Applied Bioinformatics

Applied Bioinformatics

Projects

Organisms

Dave Edwards, Head of Group

About Me

Originally from the UK, I moved to DPI Victoria in 2002 to work with German Spangenberg as leader of the Computational Biology and Discovery Technologies sub-platform, leading research groups in bioinformatics, microarray technology as well as genome sequencing and Brassica genetics. Previously I worked with Keith Edwards at Long Ashton Research Station near Bristol, and the University of Cambridge, where I had gained my PhD on a study of transcriptional regulators that are functionally conserved between animals and plants. Previous to this, I backpacked around the world taking employment at McGill University and gaining an early appreciation of Australian cereal research at Adelaide University under Peter Langridge. My undergraduate days at Nottingham University introduced me to plant molecular genetics and I later had the opportunity to hone these skills (again under Keith Edwards) at ICI Seeds (now Syngenta). I am currently working with Kaye Basford at the University of Queensland node of ACPFG to provide the bioinformatics that underlies ACPFG research activities, with an emphasis on applying the vast quantities of ‘omic data to cereal crop improvement. I am based in the Institute for Molecular Biosciences (IMB) which provides a vibrant and diverse research environment with excellent bioinformatics infrastructure.

Publications

JOURNAL ARTICLES

• Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Batley J, Spangenberg G and Edwards D. A Comparative Map Viewer Integrating Genetic Maps for Brassica and Arabidopsis. BMC Plant Biology (In Press, accepted July 2007)
• Hong CP, Piao ZY, Kang TW, Batley J, Yang TJ, Hur YK, Bhak J, Edwards D and Lim YP. Genomic distribution of Simple Sequence Repeats in Brassica rapa. 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. Identification and characterisation of Simple Sequence Repeat (SSR) markers from Brassica napus expressed sequences. Molecular Ecology Notes (In Press, accepted February 2007)
• 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. Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Plant Biotechnology Journal 2: 495-506
• Edwards D and Batley J. (2004) Plant Bioinformatics: From Genome to Phenome. 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. 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. 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. 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. 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. 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. Theoretical and Applied Genetics 105: 532-543
• O’ Sullivan D, Edwards D, Edwards KJ. Maize Genomics. 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. Plant Journal (2000)
• Edwards D, Murray JAH, Smith AG. Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. Plant Physiology (1998) 117 (3): 1015-1022
• Edwards KJ, Thompson H, Edwards D, DeSaizeu A, Sparks C, Thompson JA, Greenland AJ, Eyers M and Schuch W. Construction and Characterisation of a Yeast Artificial Chromosome Library Containing 3 Haploid Maize Genome Equivalents. Plant Molecular Biology (1992) 19: (2) 299-308

BOOKS

• Plant Bioinformatics. Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA). (In press, accepted August 2006)

BOOK CHAPTERS

• Batley J and Edwards D. Mining for Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: Bioinformatics for DNA Sequence Analysis. Ed. David Posada Methods in Molecular Biology, Humana Press (USA)
• Edwards D. Bioinformatics. In: The World Wheat Book. Eds. Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) (In press, accepted January 2007)
• Batley J and Edwards D. Bioinformatics: Fundamentals and Applications in Plant Genetics and Breeding. In: Principles and Practices of Plant Molecular Mapping and Breeding. Eds. Kole C and Abbott AG. Science Publishers, Inc., (USA) (In press, accepted January 2007)
• Edwards D. Bioinformatics and plant genomics for staple crops improvement. In: Breeding Major Food Staples for the 21st Century. Eds. Kang MS and Priyadarshan PM. Blackwell (In press, accepted August 2006)
• Batley J, Jewell E and Edwards D. 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) (In press, accepted August 2006)
• Love CG and Edwards D. Accessing integrated Brassica genetic and genomic data using the BASC server. In: Plant Bioinformatics. Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA) (In press, accepted August 2006)
• 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
• 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.
• 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.
• 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.
• 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.
• 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.
• 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

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 Newsletter27
• 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 Newsletter27
• 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