Difference between revisions of "Publications DE"

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===BOOKS:===
 
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## [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)
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# [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)
 
## [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)
  

Revision as of 11:03, 30 January 2011

Publications - David Edwards

BOOKS:

  1. Bioinformatics: Tools and Applications. Ed. Edwards D, Hanson D and Stajich J. Springer (USA). (2009)
    1. Plant Bioinformatics. Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA). (2007)

BOOK CHAPTERS:

    1. Duran C, Boskovic Z, Batley J and Edwards D. Brassica Bioinformatics. In Vegetable Brassicas Ed. Sadowski J. Science Publishers, Inc., New Hampshire (In press)
    2. Edwards D. Bioinformatics. In: The World Wheat Book. Eds. Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) (In press)
    3. Edwards D, Hansen D and Stajich J. (2009) DNA Sequence Databases. In Bioinformatics: Tools and Applications. Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 1-11
    4. Duran C, Edwards D and Batley J. (2009) Molecular Marker Discovery and Genetic map Visualisation. In Bioinformatics: Tools and Applications. Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 165-189
    5. Imelfort M, Batley J, Grimmond S and Edwards D. (2009) Genome sequencing approaches and successes. In: Plant Genomics. Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 345-358
    6. Batley J and Edwards D. (2009) Mining for Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: Bioinformatics for DNA Sequence Analysis. Ed. Posada D. Methods in Molecular Biology, Humana Press (USA), pp 303-322
    7. Appleby N, Edwards D and Batley J. (2009) New technologies for ultra-high throughput genotyping in plants. In: Plant Genomics. Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press, (USA), pp 19-40
    8. Duran C, Edwards D and Batley J. (2009) Genetic maps and the use of synteny. In: Plant Genomics. Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 41-56
    9. Edwards D and Batley J. (2008) Bioinformatics: Fundamentals and Applications in Plant Genetics, Mapping and Breeding. In: Principles and Practices of Plant Genomics. Eds. Kole C and Abbott AG. Science Publishers, Inc., (USA), pp 269-302
    10. Edwards D. (2007) Bioinformatics and plant genomics for staple crops improvement. In: Breeding Major Food Staples. Eds. Kang MS and Priyadarshan PM. Blackwell, pp 93-106
    11. Batley J, Jewell E and Edwards D. (2007) Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: Plant Bioinformatics. Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA), pp. 473-494
    12. Love CG and Edwards D. (2007) Accessing integrated Brassica genetic and genomic data using the BASC server. In: Plant Bioinformatics. Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA) (2007), pp. 229-244
    13. Edwards D, Salisbury PA, Burton WA, Hopkins CJ and Batley J. (2007) Indian Mustard, in Genome Mapping and Molecular Breeding in Plants, Vol. 2. Ed. Kole C. Springer NY, pp 179-210
    14. Edwards D, Forster JW, Chagné D and Batley J. (2007) What are SNPs? In: Association Mapping in Plants Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 41-52.
    15. Edwards D, Batley J, Cogan NOI, Forster JW and Chagné D. 2007. Single Nucleotide Polymorphism Discovery. In: Association Mapping in Plants Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 53-76.
    16. Chagné D, Batley J, Edwards D, and Forster JW. (2007) Single Nucleotide Polymorphisms genotyping in plants. In: Association Mapping in Plants Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 77-94.
    17. Batley J and Edwards D. (2007) SNP applications in plants. In: Association Mapping in Plants Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 95-102.
    18. 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: Molecular Breeding for Genetic Improvement of Forage Crops and Turf. Ed. Humphreys MO. Wageningen Academic Publishers, pp 83-97.
    19. 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: Neotyphodium in Cool Season Grasses. Eds. Roberts CA, West CP and Spiers DE. Blackwell, pp 103-140

JOURNAL ARTICLES:

    1. 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. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal (accepted November 2010)
    2. 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. Genome Biology (accepted September 2010)
    3. 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. Genomics (accepted September 2010)
    4. 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. Genome (accepted June 2010).
    5. 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. Plant Methods 6:19
    6. Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. Bioinformatics 26 (2) 273-274
    7. Edwards D and Batley J. (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnology Journal 8: 2–9
    8. 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. Theoretical and Applied Genetics 120 (1): 71-83
    9. Imelfort M and Edwards D. (2009) De novo sequencing of plant genomes using second-generation technologies. Briefings in Bioinformatics 10: 609-618
    10. Batley J and Edwards D. (2009) Genome sequence data: management, storage, and visualization. Biotechniques 46:333-336
    11. Duran C, Appleby N, Vardy M, Imelfort M, Edwards D and Batley J. (2009) Single Nucleotide Polymorphism Discovery in Barley using AutoSNPdb. Plant Biotechnology Journal 7 (4): 326 – 333
    12. Imelfort M, Duran C, Batley J and Edwards D. (2009) Discovering genetic polymorphisms in next generation sequencing data. Plant Biotechnology Journal 7 (4): 312 – 317
    13. Duran C, Appleby N,, Edwards D and Batley J. (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. Current Bioinformatics 4:16-27
    14. 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. Nucleic Acids Research 37: 951–953
    15. 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. Theoretical and Applied Genetics 115 (6): 777-792
    16. 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. BMC Plant Biology 7: 40
    17. 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. Molecules and Cells 23 (3) 349-356
    18. 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. Molecular Ecology Notes 7: 886–889.
    19. 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. Molecular Ecology Notes 7: 697-700
    20. 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. Molecular Ecology Notes 7: 273-277
    21. 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. Nucleic Acids Research 35: D870–D873
    22. 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. New Phytologist 173: 481-494
    23. 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. Molecular Ecology Notes 6: 1191-1194
    24. 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. Molecules and Cells 22: 300-307
    25. 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. Plant Molecular Biology 61: 757-768
    26. 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. Nucleic Acids Research 34: W656–W659
    27. 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. Acta Horticulturae 706: 99-104
    28. 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. Acta Horticulturae 706: 77-82
    29. 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. Acta Horticulturae 706: 115-119
    30. 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. Molecular Ecology Notes 6: 319-322
    31. 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. Fungal Genetics and Biology 43: 465-475
    32. 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. FEMS Microbiology Letters 258: 150-160
    33. 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. Nucleic Acids Research 33: D656-D659
    34. 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
    35. 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. Nucleic Acids Research 33: W493-W495
    36. Robinson AJ, Love CG, Batley J, Barker G and Edwards D. (2004) Simple Sequence Repeat Marker Loci Discovery using SSR Primer. Bioinformatics 20: 1475-1476
    37. 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. Plant Biotechnology Journal 2: 495-506
    38. Edwards D and Batley J. (2004) Plant Bioinformatics: From Genome to Phenome. Trends in Biotechnology 22: 232-237
    39. 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. Comparative and Functional Genomics 5: 276-280
    40. Love CG, Batley J and Edwards D. (2003) Applied Computational Tools for Crop Genome Research. Journal of Plant Biotechnology 5: 193-195
    41. 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. Plant Physiology 132: 84-91
    42. 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. Molecular Breeding 11: 111-120
    43. 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. Bioinformatics 19: 421-422
    44. Edwards D, Coghill J, Batley J, Holdsworth M and Edwards KJ. (2002) Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. Biotechniques 32: 1090-1097
    45. 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
    46. 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. Theoretical and Applied Genetics 105: 532-543
    47. O’ Sullivan D, Edwards D, Edwards KJ. Maize Genomics. AgBiotechNet (2000) 2
    48. 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. Plant Journal (2000) 23 (4):557-566
    49. Edwards D, Murray JAH, Smith AG. (1998) Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. Plant Physiology 117 (3): 1015-1022
    50. 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. Plant Molecular Biology 19: (2) 299-308

CONFERENCE PAPERS:

    1. 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
    2. 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
    3. 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
    4. 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
    5. 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:

    1. 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
    2. 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
    3. 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
    4. 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
    5. 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
    6. 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
    7. 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
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