Integrated Bioinformatics System for Brassica Research. Cruciferae Newsletter 27
#Kaur J, Webster T, Chapman R, Batley J, Salisbury P, Spangenberg GC and Edwards D. (2007) Gene Expression Studies in Canola in Response to Blackleg (Leptosphaeria maculans) Infection. Cruciferae Newsletter 27
#Savage D, Logan E, Erwin T, Robinson A, Love CG, Barker G, Batley J and Edwards D. (2007) Real-time mining of maize genome data for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular genetic markers. Maize Newsletter 79
#Swarbreck D, O’Sullivan D, Ripoll PJ, Edwards D, Edwards KJ and Theodoulou F. (2002) Unravelling the MRP family in monocots. Comparative Biochemistry and Physiology A: Molecular & Integrative Physiology 32: S1

Publications DE

2015-08-11T04:20:11Z

Appbio: /* JOURNAL ARTICLES: */

==Publications - David Edwards==

===BOOKS:===

#[http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA). (2012)
#[http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA). (2009)
#[http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA). (2007)

===BOOK CHAPTERS:===

#Visendi P, Batley J and Edwards D. Next Generation Sequencing and Germplasm Resources. In Advances in Genomics of Plant Genetic resources. Volume 1. Genomics platforms, crop domestication and allele mining. Ed. Tuberosa R. Springer (USA) (accepted August 2012)
#Edwards D. (2013) Bioinformatics tools to assist breeding for climate change. In Genomics and breeding for climate resilient crops. Ed, Kole C. Springer (USA), pp 391-414
#Edwards D and Gupta PK. (2013) Sequence based DNA markers and genotyping for cereal genomics and breeding. In Cereal Genomics II. Eds. Gupta PK and Varshney, RK. Springer (USA) pp 57-76
#Edwards D and Wang X. (2012) Genome Sequencing Initiatives. In [http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 152-157
#Lorenc M, Boskovic Z, Stiller J, Duran C and Edwards D. (2012) Role of Bioinformatics as a Tool for Oilseed Brassica Species. In [http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 194-205
#Edwards D. (2011) Wheat Bioinformatics. In: [http://www.cplbookshop.com/contents/C63.htm The World Wheat Book II.] Eds. Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) pp 851-875
#Duran C, Boskovic Z, Batley J and Edwards D. (2011) Brassica Bioinformatics. In [http://www.scipub.net/agriculture/genetics-genomics-and-breeding-of-vegetable-brassicas.html Vegetable Brassicas] Ed. Sadowski J. Science Publishers, Inc., New Hampshire pp 406-418
#Edwards D, Hansen D and Stajich J. (2009) DNA Sequence Databases. In [http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 1-11
#Duran C, Edwards D and Batley J. (2009) Molecular Marker Discovery and Genetic map Visualisation. In [http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 165-189
#Imelfort M, Batley J, Grimmond S and Edwards D. (2009) Genome sequencing approaches and successes. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 345-358
#Batley J and Edwards D. (2009) Mining for Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: [http://www.springer.com/life+sciences/bioinformatics/book/978-1-58829-910-9 Bioinformatics for DNA Sequence Analysis.] Ed. Posada D. Methods in Molecular Biology, Humana Press (USA), pp 303-322
#Appleby N, Edwards D and Batley J. (2009) New technologies for ultra-high throughput genotyping in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press, (USA), pp 19-40
#Duran C, Edwards D and Batley J. (2009) Genetic maps and the use of synteny. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 41-56
#Edwards D and Batley J. (2008) Bioinformatics: Fundamentals and Applications in Plant Genetics, Mapping and Breeding. In: [http://aob.oxfordjournals.org/content/102/5/879.full Principles and Practices of Plant Genomics.] Eds. Kole C and Abbott AG. Science Publishers, Inc., (USA), pp 269-302
#Edwards D. (2007) Bioinformatics and plant genomics for staple crops improvement. In: [http://au.wiley.com/WileyCDA/WileyTitle/productCd-0813818354.html Breeding Major Food Staples.] Eds. Kang MS and Priyadarshan PM. Blackwell, pp 93-106
#Batley J, Jewell E and Edwards D. (2007) Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA), pp. 473-494
#Love CG and Edwards D. (2007) Accessing integrated Brassica genetic and genomic data using the BASC server. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA) (2007), pp. 229-244
#Edwards D, Salisbury PA, Burton WA, Hopkins CJ and Batley J. (2007) Indian Mustard, in [http://www.springer.com/series/7367 Genome Mapping and Molecular Breeding in Plants, Vol. 2.] Ed. Kole C. Springer NY, pp 179-210
#Edwards D, Forster JW, Chagné D and Batley J. (2007) What are SNPs? In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 41-52.
#Edwards D, Batley J, Cogan NOI, Forster JW and Chagné D. 2007. Single Nucleotide Polymorphism Discovery. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 53-76.
#Chagné D, Batley J, Edwards D, and Forster JW. (2007) Single Nucleotide Polymorphisms genotyping in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 77-94.
#Batley J and Edwards D. (2007) SNP applications in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 95-102.
#Spangenberg GC, Forster JW, Edwards D, John U, Mouradov A, Emmerling M, Batley J, Felitti S, Cogan NOI, Smith KF and Dobrowolski M. (2005) Future Directions in the Molecular Breeding of Forage and Turf. In: [http://www.wageningenacademic.com/molecular Molecular Breeding for Genetic Improvement of Forage Crops and Turf.] Ed. Humphreys MO. Wageningen Academic Publishers, pp 83-97.
#Spangenberg GC, Felitti SA, Shields K, Ramsperger M, Tian P, Ong EK, Singh D, Logan E and Edwards D. (2005) Gene Discovery and Microarray-Based Transcriptome Analysis of the Grass-Endophyte Association. In: [http://onlinelibrary.wiley.com/book/10.1002/9780470384916 Neotyphodium in Cool Season Grasses.] Eds. Roberts CA, West CP and Spiers DE. Blackwell, pp 103-140

===JOURNAL ARTICLES:===

# Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke L, Dempewolf H, De Pace C, Edwards D, Gepts P , Greenland A, Hall A, Henry R, Hori K, Howe G, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen H, Ogbonnaya F, Ortiz R, Paterson A, Tuberosa R, Valliyodan B, Varshney R, Yano M. (2015) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnology Journal (accepted August 2015)
# Gou L, Hattori J, Fedak G, Balcerzak M, Klassen D, Sharpe A, Visendi P, Edwards D, Tinker N, Wei Y, Chen G and Ouellet T. (2015) Development and validation of Thinopyrum elongatum expressed molecular markers specific for the long arm of chromosome 7E. Crop Science (accepted July 2015)
# Cai G, Yang Q, Yi B, Fan C, Zhang C, Edwards D, Batley J and Zhou Y. (2015) A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics 16, 409
# Pang W, Li X, Choi SR, Nguyen VD, Dhandapani V, Kim YY, Ramchiary N, Kim JG, Edwards D, Batley J, Na J, Kim HR, Lim YP. (2015) Mapping QTLs of resistance to head splitting in cabbage (Brassica oleracea L.var. capitata L). Molecular Breeding 35:126
# Patel DA, Zander M, Van de Wouw AP, Mason AS, Edwards D, Batley J. (2015) Population Diversity of Leptosphaeria maculans in Australia. International Journal of Biology 7 (3): 18-36
# Mohd-Yusoff NF, Ruperao P, Tomoyoshi NE, Edwards D, Gresshoff PM, Biswas B and Batley J. (2015) Scanning ethyl methanesulphonate effects on the whole genome of Lotus japonicus using second generation sequencing analysis. G3. 5 (4): 559-67
# Bayer PE, Ruperao P, Mason AS, Stiller J, Chan CKK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J, Edwards D. (2015) High resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 128 (6): 1039-1047.
# Mason M, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J. (2015) High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources (Accepted January 2015).
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan CKK, Sablok G, Ralph PJ, Edwards D. (2015) Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany. 66 (5):1489-98
# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13 (1):97-104.
# Rosic N, Kaniewska P, Chan K, Ling E, Edwards D, Dove D and Hoegh-Guldberg O. (2014) Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 15:1052.
# Shin SC, Ahn DH, Kim SJ, Pyo CW, Lee H, Kim MK, Lee J, Lee JE, H. Detrich III HW, Postlethwait JH, Edwards D, Lee SG, Lee JH, Park H. The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment. (2014) Genome Biology 15:468.
# Chalhoub B., Denoeud F., Liu S., Parkin I.A.P., Tang H., Wang X., Chiquet J., Belcram H., Tong C., Samans B., Corréa M., Da Silva C., Just J., Falentin C., Koh C.S., Le Clainche I., Bernard M., Bento P., Noel B., Labadie K., Alberti A., Charles M., Arnaud D., Guo H., Daviaud C., Alamery S., Jabbari K., Zhao M., Edger P.P., Chelaifa H., Tack D., Lassalle G., Mestiri I., Schnel N., Le Paslier M.-C., Fan G., Renault V., Bayer P.E., Golicz A.A., Manoli S., Lee T.-H., Thi V.H.D., Chalabi S., Hu Q., Fan C., Tollenaere R., Lu Y., Battail C., Shen J., Sidebottom C.H.D., Wang X., Canaguier A., Chauveau A., Bérard A., Deniot G., Guan M., Liu Z., Sun F., Lim Y.P., Lyons E., Town C.D., Bancroft I., Wang X., Meng J., Ma J., Pires J.C., King G.J., Brunel D., Delourme R., Renard M., Aury J.-M., Adams K.L., Batley J., Snowdon R.J., Tost J., Edwards D., Zhou Y., Hua W., Sharpe A.G., Paterson A.H., Guan C., Wincker P. (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. [http://www.sciencemag.org/content/345/6199/950.full Science 345:950-953.]
# Rosic N, Ling E, Chan K, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O, and Lee H. (2014) Unfolding the secrets of coral-algal symbiosis. The ISME Journal (accepted August 2014)
# International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. [http://www.sciencemag.org/content/345/6194/1251788.abstract Science 345:1251788-1251788]
# Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., Jakobsen K.S., Wulff B.B.H., Steuernagel B., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. [http://www.sciencemag.org/content/345/6194/1250092.abstract Science 345:1250092-1250092]
# Pfeifer M., Kugler K.G., Sandve S.R., Zhan B., Rudi H., Hvidsten T.R., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. [http://www.sciencemag.org/content/345/6194/1250091.abstract Science 345:1250091-1250091]
# Parkin, I., Koh, C., Tang, H., Robinson, S., Kagale, S., Clarke, W., Town, C., Nixon, J., Krishnakumar, V., Bidwell, S., Denoeud, F., Belcram, H., Links, M., Just, J., Clarke, C., Bender, T., Huebert, T., Mason, A., Pires, J., Barker, G., Moore, J., Walley, P., Manoli, S., Batley, J., Edwards, D., Nelson, M., Wang, X., Paterson, A., King, G., Bancroft, I., Chalhoub, B. and Sharpe, A. (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. [http://genomebiology.com/2014/15/6/R77 Genome Biology 15, R77]
# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. [http://www.onlinelibrary.wiley.com/doi/10.1111/pbi.12240/abstract Plant Biotechnology Journal 13 (1), 97-104]
# Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M, Kumar P, Parkin I, Batley J, Luckett D, and Wratten N. (2014) Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101673 PLOS ONE. 9(7): e101673]
# Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, Zhao M, Ma J, Yu J, SH, Wang X, Wang J, Lu K, Fan Z, Bancroft I, Yang TJ, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee TH, Wang J, Jin H, Li Z, Li X, Zhang J, L Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. [http://www.nature.com/ncomms/2014/140523/ncomms4930/full/ncomms4930.html Nature Communications. 5. DOI: 10.1038/ncomms4930]
# Raman H, Dalton-Morgan J, Diffey S, Raman R, Alamery S, Edwards D and Batley, J. (2014) High-density SNP markers based map construction and genome-wide linkage analysis in Brassica napus. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12186/abstract Plant Biotechnology Journal. 12:851-860]
# Ruperao P, Chan KCK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J, Chitikineni A, Visendi P, Gaur PM, Millán T, Singh KB, Taran B, Wang J, Batley J, Doležel J, Varshney RK and Edwards D. (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12182/abstract Plant Biotechnology Journal. 12:778-786]
# Visendi P, Batley J, Edwards D. (2013) Next generation characterisation of cereal genomes for marker discovery. Biology 2: 1357-1377 [http://www.mdpi.com/2079-7737/2/4/1357/pdf Biology 2: 1357-1377]
# Golicz AA, Bayer PE, Martinez PA, Lai K, Lorenc MT, Alamery S, Hayward A, Tollenaere R, Long Y, Meng J, Batley J, Edwards D. (2013) Characterising diversity in the Brassica genomes. [http://www.actahort.org/books/1005/ Acta Horticulturae. 1005: 33-48]
# Deng P, Nie X, Wang L, Cui L, Liu P, Tong W, Biradar SS, Edwards D, Berkman P, Šimková H, Doležel J, Luo M, You F, Batley J, Fleury D, Appels R, Weining S. (2013) Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes. [http://link.springer.com/article/10.1007%2Fs11105-013-0669-x Plant Molecular Biology Reporter. 1-14]
# Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang WJ, Liang X , Kahl G, Edwards D, Varshney RK. (2013) Functional genomics to study stress responses in crop legumes: Progress and prospects. [http://www.publish.csiro.au/paper/FP13191.htm Functional Plant Biology. 40(12) 1221-1233]
# Zander M, Patel DA, Van de Wouw A, Lai K, Lorenc MY, Campbell E, Hayward A, Edwards D, Raman H and Batley J. (2013) Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. [http://link.springer.com/article/10.1007%2Fs10142-013-0324-5 Functional and Integrative Genomics. 13: 295–308]
# Raman H, Raman R, Kilian A, Detering F, Long Y, Edwards D, Parkin IAP, Sharpe AG, Nelson MN, Larkan N, Zou J, Meng J, Aslam MN, Batley J, Cowling WA, Lydiate D. (2013) A consensus map of rapeseed (Brassica napus L) based on diversity array technology markers: Applications in genetic dissection of qualitative and quantitative traits. [http://www.biomedcentral.com/1471-2164/14/277 BMC Genomics 14: 277]
# Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Tar'an B, Millan T, Zhang X, Rosen B, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Thudi M, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, SinghKB, Datta SK, Jackson SA, Wang J, Cook D. (2013) Draft genome sequence of kabuli chickpea (Cicer arietinum): genetic structure and breeding constraints for crop improvement. [http://www.nature.com/nbt/journal/v31/n3/full/nbt.2491.html Nature Biotechnology 31, 240–246]
# Duran C, Singhania R, Raman H, Batley J, Edwards D. Predicting polymorphic EST-SSRs in silico. (2013) [http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12078/abstract Molecular Ecology Resources 13 (3): 538-45]
# Berkman, P.J., Visendi, P., Lee, H.C., Stiller, J., Manoli, S., Lorenc, M.T., Lai, K., Batley, J., Fleury, D., Šimková, H., Kubaláková, M., Weining, S., Doležel, J. and Edwards, D. (2013) Dispersion and domestication shaped the genome of bread wheat. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12044/full Plant Biotechnology Journal 11 (5): 564-571]
# Kazakoff SH, Imelfort M, Edwards D, Koehorst J, Biswas B, Batley J, Scott PT, Gresshoff PM. (2012) Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0051687 PLOS ONE e51687]
# Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J,Luckett D, Wratten N, Dennis E. (2013) Genetic and physical mapping of flowering time loci in canola (Brassica napus L.) [http://link.springer.com/article/10.1007/s00122-012-1966-8 Theoretical and Applied Genetics 126 (1): 119-132]
# Edwards D, Batley J and Snowdon, R. (2013) Accessing complex crop genomes with next-generation sequencing. [http://link.springer.com/article/10.1007/s00122-012-1964-x Theoretical and Applied Genetics 126 (1): 1-11]
# Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, J. Berkman PJ, Lai K, Batley J and Edwards D. (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. [http://www.mdpi.com/2079-7737/1/2/370 Biology 1(2): 370-38]
# Edwards D, Henry RJ and Edwards KJ. (2012) Advances in DNA sequencing accelerating plant biotechnology. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00724.x/full Plant Biotechnology Journal. 10 (6): 621–622]
# Hayashi S, Reid D, Lorenc M, Stiller J, Edwards D, Gresshoff PM and Ferguson BJ. (2012) Transient Nod-factor dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00729.x/abstract Plant Biotechnology Journal. 8: 995–1010]
# Jiang Q, Yen SH, Stiller J, Edwards D, Scott PT and Gresshoff PM. (2012) Diversity Analysis of the Tree Legume Pongamia pinnata using PISSRs (Pongamia Inter-Simple Sequence Repeats). Journal of Plant Genome Sciences. 1 (3): 54–67
# Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D. (2012) Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00718.x/abstract Plant Biotechnology Journal. 10 (6): 743-749]
# Hayward A, Vighnesh G, Delay G, Samian MR, Manoli SM, Stiller J, McKenzie M, Edwards D and Batley J. (2012) Second Generation Sequencing for Gene Discovery in the Brassicaceae. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00719.x/abstract Plant Biotechnology Journal. 10 (6): 750-759]
# Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, McLanders J, Lorenc M, Manoli S, Stiller J, Raman R, Raman H, Edwards D and Batley J. (2012) Identification and characterisation of candidate Rlm4 blackleg resistance genes in Brassica napus using next generation sequencing. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00716.x/abstract Plant Biotechnology Journal. 10 (6): 709-715]
# Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A. (2012) Bread matters: A national initiative to profile the genetic diversity of Australian wheat. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00717.x/abstract Plant Biotechnology Journal. 10 (6): 703-708]
# Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S. (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. [http://www.amjbot.org/content/99/9/e369.short American Journal of Botany. 99 (9) e369-e371]
# Reid DE, Hayashi S, Lorenc M, Stiller J, Edwards D, Gresshoff PM, Ferguson BJ. (2012) Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00706.x/abstract Plant Biotechnology Journal. 10 (6): 680-689]
#Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D and Batley J. (2012) SNP discovery and applications in Brassica napus. Journal of Plant Biotechnology. 39: 1-12
#Raman R, Taylor B, Marcroft S, Stiller J, Eckermann P, Coombes N, Rehman A, Lindbeck K, Luckett D, Wratten N, Batley J, Edwards D, Wang X, Raman H. Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.) [http://www.springerlink.com/content/a1h7t6648087735w/abstract/ Theoretical and Applied Genetics 125: 405-415]
#Lai K, Lorenc MT and Edwards D. (2012) Genomic databases for crop improvement. [http://www.mdpi.com/2073-4395/2/1/62/ Agronomy 2: 67-73]
#Azam S, Thakur V, Pradeep R, Shah T, Jayashree B, BhanuPrakash A, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JDG and Varshney R. (2012) Coverage based consensus calling (CBCC) of short sequence reads and comparison of CBCC-results for the identification of SNPs in chickpea, a crop species without the reference genome. [http://www.amjbot.org/content/early/2012/01/31/ajb.1100419 American Journal of Botany 99 (2): 186-192]
#Hayward A, McLanders J, Campbell E, Edwards D and Batley J. (2012) Genomic advances will herald new insights into the Brassica:Leptosphaeria maculans pathosystem. [http://onlinelibrary.wiley.com/doi/10.1111/j.1438-8677.2011.00481.x/abstract Plant Biology 14 (1): 1-10]
#Berkman PJ, Lai K, Lorenc MT and Edwards D. Next generation sequencing applications for wheat crop improvement. (2012) [http://www.amjbot.org/content/99/2/365.short American Journal of Botany 99 (2): 365-371]
#Lee H, Lai K, Lorenc MT, Imelfort M, Duran C and Edwards D. (2012) Bioinformatics tools and databases for analysis of next generation sequence data. [http://bfg.oxfordjournals.org/content/early/2011/12/18/bfgp.elr037.abstract Briefings in Functional Genomics 11 (1), 12-24]
#Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J and Edwards D. (2012) WheatGenome.info: An integrated database and portal for wheat genome information. [http://pcp.oxfordjournals.org/content/early/2011/10/18/pcp.pcr141.short Plant and Cell Physiology 53(2): e2(1–7)]
#Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Pilar Hernandez P, and Edwards D. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. [http://www.springerlink.com/content/uk508r17832pkht8/ Theoretical and Applied Genetics 3: 423-432]
#Rosic N, Kaniewska P, Ling E, Edwards D, Dove S, Hoegh-Guldberg O. (2011) Transcriptomics of the Coral-Algal Symbiosis in Response to Environmental Stress. European Journal of Phycology 46, 97
#The Brassica rapa Genome Sequencing Project Consortium. (2011) The genome of the mesopolyploid crop species Brassica rapa. [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html Nature Genetics 43: 1035-1040]
#Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J and Edwards D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract Plant Biotechnology Journal 9 (7): 768-775]
#Mun JH, Kwon SJ, Seol YJ, Kim JA, Jin M, Kim JS, Lim MH, Lee SI, Hong JK, Park TH, Lee SC, Kim BJ, Seo MS, Baek S, Lee MJ, Shin JY, Hahn JH, Hwang YJ, Lim KB, Park JY, Lee J, Yang TJ, Yu HJ, Choi SR, Ramchiary N, Lim YP, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Parkin IAP, Batley J, Edwards D and Park BS. (2010) Sequence and structure of Brassica rapa chromosome A3. [http://genomebiology.com/2010/11/9/R94 Genome Biology 11: R94]
#Koo DH, Hong CP, Batley J, Chung YS, Edwards D, Bang JW, PhD; Hur Y and Lim YP. (2010) Rapid Divergence of Repetitive DNAs in Brassica Relatives. [http://dx.doi.org/10.1016/j.ygeno.2010.12.002 Genomics 97(3): 173-185 ]
#Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman P, Clark T, McKenzie M, Appleby N, Batley J, Basford K, and Edwards D. (2010) Future tools for association mapping in crop plants. [http://rparticle.web-p.cisti.nrc.ca/rparticle/AbstractTemplateServlet?calyLang=eng&journal=gen&volume=53&year=2010&issue=11&msno=g10-057 Genome 53: 1017-1023]
#Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. [http://www.plantmethods.com/content/6/1/19 Plant Methods 6:19]
#Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. [http://bioinformatics.oxfordjournals.org/content/26/2/273.short Bioinformatics 26 (2): 273-274]
#Edwards D and Batley J. (2010) Plant genome sequencing: applications for crop improvement. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00459.x/abstract Plant Biotechnology Journal 8: 2–9]
#Kaur S, Cogan N.O.I, Ye G, Baillie R.C, M. L. Hand M.L, Ling A.E., Mcgearey A.K., Kaur J, Hopkins C.J, Todorovic M, Mountford H, Edwards D, Batley J, Burton W, Salisbury P, Gororo N, Marcroft S, Kearney G, Smith K.F, Forster J.W, Spangenberg G.C. (2009) Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. [http://www.springerlink.com/content/lk759m559hl8quw2/ Theoretical and Applied Genetics 120 (1): 71-83]
#Imelfort M and Edwards D. (2009) De novo sequencing of plant genomes using second-generation technologies. [http://bib.oxfordjournals.org/content/10/6/609.abstract Briefings in Bioinformatics 10: 609-618]
#Batley J and Edwards D. (2009) Genome sequence data: management, storage, and visualization. [http://www.biotechniques.com/multimedia/archive/00044/BTN_A_000113134_O_44655a.pdf Biotechniques 46:333-336]
#Duran C, Appleby N, Vardy M, Imelfort M, Edwards D and Batley J. (2009) Single Nucleotide Polymorphism Discovery in Barley using AutoSNPdb. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00407.x/abstract Plant Biotechnology Journal 7 (4): 326 – 333]
#Imelfort M, Duran C, Batley J and Edwards D. (2009) Discovering genetic polymorphisms in next generation sequencing data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00406.x/abstract Plant Biotechnology Journal 7 (4): 312 – 317]
#Duran C, Appleby N,, Edwards D and Batley J. (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. [http://www.bentham.org/cbio/Samples/cbio%204-1/0003CBIO.pdf Current Bioinformatics 4: 16-27]
#Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J and Edwards D. (2009) AutoSNPdb: An Annotated Single Nucleotide Polymorphism Database for Crop Plants. [http://nar.oxfordjournals.org/content/37/suppl_1/D951.short Nucleic Acids Research 37: 951–953]
#Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ, Barker GC, Hand P, Lydiate DJ, Batley J, Edwards D, Koo DH, Bang JW, Park BS and Lim YP. (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. [http://www.springerlink.com/content/n6h2q013qn105667/ Theoretical and Applied Genetics 115 (6): 777-792]
#Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Batley J, Spangenberg G and Edwards D. (2007) A Comparative Map Viewer Integrating Genetic Maps for Brassica and Arabidopsis. [http://www.biomedcentral.com/1471-2229/7/40 BMC Plant Biology 7: 40]
#Hong CP, Piao ZY, Kang TW, Batley J, Yang TJ, Hur YK, Bhak J, Edwards D and Lim YP. (2007) Genomic distribution of Simple Sequence Repeats in Brassica rapa. [http://molcells.inforang.com/article_pdf/Ksmcb/23/Ksmcb23-3-10.pdf Molecules and Cells 23 (3): 349-356]
#Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Kaur S, Li X, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Walkiewicz M, Spangenberg GC and Edwards D. (2007) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Brassica napus expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01738.x/abstract Molecular Ecology Notes 7: 886–889.]
#Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X, Lim GAC, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Spangenberg GC, Edwards D and Batley J. (2007) Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01681.x/abstract Molecular Ecology Notes 7: 697-700]
#Ling AE, Kaur J, Burgess B, Hand M, Hopkins CJ, Li X, Love CG, Vardy M, Walkiwiecz M, Spangenberg G, Edwards D and Batley J. (2007) Characterisation of Simple Sequence Repeat markers derived in silico from Brassica rapa Bacterial Artificial Chromosome sequences and their application in Brassica napus. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01578.x/abstract Molecular Ecology Notes 7: 273-277]
#Erwin T, Jewell E, Love C, Lim G, Li X, Chapman R, Batley J, Stajich J, Mongin E, Stupka E, Ross B, Spangenberg G and Edwards D. (2007) BASC: an integrated bioinformatics system for Brassica research. [http://nar.oxfordjournals.org/content/35/suppl_1/D870.full Nucleic Acids Research 35: D870–D873]
#Donnison IS, Gay AP, Thomas H, Edwards KJ, Edwards D, James CL, Thomas AM, Ougham HJ. (2007) Modification of nitrogen remobilisation, grain fill and leaf senescence in maize (Zea mays L.) by transposon insertional mutagenesis. [http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2006.01928.x/abstract New Phytologist 173: 481-494]
#Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg G, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01488.x/abstract Molecular Ecology Notes 6: 1191-1194]
#Hong CP, Plaha P, Koo DH, Yang TJ, Choi SR, Lee YK, Uhm T, Bang JW, Edwards D, Bancroft I, Park BS, Lee J, and Lim YP. (2006) A Survey of the Brassica rapa Genome through BAC-End Sequence Analysis, and Comparative Analysis with Arabidopsis thaliana. [http://molcells.inforang.com/article_pdf/Ksmcb/22/Ksmcb22-3-8.pdf Molecules and Cells 22: 300-307]
#Philippar K, Büchsenschütz K, Edwards D, Löffler J, Lüthen H, Kranz E, Edwards KJ and Hedrich R. (2006) The auxin-induced K+ channel gene Zmk1 in maize functions in coleoptile growth and is required for embryo development. [http://www.springerlink.com/content/aj37695670l2h21g/ Plant Molecular Biology 61: 757-768]
#Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GAC, Li X, Batley J, Spangenberg GC and Edwards D. (2006) SSR Primer and SSR Taxonomy Tree: Biome SSR discovery. [http://nar.oxfordjournals.org/content/34/suppl_2/W656.abstract Nucleic Acids Research 34: W656–W659]
#Love C, Logan E, Erwin T, Spangenberg G and Edwards D. (2006) Analysis of the Brassica A and C Genomes and Comparison with the Genome of Arabidopsis thaliana. [http://www.actahort.org/books/706/706_9.htm Acta Horticulturae 706: 99-104]
#Love C, Logan E, Erwin T, Kaur J, Lim GAC, Hopkins C, Batley J, James N, May S, Spangenberg G and Edwards D. (2006) Integrating and interrogating diverse Brassica data within an EnsEMBL structured database. [http://www.actahort.org/books/706/706_7.htm Acta Horticulturae 706: 77-82]
#Hopkins C, Mogg R, Gororo N, Salisbury PA, Burton WA, Love C, Spangenberg GC, Edwards D and Batley J. (2006) An assessment of genetic diversity within and between Brassica napus and Brassica juncea lines from international germplasm collections. [http://www.actahort.org/books/706/706_11.htm Acta Horticulturae 706: 115-119]
#Keniry A, Hopkins CJ, Jewell E, Morrison B, Spangenberg GS, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Fragaria x ananassa expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2005.01215.x/abstract Molecular Ecology Notes 6: 319-322]
#Felitti S, Shields K, Ramsperger M, Tian P, Sawbridge T, Webster T, Logan E, Erwin T, Forster J, Edwards D and Spangenberg G. (2006) Transcriptome analysis of Neotyphodium and Epichloë grass endophytes. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WFV-4JJ2BVB-1&_user=10&_coverDate=07%2F31%2F2006&_rdoc=2&_fmt=high&_orig=browse&_origin=browse&_zone=rslt_list_item&_srch=doc-info%28%23toc%236804%232006%23999569992%23623142%23FLA%23display%23Volume%29&_cdi=6804&_sort=d&_docanchor=&_ct=6&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=946ca03d60d162de79d2b5c3c8079bdc&searchtype=a Fungal Genetics and Biology 43: 465-475]
#Sexton A, Cozijnsen A, Keniry A, Logan E, Love C, Batley J, Edwards D and Howlett B. (2006) Transcription profile of genes from three developmental stages of the plant pathogen Sclerotinia sclerotiorum. [http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2006.00212.x/abstract FEMS Microbiology Letters 258: 150-160]
#Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker GLA, Spangenberg GC and Edwards D. (2005) SNPServer: A Realtime SNP Discovery tool. [http://nar.oxfordjournals.org/content/33/suppl_1/D656.abstract Nucleic Acids Research 33: D656-D659]
#Mortimer J, Batley J, Love C, Logan E and Edwards D. (2005) Simple Sequence Repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. Journal of Plant Biotechnology 7: 17-25
#Love C, Robinson A, Lim G, Hopkins C, Batley J, Barker G, Spangenberg G and Edwards D. (2005) Brassica ASTRA: An Integrated Database for Brassica Genomic Research. [http://nar.oxfordjournals.org/content/33/suppl_2/W493.abstract Nucleic Acids Research 33: W493-W495]
#Robinson AJ, Love CG, Batley J, Barker G and Edwards D. (2004) Simple Sequence Repeat Marker Loci Discovery using SSR Primer. [http://bioinformatics.oxfordjournals.org/content/20/9/1475.abstract Bioinformatics 20: 1475-1476]
#Wilson ID, Barker GLA, Beswick RW, Shepherd SK, Lu C, Coghill JA, Edwards D, Owen P, Lyons R, Parker JS, Lenton JR, Holdsworth MJ, Shewry PR and Edwards KJ. (2004) A transcriptomics resource for wheat functional genomics. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2004.00096.x/abstract Plant Biotechnology Journal 2: 495-506]
#Edwards D and Batley J. (2004) Plant Bioinformatics: From Genome to Phenome. [http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2804%2900076-9 Trends in Biotechnology 22: 232-237]
#Love CG, Batley J, Lim G, Robinson AJ, Savage D, Singh D, Spangenberg GC, and Edwards D. (2004) New computational tools for Brassica genome research. [http://www.hindawi.com/journals/cfg/2004/160354.abs.html Comparative and Functional Genomics 5: 276-280]
#Love CG, Batley J and Edwards D. (2003) Applied Computational Tools for Crop Genome Research. Journal of Plant Biotechnology 5: 193-195
#Batley J, Barker G, O'Sullivan H, Edwards KJ and Edwards D. (2003) Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data. [http://www.plantphysiol.org/cgi/content/abstract/132/1/84 Plant Physiology 132: 84-91]
#Batley J, Mogg R, Edwards D, O’Sullivan H and Edwards KJ. (2003) A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. [http://www.springerlink.com/content/q142t023674pl328/ Molecular Breeding 11: 111-120]
#Barker G, Batley J, O'Sullivan H, Edwards KJ and Edwards D. (2003) Redundancy Based Detection of Sequence Polymorphisms in Expressed Sequence Tag Data using AutoSNP. [http://bioinformatics.oxfordjournals.org/content/19/3/421.abstract Bioinformatics 19: 421-422]
#Edwards D, Coghill J, Batley J, Holdsworth M and Edwards KJ. (2002) Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. [http://www.biotechniques.com/multimedia/archive/00011/02325rr04_11101a.pdf Biotechniques 32: 1090-1097]
#Edwards D, Stevenson D, Forsyth A, Hegarty M, Batley J, Holdsworth M and Edwards KJ. (2002) Identification of transposon-tagged maize genes displaying homology to arrayed cDNA clones using Mutator insertion display. Genome letters 1: 48-55
#Mogg R, Batley J, Hanley S, Edwards D, O’Sullivan H and Edwards KJ. (2002) Characterisation of the flanking regions of Zea Mays microsatellites reveals a large number of useful sequence polymorphisms. [http://www.ingentaconnect.com/content/asp/glet/2002/00000001/00000001/art00006 Theoretical and Applied Genetics 105: 532-543]
#O’ Sullivan D, Edwards D, Edwards KJ. Maize Genomics. [http://www.cabi.org/AgBioTechNet/ AgBiotechNet (2000) 2]
#Hanley S, Edwards D, Stevenson D, Haines S, Hegarty M, Schuch W, Edwards KJ. Identification of transposon tagged genes by the random sequencing of Mutator-tagged DNA fragments from Zea mays. [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313x.2000.00830.x/abstract Plant Journal (2000) 23 (4):557-566]
#Edwards D, Murray JAH, Smith AG. (1998) Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. [http://www.plantphysiol.org/cgi/content/abstract/117/3/1015 Plant Physiology 117 (3): 1015-1022]
#Edwards KJ, Thompson H, Edwards D, DeSaizeu A, Sparks C, Thompson JA, Greenland AJ, Eyers M and Schuch W. (1992) Construction and Characterisation of a Yeast Artificial Chromosome Library Containing 3 Haploid Maize Genome Equivalents. [http://www.springerlink.com/content/t44p88j375vr2522/ Plant Molecular Biology 19: (2) 299-308]

===CONFERENCE PAPERS: ===

#Batley J, Edwards D, Spangenberg G, Burgess BR, Burton W, Erwin T, Hand M, Hopkins C, Howlett B, Jewell E, Kaur J, Keniry A, Li X, Love CG, Marcroft S, Mountford H, Salisbury P and Walkiewicz M. (2005) Development of molecular markers for implementation in Australian Brassica Improvement. In: 14th Australian Research Assembly on Brassicas. of a conference, Port Lincoln 2005. Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 65-69
#Edwards D, Batley J, Spangenberg G, Burgess BR, Erwin T, Hand M, Hopkins C, Jewell E, Keniry A, Li X, Love CG, Mountford H and Walkiewicz M. (2005) The Multinational Brassica Genome Project. In: 14th Australian Research Assembly on Brassicas. Port Lincoln 2005, Proceedings Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 70-72
#Batley J and Edwards D. (2004) Molecular Tools for Plant Biology. In: Proceedings of Vision for Practical Use of Biotechnology. The Korean Society of Plant Biotechnology. Korea pp 19-24
#Batley J, Vecchies A, Mogg R, Bond J, Cogan N, Hopkins C, Gororo N, Marcroft S, Forster J, Spangenberg G and Edwards D. (2003) A study of genetic diversity among Brassica napus and Brassica juncea germplasm collections using Simple Sequence Repeat (SSR) markers. Thirteen Biennial Australian Research Assembly on Brassicas. Proceedings of a conference, Tamworth, New South Wales. pp 84-86
#Edwards D. (2003) Applied Computational Tools for Crop Genome Research. In: Proceedings of Development of Core Biotechnology for Next Generation. The Korean Society of Plant Biotechnology. Korea 33-34

===OTHER PUBLICATIONS:===

#Li X, Jewell E, Erwin TA, Lim GAC, Love CG, Batley J, Spangenberg GC and Edwards D. (2007) Brassica Bacterial Artificial Chromosome (BAC) and Gene Annotator. Cruciferae Newsletter 27
#Ling A, Hopkins C, Burton W, Hand M, Kaur S, McGearey A, Kaur J, Love C, Salisbury P, Todorovic M, Vardy M, Walkiewicz M, Spangenberg G, Edwards D and Batley J. (2007) Development of Molecular Markers for Implementation in the Australian National Brassica Improvement Program. Cruciferae Newsletter 27
#Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Spangenberg GC and Edwards D. (2007) CMap: A Comparative Mapping Tool for Brassica. Cruciferae Newsletter 27
#Erwin TA, Jewell E, Love CG, Xi Li, Lim GAC, Chapman R, Spangenberg G, and Edwards D. (2007) Brassica BASC: An Integrated Bioinformatics System for Brassica Research. Cruciferae Newsletter 27
#Kaur J, Webster T, Chapman R, Batley J, Salisbury P, Spangenberg GC and Edwards D. (2007) Gene Expression Studies in Canola in Response to Blackleg (Leptosphaeria maculans) Infection. Cruciferae Newsletter 27
#Savage D, Logan E, Erwin T, Robinson A, Love CG, Barker G, Batley J and Edwards D. (2007) Real-time mining of maize genome data for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular genetic markers. Maize Newsletter 79
#Swarbreck D, O’Sullivan D, Ripoll PJ, Edwards D, Edwards KJ and Theodoulou F. (2002) Unravelling the MRP family in monocots. Comparative Biochemistry and Physiology A: Molecular & Integrative Physiology 32: S1

Publications DE

2015-08-11T04:18:40Z

Appbio: /* JOURNAL ARTICLES: */

==Publications - David Edwards==

===BOOKS:===

#[http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA). (2012)
#[http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA). (2009)
#[http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA). (2007)

===BOOK CHAPTERS:===

#Visendi P, Batley J and Edwards D. Next Generation Sequencing and Germplasm Resources. In Advances in Genomics of Plant Genetic resources. Volume 1. Genomics platforms, crop domestication and allele mining. Ed. Tuberosa R. Springer (USA) (accepted August 2012)
#Edwards D. (2013) Bioinformatics tools to assist breeding for climate change. In Genomics and breeding for climate resilient crops. Ed, Kole C. Springer (USA), pp 391-414
#Edwards D and Gupta PK. (2013) Sequence based DNA markers and genotyping for cereal genomics and breeding. In Cereal Genomics II. Eds. Gupta PK and Varshney, RK. Springer (USA) pp 57-76
#Edwards D and Wang X. (2012) Genome Sequencing Initiatives. In [http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 152-157
#Lorenc M, Boskovic Z, Stiller J, Duran C and Edwards D. (2012) Role of Bioinformatics as a Tool for Oilseed Brassica Species. In [http://www.scipub.net/botany/genetics-genomics-and-breeding-of-oilseed-brassicas.html Genetics, Genomics and Breeding of Oilseed Brassicas.] Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 194-205
#Edwards D. (2011) Wheat Bioinformatics. In: [http://www.cplbookshop.com/contents/C63.htm The World Wheat Book II.] Eds. Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) pp 851-875
#Duran C, Boskovic Z, Batley J and Edwards D. (2011) Brassica Bioinformatics. In [http://www.scipub.net/agriculture/genetics-genomics-and-breeding-of-vegetable-brassicas.html Vegetable Brassicas] Ed. Sadowski J. Science Publishers, Inc., New Hampshire pp 406-418
#Edwards D, Hansen D and Stajich J. (2009) DNA Sequence Databases. In [http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 1-11
#Duran C, Edwards D and Batley J. (2009) Molecular Marker Discovery and Genetic map Visualisation. In [http://www.springer.com/life+sciences/bioinformatics/book/978-0-387-92737-4 Bioinformatics: Tools and Applications.] Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 165-189
#Imelfort M, Batley J, Grimmond S and Edwards D. (2009) Genome sequencing approaches and successes. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 345-358
#Batley J and Edwards D. (2009) Mining for Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: [http://www.springer.com/life+sciences/bioinformatics/book/978-1-58829-910-9 Bioinformatics for DNA Sequence Analysis.] Ed. Posada D. Methods in Molecular Biology, Humana Press (USA), pp 303-322
#Appleby N, Edwards D and Batley J. (2009) New technologies for ultra-high throughput genotyping in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press, (USA), pp 19-40
#Duran C, Edwards D and Batley J. (2009) Genetic maps and the use of synteny. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-997-0 Plant Genomics.] Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 41-56
#Edwards D and Batley J. (2008) Bioinformatics: Fundamentals and Applications in Plant Genetics, Mapping and Breeding. In: [http://aob.oxfordjournals.org/content/102/5/879.full Principles and Practices of Plant Genomics.] Eds. Kole C and Abbott AG. Science Publishers, Inc., (USA), pp 269-302
#Edwards D. (2007) Bioinformatics and plant genomics for staple crops improvement. In: [http://au.wiley.com/WileyCDA/WileyTitle/productCd-0813818354.html Breeding Major Food Staples.] Eds. Kang MS and Priyadarshan PM. Blackwell, pp 93-106
#Batley J, Jewell E and Edwards D. (2007) Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA), pp. 473-494
#Love CG and Edwards D. (2007) Accessing integrated Brassica genetic and genomic data using the BASC server. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-1-58829-653-5 Plant Bioinformatics.] Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA) (2007), pp. 229-244
#Edwards D, Salisbury PA, Burton WA, Hopkins CJ and Batley J. (2007) Indian Mustard, in [http://www.springer.com/series/7367 Genome Mapping and Molecular Breeding in Plants, Vol. 2.] Ed. Kole C. Springer NY, pp 179-210
#Edwards D, Forster JW, Chagné D and Batley J. (2007) What are SNPs? In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 41-52.
#Edwards D, Batley J, Cogan NOI, Forster JW and Chagné D. 2007. Single Nucleotide Polymorphism Discovery. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 53-76.
#Chagné D, Batley J, Edwards D, and Forster JW. (2007) Single Nucleotide Polymorphisms genotyping in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 77-94.
#Batley J and Edwards D. (2007) SNP applications in plants. In: [http://www.springer.com/life+sciences/plant+sciences/book/978-0-387-35844-4 Association Mapping in Plants] Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 95-102.
#Spangenberg GC, Forster JW, Edwards D, John U, Mouradov A, Emmerling M, Batley J, Felitti S, Cogan NOI, Smith KF and Dobrowolski M. (2005) Future Directions in the Molecular Breeding of Forage and Turf. In: [http://www.wageningenacademic.com/molecular Molecular Breeding for Genetic Improvement of Forage Crops and Turf.] Ed. Humphreys MO. Wageningen Academic Publishers, pp 83-97.
#Spangenberg GC, Felitti SA, Shields K, Ramsperger M, Tian P, Ong EK, Singh D, Logan E and Edwards D. (2005) Gene Discovery and Microarray-Based Transcriptome Analysis of the Grass-Endophyte Association. In: [http://onlinelibrary.wiley.com/book/10.1002/9780470384916 Neotyphodium in Cool Season Grasses.] Eds. Roberts CA, West CP and Spiers DE. Blackwell, pp 103-140

===JOURNAL ARTICLES:===

# Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke L, Dempewolf H, De Pace C, Edwards D, Gepts P , Greenland A, Hall A, Henry R, Hori K, Howe G, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen H, Ogbonnaya F, Ortiz R, Paterson A, Tuberosa R, Valliyodan B, Varshney R, Yano M. (2015) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnology Journal (accepted August 2015)
# Gou L, Hattori J, Fedak G, Balcerzak M, Klassen D, Sharpe A, Visendi P, Edwards D, Tinker N, Wei Y, Chen G and Ouellet T. (2015) Development and validation of Thinopyrum elongatum expressed molecular markers specific for the long arm of chromosome 7E. Crop Science (accepted July 2015)
# Cai G, Yang Q, Yi B, Fan C, Zhang C, Edwards D, Batley J and Zhou Y. (2015) A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics 16, 409
# Pang W, Li X, Choi SR, Nguyen VD, Dhandapani V, Kim YY, Ramchiary N, Kim JG, Edwards D, Batley J, Na J, Kim HR, Lim YP. (2015) Mapping QTLs of resistance to head splitting in cabbage (Brassica oleracea L.var. capitata L). Molecular Breeding 35:126
# Patel DA, Zander M, Van de Wouw AP, Mason AS, Edwards D, Batley J. (2015) Population Diversity of Leptosphaeria maculans in Australia. International Journal of Biology 7 (3): 18-36
# Mohd-Yusoff NF, Ruperao P, Tomoyoshi NE, Edwards D, Gresshoff PM, Biswas B and Batley J. (2015) Scanning ethyl methanesulphonate effects on the whole genome of Lotus japonicus using second generation sequencing analysis. G3. 5 (4): 559-67
# Bayer PE, Ruperao P, Mason AS, Stiller J, Chan CKK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J, Edwards D. (2015) High resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 128 (6): 1039-1047.
# Mason M, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J. (2015) High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources (Accepted January 2015).
# Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan CKK, Sablok G, Ralph PJ, Edwards D. (2015) Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany. 66 (5):1489-98
# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13 (1):97-104.
# Rosic N, Kaniewska P, Chan K, Ling E, Edwards D, Dove D and Hoegh-Guldberg O. (2014) Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 15:1052.
# The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment. (2014) Shin SC, Ahn DH, Kim SJ, Pyo CW, Lee H, Kim MK, Lee J, Lee JE, H. Detrich III HW, Postlethwait JH, Edwards D, Lee SG, Lee JH, Park H. Genome Biology 15:468.
# Chalhoub B., Denoeud F., Liu S., Parkin I.A.P., Tang H., Wang X., Chiquet J., Belcram H., Tong C., Samans B., Corréa M., Da Silva C., Just J., Falentin C., Koh C.S., Le Clainche I., Bernard M., Bento P., Noel B., Labadie K., Alberti A., Charles M., Arnaud D., Guo H., Daviaud C., Alamery S., Jabbari K., Zhao M., Edger P.P., Chelaifa H., Tack D., Lassalle G., Mestiri I., Schnel N., Le Paslier M.-C., Fan G., Renault V., Bayer P.E., Golicz A.A., Manoli S., Lee T.-H., Thi V.H.D., Chalabi S., Hu Q., Fan C., Tollenaere R., Lu Y., Battail C., Shen J., Sidebottom C.H.D., Wang X., Canaguier A., Chauveau A., Bérard A., Deniot G., Guan M., Liu Z., Sun F., Lim Y.P., Lyons E., Town C.D., Bancroft I., Wang X., Meng J., Ma J., Pires J.C., King G.J., Brunel D., Delourme R., Renard M., Aury J.-M., Adams K.L., Batley J., Snowdon R.J., Tost J., Edwards D., Zhou Y., Hua W., Sharpe A.G., Paterson A.H., Guan C., Wincker P. (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. [http://www.sciencemag.org/content/345/6199/950.full Science 345:950-953.]
# Rosic N, Ling E, Chan K, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O, and Lee H. (2014) Unfolding the secrets of coral-algal symbiosis. The ISME Journal (accepted August 2014)
# International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. [http://www.sciencemag.org/content/345/6194/1251788.abstract Science 345:1251788-1251788]
# Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., Jakobsen K.S., Wulff B.B.H., Steuernagel B., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. [http://www.sciencemag.org/content/345/6194/1250092.abstract Science 345:1250092-1250092]
# Pfeifer M., Kugler K.G., Sandve S.R., Zhan B., Rudi H., Hvidsten T.R., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. [http://www.sciencemag.org/content/345/6194/1250091.abstract Science 345:1250091-1250091]
# Parkin, I., Koh, C., Tang, H., Robinson, S., Kagale, S., Clarke, W., Town, C., Nixon, J., Krishnakumar, V., Bidwell, S., Denoeud, F., Belcram, H., Links, M., Just, J., Clarke, C., Bender, T., Huebert, T., Mason, A., Pires, J., Barker, G., Moore, J., Walley, P., Manoli, S., Batley, J., Edwards, D., Nelson, M., Wang, X., Paterson, A., King, G., Bancroft, I., Chalhoub, B. and Sharpe, A. (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. [http://genomebiology.com/2014/15/6/R77 Genome Biology 15, R77]
# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. [http://www.onlinelibrary.wiley.com/doi/10.1111/pbi.12240/abstract Plant Biotechnology Journal 13 (1), 97-104]
# Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M, Kumar P, Parkin I, Batley J, Luckett D, and Wratten N. (2014) Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101673 PLOS ONE. 9(7): e101673]
# Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, Zhao M, Ma J, Yu J, SH, Wang X, Wang J, Lu K, Fan Z, Bancroft I, Yang TJ, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee TH, Wang J, Jin H, Li Z, Li X, Zhang J, L Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. [http://www.nature.com/ncomms/2014/140523/ncomms4930/full/ncomms4930.html Nature Communications. 5. DOI: 10.1038/ncomms4930]
# Raman H, Dalton-Morgan J, Diffey S, Raman R, Alamery S, Edwards D and Batley, J. (2014) High-density SNP markers based map construction and genome-wide linkage analysis in Brassica napus. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12186/abstract Plant Biotechnology Journal. 12:851-860]
# Ruperao P, Chan KCK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J, Chitikineni A, Visendi P, Gaur PM, Millán T, Singh KB, Taran B, Wang J, Batley J, Doležel J, Varshney RK and Edwards D. (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12182/abstract Plant Biotechnology Journal. 12:778-786]
# Visendi P, Batley J, Edwards D. (2013) Next generation characterisation of cereal genomes for marker discovery. Biology 2: 1357-1377 [http://www.mdpi.com/2079-7737/2/4/1357/pdf Biology 2: 1357-1377]
# Golicz AA, Bayer PE, Martinez PA, Lai K, Lorenc MT, Alamery S, Hayward A, Tollenaere R, Long Y, Meng J, Batley J, Edwards D. (2013) Characterising diversity in the Brassica genomes. [http://www.actahort.org/books/1005/ Acta Horticulturae. 1005: 33-48]
# Deng P, Nie X, Wang L, Cui L, Liu P, Tong W, Biradar SS, Edwards D, Berkman P, Šimková H, Doležel J, Luo M, You F, Batley J, Fleury D, Appels R, Weining S. (2013) Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes. [http://link.springer.com/article/10.1007%2Fs11105-013-0669-x Plant Molecular Biology Reporter. 1-14]
# Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang WJ, Liang X , Kahl G, Edwards D, Varshney RK. (2013) Functional genomics to study stress responses in crop legumes: Progress and prospects. [http://www.publish.csiro.au/paper/FP13191.htm Functional Plant Biology. 40(12) 1221-1233]
# Zander M, Patel DA, Van de Wouw A, Lai K, Lorenc MY, Campbell E, Hayward A, Edwards D, Raman H and Batley J. (2013) Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. [http://link.springer.com/article/10.1007%2Fs10142-013-0324-5 Functional and Integrative Genomics. 13: 295–308]
# Raman H, Raman R, Kilian A, Detering F, Long Y, Edwards D, Parkin IAP, Sharpe AG, Nelson MN, Larkan N, Zou J, Meng J, Aslam MN, Batley J, Cowling WA, Lydiate D. (2013) A consensus map of rapeseed (Brassica napus L) based on diversity array technology markers: Applications in genetic dissection of qualitative and quantitative traits. [http://www.biomedcentral.com/1471-2164/14/277 BMC Genomics 14: 277]
# Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Tar'an B, Millan T, Zhang X, Rosen B, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Thudi M, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, SinghKB, Datta SK, Jackson SA, Wang J, Cook D. (2013) Draft genome sequence of kabuli chickpea (Cicer arietinum): genetic structure and breeding constraints for crop improvement. [http://www.nature.com/nbt/journal/v31/n3/full/nbt.2491.html Nature Biotechnology 31, 240–246]
# Duran C, Singhania R, Raman H, Batley J, Edwards D. Predicting polymorphic EST-SSRs in silico. (2013) [http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12078/abstract Molecular Ecology Resources 13 (3): 538-45]
# Berkman, P.J., Visendi, P., Lee, H.C., Stiller, J., Manoli, S., Lorenc, M.T., Lai, K., Batley, J., Fleury, D., Šimková, H., Kubaláková, M., Weining, S., Doležel, J. and Edwards, D. (2013) Dispersion and domestication shaped the genome of bread wheat. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12044/full Plant Biotechnology Journal 11 (5): 564-571]
# Kazakoff SH, Imelfort M, Edwards D, Koehorst J, Biswas B, Batley J, Scott PT, Gresshoff PM. (2012) Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0051687 PLOS ONE e51687]
# Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J,Luckett D, Wratten N, Dennis E. (2013) Genetic and physical mapping of flowering time loci in canola (Brassica napus L.) [http://link.springer.com/article/10.1007/s00122-012-1966-8 Theoretical and Applied Genetics 126 (1): 119-132]
# Edwards D, Batley J and Snowdon, R. (2013) Accessing complex crop genomes with next-generation sequencing. [http://link.springer.com/article/10.1007/s00122-012-1964-x Theoretical and Applied Genetics 126 (1): 1-11]
# Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, J. Berkman PJ, Lai K, Batley J and Edwards D. (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. [http://www.mdpi.com/2079-7737/1/2/370 Biology 1(2): 370-38]
# Edwards D, Henry RJ and Edwards KJ. (2012) Advances in DNA sequencing accelerating plant biotechnology. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00724.x/full Plant Biotechnology Journal. 10 (6): 621–622]
# Hayashi S, Reid D, Lorenc M, Stiller J, Edwards D, Gresshoff PM and Ferguson BJ. (2012) Transient Nod-factor dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00729.x/abstract Plant Biotechnology Journal. 8: 995–1010]
# Jiang Q, Yen SH, Stiller J, Edwards D, Scott PT and Gresshoff PM. (2012) Diversity Analysis of the Tree Legume Pongamia pinnata using PISSRs (Pongamia Inter-Simple Sequence Repeats). Journal of Plant Genome Sciences. 1 (3): 54–67
# Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D. (2012) Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00718.x/abstract Plant Biotechnology Journal. 10 (6): 743-749]
# Hayward A, Vighnesh G, Delay G, Samian MR, Manoli SM, Stiller J, McKenzie M, Edwards D and Batley J. (2012) Second Generation Sequencing for Gene Discovery in the Brassicaceae. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00719.x/abstract Plant Biotechnology Journal. 10 (6): 750-759]
# Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, McLanders J, Lorenc M, Manoli S, Stiller J, Raman R, Raman H, Edwards D and Batley J. (2012) Identification and characterisation of candidate Rlm4 blackleg resistance genes in Brassica napus using next generation sequencing. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00716.x/abstract Plant Biotechnology Journal. 10 (6): 709-715]
# Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A. (2012) Bread matters: A national initiative to profile the genetic diversity of Australian wheat. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00717.x/abstract Plant Biotechnology Journal. 10 (6): 703-708]
# Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S. (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. [http://www.amjbot.org/content/99/9/e369.short American Journal of Botany. 99 (9) e369-e371]
# Reid DE, Hayashi S, Lorenc M, Stiller J, Edwards D, Gresshoff PM, Ferguson BJ. (2012) Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00706.x/abstract Plant Biotechnology Journal. 10 (6): 680-689]
#Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D and Batley J. (2012) SNP discovery and applications in Brassica napus. Journal of Plant Biotechnology. 39: 1-12
#Raman R, Taylor B, Marcroft S, Stiller J, Eckermann P, Coombes N, Rehman A, Lindbeck K, Luckett D, Wratten N, Batley J, Edwards D, Wang X, Raman H. Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.) [http://www.springerlink.com/content/a1h7t6648087735w/abstract/ Theoretical and Applied Genetics 125: 405-415]
#Lai K, Lorenc MT and Edwards D. (2012) Genomic databases for crop improvement. [http://www.mdpi.com/2073-4395/2/1/62/ Agronomy 2: 67-73]
#Azam S, Thakur V, Pradeep R, Shah T, Jayashree B, BhanuPrakash A, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JDG and Varshney R. (2012) Coverage based consensus calling (CBCC) of short sequence reads and comparison of CBCC-results for the identification of SNPs in chickpea, a crop species without the reference genome. [http://www.amjbot.org/content/early/2012/01/31/ajb.1100419 American Journal of Botany 99 (2): 186-192]
#Hayward A, McLanders J, Campbell E, Edwards D and Batley J. (2012) Genomic advances will herald new insights into the Brassica:Leptosphaeria maculans pathosystem. [http://onlinelibrary.wiley.com/doi/10.1111/j.1438-8677.2011.00481.x/abstract Plant Biology 14 (1): 1-10]
#Berkman PJ, Lai K, Lorenc MT and Edwards D. Next generation sequencing applications for wheat crop improvement. (2012) [http://www.amjbot.org/content/99/2/365.short American Journal of Botany 99 (2): 365-371]
#Lee H, Lai K, Lorenc MT, Imelfort M, Duran C and Edwards D. (2012) Bioinformatics tools and databases for analysis of next generation sequence data. [http://bfg.oxfordjournals.org/content/early/2011/12/18/bfgp.elr037.abstract Briefings in Functional Genomics 11 (1), 12-24]
#Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J and Edwards D. (2012) WheatGenome.info: An integrated database and portal for wheat genome information. [http://pcp.oxfordjournals.org/content/early/2011/10/18/pcp.pcr141.short Plant and Cell Physiology 53(2): e2(1–7)]
#Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Pilar Hernandez P, and Edwards D. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. [http://www.springerlink.com/content/uk508r17832pkht8/ Theoretical and Applied Genetics 3: 423-432]
#Rosic N, Kaniewska P, Ling E, Edwards D, Dove S, Hoegh-Guldberg O. (2011) Transcriptomics of the Coral-Algal Symbiosis in Response to Environmental Stress. European Journal of Phycology 46, 97
#The Brassica rapa Genome Sequencing Project Consortium. (2011) The genome of the mesopolyploid crop species Brassica rapa. [http://www.nature.com/ng/journal/v43/n10/full/ng.919.html Nature Genetics 43: 1035-1040]
#Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J and Edwards D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract Plant Biotechnology Journal 9 (7): 768-775]
#Mun JH, Kwon SJ, Seol YJ, Kim JA, Jin M, Kim JS, Lim MH, Lee SI, Hong JK, Park TH, Lee SC, Kim BJ, Seo MS, Baek S, Lee MJ, Shin JY, Hahn JH, Hwang YJ, Lim KB, Park JY, Lee J, Yang TJ, Yu HJ, Choi SR, Ramchiary N, Lim YP, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Parkin IAP, Batley J, Edwards D and Park BS. (2010) Sequence and structure of Brassica rapa chromosome A3. [http://genomebiology.com/2010/11/9/R94 Genome Biology 11: R94]
#Koo DH, Hong CP, Batley J, Chung YS, Edwards D, Bang JW, PhD; Hur Y and Lim YP. (2010) Rapid Divergence of Repetitive DNAs in Brassica Relatives. [http://dx.doi.org/10.1016/j.ygeno.2010.12.002 Genomics 97(3): 173-185 ]
#Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman P, Clark T, McKenzie M, Appleby N, Batley J, Basford K, and Edwards D. (2010) Future tools for association mapping in crop plants. [http://rparticle.web-p.cisti.nrc.ca/rparticle/AbstractTemplateServlet?calyLang=eng&journal=gen&volume=53&year=2010&issue=11&msno=g10-057 Genome 53: 1017-1023]
#Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. [http://www.plantmethods.com/content/6/1/19 Plant Methods 6:19]
#Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. [http://bioinformatics.oxfordjournals.org/content/26/2/273.short Bioinformatics 26 (2): 273-274]
#Edwards D and Batley J. (2010) Plant genome sequencing: applications for crop improvement. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00459.x/abstract Plant Biotechnology Journal 8: 2–9]
#Kaur S, Cogan N.O.I, Ye G, Baillie R.C, M. L. Hand M.L, Ling A.E., Mcgearey A.K., Kaur J, Hopkins C.J, Todorovic M, Mountford H, Edwards D, Batley J, Burton W, Salisbury P, Gororo N, Marcroft S, Kearney G, Smith K.F, Forster J.W, Spangenberg G.C. (2009) Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. [http://www.springerlink.com/content/lk759m559hl8quw2/ Theoretical and Applied Genetics 120 (1): 71-83]
#Imelfort M and Edwards D. (2009) De novo sequencing of plant genomes using second-generation technologies. [http://bib.oxfordjournals.org/content/10/6/609.abstract Briefings in Bioinformatics 10: 609-618]
#Batley J and Edwards D. (2009) Genome sequence data: management, storage, and visualization. [http://www.biotechniques.com/multimedia/archive/00044/BTN_A_000113134_O_44655a.pdf Biotechniques 46:333-336]
#Duran C, Appleby N, Vardy M, Imelfort M, Edwards D and Batley J. (2009) Single Nucleotide Polymorphism Discovery in Barley using AutoSNPdb. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00407.x/abstract Plant Biotechnology Journal 7 (4): 326 – 333]
#Imelfort M, Duran C, Batley J and Edwards D. (2009) Discovering genetic polymorphisms in next generation sequencing data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00406.x/abstract Plant Biotechnology Journal 7 (4): 312 – 317]
#Duran C, Appleby N,, Edwards D and Batley J. (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. [http://www.bentham.org/cbio/Samples/cbio%204-1/0003CBIO.pdf Current Bioinformatics 4: 16-27]
#Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J and Edwards D. (2009) AutoSNPdb: An Annotated Single Nucleotide Polymorphism Database for Crop Plants. [http://nar.oxfordjournals.org/content/37/suppl_1/D951.short Nucleic Acids Research 37: 951–953]
#Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ, Barker GC, Hand P, Lydiate DJ, Batley J, Edwards D, Koo DH, Bang JW, Park BS and Lim YP. (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. [http://www.springerlink.com/content/n6h2q013qn105667/ Theoretical and Applied Genetics 115 (6): 777-792]
#Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Batley J, Spangenberg G and Edwards D. (2007) A Comparative Map Viewer Integrating Genetic Maps for Brassica and Arabidopsis. [http://www.biomedcentral.com/1471-2229/7/40 BMC Plant Biology 7: 40]
#Hong CP, Piao ZY, Kang TW, Batley J, Yang TJ, Hur YK, Bhak J, Edwards D and Lim YP. (2007) Genomic distribution of Simple Sequence Repeats in Brassica rapa. [http://molcells.inforang.com/article_pdf/Ksmcb/23/Ksmcb23-3-10.pdf Molecules and Cells 23 (3): 349-356]
#Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Kaur S, Li X, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Walkiewicz M, Spangenberg GC and Edwards D. (2007) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Brassica napus expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01738.x/abstract Molecular Ecology Notes 7: 886–889.]
#Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X, Lim GAC, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Spangenberg GC, Edwards D and Batley J. (2007) Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2007.01681.x/abstract Molecular Ecology Notes 7: 697-700]
#Ling AE, Kaur J, Burgess B, Hand M, Hopkins CJ, Li X, Love CG, Vardy M, Walkiwiecz M, Spangenberg G, Edwards D and Batley J. (2007) Characterisation of Simple Sequence Repeat markers derived in silico from Brassica rapa Bacterial Artificial Chromosome sequences and their application in Brassica napus. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01578.x/abstract Molecular Ecology Notes 7: 273-277]
#Erwin T, Jewell E, Love C, Lim G, Li X, Chapman R, Batley J, Stajich J, Mongin E, Stupka E, Ross B, Spangenberg G and Edwards D. (2007) BASC: an integrated bioinformatics system for Brassica research. [http://nar.oxfordjournals.org/content/35/suppl_1/D870.full Nucleic Acids Research 35: D870–D873]
#Donnison IS, Gay AP, Thomas H, Edwards KJ, Edwards D, James CL, Thomas AM, Ougham HJ. (2007) Modification of nitrogen remobilisation, grain fill and leaf senescence in maize (Zea mays L.) by transposon insertional mutagenesis. [http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2006.01928.x/abstract New Phytologist 173: 481-494]
#Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg G, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2006.01488.x/abstract Molecular Ecology Notes 6: 1191-1194]
#Hong CP, Plaha P, Koo DH, Yang TJ, Choi SR, Lee YK, Uhm T, Bang JW, Edwards D, Bancroft I, Park BS, Lee J, and Lim YP. (2006) A Survey of the Brassica rapa Genome through BAC-End Sequence Analysis, and Comparative Analysis with Arabidopsis thaliana. [http://molcells.inforang.com/article_pdf/Ksmcb/22/Ksmcb22-3-8.pdf Molecules and Cells 22: 300-307]
#Philippar K, Büchsenschütz K, Edwards D, Löffler J, Lüthen H, Kranz E, Edwards KJ and Hedrich R. (2006) The auxin-induced K+ channel gene Zmk1 in maize functions in coleoptile growth and is required for embryo development. [http://www.springerlink.com/content/aj37695670l2h21g/ Plant Molecular Biology 61: 757-768]
#Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GAC, Li X, Batley J, Spangenberg GC and Edwards D. (2006) SSR Primer and SSR Taxonomy Tree: Biome SSR discovery. [http://nar.oxfordjournals.org/content/34/suppl_2/W656.abstract Nucleic Acids Research 34: W656–W659]
#Love C, Logan E, Erwin T, Spangenberg G and Edwards D. (2006) Analysis of the Brassica A and C Genomes and Comparison with the Genome of Arabidopsis thaliana. [http://www.actahort.org/books/706/706_9.htm Acta Horticulturae 706: 99-104]
#Love C, Logan E, Erwin T, Kaur J, Lim GAC, Hopkins C, Batley J, James N, May S, Spangenberg G and Edwards D. (2006) Integrating and interrogating diverse Brassica data within an EnsEMBL structured database. [http://www.actahort.org/books/706/706_7.htm Acta Horticulturae 706: 77-82]
#Hopkins C, Mogg R, Gororo N, Salisbury PA, Burton WA, Love C, Spangenberg GC, Edwards D and Batley J. (2006) An assessment of genetic diversity within and between Brassica napus and Brassica juncea lines from international germplasm collections. [http://www.actahort.org/books/706/706_11.htm Acta Horticulturae 706: 115-119]
#Keniry A, Hopkins CJ, Jewell E, Morrison B, Spangenberg GS, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Fragaria x ananassa expressed sequences. [http://onlinelibrary.wiley.com/doi/10.1111/j.1471-8286.2005.01215.x/abstract Molecular Ecology Notes 6: 319-322]
#Felitti S, Shields K, Ramsperger M, Tian P, Sawbridge T, Webster T, Logan E, Erwin T, Forster J, Edwards D and Spangenberg G. (2006) Transcriptome analysis of Neotyphodium and Epichloë grass endophytes. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WFV-4JJ2BVB-1&_user=10&_coverDate=07%2F31%2F2006&_rdoc=2&_fmt=high&_orig=browse&_origin=browse&_zone=rslt_list_item&_srch=doc-info%28%23toc%236804%232006%23999569992%23623142%23FLA%23display%23Volume%29&_cdi=6804&_sort=d&_docanchor=&_ct=6&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=946ca03d60d162de79d2b5c3c8079bdc&searchtype=a Fungal Genetics and Biology 43: 465-475]
#Sexton A, Cozijnsen A, Keniry A, Logan E, Love C, Batley J, Edwards D and Howlett B. (2006) Transcription profile of genes from three developmental stages of the plant pathogen Sclerotinia sclerotiorum. [http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2006.00212.x/abstract FEMS Microbiology Letters 258: 150-160]
#Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker GLA, Spangenberg GC and Edwards D. (2005) SNPServer: A Realtime SNP Discovery tool. [http://nar.oxfordjournals.org/content/33/suppl_1/D656.abstract Nucleic Acids Research 33: D656-D659]
#Mortimer J, Batley J, Love C, Logan E and Edwards D. (2005) Simple Sequence Repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. Journal of Plant Biotechnology 7: 17-25
#Love C, Robinson A, Lim G, Hopkins C, Batley J, Barker G, Spangenberg G and Edwards D. (2005) Brassica ASTRA: An Integrated Database for Brassica Genomic Research. [http://nar.oxfordjournals.org/content/33/suppl_2/W493.abstract Nucleic Acids Research 33: W493-W495]
#Robinson AJ, Love CG, Batley J, Barker G and Edwards D. (2004) Simple Sequence Repeat Marker Loci Discovery using SSR Primer. [http://bioinformatics.oxfordjournals.org/content/20/9/1475.abstract Bioinformatics 20: 1475-1476]
#Wilson ID, Barker GLA, Beswick RW, Shepherd SK, Lu C, Coghill JA, Edwards D, Owen P, Lyons R, Parker JS, Lenton JR, Holdsworth MJ, Shewry PR and Edwards KJ. (2004) A transcriptomics resource for wheat functional genomics. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2004.00096.x/abstract Plant Biotechnology Journal 2: 495-506]
#Edwards D and Batley J. (2004) Plant Bioinformatics: From Genome to Phenome. [http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2804%2900076-9 Trends in Biotechnology 22: 232-237]
#Love CG, Batley J, Lim G, Robinson AJ, Savage D, Singh D, Spangenberg GC, and Edwards D. (2004) New computational tools for Brassica genome research. [http://www.hindawi.com/journals/cfg/2004/160354.abs.html Comparative and Functional Genomics 5: 276-280]
#Love CG, Batley J and Edwards D. (2003) Applied Computational Tools for Crop Genome Research. Journal of Plant Biotechnology 5: 193-195
#Batley J, Barker G, O'Sullivan H, Edwards KJ and Edwards D. (2003) Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data. [http://www.plantphysiol.org/cgi/content/abstract/132/1/84 Plant Physiology 132: 84-91]
#Batley J, Mogg R, Edwards D, O’Sullivan H and Edwards KJ. (2003) A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. [http://www.springerlink.com/content/q142t023674pl328/ Molecular Breeding 11: 111-120]
#Barker G, Batley J, O'Sullivan H, Edwards KJ and Edwards D. (2003) Redundancy Based Detection of Sequence Polymorphisms in Expressed Sequence Tag Data using AutoSNP. [http://bioinformatics.oxfordjournals.org/content/19/3/421.abstract Bioinformatics 19: 421-422]
#Edwards D, Coghill J, Batley J, Holdsworth M and Edwards KJ. (2002) Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. [http://www.biotechniques.com/multimedia/archive/00011/02325rr04_11101a.pdf Biotechniques 32: 1090-1097]
#Edwards D, Stevenson D, Forsyth A, Hegarty M, Batley J, Holdsworth M and Edwards KJ. (2002) Identification of transposon-tagged maize genes displaying homology to arrayed cDNA clones using Mutator insertion display. Genome letters 1: 48-55
#Mogg R, Batley J, Hanley S, Edwards D, O’Sullivan H and Edwards KJ. (2002) Characterisation of the flanking regions of Zea Mays microsatellites reveals a large number of useful sequence polymorphisms. [http://www.ingentaconnect.com/content/asp/glet/2002/00000001/00000001/art00006 Theoretical and Applied Genetics 105: 532-543]
#O’ Sullivan D, Edwards D, Edwards KJ. Maize Genomics. [http://www.cabi.org/AgBioTechNet/ AgBiotechNet (2000) 2]
#Hanley S, Edwards D, Stevenson D, Haines S, Hegarty M, Schuch W, Edwards KJ. Identification of transposon tagged genes by the random sequencing of Mutator-tagged DNA fragments from Zea mays. [http://onlinelibrary.wiley.com/doi/10.1046/j.1365-313x.2000.00830.x/abstract Plant Journal (2000) 23 (4):557-566]
#Edwards D, Murray JAH, Smith AG. (1998) Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. [http://www.plantphysiol.org/cgi/content/abstract/117/3/1015 Plant Physiology 117 (3): 1015-1022]
#Edwards KJ, Thompson H, Edwards D, DeSaizeu A, Sparks C, Thompson JA, Greenland AJ, Eyers M and Schuch W. (1992) Construction and Characterisation of a Yeast Artificial Chromosome Library Containing 3 Haploid Maize Genome Equivalents. [http://www.springerlink.com/content/t44p88j375vr2522/ Plant Molecular Biology 19: (2) 299-308]

===CONFERENCE PAPERS: ===

#Batley J, Edwards D, Spangenberg G, Burgess BR, Burton W, Erwin T, Hand M, Hopkins C, Howlett B, Jewell E, Kaur J, Keniry A, Li X, Love CG, Marcroft S, Mountford H, Salisbury P and Walkiewicz M. (2005) Development of molecular markers for implementation in Australian Brassica Improvement. In: 14th Australian Research Assembly on Brassicas. of a conference, Port Lincoln 2005. Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 65-69
#Edwards D, Batley J, Spangenberg G, Burgess BR, Erwin T, Hand M, Hopkins C, Jewell E, Keniry A, Li X, Love CG, Mountford H and Walkiewicz M. (2005) The Multinational Brassica Genome Project. In: 14th Australian Research Assembly on Brassicas. Port Lincoln 2005, Proceedings Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 70-72
#Batley J and Edwards D. (2004) Molecular Tools for Plant Biology. In: Proceedings of Vision for Practical Use of Biotechnology. The Korean Society of Plant Biotechnology. Korea pp 19-24
#Batley J, Vecchies A, Mogg R, Bond J, Cogan N, Hopkins C, Gororo N, Marcroft S, Forster J, Spangenberg G and Edwards D. (2003) A study of genetic diversity among Brassica napus and Brassica juncea germplasm collections using Simple Sequence Repeat (SSR) markers. Thirteen Biennial Australian Research Assembly on Brassicas. Proceedings of a conference, Tamworth, New South Wales. pp 84-86
#Edwards D. (2003) Applied Computational Tools for Crop Genome Research. In: Proceedings of Development of Core Biotechnology for Next Generation. The Korean Society of Plant Biotechnology. Korea 33-34

===OTHER PUBLICATIONS:===

#Li X, Jewell E, Erwin TA, Lim GAC, Love CG, Batley J, Spangenberg GC and Edwards D. (2007) Brassica Bacterial Artificial Chromosome (BAC) and Gene Annotator. Cruciferae Newsletter 27
#Ling A, Hopkins C, Burton W, Hand M, Kaur S, McGearey A, Kaur J, Love C, Salisbury P, Todorovic M, Vardy M, Walkiewicz M, Spangenberg G, Edwards D and Batley J. (2007) Development of Molecular Markers for Implementation in the Australian National Brassica Improvement Program. Cruciferae Newsletter 27
#Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Spangenberg GC and Edwards D. (2007) CMap: A Comparative Mapping Tool for Brassica. Cruciferae Newsletter 27
#Erwin TA, Jewell E, Love CG, Xi Li, Lim GAC, Chapman R, Spangenberg G, and Edwards D. (2007) Brassica BASC: An Integrated Bioinformatics System for Brassica Research. Cruciferae Newsletter 27
#Kaur J, Webster T, Chapman R, Batley J, Salisbury P, Spangenberg GC and Edwards D. (2007) Gene Expression Studies in Canola in Response to Blackleg (Leptosphaeria maculans) Infection. Cruciferae Newsletter 27
#Savage D, Logan E, Erwin T, Robinson A, Love CG, Barker G, Batley J and Edwards D. (2007) Real-time mining of maize genome data for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular genetic markers. Maize Newsletter 79
#Swarbreck D, O’Sullivan D, Ripoll PJ, Edwards D, Edwards KJ and Theodoulou F. (2002) Unravelling the MRP family in monocots. Comparative Biochemistry and Physiology A: Molecular & Integrative Physiology 32: S1

A differential kmer analysis pipeline

2015-07-27T07:44:22Z

Appbio: Created page with "Most next generation transcriptome sequencing projects rely on either mapping sequenced reads to a reference of the assembly of the reads themselves to produce a reference for ma..."

Most next generation transcriptome sequencing projects rely on either mapping sequenced reads to a reference of the assembly of the reads themselves to produce a reference for mapping.

As an alternative approach, we have established a non-mapping method where differential expressed reads are determined by examining kmer abundance. While computationally expensive, this approach has the advantage in that it works well for metagenomic samples and can differentiate between very similar genes from the same or related organisms.

Back to [[Main_Page]]

Main Page

2015-07-27T07:40:57Z

Appbio: /* Transcriptomics */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:[[A differential kmer analysis pipeline]]

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Philipp Bayer]]

[[Agnieszka Golicz]]

[[Bhavna Hurgobin]]

[[Kaitao Lai]]

[[Jenny (Huey Tyng) Lee]]

[[Michal Lorenc]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

[[Pradeep Ruperao]]

Co supervisor:

[[Salman Alamery]]

[[Fabian Inturrsis]]

[[Sarah Loberg]]

[[Dhwani Patel]]

[[Reece Tollenaere]]

[[Manuel Zander]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions availble at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Main Page

2015-07-27T07:40:00Z

Appbio: /* Species of interest include: */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:A differential kmer analysis pipeline

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Philipp Bayer]]

[[Agnieszka Golicz]]

[[Bhavna Hurgobin]]

[[Kaitao Lai]]

[[Jenny (Huey Tyng) Lee]]

[[Michal Lorenc]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

[[Pradeep Ruperao]]

Co supervisor:

[[Salman Alamery]]

[[Fabian Inturrsis]]

[[Sarah Loberg]]

[[Dhwani Patel]]

[[Reece Tollenaere]]

[[Manuel Zander]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions availble at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Other legumes

2015-07-27T07:39:44Z

Appbio:

In addition to chickpea, we contribute to a range of legume genome projects including.

Pea: We are members of an international consortium to sequence the pea genome, led by INRA, France. As part of this endeavour, we are sequencing isolated chromosomes (from Jaroslav Dolezel) and undertaking skimGBS to assess contig assembly quality and placement.

Pigeonpea: We are working with colleagues at ICRISAT to improve the pigeonpea genome assembly using skimGBS

Lentil: We are members of an international consortium to sequence the lentil genome led by Kirstin Bett in Saskatoon, we are sequencing isolated chromosomes (from Jaroslav Dolezel) and undertaking skimGBS to assess contig assembly quality and placement.

Lupin: I am an adviser for a lupin genome project at WA

Clover: I am an adviser and contribute to a clover genome project at WA

Pongamia: I have previously contributed towards the analysis of the Pongamia Pinnata genome in a project led by Peter Gresshoff at the University of Queensland

Back to [[Main_Page]]

Other legumes

2015-07-27T07:39:11Z

Appbio:

Other legumes

2015-07-27T07:38:56Z

Appbio: Created page with "In addition to chickpea, we contribute to a range of legume genome projects including. Pea: We are members of an international consortium to sequence the pea genome, led by INRA..."

In addition to chickpea, we contribute to a range of legume genome projects including.

Pea: We are members of an international consortium to sequence the pea genome, led by INRA, France. As part of this endeavour, we are sequencing isolated chromosomes (from Jaroslav Dolezel) and undertaking skimGBS to assess contig assembly quality and placement.
Pigeonpea: We are working with colleagues at ICRISAT to improve the pigeonpea genome assembly using skimGBS
Lentil: We are members of an international consortium to sequence the lentil genome led by Kirstin Bett in Saskatoon, we are sequencing isolated chromosomes (from Jaroslav Dolezel) and undertaking skimGBS to assess contig assembly quality and placement.
Lupin: I am an adviser for a lupin genome project at WA
Clover: I am an adviser and contribute to a clover genome project at WA
Pongamia: I have previously contributed towards the analysis of the Pongamia Pinnata genome in a project led by Peter Gresshoff at the University of Queensland

Main Page

2015-07-27T07:29:18Z

Appbio: /* Species of interest include: */

==About the group==

The applied bioinformatics group was founded in 2007 at the University of Queensland and moved to the University of Western Australia in January 2015. Since this time, the group has established itself as a leading bioinformatics group in Australia. Our current research activities include the second generation sequencing of complex genomes and metagenomic populations, genome annotation, diversity analysis, trait association and data visualisation.

The group receives funding from the [http://www.uwa.edu.au/ University of Western Australia], the [http://www.arc.gov.au/ Australian Research Council], the [http://www.grdc.com.au/ Grains Research and Development Corporation] and several industry partners to undertake applied bioinformatics research in genetics and genomics.

The group is led by Professor [[David Edwards]] and consists of researchers with diverse backgrounds. We offer training in applied bioinformatics at all levels and [[publications_DE|publish]] widely in the fields of genomics, genetics and bioinformatics. Please contact [mailto:Dave.Edwards@uwa.edu.au David Edwards] for further information.

We are based at the University of Western Australia's Crawley campus in Perth, Australia.

==Publications==

We publish extensively in major journals. A current list of publications can be found here [[publications_DE|'publications']]

==Public research projects==

The applied bioinformatics research group works in several areas associated with second generation sequencing and assembly, genetic and genomic variation analysis and the discovery and application of molecular genetic markers. We work with a range of species, mostly in collaboration with a broad range of national and international research groups.

===[[Genome sequencing]]===

:[http://www.wheatgenome.info Wheat genome sequencing]

:[http://www.brassicagenome.net Brassica genome sequencing]

:[http://www.cicer.info/ Chickpea genome sequencing]

:[[Metagenomics]]

:[[TAGdb]]

===Transcriptomics===

:A differential kmer analysis pipeline

===Molecular marker discovery===

:[[SNP discovery]]

:[[SSR discovery]]

:[[Genetic map visualisation]]

===Genome annotation and visualisation===

:[[Gene and genome annotation]]

===Species of interest include:===

:[[Brassica]]

:[[Chickpea]]

:[[Wheat]]

:[[Pea]]

:[[Other legumes]]

:[[Metagenomics]]

==Group members==

===Group leader===

[[David Edwards]]

===Postdocs===

[[Kenneth Chan]]

Positions available, please contact David Edwards if interested

===Research Assistants===

===PhD students===

Primary supervisor:

[[Philipp Bayer]]

[[Agnieszka Golicz]]

[[Bhavna Hurgobin]]

[[Kaitao Lai]]

[[Jenny (Huey Tyng) Lee]]

[[Michal Lorenc]]

[[Paula Andrea Martinez]]

[[Juan Montenegro]]

[[Paul Visendi Muhindira]]

[[Pradeep Ruperao]]

Co supervisor:

[[Salman Alamery]]

[[Fabian Inturrsis]]

[[Sarah Loberg]]

[[Dhwani Patel]]

[[Reece Tollenaere]]

[[Manuel Zander]]

Positions available, please contact David Edwards if interested

=== Master students ===

Positions available, please contact David Edwards if interested

=== Honours students ===

Positions available, please contact David Edwards if interested

=== Interns ===

Positions available, please contact David Edwards if interested

===[[Alumni]]===

===Positions available===

There are current positions availble at all levels including Postdoc, PhD students and Interns. Candidates should have a good understanding of one or more areas of Computing, Software development, Complex data analysis, Bioinformatics or Genomics. For consideration, please forward your cv and cover letter to Dave.Edwards@uwa.edu.au.

Pea

2015-07-27T07:28:37Z

Appbio: Created page with "We are contributing to an international consortium to sequence the pea genome, led by INRA, France. As part of this endeavour, we are sequencing isolated chromosomes (from Jarosl..."

We are contributing to an international consortium to sequence the pea genome, led by INRA, France. As part of this endeavour, we are sequencing isolated chromosomes (from Jaroslav Dolezel) and undertaking skimGBS to assess contig assembly quality and placement.

Wheat

2015-07-27T07:26:11Z

Appbio:

Wheat is a major human staple used for the production of bread, pasta, noodles, beer and even ethanol biofuel. The hexaploid genome of bread wheat is extremely large, 16,000 million basepairs (Mbp), making it difficult to characterise and confounding many traditional bioinformatics analysis tools. We are developing bioinformatics tools for the analysis of this complex crop genome with the aim of supporting applied crop research and improvement.

Wheat is probably the most important crop in the world, yet it has one of the most challenging genomes. Bread wheat is a hexaploid, with three complete genomes termed A, B and D in the nucleus of each cell. Each of these genomes is almost twice of the human genome and consists of around 5,500 million letters. Several groups around the world are working towards sequencing wheat. Details of individual efforts can be found on the wiki below.

Genome sequencing projects can be generally divided into whole genome shotgun (WGS) methods or BAC by BAC methods.

WGS attempts to sequence the genome in one go, by generating a large amount of sequence data and then assembling this to produce a representation of the string of letters which make up the genome. WGS has the benefit in that it is quick and relatively inexpensive, but it is often confounded by the inability to stitch the individual sequence reads together, resulting in a poor quality assembly. This is particularly problematic for polyploids, where more than one genome is present in each cell, or where there is a substantial quantity of repetitive sequences. Wheat is a polyploid with 3 genomes, each of which is 80% repetitive, making WGS unattractive.

The alternative BAC by BAC approach requires breaking the genome down to relatively small pieces (c. 120 kbp), ordering these as a minimal tiling path, then sequencing each of the BACs in the tiling path. While sequence assembly or repetitive regions remains problematic, this approach offers the potential to produce the best quality finished genome. However, BAC by BAC sequencing of wheat is hugely expensive, time consuming and is still not guaranteed to produce a complete genome due to some regions being underrepresented in BAC libraries.

We have taken an alternative approach, combining their experience of second generation sequencing technology with the ability of the Dolezel group in the Czech Republic to isolate individual chromosome arms. We have demonstrated that we can produce sequence data and assemble all genes for a specific chromosome arm. By including comparative genomic and molecular genetic marker data, we can produce an assembled sequence representing all known genes, including gene promoters and surrounding genome sequence. This syntenic build is the basis for studies of genome evolution and function with the aim of improving this important crop plant. As we assemble and annotate wheat chromosome arms, they are made publically available using the genome viewer GBrowse2.

The results are presented in the publications below.

# International Wheat Genome Sequencing Consortium. (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. [http://www.sciencemag.org/content/345/6194/1251788.abstract Science 345:1251788-1251788]
# Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., Jakobsen K.S., Wulff B.B.H., Steuernagel B., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. [http://www.sciencemag.org/content/345/6194/1250092.abstract Science 345:1250092-1250092]
# Pfeifer M., Kugler K.G., Sandve S.R., Zhan B., Rudi H., Hvidsten T.R., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. [http://www.sciencemag.org/content/345/6194/1250091.abstract Science 345:1250091-1250091]
# Berkman, P.J., Visendi, P., Lee, H.C., Stiller, J., Manoli, S., Lorenc, M.T., Lai, K., Batley, J., Fleury, D., Šimková, H., Kubaláková, M., Weining, S., Doležel, J. and Edwards, D. (2013) Dispersion and domestication shaped the genome of bread wheat. [http://onlinelibrary.wiley.com/doi/10.1111/pbi.12044/full Plant Biotechnology Journal 11 (5): 564-571]
#Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Pilar Hernandez P, and Edwards D. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. [http://www.springerlink.com/content/uk508r17832pkht8/ Theoretical and Applied Genetics 3: 423-432]
#Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J and Edwards D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract Plant Biotechnology Journal 9 (7): 768-775]

In addition to chromosome arm shotgun sequencing, we contribute to the IWGSC assembly of the BAC minimum tiling path led by Jaroslav Dolezel.

A major effort of the group is the translation of genomics for crop improvement. We led an Australian consortium to resequence a set of diverse Australian bread wheat line and have identified more than 20 million SNP molecular markers across teh bread wheat genome. Related papers are listed below.

# Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. [http://www.onlinelibrary.wiley.com/doi/10.1111/pbi.12240/abstract Plant Biotechnology Journal 13 (1), 97-104]
# Visendi P, Batley J, Edwards D. (2013) Next generation characterisation of cereal genomes for marker discovery. Biology 2: 1357-1377 [http://www.mdpi.com/2079-7737/2/4/1357/pdf Biology 2: 1357-1377]
# Deng P, Nie X, Wang L, Cui L, Liu P, Tong W, Biradar SS, Edwards D, Berkman P, Šimková H, Doležel J, Luo M, You F, Batley J, Fleury D, Appels R, Weining S. (2013) Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes. [http://link.springer.com/article/10.1007%2Fs11105-013-0669-x Plant Molecular Biology Reporter. 1-14]
# Edwards D, Batley J and Snowdon, R. (2013) Accessing complex crop genomes with next-generation sequencing. [http://link.springer.com/article/10.1007/s00122-012-1964-x Theoretical and Applied Genetics 126 (1): 1-11]
# Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, J. Berkman PJ, Lai K, Batley J and Edwards D. (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. [http://www.mdpi.com/2079-7737/1/2/370 Biology 1(2): 370-38]
# Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D. (2012) Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00718.x/abstract Plant Biotechnology Journal. 10 (6): 743-749]
# Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A. (2012) Bread matters: A national initiative to profile the genetic diversity of Australian wheat. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00717.x/abstract Plant Biotechnology Journal. 10 (6): 703-708]
# Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S. (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. [http://www.amjbot.org/content/99/9/e369.short American Journal of Botany. 99 (9) e369-e371]
#Berkman PJ, Lai K, Lorenc MT and Edwards D. Next generation sequencing applications for wheat crop improvement. (2012) [http://www.amjbot.org/content/99/2/365.short American Journal of Botany 99 (2): 365-371]
#Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J and Edwards D. (2012) WheatGenome.info: An integrated database and portal for wheat genome information. [http://pcp.oxfordjournals.org/content/early/2011/10/18/pcp.pcr141.short Plant and Cell Physiology 53(2): e2(1–7)]
#Edwards D and Batley J. (2010) Plant genome sequencing: applications for crop improvement. [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2009.00459.x/abstract Plant Biotechnology Journal 8: 2–9]

Further information on our wheat research is available at [http://www.wheatgenome.info/ wheatgenome.info]

Back to [[Main_Page]]

Wheat

2015-07-27T07:25:49Z

Appbio:

Wheat

2015-07-27T07:16:56Z

Appbio:

2014-02-10T21:15:32Z

Appbio: /* Publications */

===Academic history ===
;Doctor of Philopsophy (July 2010 - present)
: School of Agriculture and Food Science, University of Queensland, Brisbane, Australia
: My PhD research interests involve analysing expression genes, and identifying genetic variations, such as genetic diversity and the assiociation of markers with important agronomic traits in Triticum aestivum (bread wheat).
: Supervisor: Dave Edwards, Jacqueline Batley, Jiri Stiller
;Master of Philosophy (Part-time study, terminated)
: Institute for Integrated and Intelligent Systems, Griffith University, Logan, Queensland, Australia, 12/2007 to 2/2010
: Research Topic: Lipreading Segmentation and Correlation between Lipreading and Speech
: Supervisors: Dr Phillip Sheridan, Dr Alan Liew

;Master of Information and Communication Technology
: Griffith University, Brisbane, Queensland, Australia，2/2005-9/2006
: Research Topic: An Investigation of Motion Tracking Algorithms
: Supervisor: Dr Phillip Sheridan

; Master of Information Technology
: University of Queensland, Brisbane, Queensland, Australia，3/2004-2/2005

; Bachelor of Science in Applied Chemistry
: Shenzhen University, Shenzhen, China，9/1998-6/2002

===Posts held===
From 3/2010 to 6/2010
: Research Assistant, Applied Bioinformatics Group, Australia Centre for Plant Functional Genomics(ACPFG), School of Land, Crop & Food Sciences, The University of Queensland
:: Participated in Brassica species genome alignment and comparative assembly.

From 12/2009 to 2/2010
: Research Scholar, Applied Bioinformatics Group, Australia Centre for Plant Functional Genomics(ACPFG), School of Land, Crop & Food Sciences, The University of Queensland
:: Participated in Next-Generation DNA Sequencing (NGS) analyzing from Brassica species.

From 01/2009 to 03/2009
: PeopleSoft Developer, Enterprise Applications Development, Information Technology Service, the University of Queensland
:: Participated in post Go-live development for SI-Net and MySI-Net these two ERP systems. Involved Perl programming on Ubuntu system.

From 09/2008 to 12/2008
: Software Developer, Software Service Development Team, Information Technology Service, the University of Queensland
:: Participated in the project the UQ Bonus Scheme. Involved developing web application by Microsoft C#.Net and Oracle PL/SQL.

From 04/2008 to 08/2008
: Java Developer (Upgrade Developer), Eyecon Pty Ltd, West End, Brisbane, Queensland, Australia
:: Participated in the SQL Server 2005 Upgrade Project and Weblogic 10 Upgrade Project. Involved developing new TSQL scripts, and migrating data from SQL Server 2000 to SQL Server 2005, and migrating game server application from WebLogic Server 7 to WebLogic Server 10, and developing WLST scripts.

From 02/2007 to 02/2008
: PeopleSoft Developer, Technical and Development Team, PeopleSoft HE Upgrade Project, Business Systems Services, Griffith University, Brisbane, Queensland, Australia
:: Participated in the 2007-2008 PeopleSoft High Education Upgrade Project. Involved developing the Student Record, Student Finance, HR Payroll system in PeopleSoft 8.48 Application Designer, PeopleCode, SQR, XML publisher and Application Engine.

From 11/2005 to 01/2006
: Email System Tester, Information and Communication Technology Services, Griffith University
:: Participated in the 2005-2006 student email expansion project and tested the latest-updated email system from view of user.

My PhD research interests involve analysing expression genes, and identifying genetic variations, such as genetic diversity and the assiociation of markers with important agronomic traits in Triticum aestivum (bread wheat). I have assembled wheat transcriptomes and identified SNPs by specific perl script, and built up the wheat autoSNPdb database. Currently, I am analysing experssion genes in Triticum aestivum.

Previously, I have developed the CMAP database for pulished Brassica genetic markers against chromosomes from Brassica rapa and CMAP database for genetic markers against wheat chromosome arm 7DS.

===Publications===
'''Journal articles'''
# Kaitao Lai, Chris Duran, Paul J. Berkman, Michał T. Lorenc, Jiri Stiller, Sahana Manoli, Matthew Hayden, Kerrie Forrest, Delphine Fleury, Ute Baumann, Manuel Zander, Annaliese Mason, Jacqueline Batley, David Edwards (2012) [http://dx.doi.org/10.1111/j.1467-7652.2012.00718.x Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data]. Plant Biotechnology Journal 10(6): 743–749.
# Kaitao Lai, Michał Tadeusz Lorenc, David Edwards (2012) [http://dx.doi.org/10.3390/agronomy2010062 Genomic Databases for Crop Improvement]. Agronomy 2(1):62-73.
# Kaitao Lai, Paul J Berkman, Michał Tadeusz Lorenc, Christopher Duran, Lars Smits, Sahana Manoli, Jiri Stiller, David Edwards (2012) [http://dx.doi.org/10.1093/pcp/pcr141 WheatGenome.info: An integrated database and portal for wheat genome information]. Plant and Cell Physiology 53(2): e2.
# Manuel Zander, Dhwani A. Patel, Angela Van de Wouw, Kaitao Lai, Michał T. Lorenc, Emma Campbell, Alice Hayward, David Edwards, Harsh Raman, Jacqueline Batley (2013) [http://dx.doi.org/10.1007/s10142-013-0324-5 Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing]. Functional & Integrative Genomics.
# Paul J. Berkman, Paul Visendi, Hong C. Lee, Jiri Stiller, Sahana Manoli, Michał T. Lorenc, Kaitao Lai, Jacqueline Batley, Delphine Fleury, Hana Šimková, Marie Kubaláková, Song Weining, Jaroslav Doležel, David Edwards (2013) [http://dx.doi.org/10.1111/pbi.12044 Dispersion and domestication shaped the genome of bread wheat]. Plant Biotechnology Journal.
# Michał T. Lorenc, Satomi Hayashi, Jiri Stiller, Hong Lee, Sahana Manoli, Pradeep Ruperao, Paul Visendi, Paul J. Berkman, Kaitao Lai, Jacqueline Batley, David Edwards (2012) [http://dx.doi.org/10.3390/biology1020370 Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP]. Biology 1(2): 370-382.
# Paul J. Berkman, Kaitao Lai, Michał T. Lorenc, David Edwards (2012) [http://dx.doi.org/10.3732/ajb.1100309 Next generation sequencing applications for wheat crop improvement]. American Journal of Botany 99(2): 365-371.
# Hong Lee, Kaitao Lai, Michał T. Lorenc, Mike Imelfort, Chris Duran, David Edwards (2012) [http://dx.doi.org/10.1093/bfgp/elr037 Bioinformatics tools and databases for analysis of next-generation sequence data]. Briefings in Functional Genomics 11(1): 12-24.
# Paul J. Berkman, Adam Skarshewski, Sahana Manoli, Michał T. Lorenc, Jiri Stiller, Lars Smits, Kaitao Lai, Emma Campbell, Marie Kubaláková, Hana Šimková, Jacqueline Batley, Jaroslav Doležel, Pilar Hernandez, David Edwards (2012) [http://dx.doi.org/10.1007/s00122-011-1717-2 Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation]. Theoretical and Applied Genetics 124(3): 423-432.
# Paul J. Berkman, Adam Skarshewski, Michał T. Lorenc, Kaitao Lai, Chris Duran, Edmund Y.S. Ling, Jiri Stiller, Lars Smits, Michael Imelfort, Sahana Manoli, Megan McKenzie, Marie Kubaláková, Hana Šimková, Jacqueline Batley, Delphine Fleury, Jaroslav Doležel, David Edwards (2011) [http://dx.doi.org/10.1111/j.1467-7652.2010.00587.x Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS]. Plant Biotechnol J 9(7), 768-775.
# Daniel J Marshall, Alice Hayward, Dominic Eales, Michael Imelfort, Jiri Stiller, Paul J Berkman, Terry Clark, Megan McKenzie, Kaitao Lai, Chris Duran, Jacqueline Batley, Dave Edwards (2010) [http://dx.doi.org/10.1186/1746-4811-6-19 Targeted identification of genomic regions using TAGdb]. Plant Methods 6: 19.

'''Book Chapters'''

'''Conference Posters'''
#Kaitao Lai, Michal Lorenc, Hong Lee, Paul Berkman, Paul Visendi Muhindira, Philipp Bayer, Pradeep Ruperao, Kenneth Chan, Sahana Manoli, Jiri Stiller, Jacqueline Batley, Dave Edwards. Genetic variation across Australian bread wheat varieties, poster for International Plant and Animal (PAG) XXI, San Diego, USA. Scheduled to present between 12th – 16th Jan, 2013.
#Manuel Matias Zander, Dhwani A. Patel, Angela Van de Wouw, Kaitao Lai, Michal T. Lorenc, Alice C Hayward, Agnieszka Golicz, Philipp Bayer, David Edwards, Jacqueline Batley. Understanding Genome Structure and Diversity of the Plant Pathogen, Leptosphaeria maculans, poster for International Plant and Animal (PAG) XXI, San Diego, USA. Presented at 13rd Jan, 2014.
#Philipp Emanuel Bayer, Paul Visendi, Kenneth Chan, Michal Lorenc, Kaitao Lai, Jessica Dalton-Morgan, Yan Long, Jinling Meng, Jacqueline Batley, David Edwards, Skim Based Genotyping by Sequencing in Complex Crop Genomes, poster for International Plant and Animal (PAG) XXI, San Diego, USA. Scheduled to present between 12th – 16th Jan, 2013.
#Paul Berkman, Paul Visendi Muhindira, Michal Lorenc, Kaitao Lai, Hong Lee, Mike Imelfort, Sahana Manoli, Pradeep Ruperao, Chris Duran, Hana Šimková, Marie Kubaláková, Emma Campbell, Pilar Hernandez, Jiri Stiller, Jaroslav Doležel, Jacqueline Batley, David Edwards, Gene content, loss, conservation and genetic variation among Triticum aestivum group 7 chromosomes, the Plant and Animal Genome XX Conference, January 14-18, 2012, California.
#Hong Lee, Paul J. Berkman, Kaitao Lai, Michal Lorenc, Mike Imelfort, Sahana Manoli, Pradeep Ruperao, Chris Duran, Emma Campbell, Alice C Hayward, Jessica Dalton-Morgan, Jiri Stiller, Jacqueline Batley, David Edwards, Finding Function in Complex Crop Genomes, the Plant and Animal Genome XX Conference, January 14-18, 2012, California.
#Paul J. Berkman, Adam Skarshewski, Michał T. Lorenc, Kaitao Lai, Chris Duran, Edmund Y.S. Ling, Jiri Stiller, Lars Smits, Michael Imelfort, Sahana Manoli, Megan McKenzie, Marie Kubaláková, Hana Šimková, Jacqueline Batley, Delphine Fleury, Jaroslav Doležel and David Edwards, Applying second-generation sequencing technology in the assembly and analysis of the wheat group 7 chromosomes, ITMI 2010, September 2010.

'''Presentations'''
#Kaitao Lai, Michal Lorenc, Chris Duran, Satomi Hayashi, Jiri Stiller, Hong Lee, Paul Visendi, Pradeep Ruperao, Sahana Manoli, Jacqueline Batley, Dave Edwards. SNP discovery in complex genomes using SGSautoSNP and autoSNPdb, computer demo for International Plant and Animal (PAG) XXI, San Diego, USA. . Scheduled to present between 12th – 16th Jan, 2013.
#Kaitao Lai, Michal Lorenc, Hong Lee, Paul Berkman, Paul Visendi Muhindira, Philipp Bayer, Kenneth Chan, Pradeep Ruperao, Sahana Manoli, Jiri Stiller, Jacqueline Batley, Dave Edwards. Characterise genetic variations across Australian bread wheat varieties, 2012 UQ seminar series: computational biology, IMB, UQ, Brisbane, Australia. Presented on 9th August 2012.
#Kaitao Lai, Nikki Appleby, Paul Berkman, Chris Duran, Michal Lorenc, Sahana Manoli, Jiri Stiller, Matt Hayden, Annalise Mason, Jacqueline Batley, David Edwards. Single nucleotide polymorphism discovery in wheat transcriptome, ACPFG Joint Research Meeting, Adelaide, Australia. Presented on 25th October 2011.

===Contact===
;Address
Applied Bioinformatics Group

Rm S424, Bld 83

Australian Centre for Plant Functional Genomics (ACPFG)

School of Land, Crop & Food Sciences

The University of Queensland

Brisbane QLD 4072

AUSTRALIA

;Phone
[+61] (0) 7 3346 7083

;Email
[mailto:k.lai1@uq.edu.au k.lai1@uq.edu.au]

Kaitao Lai

2014-02-10T21:15:06Z

Appbio: /* Publications */

===Academic history ===
;Doctor of Philopsophy (July 2010 - present)
: School of Agriculture and Food Science, University of Queensland, Brisbane, Australia
: My PhD research interests involve analysing expression genes, and identifying genetic variations, such as genetic diversity and the assiociation of markers with important agronomic traits in Triticum aestivum (bread wheat).
: Supervisor: Dave Edwards, Jacqueline Batley, Jiri Stiller
;Master of Philosophy (Part-time study, terminated)
: Institute for Integrated and Intelligent Systems, Griffith University, Logan, Queensland, Australia, 12/2007 to 2/2010
: Research Topic: Lipreading Segmentation and Correlation between Lipreading and Speech
: Supervisors: Dr Phillip Sheridan, Dr Alan Liew

;Master of Information and Communication Technology
: Griffith University, Brisbane, Queensland, Australia，2/2005-9/2006
: Research Topic: An Investigation of Motion Tracking Algorithms
: Supervisor: Dr Phillip Sheridan

; Master of Information Technology
: University of Queensland, Brisbane, Queensland, Australia，3/2004-2/2005

; Bachelor of Science in Applied Chemistry
: Shenzhen University, Shenzhen, China，9/1998-6/2002

===Posts held===
From 3/2010 to 6/2010
: Research Assistant, Applied Bioinformatics Group, Australia Centre for Plant Functional Genomics(ACPFG), School of Land, Crop & Food Sciences, The University of Queensland
:: Participated in Brassica species genome alignment and comparative assembly.

From 12/2009 to 2/2010
: Research Scholar, Applied Bioinformatics Group, Australia Centre for Plant Functional Genomics(ACPFG), School of Land, Crop & Food Sciences, The University of Queensland
:: Participated in Next-Generation DNA Sequencing (NGS) analyzing from Brassica species.

From 01/2009 to 03/2009
: PeopleSoft Developer, Enterprise Applications Development, Information Technology Service, the University of Queensland
:: Participated in post Go-live development for SI-Net and MySI-Net these two ERP systems. Involved Perl programming on Ubuntu system.

From 09/2008 to 12/2008
: Software Developer, Software Service Development Team, Information Technology Service, the University of Queensland
:: Participated in the project the UQ Bonus Scheme. Involved developing web application by Microsoft C#.Net and Oracle PL/SQL.

From 04/2008 to 08/2008
: Java Developer (Upgrade Developer), Eyecon Pty Ltd, West End, Brisbane, Queensland, Australia
:: Participated in the SQL Server 2005 Upgrade Project and Weblogic 10 Upgrade Project. Involved developing new TSQL scripts, and migrating data from SQL Server 2000 to SQL Server 2005, and migrating game server application from WebLogic Server 7 to WebLogic Server 10, and developing WLST scripts.

From 02/2007 to 02/2008
: PeopleSoft Developer, Technical and Development Team, PeopleSoft HE Upgrade Project, Business Systems Services, Griffith University, Brisbane, Queensland, Australia
:: Participated in the 2007-2008 PeopleSoft High Education Upgrade Project. Involved developing the Student Record, Student Finance, HR Payroll system in PeopleSoft 8.48 Application Designer, PeopleCode, SQR, XML publisher and Application Engine.

From 11/2005 to 01/2006
: Email System Tester, Information and Communication Technology Services, Griffith University
:: Participated in the 2005-2006 student email expansion project and tested the latest-updated email system from view of user.

My PhD research interests involve analysing expression genes, and identifying genetic variations, such as genetic diversity and the assiociation of markers with important agronomic traits in Triticum aestivum (bread wheat). I have assembled wheat transcriptomes and identified SNPs by specific perl script, and built up the wheat autoSNPdb database. Currently, I am analysing experssion genes in Triticum aestivum.

Previously, I have developed the CMAP database for pulished Brassica genetic markers against chromosomes from Brassica rapa and CMAP database for genetic markers against wheat chromosome arm 7DS.

===Publications===
'''Journal articles'''
# Kaitao Lai, Chris Duran, Paul J. Berkman, Michał T. Lorenc, Jiri Stiller, Sahana Manoli, Matthew Hayden, Kerrie Forrest, Delphine Fleury, Ute Baumann, Manuel Zander, Annaliese Mason, Jacqueline Batley, David Edwards (2012) [http://dx.doi.org/10.1111/j.1467-7652.2012.00718.x Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data]. Plant Biotechnology Journal 10(6): 743–749.
# Kaitao Lai, Michał Tadeusz Lorenc, David Edwards (2012) [http://dx.doi.org/10.3390/agronomy2010062 Genomic Databases for Crop Improvement]. Agronomy 2(1):62-73.
# Kaitao Lai, Paul J Berkman, Michał Tadeusz Lorenc, Christopher Duran, Lars Smits, Sahana Manoli, Jiri Stiller, David Edwards (2012) [http://dx.doi.org/10.1093/pcp/pcr141 WheatGenome.info: An integrated database and portal for wheat genome information]. Plant and Cell Physiology 53(2): e2.
# Manuel Zander, Dhwani A. Patel, Angela Van de Wouw, Kaitao Lai, Michał T. Lorenc, Emma Campbell, Alice Hayward, David Edwards, Harsh Raman, Jacqueline Batley (2013) [http://dx.doi.org/10.1007/s10142-013-0324-5 Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing]. Functional & Integrative Genomics.
# Paul J. Berkman, Paul Visendi, Hong C. Lee, Jiri Stiller, Sahana Manoli, Michał T. Lorenc, Kaitao Lai, Jacqueline Batley, Delphine Fleury, Hana Šimková, Marie Kubaláková, Song Weining, Jaroslav Doležel, David Edwards (2013) [http://dx.doi.org/10.1111/pbi.12044 Dispersion and domestication shaped the genome of bread wheat]. Plant Biotechnology Journal.
# Michał T. Lorenc, Satomi Hayashi, Jiri Stiller, Hong Lee, Sahana Manoli, Pradeep Ruperao, Paul Visendi, Paul J. Berkman, Kaitao Lai, Jacqueline Batley, David Edwards (2012) [http://dx.doi.org/10.3390/biology1020370 Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP]. Biology 1(2): 370-382.
# Paul J. Berkman, Kaitao Lai, Michał T. Lorenc, David Edwards (2012) [http://dx.doi.org/10.3732/ajb.1100309 Next generation sequencing applications for wheat crop improvement]. American Journal of Botany 99(2): 365-371.
# Hong Lee, Kaitao Lai, Michał T. Lorenc, Mike Imelfort, Chris Duran, David Edwards (2012) [http://dx.doi.org/10.1093/bfgp/elr037 Bioinformatics tools and databases for analysis of next-generation sequence data]. Briefings in Functional Genomics 11(1): 12-24.
# Paul J. Berkman, Adam Skarshewski, Sahana Manoli, Michał T. Lorenc, Jiri Stiller, Lars Smits, Kaitao Lai, Emma Campbell, Marie Kubaláková, Hana Šimková, Jacqueline Batley, Jaroslav Doležel, Pilar Hernandez, David Edwards (2012) [http://dx.doi.org/10.1007/s00122-011-1717-2 Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation]. Theoretical and Applied Genetics 124(3): 423-432.
# Paul J. Berkman, Adam Skarshewski, Michał T. Lorenc, Kaitao Lai, Chris Duran, Edmund Y.S. Ling, Jiri Stiller, Lars Smits, Michael Imelfort, Sahana Manoli, Megan McKenzie, Marie Kubaláková, Hana Šimková, Jacqueline Batley, Delphine Fleury, Jaroslav Doležel, David Edwards (2011) [http://dx.doi.org/10.1111/j.1467-7652.2010.00587.x Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS]. Plant Biotechnol J 9(7), 768-775.
# Daniel J Marshall, Alice Hayward, Dominic Eales, Michael Imelfort, Jiri Stiller, Paul J Berkman, Terry Clark, Megan McKenzie, Kaitao Lai, Chris Duran, Jacqueline Batley, Dave Edwards (2010) [http://dx.doi.org/10.1186/1746-4811-6-19 Targeted identification of genomic regions using TAGdb]. Plant Methods 6: 19.

'''Book Chapters'''

'''Conference Posters'''
#Kaitao Lai, Michal Lorenc, Hong Lee, Paul Berkman, Paul Visendi Muhindira, Philipp Bayer, Pradeep Ruperao, Kenneth Chan, Sahana Manoli, Jiri Stiller, Jacqueline Batley, Dave Edwards. Genetic variation across Australian bread wheat varieties, poster for International Plant and Animal (PAG) XXI, San Diego, USA. Scheduled to present between 12th – 16th Jan, 2013.
Manuel Matias Zander, Dhwani A. Patel, Angela Van de Wouw, Kaitao Lai, Michal T. Lorenc, Alice C Hayward, Agnieszka Golicz, Philipp Bayer, David Edwards, Jacqueline Batley. Understanding Genome Structure and Diversity of the Plant Pathogen, Leptosphaeria maculans, poster for International Plant and Animal (PAG) XXI, San Diego, USA. Presented at 13rd Jan, 2014.
#Philipp Emanuel Bayer, Paul Visendi, Kenneth Chan, Michal Lorenc, Kaitao Lai, Jessica Dalton-Morgan, Yan Long, Jinling Meng, Jacqueline Batley, David Edwards, Skim Based Genotyping by Sequencing in Complex Crop Genomes, poster for International Plant and Animal (PAG) XXI, San Diego, USA. Scheduled to present between 12th – 16th Jan, 2013.
#Paul Berkman, Paul Visendi Muhindira, Michal Lorenc, Kaitao Lai, Hong Lee, Mike Imelfort, Sahana Manoli, Pradeep Ruperao, Chris Duran, Hana Šimková, Marie Kubaláková, Emma Campbell, Pilar Hernandez, Jiri Stiller, Jaroslav Doležel, Jacqueline Batley, David Edwards, Gene content, loss, conservation and genetic variation among Triticum aestivum group 7 chromosomes, the Plant and Animal Genome XX Conference, January 14-18, 2012, California.
#Hong Lee, Paul J. Berkman, Kaitao Lai, Michal Lorenc, Mike Imelfort, Sahana Manoli, Pradeep Ruperao, Chris Duran, Emma Campbell, Alice C Hayward, Jessica Dalton-Morgan, Jiri Stiller, Jacqueline Batley, David Edwards, Finding Function in Complex Crop Genomes, the Plant and Animal Genome XX Conference, January 14-18, 2012, California.
#Paul J. Berkman, Adam Skarshewski, Michał T. Lorenc, Kaitao Lai, Chris Duran, Edmund Y.S. Ling, Jiri Stiller, Lars Smits, Michael Imelfort, Sahana Manoli, Megan McKenzie, Marie Kubaláková, Hana Šimková, Jacqueline Batley, Delphine Fleury, Jaroslav Doležel and David Edwards, Applying second-generation sequencing technology in the assembly and analysis of the wheat group 7 chromosomes, ITMI 2010, September 2010.

'''Presentations'''
#Kaitao Lai, Michal Lorenc, Chris Duran, Satomi Hayashi, Jiri Stiller, Hong Lee, Paul Visendi, Pradeep Ruperao, Sahana Manoli, Jacqueline Batley, Dave Edwards. SNP discovery in complex genomes using SGSautoSNP and autoSNPdb, computer demo for International Plant and Animal (PAG) XXI, San Diego, USA. . Scheduled to present between 12th – 16th Jan, 2013.
#Kaitao Lai, Michal Lorenc, Hong Lee, Paul Berkman, Paul Visendi Muhindira, Philipp Bayer, Kenneth Chan, Pradeep Ruperao, Sahana Manoli, Jiri Stiller, Jacqueline Batley, Dave Edwards. Characterise genetic variations across Australian bread wheat varieties, 2012 UQ seminar series: computational biology, IMB, UQ, Brisbane, Australia. Presented on 9th August 2012.
#Kaitao Lai, Nikki Appleby, Paul Berkman, Chris Duran, Michal Lorenc, Sahana Manoli, Jiri Stiller, Matt Hayden, Annalise Mason, Jacqueline Batley, David Edwards. Single nucleotide polymorphism discovery in wheat transcriptome, ACPFG Joint Research Meeting, Adelaide, Australia. Presented on 25th October 2011.

===Contact===
;Address
Applied Bioinformatics Group

Rm S424, Bld 83

Australian Centre for Plant Functional Genomics (ACPFG)

School of Land, Crop & Food Sciences

The University of Queensland

Brisbane QLD 4072

AUSTRALIA

;Phone
[+61] (0) 7 3346 7083

;Email
[mailto:k.lai1@uq.edu.au k.lai1@uq.edu.au]