Scientific Publications

2003

Ablett GA, Karakousis A, Cakir M, Holton TA, Banbury L, Langridge P,Henry RJ. (2003) Application of SR markersin the construction of Australian barley genetic maps, Aust. J. Agric Res. 54, 1187-1195.

Barr AR, Jefferies SP,Warner P,Eglinton JK,Moody DM, Chalmers KJ, Langridge P (2003) Marker assisted selection in barley in theory and practice, Aust. J. Agric Res.

Barr AR, Karakousis A, Lance RCM, Logue SJ, Manning S, Chalmers KJ, Kretschmer JM, Collins HM, Roumeliotis S, Coventry SJ, Moody DM, Read BJ, Poulsen D, Li CD, Platz GJ, Inkerman A, Panozzo JF, Cullis BR, Smith AB, Lim P, Langridge P, Boyd WJR. (2003) Mapping and QTL analysis of the barley population Chebec x Harrington, Aust. J. Agric Res. 54, 1125-1130.

Basford KE (2003) Review of GGE Biplot Analysis: A Graphical Tool for Breeders, Geneticists, and Agronomists. W. Yan and M.S. Kang., Biometrics 59, 735-736

Cakir M, PoulsenD, Galwey NW, Ablett GA, Chalmers KJ, Platz GJ, Park RF, Lance RCM, anozzo JF, Read BJ, Moody DB, Barr AR, Johnston P, Li CD, Grime CR, Appels R, Jones MGK, Langridge P, Boyd WJR. (2003) Mapping and QTL analysis of the barley population Tallon x Kaputar, Aust. J. Agric Res. 54, 1155-1162

Chalmers J, Johnson X, Lidgett A, Spangenberg G (2003) (2003) Isolation and characterisation of a sucrose: sucrose 1 fructosyl transferase gene from perennial ryegrass (Lolium perenne L.)., J. Plant Physiol 160: 1385-1391

Chiovitti A, Bacic A, Burke J, Wetherbee R (2003) Heterogeneous xylose-rich glycans are associated with extracellular glycoconjugates from the biofouling diatom Craspedostauros australis (Bacillariophyceae)., European Journal of Phycology 38: 351-360

Chiovitti A, Higgins MJ, Harper RE, Wetherbee R, Bacic A (2003) The complex polysaccharides of the raphid diatom Pinularia viridis (Bacillariophyceae), Journal of Phycology 39(2): 543-554.

Coventry SJ, Collins HM, Barr AR, Jefferies SP, Chalmers KJ, Logue SJ, Langridge P. (2003) Use of putative QTL and structural genes in marker assisted selection for diastatic power in malting barley (Hordeum vulgare L.)., Aust. J. Agric Res. 54, 1241-1250.

Ding Y, Aldao-Humble G, Ludlow E, Drayton M, Lin Y, Nagel J, Dupal M, Zhao G, Pallaghy C, Kalla R, Emmerling M, Spangenberg G (2003) Efficient plant regeneration and Agrobacterium-mediated transformation in Medicago and Trifolium species., Plant Science 165:1419-1427

Doblin MS, Vergara CE, Read S, Newbigin E, Bacic A (2003) Plant cell wall biosynthesis: making the bricks., In: The Plant Cell Wall, J Rose (ed),Blackwell Publishing, UK, ch 6, pp.183-222.

Fairweather, J.K., Rutten, S.J., Hrmova, M., Fincher, G.B. and Driguez, H. ( (2003) Synthesis o f complex oligosaccharides using a mutated (1,3)-ß-D-glucan endohydrolase from barley., Chem. Europ. J. 9, 2603-2610

Fincher, G.B. and Stone, B.A. (2003) Chemistry of non-starch polysaccharides from cereal grains, Encyclopedia of Grain Science

Griffiths KM, Bacic A, Howlett BJ (2003) Sterol composition o mycelia of the plant pathogenic ascomycete Leptosphaeria maculans, Phytochemistry 62:147-153

Huang C Y, Ayliffe M A and Timmis J N (2003) Direct measurement of the transfer rate of chloroplast DNA into the nucleus., Nature 422, 72-76

Huang C Y, Ayliffe M A and Timmis J N (2003) Organelle evolution meets biotechnology., Nature Biotechnol. 21, 489-490

Irwin JAG, Musial JM, Mackie JM and Basford KE (2003) . Utilityof cotyledon and detached leaf assays for assessing root reactions of lucerne to Phytophthora root rot caused by Phytophthora medicaginis., Australasian Plant Pathology 32, 263-268

Jacobs, A.K., Lipka, V., Burton, R.A., Panstruga, R., Strizhov, N., Schulze-Lefert, P. and Fincher, G.B. (2003) An Arabidopsis thaliana callose synthase, GSL5, is required for wound and papillary callose formation., Plant Cell 15, 2503-2513

Jefferies SP, King BJ, Barr AR, Warner P, Logue SJ, Langridge P (2003) Marker-assisted backcross introgression of the Yd2 gene conferring resistance to barley yellow dwarf virus in barley., Plant Breeding 122, 52-56

Johnson K, Jones B, Schultz CJ, Bacic A (2003) Non-enzymic cell wall (glyco)proteins., In: The Plant Cell Wall, ed J. Rose, Blackwell Publishing, Ch 4, pp 124-154

Johnson KL, Jones BJ, Bacic A, Schultz CJ (2003) The Fasciclin like arabino galactan-proteins of Arabidopsis: A multigene family of putative cell adhesion molecules., Plant Physiol. 133, 1911-1925

Johnson X, Lidgett A, Chalmers J, Guthridge K, Jones E, Cummings N, Spangenberg G (2003) Isolation and characterisation of an invertase cDNA from perennial ryegrass, J. Plant Physiol 160: 903-911

Kalyna M, Lopato S, Barta A. (2003) Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development., Mol Biol Cell. 14(9):3565-77

Karakousis A, Barr AR, Chalmers KJ, Ablett GA, Holton TA, Henry RJ, Lim P, Langridge P. (2003) Potential of SSR markers forplant breeding andvarietyidentification in Australian barley germplasm., Aust. J. Agric Res. 54, 1197-1210

Karakousis A, Barr, AR, Kretschmer JM, Manning S, Logue SJ, Roumeliotis S, Collins HM, Chalmers KJ, Lance RCM, Langridge P, Li CD. Mapping and QTL analysis of the barley population Galleon x Haruna Nijo. Aust. J. Agric Res. 54, 1131-1135.

Karakousis A, Barr AR, Kretschmer JM, Manning S, Islam AKM, Langridge P, Chalmers KJ, Jefferies SP. (2003) Mapping and QTL analysis of the barley population Clipperx Sahara., Aust. J. Agric Res. 54, 1137-1140

Karakousis A, Gustafson JP, Chalmers KJ, Barr AR, Langridge, P. (2003) A consensus map of barley integrating SSR, RFLP, and AFLP markers., Aust.J. Agric Res. 54, 1173-1185

Karakousis A, Langridge P. (2003) A high throughput plant DNA extraction method for marker analysis., Plant Mol. Biol. Rep.

Langridge P, Barr AR (2003) Better barley faster--the role of marker assisted selection;, Preface, Aust. J. Agric Res. 54, I-IV

Langridge P, Chalmers K. (2003) The principle of molecular markers. In “Molecular Marker in Plant Breeding and Crop Improvement” , Eds G Wenzel H Loerz

Langridge, P. and Fincher, G.B. (2003) Functional Genomics. , Encyclopedia of Grain Science

Lee, R.C., Hrmova, M., Burton, R.A., Lahnstein, J. and Fincher, G.B. (2003) Bifunctional Family 3 Glycoside Hydrolases from Barley with α-L-Arabinofuranosidase and ß-DXylosidase Activity: Characterization, Primary Structures and COOH-terminal processing., J. Biol. Chem. 278, 5377-5387

Li J, Burton, RA, Harvey AJ, Hrmova M, Wardak AZ, Stone, BA and Fincher GB. (2003) Biochemical evidence linking a putative callose synthase gene with (1-3)-ß-D-glucan biosynthesis in barley. Plant Molec. Biol. 53, 213-225.

Lin Y, Ludlow E, Kalla R, Pallaghy C, Emmerling M, Spangenberg G (2003) Organ-specific developmentally-regulated and abiotic stress-induced activities of four Arabidopsis thaliana promoters in transgenic white clover, Plant Science 165:1437-1444

Madsen LH, Collins NC, Rakwalska M, Backes G, Sandal N, Krusell L, Jensen J, Waterman EH, Jahoor A, AyliffeM, Pryor AJ,Langridge P, Schulze-LefertP, Stougaard J. (2003) Barley disease resistance gene analogs of the NBS-LRR class - identification and mapping., Mol. Genet. Genom. 269, 150-161

Mares DJ, Mrva K, and Fincher GB (2003) Enzyme Activities. In Encyclopaedia of Grain Science.

Mayo, G, Langridge P (2003) Modes of reproduction in Australian populations of Hypericum perforatum L. (St John's wort) revealed by DNA fingerprinting and cytological methods. Genome 46, 573-579.

Meissner M, Lopato S, Gotzmann J, Sauermann G, Barta A. (2003) Proto-oncoprotein TLS/FUS is associated to the nuclear matrix and complexed with splicing factors PTB, SRm160, and SR proteins., Exp Cell Res. 283(2):184-95.

Milligan AS, Lopato S, Langridge P (2003). Functional genomics studies for seed development in cereals. In 'Cereal genomics' Eds. PK Gupta & RA Varshney.

Sawbridge T, Ong E, Binnion C, Emmerling M, Meath K, Nunan K, O’Neill M, O’Toole F, Simmonds J, Wearne K,Winkworth A,Spangenberg G (2003) Generation and analysis of expressed sequence tags in white clover, Plant Science 165:1077-1087

Simpson, D.J., Fincher, G.B. Huang, A.H.C. and Cameron-Mills, V. (2003) Structure and function of cereal and related higher plant, J. Cereal Sci. 37, 111-127

Sutherland CM, Henschke PA, Langridge P, and de Barros Lopes M. (2003) Subunit and cofactor binding of Saccharomyces cerevisiae sulfite reductase - towards developing wine yeast with lowered ability to produce hydrogen sulfide., Aust. J. Grape Wine Res. 9, 186-193

Sutton T, Whitford R, Baumann U, Dong C, Able JA, Langridge P (2003) The Ph2 pairing homoeologous locus of wheat, Plant J 36, 443- 456

Teng R, Ang C, McManus D, Armstrong D, Mau S-L, Bacic A (2003) Regioselective acylation of ginsenosides by Novozyme 435. Tetrahedron Letters 44(30): 5661-5664.

van Zijll de Jong E, Guthridge, K, Spangenberg, G, Forster J (2003) Development and characterisation of EST-derived simple sequence repeat, Genome 46:277-290

Zhu M Y, Pan J W, Wang L L, Gu Q, Huang C Y (2003) Mutation induced enhancement of Al tolerance in barley cell lines., Plant Sci.164: 17-23

 

 

2004

Barrett B, Griffiths A., Schreiber M, EllisonC, Mercer C, Bouton J, Sawbridge T, ForsterJ W, Spangenberg G, Bryan G, WoodfieldD (2004) A microsatellite map of whiteclover (Trifolium repens L.)., Theoretical and Applied Genetics 109, 596-608.

Basford, K E, Federer, W T and DeLacy, I H (2004) Mixed model formulations for multi environment trials., Agronomy Journal 96,143-147.

Bian X Y, Friedrich A, Bai J R, Baumann U,Hayman D L, Barker S J, Langridge P (2004) High-resolution mapping of the S & Z lociof Phalaris coerulescens., Genome 47,918-930.

Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner -Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Science 9, 418-425.

Burton, R A, Shirley, N J, King, B J, Harvey,A J and Fincher, G B (2004) The CesAGene Family of Barley, Trends in Plant Science 9, 418-425.

Caldwell K S, Langridge P, Powell W, (2004) Comparative sequence analysis of the region harbouring the hardness locus in barley and its co linear region in rice, Plant Physiology 136, 3177-3190.

Chiovitti A, Bacic A, Craik D J, Kraft G T,Liao M-L (2004) A nearly idealized 6’-Omethylated-carrageenan from the redalga Claviclonium ovatum, Carbohydrate Research 339, 1459-1466.

Chiovitti A, McManus L J, Kraft G T, Bacic A, Liao M-L (2004) Extraction and characterization of agar from Australian Pterocladia lucida., Journal of Applied Phycology 16, 41-48.

Cunliffe K V, Vecchies A C, Jones E S, Kearney G A, Forster J W, Spangenberg GC, Smith K F (2004) Assessment of gene flow using novel donor genotypes of perennial ryegrass, Australian Journal of Agricultural Research 55,389-396.

Demidchik, V, Essah, P and Tester, M (2004) Glutamate activates sodium and calcium currents in the plasma membraneof Arabidopsis root cells., Planta 219: 167-175.

Ellis, R N, Basford, K E, Leslie, J K, Hogarth,D M and Cooper, M (2004) . A methodologyfor analysis of sugarcane productivity trends -2. Comparing variety trials with commercialproductivity., Australian Journal ofAgricultural Research 55, 109-116.

Ellis, R N, Harch, B D, Basford, K E andPitcher, C R (2004) . Understandingepibenthic community structure in theGreat Barrier Reef using various ordinationtechniques., Centre for Statistics ResearchReport 107, 22.

Emmerling M, Chu P, Smith K F, Kalla R, Spangenberg G (2004) Field evaluation of transgenic white clover with AMV immunityand development of elite transgenic germplasm. In ‘‘, ‘‘Molecular Breeding of Forage and Turf” Proceedings of the 3rd International Symposium, Molecular Breeding of Forage and Crops. WangZ.-Y. (ed), 359-366. Kluwer Academic Publishers, Dallas, Texas.

Faville M J, Vecchies A C, Schreiber M, Drayton M C, Hughes L J, Jones E S, Guthridge K M, Smith K F, Sawbridge T, Spangenberg G C, Bryan G T, Forster J W (2004) Functionally associated molecular genetic marker map construction in perennial ryegrass, Molecular Breeding of Forage and Turf” Proceedings of the 3rd International Symposium.

Felitti S, Shields K, Ramsperger R, Webster T, Ong B, Sawbridge T, Spangenberg G (2004) Gene discovery and microarray based transcriptome analysis in grass endophytes ‘‘Molecular Breeding of Forage and Turf, Proceedings of the 3rd International Symposium, Molecular Breeding of Forage and Crops.

Fincher, G B and Langridge, P (2004) Genomics., Encyclopedia of Grain Science (C Wrigley, H Corke and CE Walker, eds) Vol 2, 16-24.

Fincher GB, and Stone BA, (2004) Chemistry of non-starch polysaccharides from cereal grains. In Encyclopaedia of Grain Science (C Wrigley, H Corke and CE Walker, eds) Vol 1, 206-223.

Garcia, A, Ward, P, Appleby, N, Basford, K and Ragan, M (2004) From genotype to phenotype: Modeling knowledge in functional plant genomics, Proceedings of the International Centre of Excellence for Education in Mathematics (ICE-EM)”Summer Symposium in Bioinformatics Bio Info Summer 2004: Genome to Phenome Modeling, Canberra, 19-20.

Gaspar Y M, Nam J, Schultz C J, Lee LY, Gilson P R, Gelvin S B, Bacic A (2004) Characterization of the Arabidopsis lysine-rich arabinogalactan-protein AtAGP17 mutant (rat1) that results in a decreased efficiency of Agrobacterium transformation, Plant Physiol. 135, 2162-2171.

Gilson P R, Vergara C E, Kjer-Nielsen L, Teasdale R, Bacic A, Gleeson P (2004) Identification of a Golgi-localised GRIP domain protein from Arabidopsis thaliana., Planta 219, 1050-1056.

Hrmova, M, De Gori, R, Smith, B J, Vasella,A, Varghese, J N and Fincher, G B (2004) Three-Dimensional Structure of the Barley ß-D-Glucan Glucohydrolase in Complex with a Transition State Mimic., Journal of Biological Chemistry, 279, 4970-4980.

Islam, F M A, Beebe, S, Munoz, M, Tohme, J, Redden, R J and Basford, K E (2004) .Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool., Theoretical and Applied Genetics 108,243-252.

Jenkins H, Hardy N, Beckmann M, Draper J, Smith A R, Taylor J, Fiehn O, Goodacre R, Bino R J, Hall R, Kopka J, Lane G A, Lange B M, Liu J R, Mendes P, Nikolau B J, Oliver S G, Paton N W, Rhee S, Roessner-TunaliU, Saito K, Smedsgaard J, Sumner L, Wang T, W (2004) A, Nature Biotechnology 22, 1601-1606.

Kremer C, Pettolino F, Bacic A, Drinnan A (2004) Distribution of cell wall components in Sphagnum hyaline cells and liver wort and hornwort elaters.,Planta 219,1023-1035.

Langridge P, Pallotta M and Hayden M, (2004) SSR Markers in Barley Breeding and Genomics,, 9th International Barley Genetics Symposium, Brno, Czech Republic 127-134.

Lawes, R A, Wegener, M K, Basford, K Eand Lawn, R J (2004) . The evaluation of the spatial and temporal stability of sugar cane farm performance based on yield and commercial cane sugar., Australian Journal of Agricultural Research 55,335-344.

Lorkovic ZJ, Lopato S, Pexa M, Lehner R, Barta A. (2004) Interactions of Arabidopsis RS domain containing cyclophilins with SR proteins and U1 and U11 small nuclear ribonucleoprotein-specific proteins suggest their involvement in pre-mRNA Splicing., J Biol Chem. 279(32):33890-8

Love C G, Batley J, Lim G, Robinson A J, Savage D, Singh D, Spangenberg G C, Edwards D (2004) New computational tools for Brassica genome research., Comparative and Functional Genomics 5, 276-280.

Macdonald, J M, Hrmova, M, Fincher, G B and Stick, R V (2004) The Synthesis of 3-O-b-Laminaribiosyl)-isofagomines, Potent Inhibitors of 1,3-b-D-Glucanendo-Hydrolases., Australian Journal of Chemistry, 57, 187-191.

Mares, D J, Mrva, K and Fincher, G B (2004) Enzyme Activities., In: Encyclopedia of Grain Science (C. Wrigley, H Corke and C.E. Walker, eds) Vol 1, pp 357-365.

Milligan A S, Lopato S and Langridge P, (2004) Functional genomics of seed development in cereals. In, Cereal Genomics, Gupta P K and Varshney R K

Newbigin E, Bacic A, Langridge P and Fincher GB, (2004) Functional Genomics in the productivity and end-use quality of barley, .Ovenden, J R, Street, R, Peel, D, Peel, SL, Courtney, A, Podlich, H, Basford, Kand Dichmont, C, 9th International Barley Genetics Symposium, Brno, Czech Republic 187-194

Oxley D, Currie G C, Bacic A (2004) Analysis of carbohydrate from glycoproteins. In: Purifying proteins for proteomics:, Purifying proteins for proteomics: A laboratory manual. R J Simpson (ed), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NewYork, USA, ch 25, pp 579-636.

Powell W and Langridge P, (2004) Unfashionable crop species flourish in the 21st century, Genome Biology 5, Article 233.

Qiao, C G, Basford K E, De Lacy I H and Cooper M (2004) . Advantage of single-trial analysis models for response to selection in wheat breeding multi-environment trials., Theoretical and Applied Genetics 108,1256-1264.

Schultz C J, Ferguson K I, Lahnstein J, Bacic A (2004) Post-translational modifications of arabino galactan-peptides of Arabidopsis thaliana: ER and GPI-anchor signal cleavage sites and hydroxylation of proline., Journal of Biological Chemistry 279,45503-45511.

Spangenberg G, Petrovska N, Kearney G A, Smith K F (2004) Low-pollen allergen ryegrasses: towards a continent free of hay fever? In: ., Allergy Matters! Kluwer Academic Press

Strohmeier, M, Hrmova, M, Fischer, M, Harvey A J, Fincher, G B and Pleiss J (2004) Molecular Modelling of Family GH16 Glycoside Hydrolases: Potential Rolesfor Xyloglucan Endotrans glucosylases / Hydrolases in Cell Wall Modification in the Poaceae., Protein Science, 13,3200-3213.

Tester, M & Morris, C (2004) World food– how to meet the growing need?, Issues, No. 69. http://www.issues.control.com.au

Tull D, Vince J E, Callaghan J M, Naderer T, Spurck T, McFadden G I, Currie G, Ferguson K, Bacic A, McConville M (2004) SMP-1, a member of a new family of small myristoylated proteins in kine to plastid parasites, is targeted to the flagellum membrane in Leishmania., Molecular Biology of the Cell 15, 4775-4786.

van Zijll de Jong E, Bannan N R, Batley J, Guthridge K M, Spangenberg G C, Smith K F and Forster J W (2004) Genetic diversity in the perennial rye grass fungal endophyte Neotyphodium lolii. ‘‘Molecular Breeding of Forage and Turf, Proceedings of the 3rd International Symposium, Molecular Breeding of Forage and Crops.

Varshney RK, Zhang HN, Potokina E, Stein N, Langridge P, Graner A (2004) A simple hybridization-based strategy for the generation of nun-redundant EST collections - a case study in barley (Hordeum vulgare L.) Plant Science 167, 629-634.

Wang Z Y, Ge Y, Scott M, Spangenberg G (2004) Viability and longevity of pollen from transgenic and non-transgenic tallfescue, American Journal of Botany 91(4), 523-530.

Wang Z.-Y (ed),155-164. Kluwer Academic Publishers, Dallas, Texas. Varshney R K, Hähnel, Thiel T, SteinN, Altschmied, Langridge P, Graner A (2004) Genetic and Physical Mapping of Genic Microsatellites in Barley, ,155-164. Kluwer Academic Publishers, Dallas, Texas.

Zhang H N, Sreenivasulu N, Weshke W, Stein N, Rudd S, Radchuk V, Potokina E, Scholz U, Schweizer P, Zierold U, Langridge P, Varshney R K, Wobus U, Graner A (2004) Large-scale analysis of the barley transcriptome based on expressed sequence tags, Plant Journal 40, 276-290.

Zhang, D, Hrmova, M, Wan, C-H, Wu,C, Balzen, J, Cai, W, Wang, J, Densmore,L D, Fincher, G B, Zhang, H and Haigler,C H (2004) Members of a new group of chitinase-like genes are expressed preferentially in cotton cells with secondary walls., Plant Molecular Biology, 54, 353-372. [Cover article]

 

 

2005

Bacic A (2005) Biopolymers., In Evans BK. et al, Biology Two. 4th Edition, Heinemann, Melbourne

Bacic A, Burton R, Doblin M, Dwivany F, Gatford KT, Medhurst A, Harvey A, Shirley N, Newbigin EJ and Fincher GB (2005) Cellulose synthase (CESA) and cellulose-synthase-like (CSL) gene families of barley, Amer. Chem Soc. 227, U292-U292

Boersma JG, Pallotta MA, Li C, Buirchell BJ, Sivasithamparam K and Yang H (2005) Construction of a genetic linkage map using MFLP, and identification of molecular markers linked to domestication genes in narrow-leafed lupins (Lupinus angustifolius L.), Cell and Mol Biol Letters Vol 10 331-344.

Bozic I, Zhang GL, Brusic V (2005) Predictive vaccinology: optimisation of predictions using support vector machine classifiers., Lecture Notes in Computer Science 3578, 375-381

Brusic V and Petrovsky N (2005) Immunoinformatics and its relevance to understanding human immune disease., Expert Review of Clinical Immunology. 1(1), 145–157.

Brusic V, August TJ and Petrovsky N (2005) Information technologies for vaccine research., Expert Review of Vaccines 4, 407-417.

Burton RA, Farrokhi N, Bacic A, Fincher GB (2005) Plant cell wall biosynthesis: real progress in the identification of participating genes, Planta 221, 309-312.

Burton RA, Wilson SM, Hrmova M, Harvey AJ, Shirley NJ, Medhurst A, Stone BA, Newbigin EJ, Bacic A, Fincher GB (2005) Cellulose Synthase-like CsIF Genes Mediate the Synthesis of Cell Wall (1,3;1,4)-β-D-Glucans; Science, 311:1940-1942.

Caldwell KS, Langridge P, Powell W (2005). Extreme population dependient linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare; Plant Physiology Vol: 136 Issue: 2 Pages: 3177-3190

Carninci P, Kasukawa T, Katayama S, Gough J et al (2005) The Transcriptional Landscape of the Mammalian Genome., Science, Sep 2;309(5740):1559-63.

Chiovittii A, Harper RE, Willis A, Bacic A, Mulvaney P, Wetherbee R (2005) Variations in the substituted 3-linked mannans closely associated with the silicified walls of diatoms., J. Phycol 41,1154-1161.

Classen B, Mau SL and Bacic A (2005) The arabinogalactan-proteins from pressed juice of Echinacea purpurea belong to the "hybrid" class of hydroxyproline-rich glycoproteins., Planta Medica 71, 59-66

Cogan N, Smith K, Yamada T, Francki M, Vecchies A, Jones E, Spangenberg G and Forster J (2005) QTL analysis and comparative genomics of herbage quality traits in perennial ryegrass (Lolium perenne L.), Theor. Appl. Genet. 110, 364-380

Davenport RJ, James RA, Zakrisson-Plogander A, Tester M and Munns RJ (2005) Control of sodium transport in durum wheat.,Plant Physiology 137, 807-818

Dong CM, Thomas S, Becker D, Löerz H, Whitford R, Sutton T, Able JA and Langridge P (2005) WM5: Isolation and characterisation of a gene expressed during early meiosis and shoot meistem development in wheat. , Functional Plant Biol. 32, 240-258.

Fincher, G.B. and Johnson, C. (2005) A cereal chemist’s quick guide to genetics, plant breeding and bioIT., Published by the Value Added Wheat CRC Ltd., North Ryde, NSW, Australia.

Gibeaut DM, Pauly M, Bacic A and Fincher GB (2005) Changes in cell wall polysaccharides in developing barley (Hordeum vulgare) coleoptiles.,Planta 221, 729-738

Gilliham M and Tester M (2005) The regulation of anion loading to the maize root xylem, Plant Physiology 137, 819-828

Hrmova M, Streltsov VA, Smith BJ, Vasella A, Varghese JN, Fincher GB (2005) Structural rationale for low nanomolar binding of transition state mimics to a family GH3 barley β-D-glucan glucohydrolase, Biochemistry (USA) 44: 16529-16539

Huang CY, Grünheit N, Ahmadinejad N, Timmis JN and Martin W (2005) Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes., Plant Physiol. 138, 1723-1733

Jarosch B, Collins NC, Zellerhoff N and Schaffrath U (2005) RAR1, ROR1, and the actin cytoskeleton contribute to basal resistance to Magnaporthe grisea in barley., Mol. Plant Microbe Interact., 18, 397-404

John UP and Spangenberg GC (2005) Xenogenomics: genomic bioprospecting in indigenous and exotic plants through EST discovery, cDNA microarray-based expression profiling and functional genomics., Comp. Funct. Genom., 230-235

Johnson AAT, Hibberd JM, Gay C, Essah PA, Haseloff J, Tester M and Guiderdoni E (2005) Spatial control of transgene expression in rice (Oryza sativa L.) using the GAL4 enhancer trapping system. Plant Journal 41, 779-789

Jones CE, Baumann U and Brown AL (2005) Automated methods of predicting the function of biological sequences using GO and BLAST., BMC Bioinformatics BMC Bioinformatics 6:272-282

Kroonenberg PM, Basford KE and Gemperline PJ (2005) Grouping three-mode data with mixture methods: the case of the diseased blue crabs., Journal of Chemometrics 18, 508-518

Langridge P and Chalmers K (2005) The principle: identification and application of molecular markers. In Molecular Marker Systems In Plant Breeding And Crop Improvement, Biotechnology In Agriculture And Forestry 55, 3-22

Lee KJD, Sakata Y, Mau S-L, Bacic A, Quatrano RS, Knight CD, Knox JP (2005) Arabinogalactan-proteins (AGPs) are required for apical cell extension in the moss Physcomitrella patens.,
The Plant Cell 17, 3051-3065

Love CG, Robinson AJ, Lim GAC, Hopkins CJ, Batley J, Barker G, Spangenberg GC and Edwards D (2005) Brassica ASTRA: an integrated database for Brassica genomic research, Nucl. Acids Res. 33, D656-D659

Miotto O, Tan TW and Brusic V (2005) Extraction by Example: Induction of Structural Rules for the Analysis of Molecular Sequence Data from Heterogeneous Sources, Lecture Notes in Computer Science 3578, 398-405

Patterson JH, Ford KL, Platt M, Sutton T, Langridge P, Fincher GB, Bacic A (2005) A proteomic investigation of the molecular mechanisms of boron tolerance in Hordeum vulgare, C.J. Li et al (Eds), Plant nutrition for food security, human health and environmental protection, Tsinghua University Press, Beijing, China, pp174-175

Petrovska N, Wu XL, Donato R, Wang ZY, Ong EK, Jones E, Forster J, Emmerling M, Sidoli A, O'Hehir R and Spangenberg G (2005) Transgenic ryegrasses (Lolium spp.) with down-regulation of main pollen allergens., Mol Breed. 14, 489-501

Rajapakse M, Wyse L, Schmidt B and Brusic V (2005) Deriving Matrix of Peptide-MHC Interactions in Diabetic Mouse by Genetic Algorithm., Lecture Notes in Computer Science 3578, 440-447

Schmidt O and Schreiber AW (2005) Integration of cell adhesion reactions – a balance of forces?, J. Theor. Biol. 238, 608-615

Schönbach C, Koh JLY, Flower DR and Brusic V (2005) An Update on Functional Molecular Immunology Database FIMM., Applied Bioinformatics 4, 25-31

Serazetdinova L, Oldach KH and Lörz H (2005) Expression of transgenic stilbene synthases in wheat causes the accumulation of unknown stilbene derivatives with antifungal activity, Journal of Plant Physiology 162, 985-1002

Shavrukov YN (2005) Modern plant breeding in Australia., Information Bulletin of the Vavilov Society of Geneticists and Breeders (Novosibirsk, Russia) 9(3), 436-439

Shavrukov YN (2005) Screening of wheat samples for the salinity tolerance and prospectives of their introduction in Australia, Theoretical and Practical Research in Plant Biology. Proceeding of the International Conference (Belgorod, Russia), 195-197.

Sprunck S, Baumann U, Edwards K, Langridge P and Dresselhaus T (2005) The transcript composition of egg cells changes significantly following fertilization in wheat (Triticum aestivum L.), Plant J. 41, 660-672

Tan PTJ, Srinivasan KN, Seah SH, Koh JLY, Tan TW, Shoba Ranganathan S and Brusic V (2005) Accurate prediction of scorpion toxin functional properties from primary sequences., Journal of Molecular Graphics and Modelling 24, 17-24

Teng R, Bui A, McManus D, Armstrong D, Mau S, Bacic A (2005) Regioselective acylation of several polyhydroxylated natural compounds by Candida antarctica Lipase B., Biocatalysis & Biotransformation 23, 109-116

Tester M and Bacic A (2005) Abiotic stress tolerance in grasses – from model plants to crop plants,
Plant Physiology 137, 791-793

Varshney RK, Balyan HS and Langridge P (2005) Wheat, The Genomes; A series on Gene Mapping, Molecular Breeding and Genomics of Economic Species, Vol 1, Cereals and Millets, Ed C. Kole, Science Publishers, pp 121-219

Varshney RK, Sigmund R, Borner A, Korzun V, Stein N, Sorrells ME, Langridge P and Graner A (2005) Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice, Plant Sci. 168, 195- 202

Walch-Liu P, Liu LH, Gilliham M, Remans T, Miller AJ, Tester M, and Forde BG (2005) Evidence that L-glutamate can act as an exogenous signal to modulate root growth and branching in Arabidopsis thaliana. , Plant & Cell Physiology 47: 1045-1057

Willsmore KL, Eckermann P, Varshnev RJ, Graner A, Langridge P, Pallotta MA, Williams K (2005) Mapping new SSRs in Australian Barley Germplasm., Proc 12th Australian Barley Technical Symposium, Hobart Tasmania 11-14 September.

Zhang G, Srinivasan KN, Veeramani A, August TJ and Brusic V (2005) PREDBALB/c: a system for prediction of peptide binding to the H2d molecules, a haplotype of the BALB/c mouse., Nucleic Acids Research 33, W180-183

Zhang GL, Khan AM, Srinivasan KN, August JT, and Brusic V (2005) MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides., Nucleic Acids Research 33, W172-179

Zhang QS, Shirley N, Lahnstein J and Fincher GB (2005) Characterization and expression patterns of UDP-D-glucuronate decarboxylase genes in barley, Plant Physiol. 138, 131-141

Zhu Y, Pettolino F, Mau S-L and Bacic A (2005) Characterization of cell wall polysaccharides from the medicinal plant Panax notoginseng. Phytochemistry 66(9), 1067-1076

 

 

2006

Able JA & Langridge P (2006) Wild sex in the grasses, Trends in Plant Science 11(6): 261-263

Babar, MA, M Van Ginkel, AR Klatt, B Prasad, and MP Reynolds. (2006) The potential of using spectral reflectance indices to estimate yield in wheat grown under reduced irrigation. , Euphytica 150:155-72.

Babar, MA, Reynolds, MP. Van Ginkel, A.R. Klatt, W.R. Raun, and M.L. Stone. (2006) Spectral Reflectance Indices as a Potential Indirect Selection Criteria for Wheat Yield under Irrigation. , Crop Science. 46: 578-588.

Bacic A (2006) Breaking an impasse in pectin biosynthesis, PNAS USA 103, 5639-5640

Brown SL, Stockdale VJ, Pettolino F, Pocock KF, de Barros Lopes M, Williams PJ, Bacic A, Fincher GB, Høj PB, Waters EJ (2006) Reducing haziness in white wine by overexpression of Saccharomyces cerevisiae genes YOL155c and YDR055w, Applied & Environ. Microbiol.

Bui AKT, Bacic A, Pettolino F (2006) Polysaccharide composition of the fruit juice of Morinda citrifolia (Noni) grown in Viet Nam , Phytochemistry 67: 1271-1275.

Burton RA, Wilson SM, Hrmova M, Harvey AJ, Shirley NJ, Medhurst A, Stone BA, Newbigin EJ, Bacic A and Fincher GB (2006) Cellulose Synthase-like CslF Genes Mediate the Synthesis of Cell Wall (1,3;1,4)-β-D-Glucans., Science 311, 1940-1942.

Calderini, D.F., Reynolds M.P, and G.A. Slafer (2006) Source-Sink Effects on Grain Weight of Bread wheat, Durum Wheat and Triticale. , Australian Journal of Agricultural Science: 57: 227-233.

Caldwell KS, Langridge P, Powell W (2006) Extreme population dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare, Genetics, 172, 557-567.

Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K, Ragan MA, Sansone SA. (2006) The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case, BMC Bioinformatics 7:267.

Crismani W, Baumann U, Sutton T, Shirley N, Webster T, Spangenberg G, Langridge P & Able JA (2006) Microarray expression analysis of meiosis and microsporogenesis in hexaploid wheat, BMC Genomics, 7: 267 (doi:10.1186/1471-2164-7-267)

Drew DP, Lunde C, Lahnstein J, Fincher GB (2006) Heterologous expression of cDNAs encoding monodehydroascorbate reductases from the moss, Physcomitrella patens and charaterizations of the expressed enzymes, Planta (Epub ahead of print

Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A , Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R (2006) An atlas of gene expression from seed to seed through barley development, Functional and Integrative Genomics 6 (2006) 202-211

Farrokhi N, Burton RA, Brownfield L, Hrmova M, Wilson SM, Bacic A, Fincher GB (2006) Plant Cell Wall Biosynthesis: Genetic, Biochemical and Functional Genomics Approaches to the Identification of Key Genes,Plant Biotechnology Journal 4, 145-167

Gang Ma, Douglas Hay, Dongmei Li, Sassan Asgari and Otto Schmidt (2006) Recognition and inactivation of LPS by lipophorin particles, Developmental and Comparative Immunology, 30(7), 617-629

Gatford KT, Basri Z, Edlington J, Lloyd J, Qureshi JA, Brettell R, Fincher GB (2006) Gene flow from transgenic wheat and barley under field conditions, Euphytica DOI 10.1007/s10681-006-9160-1

Gutiérrez-Rodríguez M, JA Escalante-Estrada, MT Rodríguez-González, MP Reynolds (2006) Canopy reflectance indices and its relationship with yield in common bean plants (Phaseolus vulgaris L.) with phosphorous supply. , International Journal of Agriculture and Biology 8: 203-7.

Hosp J, Tashpulatov A, Roessner U, Barsova E, Katholnigg H, Steinborn R, Melikant B, Lukyanov S, Heberle-Bors E, Touraev A (2006) Transcriptional and metabolic profiles of stress-induced, embryogenic tobacco microspores., Plant Mol Biol. 63, 137-149

Hrmova M, Burton RA, Biely P, Lahnstein J, Fincher GB (2006) Hydrolysis of (1,4)-β-D-Mannans in Barley (Hordeum vulgare L.) Is Mediated by the Concerted Action of (1,4)-β-D-Mannan Endohydrolase and β-D-Mannosidase, Biochem. J. 398,

Johnson AAT, Yu SM, Tester M. (2006) Activation tagging systems in rice., In: Uphadyana, N., ed., ‘Rice Functional Genomics’. Springer, pp. 343-364

Kuchel H, Hollamby G, Langridge P, Williams K, Jefferies SP, (2006) Identification of genetic loci associated with ear emergence in bread wheat, Australian Journal of Agricultural Research

Kuchel H, Langridge P, Mosionek L, Williams K, Jefferies SP (2006) The genetic control of milling yield, dough rheology and baking quality of wheat, Theor Appl Genet

Langridge P, Paltridge N, Fincher GB (2006) Functional Genomics of Abiotic Stress Tolerance, Briefings in Functional Genomics and Proteomics, V. 4 Issue 4

Lopato S, Bazanova N, Morran S, Milligan AS, Shirley S, and Langridge P (2006) Isolation of plant transcription factors using a modified yeast one-hybrid system, Plant Methods 2:3

Lunde C, Baumann U, Shirley NJ, Drew DP, Fincher GB (2006) Gene structure and expression pattern analysis of three monodehydroascorbate reductase (Mdhar) genes in Physcomitrella patens: Implications for the evolution of the MDHAR family in plants, Plant Molecular Biology 2006, Jan; 60(2):259-75

Mahbubur Rahman, Gang Ma, Harry L.S. Roberts and Otto Schmidt (2006) Cell-free immune reactions in insects, Journal of Insect Physiology, 52 (7), 754-762

McDonagh H, Ferguson K, Bacic A (2006) Variation in protein abundance profiles in the M. semitendinosus of lambs bred from sires selected on the basis of growth and muscling potential., Aust. J.Agric. Res.57, 671-682.

Mulvenna JP, Bharathi R, Burton RA, Shirley NJ, Fincher GB, Anderson MA and Craik DJ (2006) Discovery of Cyclotide-like Protein Sequences in Graminaceous Crop Plants: Ancestral Precursors of Circular Proteins?, Plant Cell 18, 2134-2144.

Murthy M and Tester M (2006) K+ and Na+ currents across the plasma membrane of protoplasts from the roots of wild type and a Na+ hyperaccumulating mutant of Capsicum,Journal of Experimental Botany, Special Issue on Salinity 57: 1171-1180

Nielsen KA, Hrmova M, Nielsen JN, Forslund K, Ebert S, Olsen CE, Fincher GB, Møller BL (2006) Reconstitution of cyanogenesis in barley (Hordeum vulgare L.) and its implications for resistance against the barley powdery mildew fungus, Planta 223, 1010-1023

Pettolino F, Liao M-L, Zhu Y, Mau S-L, Bacic A (2006) Structure, function and cloning of arabinogalactan-proteins (AGPs): An overview.,Food and Food Ingredients Journal of Japan 211, 12-25

Platten JD, Cotsaftis O, Berthomieu P, Bohnert H, Davenport RJ, Fairbairn DJ, Horie T, Leigh RA, Lin HX, Luan S, Mäser P, Pantoja O, Rodríguez-Navarro A, Schachtman DP, Schroeder JI, Sentenac H, Uozumi N, Véry AA, Zhu JK, Dennis ES and Tester M (2006) Nomenclature for HKT transporters, key determinants of plant salinity tolerance, Trends in Plant Sciences 11, 372-374

Reynolds MP and Borlaug NE (2006) Applying innovations and new technologies for international collaborative wheat improvement. , Journal of Agricultural Science 144: 95-110.

Reynolds MP and Borlaug NE (2006) Impacts of breeding on international collaborative wheat improvement. , Journal of Agricultural Science 144: 3-7.

Reynolds, MP, Rebetzke G, Pellegrinesci A, Trethowan R (2006) Drought Tolerance in Cereals , In (Ed) JM Ribaut. Haworth's Food Products Press, New York

Roessner U, Patterson J, Forbes M, Fincher G, Langridge P, Bacic A (2006) An investigation of boron toxicity in barley using metabolomics., Plant Physiology 142, 1087-1101

Roy, SJ (2006) The Salt Focus group at the Australian Centre for Plant Functional Genomics, Phytogen 8:19-20

Schreiber AW and Baumann U (2006) A framework for gene expression analysis., Bioinformatics. 2007 Jan 15;23(2):191-7. Epub 2006 Nov 21

Shavrukov Y, Bowne J, Langridge P and Tester M (2006) Screening for sodium exclusion in wheat and barley, Proceedings of 13th Conference of the Australian Society of Agronomy

Shavrukov Y, Sokolov V, Langridge P and Tester M (2006) Interspecific hybrid, Zea mays L. x Tripsacum dactiloides L., a new fodder crop with large silage biomass production under abiotic stresses, Proceedings of 13th Conference of the Australian Society of Agronomy

Symons GM, Davies C, Shavrukov Y, Dry IB, Reid JB and Thomas MR (2006) Grapes on steroids. Brassinosteroids are involved in grape berry ripening, Plant Physiology 140 (1), 150-158

Tacconi G, Baldassarre V, Collins NC , Bulgarelli D, Stanca AM, and Valè G. (2006) Haplotype characterization and markers at the barley Mlo powdery mildew resistance locus as tools for marker-assisted selection., Genome 49: 864-872

Varshney RK, Grosse I, Haehnel U, Siefken R, Prasad M, Stein N, Langridge P, Altschmied L, Graner A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome, Theor Appl Genet. 113, 239-250

Whitford R, Baumann U, Sutton T, Gumaelius L, Wolters P, Tingey S, Able JA and Langridge P. (2006) Identification of transposons, retroelements, and a gene family predominantly expressed in floral tissues in chromosome 3DS of the hexaploid wheat progenitor Aegilops tauschii., Functional and Integrative Genomics DOI:http://dx.doi.org/10.1007/s10142-006-0026-3

Whitney S, Wilson E, Reid JSG, Webster J, Bacic A, Gidley MJ (2006) Effects of structural variation in xyloglucan polymers on interactions with bacterial cellulose, American Journal of Botany 93, 1402-1414

Willsmore KL, Eckermann P, Varshney RK, Graner A, Langridge P, Pallotta M, Cheong J, Williams KJ (2006) New eSSR and gSSR markers added to Australian barley maps, Aust. J. Agric, Res. 57:953-959

Wilson SM, Burton RA, Doblin MS, Stone BA, Newbigin EJ, Fincher GB and Bacic A (2006) Temporal and spatial appearance of wall polysaccharides during cellularization of barley (Hordeum vulgare) endosperm, Planta 224, 655-667

Zhang Q, Maria Hrmova, Neil J Shirley, Jelle Lahnstein, Geoffrey B Fincher (2006) Gene expression patterns and catalytic properties of UDP-D-glucose 4-epimerases from barley (Hordeum vulgare L.), Biochemical Journal 394:115-124 (2006)

Zhao T, Pallotta M, Langridge P, Prasad M, Graner A, Schulze-Lefert P, Koprek T (2006) Mapped Ds/T-DNA launch pads for functional genomics in barley, The Plant Journal

Zhu Y, Pettolino F, Mau S-L, Shen Y-C, Chen C-F, Bacic A (2006) Immunoactive polysaccharide-rich fractions from Panax notoginseng, Planta Medica 72: 1-7

 

 

2007

Able JA, Langridge P & Milligan AS (2007) Capturing diversity in the cereals: many options but little promiscuity, Trends in Plant Science, 12(2): 71-79

Appleby N, Edwards D and Batley J, (2007) New technologies for ultra-high throughput genotyping in plants  Ed  Somers D, Langridge P, and Gustafson JP, Methods in Molecular Biology, Humana Press (USA)

Ayliffe MA, Pallotta M, Langridge P and Pryor AJ (2007) A Barley Activation Tagging System, Plant Mol  Biol  64:329-47

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

Batley J, Jewell E and Edwards D, 2007. Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers, Plant Bioinformatics  Ed  Edwards D  Methods in Molecular Biology, Humana Press (USA).

Boden SA, Shadiac N, Tucker E, Langridge P & Able JA, (2007) Expression and functional analysis of TaASY1 during meiosis of bread wheat (Triticum aestivum), BMC Molecular Biology 8:65

Brownfield L, Ford K, Doblin M, Newbigin E, Read S, Bacic A, (2007) Proteomic and biochemical evidence links the callose synthase in Nicotiana alata pollen tubes to the product of the NaGSL1 gene, Plant Journal 52, 147-156.

Byrt, C S, Platten, J D, Spielmeyer, W, James, R A, Lagudah, E S, Dennis, E S, Tester, M  & Munns, R, (2007) HKT1;5-like cation transporters linked to Na+ exclusion loci in wheat, Nax2 and Kna1, Plant Physiology, 143, 1918-1928.

Chen Z, Pottosin I, Cuin T, Funglsang A, Tester M, Jha D, Zepeda-Jazo I, Zhon M, Palmgren M; Newman I; Shabala S, (2007) Root plasma membrane transporters controlling K+/Na+ homeostasis in salt stressed barley, Plant Physiology, 145:1714-1725.

Collins NC, Niks RE and Schulze-Lefert P, (2007) Resistance to cereal rusts at the plant cell wall - what can we learn from other host-pathogen systems?, Australian Journal of Agricultural Research, 58, 476 - 489

Davenport RJ, Munoz-Mayor A, Jha D, Essah PA, Rus A  & Tester M, (2007) The Na+ transporter AtHKT1 controls xylem retrieval of Na+ in Arabidopsis, Plant, Cell & Environment 30, 497-507

Edwards D, Bioinformatics and plant genomics for staple crops improvement, Breeding Major Food Staples for the 21st Century  2007. Eds  Kang MS and Priyadarshan PM  Blackwell

Gang Ma (2007) The molecular biology of tolerance to Bacillus thuringiensis endotoxin in Helicoverpa armigera: a novel mechanism and genetic transmission, Australian Journal of Entomology, 46(1), 86

Genc Y, Huang CY and Langridge P, (2007) A study of the role of root morphological traits in growthof barley in zinc-deficient soil, Journal of Experimental Botany 58: 2775–2784

Genc, Y, McDonald, G K  & Tester, M, (2007) Reassessment of tissue Na+ concentration as a criterion for salinity tolerance in bread wheat, Plant, Cell & Environment, doi: 10 1111/j 1365-3040 2007 01726 x

Glassop D, Roessner U, Bacic A, Bonnett G, (2007) Changes in the sugarcane metabolome with stem development  Are they related to sucrose accumulation?, Plant Cell Physiol  48, 573-584

Hrmova M, Farkas V, Lahnstein J, Fincher GB, (2007) A barley xyloglucan xyloglucosyl transferase covalently links xyloglucan, cellulosic substrates and (1, 3;1, 4)-β-D-glucans, Journal of Biological Chemistry 282, 12951-12962

Hrmova M, Fincher GB, (2007) Dissecting the catalytic mechanism of a plant β-D-glucan glucohydrolase through structural biology using inhibitors and substrate analogues  Invited review, Carbohydrate Research 342, 1613-1623 

Jacobs A, Lunde C, Bacic A, Tester M, Roessner U, (2007) The impact of constitutive heterologous expression of a moss Na+ transporter on the metabolomes of rice and barley, Metabolomics3(3): 307-317

Jones CE, Brown AL, Baumann U, (2007) Estimating the annotation error rate of curated GO database sequence annotations, BMC Bioinformatics  8: 170

Kuchel H, Williams KJ, Langridge P, Eagles HA, Jefferies SP, (2007) Genetic dissection of grain yield in bread wheat  II  QTL-by-environment interaction, Theor Appl Genet  115:1015-27 

Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C, Martin J, Morel JB, Johnson AAT, Bourgis F, Ghesquière A, Ruiz M, Courtois B, Guiderdoni E, (2007) Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library, Nucleic Acids Research

Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Batley J, Spangenberg G, Edwards D, (2007) A Comparative Map Viewer Integrating Genetic Maps for Brassica and Arabidopsis, BMC Plant Biology, 7: 40

Lloyd AH, Milligan AS, Langridge P, Able JA, (2007) TaMSH7: A cereal mismatch repair gene that affects fertility in transgenic barley (Hordeum vulgare L ), BMC Plant Biol  7:67

Lopato S, Borisjuk L, Milligan AS, Shirley N, Bazanova N, Langridge P, (2007) Systematic identification of factors involved in post-transcriptional processes in wheat grain, Plant Mol Biol  62; 637-653 

Love CG, Edwards D, (2007) Accessing integrated Brassica genetic and genomic data using the BASC server, Plant Bioinformatics  Ed  Edwards D  Methods in Molecular Biology, Humana Press (USA), pp  229-244

Lunde C, Drew D, Jacobs A and Tester M, (2007) Exclusion of Na+ via a sodium ATPase (PpENA1) ensures normal growth of Physcomitrella patens under moderate salt stress, Plant Physiology 144: 1786-1796

Møller I and Tester M, (2007) Salinity tolerance of Arabidopsis: a good model for cereals?, Trends in Plant Science 12: 534-540

Moller I, Sorensen I, Bernal AJ, Blaukopf C, Lee K, Øbro J, Pettolino F, Roberts A, Mikkelsen JD, Knox JP, Bacic A, Willats WGT, (2007) High-throughput mapping of cell wall polymers within and between plants using novel microarrays, Plant Journal 50, 1118-1128

Paltridge N, Langridge P and Fincher GB, (2007) GM Wheat and Barley I: Genetics, reproductive biology and agronomic considerations. Australian Institute of Agricultural Science and Technology, (ed  Reuter D), 11-18

Patterson J, Ford K, Cassin A, Natera, Bacic A, (2007) Increased abundance of proteins involved in phytosiderophore production in boron tolerant barley, Plant Physiology 144, 1612-1631

Périn C, Rebouillat J, Brasileiro AMC, Diévart A, Gantet P, Breitler JC, Johnson AAT, Courtois B, Ahmadi N, de Raissac M, Luquet D, Conte M, This D, Pati PK, Le QH, Meynard D, Verdeil JL, Guiderdoni E, (2007) Novel insights into the genomics of rice root adaptive development, In Brar DS, Mackill DJ, Hardy B (Eds ) Rice Genetics V, Proceedings of the Fifth International Rice Genomics Symposium (pp  117-141)  Los Banos, Philippines: International Rice Research Institute

Reynolds MP, Saint Pierre C, Vargas M, Condon AG, 2007. Evaluating potential genetic gains in wheat associated with stress-adaptive trait expression in diverse germplasm under drought and heat stress, Crop Science 47(53):172-189.

Roessner U, Pettolino F, 2007. The importance of anatomy and physiology in plant metabolomics, In “Metabolomics: A Powerful tool in Systems Biology” of the book series Topics in Current Genetics, Jewett MC and Nielson J, eds, Springer, Heidelberg, Germany

Schnurbusch T, Huang C, Collins NC, Sutton T, John U, Roy S, Paltridge N, Tester MA, Langridge P and Fincher GB, (2007) GM Wheat and Barley II  Prospects for Enhanced Productivity and Quality, Australian Institute of Agricultural Science and Technology, (ed  Reuter D), 21; 4-11

Schnurbusch, T, Collins N, Eastwood R, Sutton T, Jefferies S, Langridge P, (2007) Fine mapping and targeted SNP survey using rice-wheat gene colinearity in the region of the Bo1 boron toxicity tolerance locus of  bread wheat, Theor  Appl  Genet  115:451-61

Shavrukov Y, Bowne JB, Langridge P  Tester M, (2007) Screening for sodium exclusion in parental species of synthetic wheat, Triticum durum and Aegilops tauschii, Aust J  Agric  Res 

Shi B-J, Collins NC, Miftahudin, Schnurbusch T, Langridge P and Gustafson JP (2007) Construction of a rye cv. Blanco BAC library, and progress towards cloning the rye Alt3 aluminium (aluminum) tolerance gene. Vorträge für Pflanzenzüchtung, 71: 205-209

Singh KM, Ghai M, Garg P, Chun EJA Schnurbusch TB, Keller B and Dhaliwal HS, (2007) An integrated molecular linkage map of diploid wheat based on a Triticum boeoticum  ×  T  monococcum RIL population, Theor Appl Genet 115: 301-312

Sutton, T, Baumann, U, Hayes, J, Collins, N C, Shi, B-J, Schnurbusch, T, Hay, A, Mayo, G, Pallotta, M, Tester, M  and Langridge, P, (2007) Boron toxicity in barley arising from efflux transporter amplification, Science, 318: 1446-1449

Tarpley L, Roessner U, (2007) Metabolomics: Enabling systems-level phenotyping in rice functional genomics, In “Rice Functional Genomics- Challenges, Progress and Prospects”, Upadhyaya NM, ed, Springer, Heidelberg, Germany, pp 91-108

Tommasini, L, Schnurbusch TB, Mascher F, Fossati D, Keller B, (2007) Association mapping and validation of Stagonospora nodorum blotch resistance in modern European winter wheat, Theor Appl Genet 115: 697–708

Varshney R, Marcel, T, Ramsay L, Russell J, Roeder M, Stein N, Waugh R, Langridge P, Niks R, Graner A, (2007) A high density barley microsatellite consensus map with 775 SSR loci, Theor  Appl  Genet  114, 1091-1103  

Varshney RK, Langridge P, Graner A, (2007) Application of genomics for molecular breeding of wheat and barley , Advances in Genetics, 58, 122-155

Villas-Boas SG, Roessner U, Hansen M, Smedsgaard J, Nielsen J, (2007) Metabolome Analysis  An introduction, Publ  Wiley & Sons, New Jersey, NJ, USA  ISBN: 978-0-471-74344-6, 311 pp

 

 

2008

Batley J and Edwards D, 2008. Bioinformatics: Fundamentals and Applications in Plant Genetics and Breeding, Principles and Practices of Plant Molecular Mapping and Breeding  Eds  Kole C and Abbott AG  Science Publishers, Inc, (USA)

Boden SA, Langridge P, Spangenberg G and Able JA. 2008. 3. TaASY1 promotes homologous chromosome interactions and is affected by deletion of Ph1. Plant Journal. 57,487–497

Brownfield L, Wilson S, Newbigin E, Bacic A and Read S. 2008. 4. Molecular control of glucan-synthase-like protein NaGSL1 and callose synthesis during growth of Nicotiana alata pollen tubes. Biochemical J. 414,43–52.

Burton RA, Jobling SA, Harvey AJ, Shirley NJ, Mather DE, Bacic A and 5. Fincher GB. 2008. The genetics and transcriptional activity of the cellulose synthase-like HvCslF gene family in barley (Hordeum vulgare L.). Plant Physiology 146, 1821–1833.

Callahan DL, Roessner U, Dumontet V, Perrier N, Wedd AG, O'Hair RAJ, Baker AJM, Kolev SD, (2008). LC-MS and GC-MS metabolite profiling of nickel(II) complexes in the latex of nickel-hyperaccumulating tree Sebertia acuminata and identification of methylated aldaric acid as a new nickel(II) ligand, Phytochemistry 69(1):240-51.

Chen A, Brûlé-Babel A, Baumann U and Collins NC. 2008. 7. Structure – function analysis of the barley genome: the gene-rich region of chromosome 2HL. Funct Integr Genomics doi: 10.1007/s10142-008-0099-2

Chiovitti A, Kraft G, Bacic A, Craik D J and Liao M-L. 2008. 8. Kappa-beta-carrageenans from Australian red algae of the Acrotylaceae (Gigartinales, Rhodophyta). Phycologia 47, 35–40.

Clark T. 2008. 9. Protein Sequence Databases. In Applied Bioinformatics Ed. Edwards D, Hanson D and Stajich J. Springer 

Collins NC, Shirley NJ, Saeed M, Pallotta M, Gustafson JP (2008). An ALMT1 gene cluster controlling aluminium (Aluminum) tolerance at the Alt4 locus of rye (Secale cereale L.). Genetics, 179: 669-682.

Collins NC, Tardieu F and Tuberosa R. 2008. 11. Quantitative trait loci and crop performance under abiotic stress: where do we stand? Plant Physiology 147: 469–486.

Conn VM, Walker AR and Franco CMM. 2008. 12. Endophytic actinobacteria induce defense pathways in Arabidopsis thaliana. Molecular Plant Microbe Interactions: 21, 208–218.

Duran C, Appleby N, Edwards D and Batley J. 2008. 13. Molecular genetic markers: discovery, applications, data storage and visualisation. Current Bioinformatics.

Duran C, Edwards D and Batley J. 2008. 14. Molecular marker discovery and genetic map visualisation. In Applied Bioinformatics Ed. Edwards D, Hanson D and Stajich J. Springer.

Duran C, Edwards D and Batley J. 2008. 15. 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) 

Edwards D and Batley J. 2008. 16. Bioinformatics: fundamentals and applications in plant genetics, mapping and breeding. Principles and Practices of Plant Genomics. Eds. Kole C and Abbott AG. Science Publishers, Inc., (USA). pp 269–302.

Farrokhi N, Hrmova M, Burton RA and Fincher GB, 2008. Heterologous and Cell Free Protein Expression Systems, in Molecular Biology; Plant Genomics  Eds  Somers D, Gustafson JP and Langridge P

Feuillet C, Langridge P and Waugh R. 2008. 18. Cereal breeding takes a walk on the wild side. Trends Gent. 24: 24–32.

Feuillet C, Langridge P and Waugh R. 2008. 19. Meeting report. The aaronsohn-itmi workshop. Israel J Plant Sci. 55:315–319.

Haegi A, Bonardi V, Dall’Aglio E, Glissant D, Tumino G, Collins NC, 24. Bulgarelli D, Infantino A, Stanca AM, Delledonne M, Valè G. 2008. Histological and molecular analysis of Rdg2a barley resistance to leaf stripe. Molecular Plant Pathology, 9: 463–478.

Hrmova M, Farkas V, Harvey AJ, Lahnstein J, Wischmann B, Kaewthai 26. N, Ezcurra I, Teeri TT and Fincher GB. 2008. Substrate specificity and catalytic mechanism of a xyloglucan xyloglucosyl transferase HvXET6 from barley (Hordeum vulgare L.). FEBS J 276, 437–456.

Hrmova M, Fincher GB, Functional genomics and structural biology in the definition of gene function, In: Methods in Molecular Biology: Plant Genomics, 2008. Humana Press Inc, Totowa, NJ, USA (Somers D, Langridge P, Gustafson P, eds) 

Huang CY, Roessner U, Eickmeier I, Genc Y, Callahan DL, Shirley N, 27. Langridge P and Bacic A. 2008. Metabolite profiling of barley (Hordeum vulgare L) plants reveal distinct responses to phosphate deficiency. Plant & Cell Physiology 49, 691–703.

Imelfort M. 2008. 30. Sequence Comparison Tools. In Applied Bioinformatics Ed. Edwards D, Hanson D and Stajich J. Springer 

Izanloo A, Condon AG, Langridge P, Tester M and Schnurbusch T. 2008. 31. Different mechanisms of adaptation to cyclic water stress in two South Australian bread wheat cultivars. J. Exp. Bot. 59:3327–3346

Jones CE, Schwerdt J, Bretag TA, Baumann U and Brown AL. 2008. 32. GOSLING: a rule-based protein annotator using BLASTand GO. Bioinformatics doi: 10.1093/bioinformatics/btn486.

Langridge P and Baumann U. 2008. 33. Self-incompatability in the Grasses. Self-Incompatability in Flowering Plants - Evolution, Diversity and Mechanisms. Chapter 13: 275–287. VE Franklin-Tong (ed.). Springer-Verlag Berlin.

Langridge P and Gilbert M. 2008. 34. From Gene Discovery to Paddock Reality. online http://www.regional.org.au/au/asa/2008/plenary/biotechnology/5944_langridgep.htm.

Li M, Singh R, Bazanova N, Milligan AS, Shirley N, Langridge P and 35. Lopato S. 2008. Spatial and temporal expression of endosperm transfer cell-specific promoters in transgenic rice and barley. Plant Biotechnol J. 6,:465–76.

Lightfoot D, Boetcher A, Little A, Shirley N and Able A. 2008. 36. Identification and characterisation of barley (Hordeum vulgare) respiratory burst oxidase homologue family members. Functional Plant Biology, 2008, 35, 347–359.

Munns R and Tester M. 2008. 37. Salinity tolerance in higher plants. Annual Reviews of Plant Biology 59, 651–681.

Myriskava R, Jenoe J, Gils A, Ismagul A, Weyen J and Gils M. 2008. 38. Expression of active Streptomyces phage phiC31 integrase in transgenic wheat plants. Plant Cell Rep 27:1821–1831

Natera S, Ford K, Cassin A, Patterson J, Newbigin E and Bacic A. 39. 2008. Analysis of the Oryza sativa plasma membrane proteome using combined protein and peptide fractionation approaches in conjunction with mass spectrometry. Journal of Proteome Research 7,1159–1187.

Pien S, Fleury D, Mylne JS, Crevillen P, Inzé D, Avramova Z, Dean C 40. and Grossniklaus U. 2008. ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation. PlantCell 20,580–8.

Qu Y, Egelund, J, Gilson PR, Houghton F, Gleeson PA, Schultz CJ and 41. Bacic A. 2008. Identification of a novel group of putative Arabidopsis thaliana β–(1,3)–galactosyltransferases. Plant Molecular Biology 68, 43–59.

Rajendran K, Tester M and Roy SJ. 2008. 42. Quantifying the three main components of salinity tolerance in cereals. Plant, Cell & Environment, 32: 237–249

Reynolds M and Tuberosa R. 2008. 43. Translational research impacting on crop productivity in drought-prone environments. Current Opinion in Plant Biology 11: 171–179.

Reynolds M, Saint Pierre C, Saad ASI, Vargas M and Condon AG. 2008. 44. Evaluating potential genetic gains in wheat associated with stress-adaptive trait expression in elite genetic resources under drought and heat stress. Crop Science S–173–189.

Roy SJ, Gilliham M, Berger B, Essah PA, Cheffings C, Miller AJ, 45. Widdowson L, Davenport RJ, Liu L.-H, Skynner MJ, Davies JM, Richardson P, Leigh RA and Tester M. 2008. Investigating glutamate receptor-like gene co-expression in Arabidopsis thaliana. Plant, Cell & Environment 31: 861–871.

Sanchez DH, Siahpoosh MR, Roessner U, Udvardi M and Kopka J. 46. 2008. Plant metabolomics reveals conserved and divergent metabolic responses to salinity. Physiologia Plantarum 132, 209–219.

Schnurbusch T, Langridge P and Sutton T. 2008. 47. The Bo1-specific PCRmarker AWW5L7 is predictive of boron tolerance status in a range of exotic durum and bread wheats. Genome 51(12): 963–971.

Schreiber AW, Shirley NJ, Burton RA and Fincher GB. 2008. 48. Combining transcriptional datasets using the generalized singular value decomposition. BMC Bioinformatics, 9: 335, doi:10.1186/1471–2105–9–355).

Somers D, Gustafson P and Langridge P Eds. 2008. 50. Methods in plant molecular biology. Hidari press.

Sørensen I, Pettolino P, Wilson SM, Doblin MS, Johansen B, Bacic A 51. and Willats WGT. 2008. Mixed linkage (13),(14)-β-D-glucan is not unique to the poales and is an abundant component of Equisetum arvense cell walls. Plant Journal 54, 510–521.

Tester M and Langridge P. 2008. 52. Crops aren’t invasive. New Scientist, 197:24.

Tracy FE, Gilliham M, Dodd, AN, Webb AAR and Tester M. 2008. 53. Cytosolic free Ca2+ in Arabidopsis thaliana are heterogeneous and modified by external ionic composition. Plant, Cell & Environment 31: 1063–1073.

Tran MK, Schultz CJ and Baumann U. 2008. 54. Conserved upstream open reading frames in higher plants. BMC Genomics 9:361.

Webster JM, Oxley D, Pettoliino FA and Bacic A. 2008. 55. Characterisation of secreted polymers from suspension cultures of Pyrus communis. Phytochemistry 69, 873–881.

Williams M, Langridge P, Trethowan R, Dreisigacker S and Crouch J. 56. 2008. Genomics of wheat, the basis of our daily bread. Chapter 22 p515–548. In “Genomics of Tropical Crop Plants.” Series: Plant Genetics and Genomics: Crops and Models , Vol. 1 Moore, Paul H.; Ming, Ray (Eds.) 2008, XXIV, 582 p

 

 

2009

Bacic A, Fincher GB, Stone BA (Eds), [2009], Chemistry, Biochemistry and Biology of (1,3)-Beta-Glucans and Related Polysaccharides, Academic Press, Book Elsevier Inc.USA Ed, 677

Batley J and Edwards D, 2009. Mining for Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers, Bioinformatics for DNA Sequence Analysis  Ed  David Posada Methods in Molecular Biology, Humana Press (USA)

Batley J, Edwards D, [2009], Genome sequence data: management, storage, and visualization, Biotechniques, 46: 333 - +Suppl.

Burton RA, Fincher GB, [2009], 1,3;1,4-ß-D-Glucans in Cell Walls of the Poaceae, Lower Plants and Fungi: A Tale of Two Linkages, Molecular Plant, 2: 873-882.

Burton, RA, Collins HM, Fincher GB, [2009], The Role of Endosperm Cell Walls in Barley Malting Quality, “Genetics and Improvement of Barley Malt Quality”, Book Springer Publishing Company Ed. G.Zhang, C. Li, P 190-237.

Callahan DL, Souza D, Bacic A, Roessner U, [2009], Profiling of polar metabolites in biological extracts using diamond hydride-based aqueous normal phase chromatography. Journal of separation science, 32: 2273-2280.

Chen A, Baumann U, Fincher GB, Collins NC, [2009], Flt-2L, a locus in barley controlling flowering time, spike density and plant height, Functional Integrative Genomics, 9, 243-254.

Chen A, Brûlé-Babel A, Baumann U, Collins NC, [2009], Structure function analysis of the barley genome: the gene-rich region of chromosome 2HL, Functional Integrative Genomics, 9, 67-79

Chen A, Gusta LV, Brûlé-Babel A, Leach A, Baumann U, Fincher GB, Collins NC, [2009], Varietal and chromosome 2H locus-specific frost tolerance in reproductive tissues of barley Hordeum vulgare L.detected using a frost simulation chamber. Theoretical Applied Genetics, 119, 685-694

Chen A, Reinheimer J, Brûlé-Babel A, Baumann U, Pallotta M, Fincher GB, Collins NC, [2009], Genes and traits associated with chromosome 1 2H and 5H regions controlling sensitivity of reproductive tissues to frost in barley, Theoretical Applied Genetics, 118, 1465-1476

Colijin C, Brandes A, Zucker J, Lun DS, Weiner B, Farhat MR, Cheng TY, Moody DB, Murray M, Galagan JE, [2009] Interpreting Expression Data With Metabolic Flux Models: Predicting Mycobacterium Tuberculosis Mycolic Acid Production. Plos Computational Biology, 5(8): Art No e1000489

DeLacy IH, Fox PN, McLaren G, Trethowan R, White JW, [2009], A conceptual model for describing processes of crop improvement in database structures. Crop Science, 49(6): 2100-2112

Doblin MS, Pettolino F, Wilson SM, Campbell R, Burton RA, Fincher GB, Newbigin E, Bacic A, [2009], A barley cellulose synthase-like CSLH gene mediates (1,3;1,4)-ß-D-glucan synthesis in transgenic Arabidopsis, Proc Natl Acad Sci (USA), 106, 5996-6001

Dong C, Dalton-Morgan J, Vincent K, Sharp P, [2009], A Modified TILLING Method for Wheat Breeding, Plant Genome, 2, 39-47 50 51

Dong C, Vincent K, Sharp P, [2009], Simultaneous mutation detection of three homoeologous genes in wheat by High Resolution Melting analysis and Mutation Surveyor, BMC Plant Biology, 9: Art No 143.

Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D, [2009], AutoSNPdb: An Annotated Single Nucleotide Polymorphism Database for Crop Plants, Nucleic Acids Research, 37: D951-953

Duran C, Appleby N, Vardy M, Imelfort M, Edwards D, Batley J, [2009], Single Nucleotide Polymorphism  Discovery in Barley using AutoSNPdb, Plant Biotechnology Journal, 7, 326-333

Dwivany FM, Yulia D, Burton RA, Shirley NJ, Wilson SM, Fincher GB, Bacic A, Newbigin E, Doblin MS, [2009], The cellulose-synthase like C (CslC) gene family of barley includes members that are integral membrane proteins targeted to the plasma membrane, Molecular Plant, 2: 1025-1039

Fauré R, Courtin CM, Delcour JA, Dumon C, Faulds CB, Fincher GB, Fort S, Fry SC, Halila S, Kabel MA, Pouvreau L, Quemener B, Rivet A, Saulnier L, Schols HA, Driguez H, O’Donohue MJ, [2009], A brief and informationally-rich naming system for oligosaccharide motifs of heteroxylans found in plant cell walls, Aust. J. Chem, 62, 533-537

Fincher GB, [2009], Exploring the evolution of (1,3;1,4)-beta-D-glucans in plant cell walls: comparative genomics can help! Current opinion in plant biology, 12: 140-147

Fincher GB, [2009], Revolutionary times in our understanding of cell wall biosynthesis and remodelling in the grasses. Plant Physiology, 149: 27-37

Fincher GB, [2009], The Evolution of 1,3;1,4-ß-D-Glucans in Cell Walls of Grasses, Current Opinions in Plant Biology, 12, 140-147

Fincher GB. 2009. 20. Biochemistry, Physiology and Genetics of Endosperm Mobilization Following Germination in Barley. In: Barley: Production, Improvements and Use. Ed. Ullrich S. Wiley-Blackwell .

Garnett T, Conn V, Kaiser B, [2009] Root based approaches to improving nitrogen use efficiency in plants. Plant Cell and Environment, 32: 1272-1283

Grace EJ, Cotsaftis O, Tester M, Smith FA, Smith SE, [2009], Arbuscular mycorrhizal inhibition of growth in barley cannot be attributed to extent of colonisation, fungal P uptake or effects on expression of plant phosphate transporter genes, New Phytologist, 181, 938-949

Harris PJ, Fincher GB, [2009], Distribution, fine structure and function of (1,3;1,4)-ß-Glucans in grasses and other taxa, Chemistry, Biochemistry and Biology of (1,3)-Beta-Glucans and Related Polysaccharides, Book Elsevier Inc. Ed. Bacic A, Fincher GB, Stone B, 621-654

Hrmova M and Fincher GB. 2009. 25. Functional genomics and structural biology in the definition of gene function. Methods in Molecular Biology, Plant Genomics. Vol 513. Eds. Somers DJ, Gustafson JP and Langridge P,. Humana Press, New York

Hrmova M, Fincher GB, [2009], Functional genomics and structural biology in the definition of gene function, Methods in Molecular Biology: Plant Genomics, Book Humana Press Inc. Ed. Somers DJ, Gustafson JP, Langridge P, P 199-227

Hrmova M, Fincher GB, [2009], Plant and microbial enzymes involved in the depolymerisation of (1,3)-ß-D-glucans and related polysaccharides, Chemistry, Biochemistry and Biology of (1,3)-Beta- Glucans and Related Polysaccharides, Book Elsevier Inc. Ed. Bacic A, Fincher GB, Stone B, 119-170

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)

Imelfort M, Duran C, Batley J, Edwards D, [2009], Discovering genetic polymorphisms in next generation sequencing data, Plant Biotechnology Journal, 7, 312-317

Imelfort M, Edwards D, [2009], Next generation sequencing of plant genomes, Briefings in Bioinformatics 10: 609-618

Jha D, Shirley N, Tester M, Roy SJ, [2009], Variation in salinity tolerance and shoot sodium accumulation in Arabidopsis ecotypes linked to differences in the natural expression levels of transporters involved in sodium transport, Plant, Cell & Environment, 32: doi: 10.1111/j.1365-3040.2009.02105.x

John UP, Polotnianka RM, Sivakumaran KA, Chew O, Mackin L, Kuiper MJ, Talbot JP, Nugent GD, Mautord J, Schrauf GE, Spangenberg GC, [2009], Ice recrystallization inhibition proteins (IRIPs) and freeze tolerance in the cryophilic Antarctic hair grass Deschampsia antarctica E. Desv, Plant Cell and Environment, 32, 336-348

Kuntothom T, Luang S, Fincher GB, Opassiri R, Hrmova M, Ketudat Cairns JR, [2009], Rice family GH1 glycoside hydrolases with ß-d-glucosidase and ß-d-mannosidase activities, Archives of Biochemistry and Biophysics, 491: 85-95

Kibble NAJ, Sohani MM, Shirley N, Byrt C, Roessner U, Bacic A, Schmidt O, Schultz CJ, [2009] Phylogenetic analysis and functional characterisation of strictosidine synthase-like genes in Arabidopsis thaliana. Functional Plant Biology, 36: 1098-1109

Kovalchuk N, Smith J, Pallotta M, Singh R, Ismagul A, Eliby S, Bazanova N, Milligan AS, Hrmova M, Langridge P, Lopato S, [2009], Characterization of the wheat endosperm transfer cell-specific protein TaPR60, Plant Mol Biol, 71, 81-98

Lehmensiek A, Bovill W, Wenzl P, Langridge P, Appels R, [2009], Genetic mapping in the Triticeae, ‘Genetics and Genomics of the Triticeae’, Book Ed. C. Feuillet, G. Muelbauer, P 201-235

Lewis D, Bacic A, Chandler PM, Newbigin EJ, [2009], Aberrant cell expansion in the elongation mutants of barley. Plant & Cell Physiology, 50, 554-571

Lonegran PF, Pallotta MA, Lorimer M, Paul JG, Barker SJ, Graham RD, [2009], Multiple genetic loci for zinc uptake and distribution in barley (Hordeum vulgare). New Phytologist, 184: 168-179

Lun DS, Sherrid A, Weiner B, Sherman DR, Galagan JE [2009] A blind deconvolution approach to high resolution mapping of transcription factor binding sites from ChIP-seq data. Gnome Biology, 10(12): Art No R142

Ma W, Anderson O, Kuchel H, Bonnardeaux Y, Collins H, Morell MK, Langridge P, Appels R, [2009], Genomics of Quality Traits, ‘Genetics and Genomics of the Triticeae’, Book Ed. C. Feuillet, G. Muelbauer, P 611-652

Møller IS, Gilliham M, Jha D, Mayo GM, Roy SJ, Coates JC, Haseloff J, Tester M, [2009], Shoot Na+ Exclusion and Increased Salinity Tolerance Engineered by Cell Type–Specific Alteration of Na+ Transport in Arabidopsis, The Plant Cell, 21: 2163-2178

Montel E, Hrmova M, Fincher GB, Driguez H, Cottaz S, [2009], A chemoenzymatic route to conjugatable ß-(1,3)-glucan oligosaccharides. , Australian Journal of Chemistry, 62, 575-58

Pereira-Netto AB, Roessner U, Fujioka S, Bacic A, Asami T, Yoshida S, Clouse SD, [2009], Shooting control by brassinosteroids: metabolomic analysis and effect of brassinazole on Malus prunifolia the Marubakaido apple rootstock. Tree Physiology, 29: 607-620

Pettolino F, Sasaki I, Turbic A, Wilson S, Felton Z, Bacic A, Hrmova M, Fincher GB, [2009], Hyphal cell walls from the plant pathogen Rhynchosporium secalis contain (1,3/1,6)-ß-D-glucans, galacto- and rhamnomannans, (1,3;1,4)-ß-D-glucans and chitin, FEBS J, 276, 4122-4133

Reynolds M, Manes Y, Izanloo A, Langridge P, [2009], Phenotyping for physiological breeding and gene discovery in wheat, Annals Appl Biol, 155: 309-320

Roessner U, Browne J, [2009], What is metabolomics all about? Biotechniques, 46: 363-365 Suppl. S

Roy SJ, [2009], Development towards salt tolerant crops - ACPFG salt focus group, Phytogen, 11, 21-23

Salekdeh GH, Reynolds M, Bennett J, Boyer J, [2009], Conceptual framework for drought Phenotyping during molecular breeding. Trends in Plant Science, 14: 488-496

Schober MS, Burton RA, Shirley NJ, Jacobs AK, Fincher GB, [2009], Analysis of the 1,3-ß-D-Glucan Synthase Gene Family of Barley, Phytochemistry, 70, 713-720

Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N, [2009], The International Barley Sequencing Consortium (IBSC) – at the threshold of efficient access to the barley genome, Plant Physiol, 149, 142-147

Shavrukov Y, Langridge P, Tester M, [2009], Salinity tolerance and sodium exclusion in genus Triticum, Breeding Science, 59, 671-678

Shi B-J, Gustafson JP, Button J, Miyazaki J, Pallotta M, Gustafson N, Zhou H, Langridge P, Collins NC, [2009], Physical analysis of the complex rye (Secale cereale L.) Alt4 aluminium (aluminum) tolerance locus using a whole-genome BAC library of rye cv. Blanco, Theoretical and Applied Genetics, 119, 695-704

Shi BJ, Gustafson PJ, Langridge P, [2009], A simple TAE-based method to generate large insert BAC libraries from plant species, Methods Mol Biol, 513, 57-80

Shi BJ, Symons RH, Palukaitis P, [2009], Stability and competiveness of interviral recombinant RNAs derived from a chimeric cucumovirus. Virus Research, 140: 216-221 54 55

Stamova BS, Roessner U, Suren S, Laudencia-Chingcuanco D, Bacic A, Beckles D, [2009], Metabolic profiling of transgenic wheat over-expressing the high-molecular-weight Dx5 glutenin subunit, Metabolomics, 5, 239-252

Vandeleur RK, Mayo G, Shelden MC, Gilliham M, Kaiser BN, Tyerman SD, [2009], The Role of Plasma Membrane Intrinsic Protein Aquaporins in Water Transport through Roots: Diurnal and Drought Stress Responses Reveal Different Strategies between Isohydric and Anisohydric Cultivars of Grapevine, Plant Physiol, 0, 149, 445-460

Widodo, Patterson JH, Newbigin EJ, Tester M, Bacic A, Roessner U, [2009], Metabolomic responses to salt stress of barley (Hordeum vulgare L) cultivars, Sahara and Clipper, which differ in salinity tolerance, Journal of Experimental Botany, 60: 4089-4103

 

 

2010

Aarao J,  Bradshaw-Hajek  B, Miklavcic SJ, Ward D, [2010], Numerical implementation of the EDEM for Modified Helmholtz BVPs on Annular Domains, Journal of Computational and Applied Mathematics, 235, 1342-1353

 Arief VN, Kroonenberg PM, DeLacy IH, Dieters MJ, Crossa J, Dreisiger S, Braun HJ, Basford KE, [2010], Construction and Three-way Ordination of the Wheat Phenome Atlas, Journal of Applied Probability and Statistics, 5, 95-118

Batley J, Edwards D, [2010], Plant genome sequencing: applications for crop improvement, Plant Biotechnology Journal, 8, 2-9

Berger B, Parent B, Tester M, [2010], High throughput imaging to study drought responses, Journal of Experimental Botany, 61, 3519-3528

Bowne J, Bacic A, Tester M, Roessner U, [2010], Abiotic stress and Metabolomics, Book Blackwell Ed. Hall RD.

Bulgarelli D, Biselli C, Collins NC, Consonni G, Stanca AM, Schulze-Lefert P, Valè G, [2010], The CC-NB-LRR-Type Rdg2a resistance gene confers immunity to the seed-borne barley leaf stripe pathogen in the absence of hypersensitive cell death, PLoS ONE, 5: e12599. doi:10.1371/journal.pone.0012599

Burton RA, Gidley MJ, Fincher GB, [2010], Heterogeneity in the chemistry, structure and function of plant cell walls, Nature Chemical Biology, 6, 724-732

Burton RA, Ma G, Baumann U, Harvey AJ, Shirley NJ, Taylor J, Pettolino F, Bacic A, Beatty M, Simmons CR, Dhugga KS, Rafalski JA, Tingey SV, Fincher GB, [2010], A Customized Gene Expression Microarray Reveals That the Brittle Stem Phenotype fs2 of Barley Is Attributable to a Retroelement in the HvCesA4 Cellulose Synthase Gene, Plant Physiology, 153, 1716-1728.

Cotsaftis O,  Plett D, Johnson A.A.T,  Walia H.,  Wilson C,  Ismail AM,  Close TJ,  Tester M,  Baumann U, [2010], Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress, Molecular Plant, doi: 10.1093/mp/ssq056

Cushman J, Tester M, [2010], Special Issue on Drought and Salinity Stress, Plant, Cell and Environment, Book  Ed. Cushman J & Tester M, 33, 453-669.

Doblin MS, Pettolino F, Bacic A, [2010], Plant cell walls: the skeleton of the plant world, Functional Plant Biology, 37, 357-381

Doblin MS, Pettolino F, Bacic A, [2010], The skeleton of the plant world and more: role in plant growth, development and biotechnology, Functional Plant Biology, 37, 357-381

Domozych DS, Sorensen I, Pettolino FA, Bacic A, (2010), The cell wall polymers of the charophycean green alga Chara corallina: Immunobinding and biochemical screening, International Journal of Plant Sciences, 171, 345-361

Drew DP, Hrmova M, Lunde C, Jacobs A, Tester M, Fincher GB, (2010) Structural and functional analyses of PpENA1 provide insights into cation binding by type IID Ptype ATPases in lower plants and fungi, Biochimica et Biophysica Acta, doi:10.1016/j.bbamem.2010.11.013

Duran C,  Eales D,  Marshall D,  Imelfort M,  Stiller J,  Berkman P,  Clark T,  McKenzie M,  Appleby N,  Batley J,  Basford K, Edwards D, [2010], Future tools for association mapping in crop plants, Genome, 53(11), 1017-1023

Duran C, Boskovic Z, Marshall D, Imelfort M, Batley J, Hamilton NA, Edwards D, [2010], CMap3D: a 3D visualization tool for comparative genetic maps, Bioinformatics, 26, 273-274

Ellis M, Egelund J, Schultz CJ, Bacic A, [2010], Arabinogalactan-Proteins: Key Regulators at the Cell Surface?, Plant Physiology, 153, 403-419.

Fleury D,  Jefferies S, Kuchel H,  Langridge P , [2010], Genetic and genomic tools to improve drought tolerance in wheat., Journal of Experimental Botany, 61, 3211-3222

Fleury D, Luo MC, Dvorak J, Ramsay L, Gill BS, Anderson OD,  You FM, Schoaei Z,  Deal KR, Langridge P, [2010], Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS., BMC Genomics, 11, 382

Gaxiola RA, Flowers TJ, Tester M, Roy SJ, [2010], Plants of Saline Environments, McGraw-Hill Encyclopaedia of Science and Technology

Genc Y, Oldach K, Verbyla AP, Lott G, Hassan M, Tester M, Wallwork H, McDonald GK, [2010], Sodium exclusion QTL associated with improved seedling growth in bread wheat under salinity stress, Theoretical and Applied Genetics, 121, 877-894

Genc Y, Tester M, McDonald GK, [2010], Calcium requirement of wheat in saline and non-saline conditions, Plant and Soil, 327, 331-345

Gupta PK, Langridge P, Mir RR , [2010], Marker-Assisted Wheat Breeding: Present Status and Future Possibilities., Molecular Breeding, 26, 145-161

Hanlin RL, Hrmova M, Harbertson JF, Downey MO , [2010], Condensed tannin and grape cell wall interactions and impact on tannin extractability into wine - a review. , Australian Journal of Grape and Wine Research, 16, 173-188

Harris BN, Sadras VO, Tester M, [2010], A water-centred framework to assess the effects of salinity on the growth and yield of wheat and barley, Plant and Soil, 336, 377-389

Hassan M, Oldach K, Bauman U, Langridge P, Sutton T, [2010], Genes mapping to boron tolerance QTL in barley identified by suppressive subtractive hybridization. , Plant, Cell and Environment, 33, 188-198

Hrmova M, Stone BA, Fincher GB, [2010], High-yield production, refolding and molecular modelling of the catalytic module of (1,3)-β-D-glucan (curdlan) synthase from Agrobacterium sp., Glycoconjugate Journal, doi 10.1007/s10719-010-9291-4

Kaewthai, N, Harvey AJ, Hrmova M, Brumer H, Ezcurra I, Teeri TT, Fincher GB, [2010], Heterologous expression of diverse barley XTH genes in the yeast Pichia pastoris., Plant Biotechnology Journal, 27, 251-258

Kosik O, Auburn RP, Stratilova E, Garajova S, Hrmova M, Farkas V, [2010], Polysaccharide micro-arrays for screening of transglycosylase activities in plant extracts, Glycoconjugate Journal, 27, 79-87

Kovalchuk N, Li M, Wittek F, Reid N, Singh R, Shirley N, Ismagul A, Eliby S, Jonson A, Milligan AS, Hrmova M, Langridge P, Lopato S, [2010], Defensin promoters as potential tools for engineering disease resistance in cereal grains, Plant Biotechnology Journal, 8, 47-64

Kuntothom T, Raab M, Tvaroška I, Fort S, Pengthaisong S, Cañada FJ, Calle L, Jiménez-Barbero J, Ketudat Cairns JR, Hrmova M, [2010], Binding of β-D-glucosides and β-D-mannosides by rice and barley β-D-glycosidases with distinct substrate specificities., Biochemistry, Book American Chemical Society Ed. , 49, 8779-8793

Liu QX, Zhang QS, Burton RA, Shirley NJ, Atwell BJ, [2010], Expression of vacuolar H+-pyrophosphatase (OVP3) is under control of an anoxia-inducible promoter in rice, Plant Molecular Biology, 72, 47-60

Luang S, Hrmova M, Ketudat Cairns JR, [2010], High-level expression of barley β-d-glucan exohydrolase HvExo I from a codon-optimized cDNA in Pichia pastoris, Protein Expression and Purification, 73, 90-98, doi:10.1016/j.pep.2010.04.011

Luang S, Ketudat Cairns JR, Streltsov VA, Hrmova M, [2010], Crystallisation of wild-type and variant forms of a recombinant β-d-glucan glucohydrolase from barley (Hordeum vulgare L.) by macroseeding with wild-type native microcrystals and preliminary X-ray analysis. , International Journal of Molecular Sciences, 11, 2759-2769

Marshall DJ,  Hayward A,  Eales D,  Imelfort M,  Stiller J,  Berkman PJ,  Clark T,  McKenzie M,  Lai K,  Duran C,  Batley J, Edwards D, [2010], Targeted identification of genomic regions using TAGdb, Plant Methods, 6

Mason MG, Jha D, Salt DE, Tester M, Hill K, Kieber JJ, Schaller GE, [2010], Type-B response regulators ARR1 and ARR12 regulate AtHKT1;1, and sodium accumulation in Arabidopsis shoots, The Plant Journal, DOI: 10.1111/j.1365-313X.2010.04366.x

Morran S, Eini O, Pyvovarenko T,  Parent B,  Singh R,  Ismagul A, Eliby S,  Shirley N, Langridge P, Lopato S, [2010], Improvement of stress tolerance of wheat and barley by modulation of expression of DREB/CBF factors. , Plant Biotechnology Journal, doi: 10.1111/j.1467-7652.2010.00547.x

Mortier V, Den Herder G, Whitford R, Van de Velde W, Rombauts S, D’haeseleer K, Holsters M, Goormatig S [2010] CLE peptides control Medicago truncatula nodulation both locally and systemically. Plant Physiology doi: 10.1104/pp.110.153718

Nelissen H, De Groeve S, Fleury D, Neyt P, Bruno L, Bitonti MB, Vandenbussche F, Van Der Straeten D, Yamaguchi T, Tsukaya H, Witters E, De Jaeger G, Houben A, Van Lijsebettens M, [2010], Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation, Proceedings of the National Academy of Sciences of USA, 107, 1678-1683

Plett D, Berger B, Tester M, [2010], Genetic determinants of salinity tolerance in crop plants, Genes for Plant abiotic stress, Book Wiley-Blackwell Ed. Jenks M & Wood A, doi: 10.1002/9780813809380.ch4

Plett D, Johnson A, Jacobs A, Tester M, [2010], Cell type-specific expression of sodium transporters improves salinity tolerance of rice, GM Crops, 5, 1-3

Plett D, Moller IS, [2010], Na(+) transport in glycophytic plants: what we know and would like to know., Plant, Cell and Environment, 33(4), 612-626

Plett D, Safwat G, Gilliham M, Møller IS,  Roy SJ, Shirley NJ, Jacobs A, Johnson A, Tester M, [2010], Improved salinity tolerance of rice through cell type-specific expression of AtHKT1;1, PLoS ONE, 5, P e12571

Plett D, Toubia J, Garnett T, Tester M, Kaiser BN, Baumann U, [2010], Dichotomy in the NRT gene families of dicots and grass species, PLoS ONE, 5: e15289

Preuss C, Huang CY, Gilliham M, Tyerman SD, [2010], Channel-Like Characteristics of the Low-Affinity Barley, Plant Physiology, 152, 1431-1441

Rivandi J,  Miyazaki J,  Hrmova M,  Pallotta M,  Tester M,  Collins NC, [2010], A SOS3 homologue maps to HvNax4,  a barley locus controlling an environmentally-sensitive Na+ exclusion trait, Journal of Experimental Botany, 38: doi: 10.1093/jxb/erq346

Robles P, Fleury D, Candela H, Cnops G, Alonso-Peral MM, Anami S, Falcone A, Caldana C, Willmitzer L, Ponce MR, Van Lijsebettens M, Micol JL, [2010], The RON1/FRY1/SAL1 gene is required for leaf morphogenesis and venation patterning in Arabidopsis, Plant Physiology, 152, 1357-1372.

Roy SJ, Tester M, [2010], Approaches for increasing the salt tolerance of crops, The Encyclopedia of Sustainable Science and Technology, Book Springer

Schnurbusch T, Hayes J, Hrmova M, Ramesh S, Tyerman S, Baumann U, Langridge P,  Sutton T, [2010], Boron toxicity tolerance in barley through reduced expression of the multifunctional aquaporin HvNIP2;1, Plant Physiology, 153, 1706-1715

Schnurbusch T, Hayes J, Sutton T, [2010], Boron toxicity tolerance in wheat and barley: Australian perspectives, Breeding Science, 60, 297-304

Shavrukov Y, Gupta N.K, Miyazaki J, Baho M.N, Chalmers K.J, Tester M., Langridge P, Collins N.C, [2010], HvNax3—a locus controlling shoot sodium exclusion derived from wild barley (Hordeum vulgare ssp. spontaneum)., Functional and Integrative Genomics, 10, 277-291

Shavrukov Y, Langridge P, Tester M, Nevo E, [2010], Wide genetic diversity of salinity tolerance, sodium exclusion and growth in wild emmer wheat, Triticum dicoccoides, Breeding Science, 60, 426-435

Shi B-J, Sutton T, Collins N, Pallotta M, Langridge P, [2010], Construction of a barley bacterial artificial chromosome (BAC) library suitable for cloning genes for boron tolerance, sodium exclusion and high grain zinc content,  Plant Breeding, 129, 291-296

Shi X, Lun DS, Médard M, Kötter R,  Meldrim JC, Barry AJ, [2010], Joint base-calling of two DNA sequences with factor graphs., IEEE Transactions on Information Theory,  56, 724-733

Tardieu F, Parent B, Simonneau T, [2010], Control of leaf growth by abscisic acid: hydraulic or non-hydraulic processes?, Plant, Cell and Environment, 33, 636-647

Tester M, Langridge P, [2010], Breeding technologies to increase crop production in a changing world., Science, 327(5967), 818-822

Tregeagle JM,, Walker RR, Tisdall JM, Tester M, [2010], Cl- uptake, transport and accumulation in grapevine rootstocks of differing capacity for Cl--exclusion, Functional Plant Biology, 37, 665-673

Vaaje-Kolstad G, Farkaš V, Fincher GB, Hrmova M, [2010], Barley xyloglucan xyloglucosyl transferases bind xyloglucan-derived oligosaccharides in their acceptor binding regions in multiple conformational states, Archives of Biochemistry and Biophysics, 496, P 61-68

Vaaje-Kolstad G, Farkaš V, Hrmova M, Fincher GB, [2010], Xyloglucan xyloglucosyl transferases from barley (Hordeum vulgare L.) bind oligomeric and polymeric xyloglucan molecules in their acceptor binding sites, Biochimica et Biophysica Acta, DOI:10.1016/j.bbagen.2010.04.001

Whitford R, Gilbert M, Langridge P [2010], Biotechnology in Agriculture. In: Reynolds, M. P. (eds.) Climate Change and Crop Production. Commonwealth Agricultural Bureaux International (CABI) publishing, Wallingford, UK.

Zhang Q, Shirley NJ, Burton RA, Lahnstein J, Hrmova M, Fincher GB, [2010], The genetics, transcriptional profiles and catalytic properties of UDP-α-d-xylose 4-epimerases from barley (Hordeum vulgare L.)., Plant Physiology, 153, 555-568, doi:10.1104/pp.110.157644

 

 

2011

Aizat, W. M., Preuss, J. M., Johnson, A. A. T., Tester, M. A. & Schultz, C. J. (2011). Investigation of a His-rich arabinogalactan-protein for micronutrient biofortification of cereal grain. Physiologia Plantarum 143, 271-286.

Berkman, P. J., Skarshewski, A., Lorenc, M. T., Lai, K., Duran, C., Ling, E. Y. S., Stiller, J., Smits, L., Imelfort, M., Manoli, S., McKenzie, M., Kubalakova, M., Simkova, H., Batley, J., Fleury, D., Dolezel, J. & Edwards, D. (2011). Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal 9, 768-775.

Boughton, B. A., Callahan, D. L., Silva, C., Bowne, J., Nahid, A., Rupasinghe, T., Tull, D. L., McConville, M. J., Bacic, A. & Roessner, U. (2011). Comprehensive Profiling and Quantitation of Amine Group Containing Metabolites. Analytical Chemistry 83, 7523-7530.

Burton, R. A., Collins, H. M., Kibble, N. A. J., Smith, J. A., Shirley, N. J., Jobling, S. A., Henderson, M., Singh, R. R., Pettolino, F., Wilson, S. M., Bird, A. R., Topping, D. L., Bacic, A. & Fincher, G. B. (2011). Over-expression of specific HvCslF cellulose synthase-like genes in transgenic barley increases the levels of cell wall (1,3;1,4)-beta-D-glucans and alters their fine structure. Plant Biotechnology Journal 9, 117-135.

Cai, J., Golzarian, M. R. & Miklavcic, S. J. (2011). Novel image segmentation based on machine learning and its application to plant analysis. Int. J. Inform & Electronics Eng. 1, 79-84.

Conn, S. J., Conn, V., Tyerman, S. D., Kaiser, B. N., Leigh, R. A. & Gilliham, M. (2011). Magnesium transporters, MGT2/MRS2-1 and MGT3/MRS2-5, are important for magnesium partitioning within Arabidopsis thaliana mesophyll vacuoles. New Phytologist 190, 583-594.

Conn, S. J., Gilliham, M., Athman, A., Schreiber, A. W., Baumann, U., Moller, I., Cheng, N.-H., Stancombe, M. A., Hirschi, K. D., Webb, A. A. R., Burton, R., Kaiser, B. N., Tyerman, S. D. & Leigh, R. A. (2011). Cell-Specific Vacuolar Calcium Storage Mediated by CAX1 Regulates Apoplastic Calcium Concentration, Gas Exchange, and Plant Productivity in Arabidopsis. Plant Cell 23, 240-257.

Cotsaftis, O., Plett, D., Johnson, A. A. T., Walia, H., Wilson, C., Ismail, A. M., Close, T. J., Tester, M. & Baumann, U. (2011). Root-Specific Transcript Profiling of Contrasting Rice Genotypes in Response to Salinity Stress. Molecular Plant 4, 25-41.

Cuin, T. A., Bose, J., Stefano, G., Jha, D., Tester, M., Mancuso, S. & Shabala, S. (2011). Assessing the role of root plasma membrane and tonoplast Na(+)/H(+) exchangers in salinity tolerance in wheat: in planta quantification methods. Plant Cell and Environment 34, 947-961.

Dortay, H., Schmöckel, S. M., Fettke, J. & Mueller-Roeber, B. (2011). Expression of human c-reactive protein in different systems and its purification from Leishmania tarentolae. Protein Expression and Purification 78, 55-60.

Drew, D. P., Hrmova, M., Lunde, C., Jacobs, A. K., Tester, M. & Fincher, G. B. (2011). Structural and functional analyses of PpENA1 provide insights into cation binding by type IID P-type ATPases in lower plants and fungi. Biochimica Et Biophysica Acta-Biomembranes 1808, 1483-1492.

Duran, C., Boskovic, Z., Batley, J. & Edwards, D. (2011). Role of bioinformatics as a tool for vegetable Brassica species. In Genetics, genomics and breeding of vegetable Brassicas (Sadowski, J. & Kole, C., eds.), pp. 406-418.   CRC Press Enfield, United States

Edwards D, Wheat Bioinformatics, The World Wheat Book  Eds  Bonjean A, Angus W and Van Ginkel M Lavoisier 2011. (France)

Edwards, D., Batley, J., Parkin, I. & Kole, C., Eds. (2011). Genetics, Genomics and Breeding of Oilseed Brassicas. Vol. 6. Genetics, Genomics and Breeding of Crop Plants. Edited by Singh, R. J. Enfield, USA: Science Publishers.

Fangel, J. U., Petersen, B. L., Jensen, N. B., Willats, W. G. T., Bacic, A. & Egelund, J. (2011). A putative Arabidopsis thaliana glycosyltransferase, At4g01220, which is closely related to three plant cell wall-specific xylosyltransferases, is differentially expressed spatially and temporally. Plant Science 180, 470-479.

Furbank, R. T. & Tester, M. (2011). Phenomics - technologies to relieve the phenotyping bottleneck. Trends in Plant Science 16, 635-644.

Gao, L.-L., Hane, J. K., Kamphuis, L. G., Foley, R., Shi, B.-J., Atkins, C. A. & Singh, K. B. (2011). Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing. Bmc Genomics 12.

Golzarian, M. R. & Frick, R. A. (2011). Classification of images of wheat, ryegrass and brome grass species at early growth stages using principal component analysis. Plant Methods 7.

Golzarian, M. R., Cai, J., Frick, R. & Miklavcic, S. J. (2011). Segmentation of cereal plant images using level set methods - A comparative study. Int. J. Inform & Electronics Eng. 1, 72-78.

Golzarian, M. R., Frick, R. A., Rajendran, K., Berger, B., Roy, S., Tester, M. & Lun, D. S. (2011). Accurate inference of shoot biomass from high-throughput images of cereal plants. Plant Methods 7.

Gong, H., Blackmore, D., Clingeleffer, P., Sykes, S., Jha, D., Tester, M. & Walker, R. (2011). Contrast in chloride exclusion between two grapevine genotypes and its variation in their hybrid progeny. Journal of Experimental Botany 62, 989-999.

Gould, S. B., Kraft, L. G. K., van Dooren, G. G., Goodman, C. D., Ford, K. L., Cassin, A. M., Bacic, A., McFadden, G. I. & Waller, R. F. (2011). Ciliate Pellicular Proteome Identifies Novel Protein Families with Characteristic Repeat Motifs That Are Common to Alveolates. Molecular Biology and Evolution 28, 1319-1331.

Gruber, B. D., Delhaize, E., Richardson, A. E., Roessner, U., James, R. A., Howitt, S. M. & Ryan, P. R. (2011). Characterisation of HvALMT1 function in transgenic barley plants. Functional Plant Biology 38, 163-175.

Hall, R. D., Wishart, D. S. & Roessner, U. (2011). Metabolomics and the move towards biology. Metabolomics 7, 454-456.

Hardner, C., Dieters, M., DeLacy, I., Neal, J., Fletcher, S., Dale, G. & Basford, K. (2011). Identifying deployment zones for Eucalyptus camaldulensis x E. globulus and x E. grandis hybrids using factor analytic modelling of genotype by environment interaction. Australian Forestry 74, 30-35.

Harris, J. C., Hrmova, M., Lopato, S. & Langridge, P. (2011). Modulation of plant growth by HD-Zip class I and II transcription factors in response to environmental stimuli. New Phytologist 190, 823-837.

Huang, C. Y., Shirley, N., Genc, Y., Shi, B. & Langridge, P. (2011). Phosphate Utilization Efficiency Correlates with Expression of Low-Affinity Phosphate Transporters and Noncoding RNA, IPS1, in Barley. Plant Physiology 156, 1217-1229.

Hussain, S. S., Ali, M., Ahmad, M. & Siddique, K. H. M. (2011). Polyamines: Natural and engineered abiotic and biotic stress tolerance in plants. Biotechnology Advances 29, 300-311.

Hussain, S. S., Kayani, M. A. & Amjad, M. (2011). Transcription Factors as Tools to Engineer Enhanced Drought Stress Tolerance in Plants. Biotechnology Progress 27, 297-306.

Ip, K., Colijn, C. & Lun, D. S. (2011). Analysis of complex metabolic behavior through pathway decomposition. Bmc Systems Biology 5.

Jacobs, A., Ford, K., Kretschmer, J. & Tester, M. (2011). Rice plants expressing the moss sodium pumping ATPase PpENA1 maintain greater biomass production under salt stress. Plant Biotechnology Journal 9, 838-847.

James, R. A., Blake, C., Byrt, C. S. & Munns, R. (2011). Major genes for Na+ exclusion, Nax1 and Nax2 (wheat HKT1;4 and HKT1;5), decrease Na+ accumulation in bread wheat leaves under saline and waterlogged conditions. Journal of Experimental Botany 62, 2939-2947.

Johnson, A. A. T., Kyriacou, B., Callahan, D. L., Carruthers, L., Stangoulis, J., Lombi, E. & Tester, M. (2011). Constitutive overexpression of the OsNAS gene family reveals single-gene strategies for effective iron- and zinc-biofortification of rice endosperm. PLoS ONE 6.

Jungreuthmayer, C., Birnbaumer, G. M., Zanghellini, J. & Ertl, P. (2011). 3D numerical simulation of a lab-on-a-chip-increasing measurement sensitivity of interdigitated capacitors by passivation optimization. Lab on a Chip 11, 1318-1325.

Kojima, S., Iwasaki, M., Takahashi, H., Imai, T., Matsumura, Y., Fleury, D., Van Lijsebettens, M., MacHida, Y. & MacHida, C. (2011). ASYMMETRIC LEAVES2 and elongator, a histone acetyltransferase complex, mediate the establishment of polarity in leaves of Arabidopsis thaliana. Plant and Cell Physiology 52, 1259-1273.

Koo, D.-H., Hong, C. P., Batley, J., Chung, Y. S., Edwards, D., Bang, J.-W., Hur, Y. & Lim, Y. P. (2011). Rapid divergence of repetitive DNAs in Brassica relatives. Genomics 97, 173-185.

Langridge, P. & Fleury, D. (2011). Making the most of 'omics' for crop breeding. Trends in Biotechnology 29, 33-40.

Li, C., Distelfeld, A., Comis, A. & Dubcovsky, J. (2011). Wheat flowering repressor VRN2 and promoter CO2 compete for interactions with NUCLEAR FACTOR-Y complexes. Plant Journal 67, 763-773.

Liu, H., McNicol, J., Bayer, M., Morris, J. A., Cardle, L., Marshall, D. F., Schulte, D., Stein, N., Shi, B.-J., Taudien, S., Waugh, R. & Hedley, P. E. (2011). Highly parallel gene-to-BAC addressing using microarrays. Biotechniques 50, 165-+.

Lukman, A. I., Gong, B., Marjo, C. E., Roessner, U. & Harris, A. T. (2011). Facile synthesis, stabilization, and anti-bacterial performance of discrete Ag nanoparticles using Medicago sativa seed exudates. Journal of Colloid and Interface Science 353, 433-444.

Nguyen, V. L., Huynh, B. L., Wallwork, H. & Stangoulis, J. (2011). Identification of quantitative trait loci for grain arabinoxylan concentration in bread wheat. Crop Science 51, 1143-1150.

Pineros, M. A. & Tester, M. (2011). Calcium Inhibits Dihydropyridine-Stimulated Increases in Opening and Unitary Conductance of a Plant Ca(2+) Channel. Journal of Membrane Biology 240, 13-20.

Preuss, C. P., Huang, C. Y. & Tyerman, S. D. (2011). Proton-coupled high-affinity phosphate transport revealed from heterologous characterization in Xenopus of barley-root plasma membrane transporter, HvPHT1;1. Plant Cell and Environment 34, 681-689.

Price, G. D., Shelden, M. C. & Howitt, S. M. (2011). Membrane topology of the cyanobacterial bicarbonate transporter, SbtA, and identification of potential regulatory loops. Molecular Membrane Biology 28, 265-275.

Pyvovarenko, T. & Lopato, S. (2011). Isolation of Plant Transcription Factors Using a Yeast One-Hybrid System. In Plant Transcription Factors: Methods and Protocols, Vol. 754, pp. 45-66.

Roy, S. J., Tucker, E. J. & Tester, M. (2011). Genetic analysis of abiotic stress tolerance in crops. Current Opinion in Plant Biology 14, 232-239.

Sammon, N. B., Harrower, K. M., Fabbro, L. D. & Reed, R. H. (2011). Three Potential Sources of Microfungi in a Treated Municipal Water Supply System in Sub-Tropical Australia. International Journal of Environmental Research and Public Health 8, 713-732.

Schreiber, A. W., Shi, B.-J., Huang, C.-Y., Langridge, P. & Baumann, U. (2011). Discovery of barley miRNAs through deep sequencing of short reads. Bmc Genomics 12.

Schulte, D., Ariyadasa, R., Shi, B., Fleury, D., Saski, C., Atkins, M., deJong, P., Wu, C.-C., Graner, A., Langridge, P. & Stein, N. (2011). BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). Bmc Genomics 12.

Shavrukov, Y., Shamaya, N., Baho, M., Edwards, J., Ramsey, C., Nevo, E., Langridge, P. & Tester, M. (2011). Salinity tolerance and Na+ exclusion in wheat: Variability, genetics, mapping populations and QTL analysis. Czech Journal of Genetics and Plant Breeding 47, S85-S93.

Shi, B. J. & Palukaitis, P. (2011). The N-terminal 12 amino acids of tomato aspermy virus 2b protein function in infection and recombination. Journal of General Virology 92, 2706-2710.

Van-Lam, N., Bao-Lam, H., Wallwork, H. & Stangoulis, J. (2011). Identification of Quantitative Trait Loci for Grain Arabinoxylan Concentration in Bread Wheat. Crop Science 51, 1143-1150.

Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J.-H., Bancroft, I., Cheng, F., Huang, S., Li, X., Hua, W., Wang, J., Wang, X., Freeling, M., Pires, J. C., Paterson, A. H., Chalhoub, B., Wang, B., Hayward, A., Sharpe, A. G., Park, B.-S., Weisshaar, B., Liu, B., Li, B., Liu, B., Tong, C., Song, C., Duran, C., Peng, C., Geng, C., Koh, C., Lin, C., Edwards, D., Mu, D., Shen, D., Soumpourou, E., Li, F., Fraser, F., Conant, G., Lassalle, G., King, G. J., Bonnema, G., Tang, H., Wang, H., Belcram, H., Zhou, H., Hirakawa, H., Abe, H., Guo, H., Wang, H., Jin, H., Parkin, I. A. P., Batley, J., Kim, J.-S., Just, J., Li, J., Xu, J., Deng, J., Kim, J. A., Li, J., Yu, J., Meng, J., Wang, J., Min, J., Poulain, J., Wang, J., Hatakeyama, K., Wu, K., Wang, L., Fang, L., Trick, M., Links, M. G., Zhao, M., Jin, M., Ramchiary, N., Drou, N., Berkman, P. J., Cai, Q., Huang, Q., Li, R., Tabata, S., Cheng, S., Zhang, S., Zhang, S., Huang, S., Sato, S., Sun, S., Kwon, S.-J., Choi, S.-R., Lee, T.-H., Fan, W., Zhao, X., Tan, X., Xu, X., Wang, Y., Qiu, Y., Yin, Y., Li, Y., et al. (2011). The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43, 1035-U157.

Xue, S., Yao, X., Luo, W., Jha, D., Tester, M., Horie, T. & Schroeder, J. I. (2011). AtHKT1;1 Mediates Nernstian Sodium Channel Transport Properties in Arabidopsis Root Stelar Cells. Plos One 6.

Zhang, Q., Pettolino, F. A., Dhugga, K. S., Rafalski, J. A., Tingey, S., Taylor, J., Shirley, N. J., Hayes, K., Beatty, M., Abrams, S. R., Zaharia, L. I., Burton, R. A., Bacic, A. & Fincher, G. B. (2011). Cell Wall Modifications in Maize Pulvini in Response to Gravitational Stress. Plant Physiology 156, 2155-2171.

 

 

2012

Azam S, Thakur V, Ruperao P, Shah T, Jayashree B, BhanuPrakash A, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JDG, Varshney RK. [2012] Coveragebased consensus calling (CbCC) of short sequence reads and comparison of CbCC results for the identification of SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome, American Journal of Botany, 99, P 186- 192.

Basford KE, McLachlan GJ, Rathnayake SI. [2012] On the classification of microarray gene-expression data, Briefings in Bioinformatics, doi: 10.1093/bib/bbs056.

Bennett D, Izanloo A, Edwards J, Kuchel H, Chalmers K, Tester M, Reynolds M, Schnurbusch T, Langridge P. [2012] Identification of novel quantitative trait loci for days to ear emergence and flag leaf glaucousness in a bread wheat (Triticum aestivum L.) population adapted to southern Australian conditions, Theoretical and Applied Genetics, 124, P 697-711.

Bennett D, Izanloo A, Reynolds M, Kuchel H, Langridge P, Schnurbusch T. [2012] Genetic dissection of grain yield and physical grain quality in bread wheat (Triticum aestivum L.) under water-limited environments, Theoretical and Applied Genetics, 125, P 255-271.

Bennett D, Reynolds M, Mullan D, Izanloo A, Kuchel H, Langridge P, Schnurbusch T. [2012] Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments, Theoretical and Applied Genetics, 125, P 1473-1485.

Berger B, de Regt B, Tester M. [2012] Applications of high-throughput plant phenotyping to study nutrient use efficiency, In Methods in Molecular Biology:Plant Mineral Nutrients – Methods and Protocols, Book (Maathuis, FJ (Ed.),Humana Press).

Berger B, de Regt B, Tester M. [2012] High-throughput phenotyping of plant shoots, In Methods in Molecular Biology: High-Throughput Phenotyping in Plants, Book (Normanly, J (Ed.), Humana Press).

Berger B, de Regt B, Tester M. [2012] Trait dissection of salinity tolerance with plant phenomics, In Plant Salt Tolerance: Methods and Protocols, Book (Shabala S, Cuin TA (Eds.), Humana Press).

Berkman PJ, Lai K, Lorenc MT, Edwards D. [2012] Next generation sequencing applications for wheat crop improvement, American Journal of Botany, 99, P 365- 371.

Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Hernandez P, Edwards D. [2012] Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation, Theoretical and Applied Genetics, 124, P 423-432.

Bowne JB, Erwin TA, Juttner J, Schnurbusch T, Langridge P, Bacic A, Roessner U. [2012] Drought responses of leaf tissues from wheat cultivars of differing drought tolerance at the metabolite level, Molecular Plant, 5, P 418-429.

Bradshaw-Hajek BH, Miklavcic SJ, Ward DA. [2012] A composite Level Set and Extended-Domain-Eigenfunction Method for simulating 2D Stokes flow involving a free surface, Journal of Computational and Applied Mathematics, 237, P 389-402.

Brien CJ, Bailey RA, Thao TT, Boland J. [2012] Quasi-Latin designs, Electronic Journal of Statistics, 6, P 1900-1925.

Brien CJ. [2012] Comment on ‘Therapist variation within randomised trials of psychotherapy: implications for precision internal and external validity’, Statistical Methods in Medical Research, 21, P 215–216.

Brien CJ. [2012] Contribution to the discussion of optimal design of experiments for statistical inference, Journal of the Royal Statistical Society Series C, 61, P 379.

Cai J, Cespedes M, Tilbrook J, Miklavcic SJ. [2012] Plant temperature measurement and analysis from infrared images, submitted for presentation and publication in the proceedings of DICTA 2012. Peer reviewed conference
proceeding.

Cai J, Miklavcic S J. [2012] The automated extraction of three-dimensional cereal plant structures from two-dimensional orthographic images, IET Image Processing,6, P 687-696.

Cai J, Miklavcic SJ. [2012] Fully automatic estimation of lens distortion parameters from single images using line rectification and voting scheme, submitted for presentation and publication in the proceedings of ECCV 2012. Peer reviewed conference proceeding.

Cai J. [2012] Integration of optical flow and dynamic programming for stereo matching, IET Image Processing, 6, P 205-212.

Cai J. [2012] Robust filtering-based thinning algorithm for pattern recognition. Computer Journal, 55, P 887-896.

Cai J. [2012] The integration of images and Kinect depth maps for better quality of 3D surface reconstruction, submitted for presentation and publication in the proceedings of ICPR 2012. Peer reviewed conference proceeding.

Chew O, Lelean S, John UP, Spangenberg GC. [2012] Cold acclimation induces rapid and dynamic changes in freeze tolerance mechanisms in the cryophile Deschampsia antarctica E. Desv, Plant Cell and Environment, 35, P 829-837.

Cotsaftis O, Plett D, Shirley N, Tester M, Hrmova M. [2012] A two-stage model of Na+ exclusion in rice explained by 3D modeling of HKT transporters and alternative splicing, PLoS One, 7: e39865.

Edwards D, Batley J, Snowdon R. [2012] Accessing complex crop genomes with next-generation sequencing, Theoretical and Applied Genetics, 126, P 1-11.

Edwards D, Henry RJ, Edwards KJ. [2012] Advances in DNA sequencing accelerating plant biotechnology, Plant Biotechnology Journal, 10, P 621-622.

Edwards D, Parkin IAP, Batley J, Kole C. [2012] Genetics, Genomics and Breeding of Oilseed Brassicas, Book, (Science Publishers), editors for this publication.

Edwards D, Wang X. [2012] Genome sequencing initiatives, In Genetics, Genomics and Breeding of Oilseed Brassicas, Book (Edwards D, Parkin IAP, Batley J, Kole C (Eds.), Science Publishers), P 152-157.

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, Plant Biotechnology Journal, 10, P 703-708.

Evrard A, Bargmann BOR, Birnbaum KD, Tester M, Baumann U, Johnson AAT. [2012] Fluorescence-activated cell sorting for analysis of cell typespecific responses to salinity stress in Arabidopsis and rice, In Plant Salt
Tolerance: Methods and Protocols, Book (Shabala S, Cuin TA (Eds.), Humana Press).

Fernandez i Marti A, Wirthensohn M, Alonso J, Socias i Company R, Hrmova M. [2012] Molecular modelling of S-RNases involved in almond self incompatibility, Frontiers in Plant Science, 3, 139.

Fleury D, Delannay X, Langridge P. [2012] Quantitative Trait Loci and Breeding, eLS, Book contribution (John Wiley & Sons).

Golzarian MR, Lee MK, Desbiolles JMA. [2012] Evaluation of colour indices for improved segmentation of plant images, Transactions of the ASABE, 55, P 261-273.

Hackenberg M, Shi BJ, Gustafson JP, Langridge P. [2012] A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs, PLoS One, 7, e42030.

Hayashi S, Reid DE, Lorenc MT, Stiller J, Edwards D, Gresshoff PM, Ferguson BJ. [2012] Transient Nod factor-dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots, Plant
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Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D, Batley J. [2012] SNP discovery and applications in Brassica napus, Plant Biotechnology Journal, 39, P 49-61.

Hayward A, McLanders J, Campbell E, Edwards D, Batley J. [2012] Genomic advances will herald new insights into the Brassica: Leptosphaeria maculans pathosystem, Plant Biology, 14, P 1-10.

Hayward A, Vighnesh G, Delay G, Samian MR, Manoli SM, Stiller J, McKenzie M, Edwards D, Batley J. [2012] Second-generation sequencing for gene discovery in the Brassicaceae, Plant Biotechnology Journal, 10, P 750-759.

Hill CB, Roessner U. [2012] Plant metabolomics using GC-MS, In GC-MS Metabolomics Handbook, Book (Weckwerth W (Ed.), Springer).

Hrmova M, Lopato S. [2012] Enhancing abiotic stress tolerance in plants by modulating properties of stress responsive transcription factors, In Advances in Genomics of Plant Genetic Resources, Book (Tuberosa R, Graner A, Frison E (Eds.), Springer Verlag).

Huynh B, Mather DE, Schreiber AW, Toubia J, Baumann U, Shoaei Z, Stein N, Ariyadasa R, Stangoulis J, Edwards J, Shirley N, Langridge P, Fleury D. [2012] Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley, Plant Molecular Biology, 80, P 299-314.

Jiang Q, Yen SH, Stiller J, Edwards D, Scott PT, Gresshoff PM. [2012] Genetic, biochemical, and morphological diversity of the legume biofuel tree Pongamia pinnata, Journal of Plant Genome Sciences, 1, P 54-67.

Johnson AAT. [2012] Enhancing the chelation capacity of rice to maximise iron and zinc concentrations under elevated atmospheric carbon dioxide. Functional Plant Biology, 40, P 101-108.

Kovalchuk N, Smith J, Bazanova N, Pyvovarenko T, Singh R, Shirley N, Ismagul A, Johnson AAT, Milligan AS, Hrmova M, Langridge P, Lopato S. [2012] Characterization of the wheat gene encoding a grain-specific lipid transfer protein TdPR61, and promoter activity in wheat, barley and rice, Journal of Experimental Botany, 63, P 2025-2040.

Kovalchuk N, Wu W, Eini O, Bazanova N, Pallotta M, Shirley N, Singh R, Ismagul A, Eliby S, Johnson A, Langridge P, Lopato S. [2012] The scutellar vascular bundle-specific promoter of the wheat HD-Zip IV transcription factor shows similar spatial and temporal activity in transgenic wheat, barley and rice, Plant Biotechnology Journal, 10, P 43-53.

Kovalchuk NV, Melynkova NM, Musatenko LI. [2012] Role of phytolectin in the life cycle of plants, Biopolymers, 28, P 171-180.

Kumar P, Cai J, Miklavcic SJ. [2012] Automated detection of root crowns using Gaussian Mixture Models and Bayesian classification, submitted for presentation and publication in the proceedings of DICTA 2012. Peer reviewed conference proceeding.

Kumar P, Cai J, Miklavcic SJ. [2012] Root crown detection using statistics of Zernike moments, accepted for presentation and publication in the proceedings of ICARCV 2012. Peer reviewed conference proceeding.

Lacroix C, Langridge P, Tuberosa R. [2012] Biotechnology for enhancing plant production and food quality – IBS 2010 Part III, Journal of Biotechnology, 159, P 249-250, and editors for this volume.

Laga H. [2012] Graspable parts recognition in man-made 3D shapes, submitted for presentation and publication in the proceedings of ACCV 2012. Peer reviewed conference proceeding.

Laga H, Kurtek S, Srivastava A, Golzarian M, Miklavcic SJ. [2012] A Riemannian elastic metric for shape-based plant leaf classification, submitted for presentation and publication in the proceedings of DICTA 2012. Peer reviewed conference proceeding.

Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, Edwards D. [2012] WheatGenome.info: An integrated database and portal for wheat genome information, Plant and Cell Physiology, 53, e2.

Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden MJ, Forrest K, Fleury D, Baumann U, Zander M, Mason AS, Batley J, Edwards D. [2012] Single nucleotide polymorphism discovery from wheat next generation sequence dData, Plant Biotechnology Journal, 10, P 743-749.

Lai K, Lorenc MT, Edwards D. [2012] Genomic databases for crop improvement, Agronomy, 2, P 62-73.
 

Lee H, Lai K, Lorenc MT, Imelfort M, Duran C, Edwards D. [2012] Bioinformatics tools and databases for analysis of next-generation sequence data, Briefings in Functional Genomics, 11, P 12-24.

Lorenc M, Boskovic Z, Stiller J, Duran C, Edwards D. [2012] Role of bioinformatics as a tool for oilseed Brassica species, In Genetics, Genomics and Breeding of Oilseed Brassicas, Book (Edwards D, Parkin IAP, Batley J, Kole C (Eds.), Science Publishers), P 194-205.

Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, J. Berkman PJ, Lai K, Batley J, Edwards D. [2012] Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP, Biology, 1, P 370-382.

Munns R, James R, Xu B, Athman A, Conn SJ, Jordans C, Byrt CS, Hare RA, Tyerman S, Tester M, Plett D, Gilliham MA. [2012] Wheat grain yield on saline soils is improved by an ancestral Na+ transporter gene, Nature Biotechnology, 30, P 360-364.

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, American Journal of Botany, 99, P E369-371.

Niepielko, MG, Ip K, Kanodia JS, Lun DS ,Yakoby N. [2012] Evolution of BMP signaling in Drosophila oogenesis: A receptor-based mechanism, Biophysical Journal, 102, P 1722-1730.

O’Callahan S, DeSouza DP, Isaac A, Wang Q, Hodkinson L, Olshansky M, Erwin T, Appelbe B, Tull DL, Roessner U, Bacic A, McConville MJ, Likic V. [2012] PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools. BMC Bioinformatics, 13, 115.

Parent B, Tardieu F. [2012] Temperature responses of developmental processes have not been affected by breeding in different ecological areas for 17 crop species, New Phytologist, 194, P 760-774.

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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. [2012] Genetic and physical mapping of flowering time loci in canola (Brassica napus L.), Theoretical and Applied Genetics, 126, P 119-132.

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. [2012] Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.), Theoretical and Applied Genetics, 125, P 405-418.

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, Plant Biotechnology Journal, 10, P 680-689.

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Roy SJ, Conn SJ, Mayo GM, Athman A, Gilliham M. [2012] Transcriptomics on small samples, Methods in Molecular Biology, 913, P 335-350.

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Temmerman L, De Livera AM, Bowne JB, Sheedy JR, Callahan DL, Nahid A, De Souza DP, Schoofs L, Tull DL, McConville MJ, Roessner U, Wentworth J. [2012] Cross-platform urine metabolomics of experimental hyperglycemia in Type 2 diabetes, Journal of Diabetes and Metabolism, doi.org/10.4172/2155-6156.S6-
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Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, McLanders J, Lorenc M, Manoli S, Stiller J, Raman R, Raman H, Batley J. Edwards D. [2012] Identification and characterisation of candidate Rlm4 blackleg resistance genes in Brassica napus using next generation sequencing, Plant Biotechnology Journal, 10, P 709-715.

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Wang W-H, Köhler B, Cao F-Q, Liu G-W, Gong Y-Y, Sheng S, Song Q-C, Cheng X-Y, Garnett T, Okamoto M, Qin R, Mueller-Roeber B, Tester M, Liu L-H. [2012] Rice DUR3 mediates high-affinity urea transport and plays an effective role in improvement of urea acquisition and utilization when expressed in Arabidopsis, New Phytologist, 193, P 432-444.

Whitford R, Fernandez A, Tejos R, Pérez AC, Kleine-Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin YC, Storme V, Van de Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson P. [2012] GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses, Developmental Cell, 22(3), P 678-85.
 

 

 

2013

Acevedo-Garcia J, Collins NC, Ahmadinejad N, Ma L, Houben A, Bednarek P, Benjdia M, Freialdenhoven A, Altmüller J, Nürnberg P, Reinhardt R, Schulze-Lefert P, Panstruga R. [2013] Fine mapping and chromosome walking towards the Ror1 locus in barley (Hordeum vulgare L.), Theoretical and Applied Genetics, 126, P 2969-2982

Adhikari BB, Mehera B, Haefele SM. [2013] Impact of rice nursery management, seeding density and seedling age on yield and yield attributes, American Journal of Plant Sciences, 4, P 146-155

Ahkami AH, Melzer M, Ghaffari MR, Pollmann S, Ghorbani Javid M, Shahinnia F, Hajirezaei MR, Druege U. [2013] Distribution of indole-3-acetic acid in Petunia hybrida shoot tip cuttings and relationship between auxin transport, carbohydrate metabolism and adventitious root formation, Planta, 238, P 499-517

Appenroth KJ, Borisjuk N, Lam E. [2013] Telling Duckweed Apart: Genotyping Technologies for the Lemnaceae, Chinese Journal of Applied & Environmental Biology, 19, P 1-10

Arief VN, DeLacy IN, Wenzl P, Dreisigacker S, Crossa J, Dieters MJ Basford KE. [2013] Comparing molecular marker combinations in natural or artificial populations, Journal of Environmental Statistics, 4, P 4

Arthur K, Collins NC, Randles JW. [2013] Mutation rate in Velvet tobacco mottle virus varies between genomic region and virus variant but is not influenced by obligatory mirid transmission, Virus Genes, 45, P 575-580

Arthur K, Collins NC, Yazarlou A, Randles JW. [2013] Nucleotide sequence diversity in Velvet tobacco mottle virus: a virus with a unique Australian pathosystem, Virus Genes, 48, P 168-173

Bashabaeva BM, Ismagul A, Abugaliyeva AI, Alimgazinova BS,  Sariev BS. [2013] Isolated microspore culture in generating genetically uniform and stable doubled haploids in barley, Biotechnology, 5, P 1-6 (In Russian, http://dx.doi.org/10.11134/btp.1.2013.5)

Berkman PJ, Visendi P, Lee HC, Stiller J, Manoli S, Lorenc MT, Lai K, Batley J, Fleury D, Šimková H, Kubaláková M, Weining S, Doležel J, Edwards D. [2013] Dispersion and domestication shaped the genome of bread wheat, Plant Biotechnology Journal, 11, P 564-571

Bonneau J, Taylor J, Parent B, Bennett D, Reynolds M, Feuillet C, Langridge P, Mather D. [2013] Multi-environment analysis and improved mapping of a yield-related QTL on chromosome 3B of wheat, Theoretical and Applied Genetics, 126, P 747-761

Bovill WD, Huang CY, McDonald GK. [2013] Genetic approaches to enhancing phosphorus-use efficiency (PUE) in crops: challenges and directions, Crop & Pasture Science, 64, P 179-198

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Buchanan M, Burton RA, Dhugga KS, Rafalski AJ, Tingey SV, Shirley NJ, Fincher GB. [2013] Endo-(1,4)- b-glucanase gene families in the grasses: temporal and spatial co-transcription of orthologous genes, BMC Plant Biology, 12, 235

Burton RA, Collins HM, Kibble NAJ, Smith JA, Shirley NJ, Jobling SA, Henderson M, Singh RR, Pettolino F, Wilson SM, Bird AR, Topping DL, Bacic A, Fincher GB. [2013] Over-expression of specific HvCslF cellulose synthase-like genes in transgenic barley increases the levels of cell wall (1,3;1,4)-b-ᴅ-glucans and alters their fine structure, Plant Biotechnology Journal, 9, P 117-135

Carter S, Shackley S, Sohi S, Suy TB, Haefele S. [2013] The impact of biochar application on soil properties and plant growth of pot grown lettuce (Lactuca sativa) and cabbage (Brassica chinensis), Agronomy, 3, P 404-418

Chew W, Hrmova M, Lopato S. [2013] Role of Homeodomain Leucine Zipper (HD-Zip) IV Transcription Factors in Plant Development and Plant Protection from Deleterious Environmental Factors, International Journal of Molecular Sciences, 14, P 8122-8147

Dreccer MF, Chapman SC, Rattey AR, Neal J, Song Y, Christopher JJ, Reynolds M. [2013] Developmental and growth controls of tillering and water-soluble carbohydrate accumulation in contrasting wheat (Triticum aestivum L.) genotypes: can we dissect them? Journal Of Experimental Botany, 64, P 143-160

Edwards D, Gupta PK. [2013] Sequence based DNA markers and genotyping for cereal genomics and breeding, In Cereal Genomics II, Book (Eds. Gupta PK and Varshney RK), Springer (USA), P 57-76

Eini O, Yang N, Pyvovarenko T, Pillman K, Bazanova N, Tikhomirov N, Eliby S, Shirley N, Sivasankar S, Tingey S, Langridge P, Hrmova M, Lopato S. [2013] Complex regulation by Apetala2 Domain-containing transcription factors revealed through analysis of the stress-responsive TdCor410b promoter from durum wheat, PLOS ONE, 8, e58713

Eini O, Dogra SC, Dry IB, Randles JW. [2013] Silencing suppressor activity of a begomovirus DNA b encoded protein and its effect on heterologous helper virus replication, Virus Research, 167, P 97-101

Fleury D, Langridge P. [2013] QTL and association mapping for plant abiotic stress tolerance: trait characterization and introgression for crop improvement, In Plant Abiotic Stress, 2nd Edition, Book  (Eds. Jenks MA and Hasegawa PM), John Wiley & Sons Inc. (USA), P 257-287

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Foster KJ, Miklavcic SJ. [2013] Mathematical modelling of the uptake and transport of salt in plant roots, Journal of Theoretical Biology, 336, P 132-143

Fuchs J, Neuberger T, Rolletschek H, Schiebold S, Nguyen TH, Borisjuk N, Börner A, Melkus G, Jakob P, Borisjuk L. [2013] A noninvasive platform for imaging and quantifying oil storage in submillimeter tobacco seed, Plant Physiology, 161, P 583-593

Gao X, Zhang Q, Newberry MP, Chalmers KJ, Mather DE. [2013] A cysteine in the repetitive domain of a high-molecular-weight glutenin subunit interferes with the mixing properties of wheat dough, Amino Acids, 44, P 1061-1071

Garnett T, Rebetzke G. [2013] Improving Crop Nitrogen Use in Dryland Farming, In Improving Water and Nutrient-Use Efficiency in Food Production Systems, Book (Ed. Rengel Z), John Wiley & Sons Inc. (USA), P 123-144

Garnett T, Conn V, Plett D, Conn S, Zanghellini J, Mackenzie N, Enju A, Francis K, Holtham L, Roessner U, Boughton B, Bacic A, Shirley N, Rafalski A, Dhugga K, Tester M, Kaiser BN. [2013] The response of the maize nitrate transport system to nitrogen demand and supply across the lifecycle, New Phytologist, 198, P 82-94

Golicz AA, Bayer PE, Martinez PA, Lai K, Lorenc MT, Alamery S, Hayward A, Tollenaere R, Batley J, Edwards D, Long Y, Meng J. [2013] Characterising diversity in the  Brassica genomes, Acta Horticulture, 1005, P 33-47

Hackenberg M, Huang P, Huang C, Shi B, Gustafson P, Langridge P. [2013] A comprehensive expression profile of microRNAs and other classes of non-coding small RNAs in barley under phosphorous-deficient and -sufficient conditions, DNA Research, 20, P 109-125

Hackenberg M, Shi B, Gustafson P, Langridge P. [2013] Characterization of phosphorus-regulated miR399 and miR827 and their isomirs in barley under phosphorus-sufficient and phosphorus-deficient conditions, BMC Plant Biology, 13, 214 

Haefele SM, Banayo NPM, Amarante ST, Siopongco JDLC, Mabesa RL. [2013] Characteristics and management options for rice-maize systems in the Philippines, Field Crops Research, 144, P 52-61

Haefele SM, Saito K, N’Diaye K, Mussgnug F, Nelson A, Wopereis MCS. [2013] Increasing rice productivity through improved nutrient use in Africa, In Realizing Africa’s Rice Promise, Book (Eds. Wopereis MCS, Johnson DE, Ahmadi N, Tollens E, Jalloh A), CABI, P 249-263

Hayes JE, Pallotta M, Baumann U, Berger B , Langridge P, Sutton T. [2013] Germanium as a tool to dissect boron toxicity effects in barley and wheat, Functional Plant Biology, 40, P 618-627

Heuer S, Chin JH, Gamuyao R, Haefele SM, Wissuwa M. [2013] Molecular breeding for phosphorus-efficient rice, In Translational Genomics in Crop Breeding: Abiotic Stress, Yield and Quality, Volume 2, Book (Eds. Varshney RJ, Tuberosa RP), John Wiley & Sons (UK), P 65-82

Hill CB, Roessner U. [2013] Metabolomic profiling of plants by GC-MS, In The Handbook of Plant Metabolomics, Book (Eds. Weckwerth W, Kahl G), Wiley-VCH (Germany), P 3-23

Hill, CB, Jha D, Bacic A, Tester M, Roessner U. [2013] Characterization of ion contents and metabolic responses to salt stress of different Arabidopsis AtHKT1;1 genotypes and their parental strains, Molecular Plant, 6, P 350-368

Hill CB, Taylor JD, Edwards J, Mather D, Bacic A, Langridge P, Roessner U. [2013] Whole genome mapping of agronomic and metabolic traits to identify novel quantitative trait loci in bread wheat grown in a water-limited environment, Plant Physiology, 162, P 1266-1281

Houston K, McKim SM, Comadran J, Bonar N, Druka I, Uzrek N, Cirillo E, Guzy-Wrobelska J, Collins NC, Halpin C, Hansson M, Dockter C, Druka A, Waugh R. [2013] Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence, Proceedings of the National Academy of Sciences, USA, 110, P 16675-16680

Huang CY, Kuchel H, Edwards J, Hall S, Parent B, Eckermann P, Herdina, Hartley DM, Langridge P, McKay AC. [2013] A DNA-based method for studying root responses to drought in field-grown wheat genotypes, Scientific Reports, 3, 3194

Jayatilake DV, Tucker EJ, Bariana H, Kuchel H, Edwards J, McKay AC, Chalmers K, Mather DE. [2013] Genetic mapping and marker development for resistance of wheat against the root lesion nematode Pratylenchus neglectus, BMC Plant Biology, 13, P 1-12

Kabir AH, Paltridge NG, Roessner U, Stangoulis JCR. [2013] Mechanisms associated with Fe-deficiency tolerance and signaling in shoots of Pisum sativum, Physiologia Plantarum, 147, P 381-395

Knauer S, Holt AL, Rubio-Somoza I, Tucker EJ, Hinze A, Pisch M, Javelle M, Timmermans MC, Tucker MR, Laux T. [2013] A protodermal miR394 signal defines a region of stem cell competence in the Arabidopsis shoot meristem, Developmental Cell, 24, P 125-132

Kovalchuk N, Jia W, Eini O, Morran S, Pyvovarenko T, Fletcher S, Bazanova N, Harris J, Beck-Oldach K, Shavrukov Y, Langridge P, Lopato S. [2013] Optimization of TaDREB3 gene expression in transgenic barley using cold-inducible promoters, Plant Biotechnology Journal, 11, P 659-670

Laga H, Mortara M, Spagnuolo M. [2013] Geometry and context for semantic correspondences and functionality recognition in man-made 3D shapes, ACM Transactions on Graphics, 32, 150

Langridge P. [2013] Food for thought,  In The Curious Country: The Role of Science in Australian Society, eBook (Ed. Dayton L), Office of the Chief Scientist, P 62-66

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Lightfoot DJ, Orford SJ, Timmis JN. [2013] Identification and characterisation of cotton boll wall-specific gene promoters for future transgenic cotton varieties, Plant Molecular Biology Reporter, 31, P 174-174

Liu D, Ford KL, Roessner U, Natera S, Cassin AM, Patterson JH, Bacic A. [2013] Rice suspension cultured cells are evaluated as a model system to study salt responsive networks in plants using a combined proteomic and metabolomic profiling approach, Proteomics, 13, P 2046-2062

Maphosa L, Langridge P, Taylor H, Chalmers KJ, Bennett D, Kuchel H, Mather DE. [2013] Genetic control of processing quality in a bread wheat mapping population grown in water-limited environments, Journal of Cereal Science, 57, P 304-311

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McDonald GK, Bovill W, Huang CY, Lightfoot D. [2013] Nutrient use efficiency, In Genomics and Breeding for Climate-Resilient Crops, Vol. 2, Book (Ed. Kole C), Springer-Verlag (Heidelberg), P 333-393

Ming L, Lopato S, Kovalchuk N, Langridge P. [2013] Functional genomics of seed development in cereals, In Cereal Genomics II, Book (Eds. Gupta PK, Varshney RK), Springer-Verlag, P 215-245

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Pavagadhi S, Natera S, Roessner U, Balasubramanian R. [2013] Insights into lipidomic perturbations in zebrafish tissues upon exposure to microcystin-LR and microcystin-RR, Environmental Science & Technology, 12, P 2046-2062

Periasamy A, Shadiac N, Amalraj A, Garajova S, Nagarajan Y, Waters S, Mertens HDT, Hrmova M. [2013] Cell-free protein synthesis of membrane (1,3)-β-ᴅ-glucan (curdlan) synthase: Co-translational insertion in liposomes and reconstitution in nanodiscs, Biochimica et Biophysica Acta - Biomembranes, 1828, P 743-757

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