Murdoch University Research Repository

Welcome to the Murdoch University Research Repository

The Murdoch University Research Repository is an open access digital collection of research
created by Murdoch University staff, researchers and postgraduate students.

Learn more

Publications: Hane, James

Stats for Hane, James
Export as [feed] RSS
Group by: Item Type | Year
Number of items: 31.

Journal Article

Andronis, C.E., Hane, J.K., Bringans, S., Hardy, G.E.S.J., Jacques, S., Lipscombe, R. and Tan, K-C (2021) Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of dieback. Frontiers in Microbiology, 12 . Art. 665396.

Shah, R.M., Williams, A.H., Hane, J.K., Lawrence, J.A., Farfan-Caceres, L.M., Debler, J.W., Oliver, R.P. and Lee, R.C. (2020) Reference genome assembly for Australian Ascochyta rabiei Isolate ArME14. Genes|Genomes|Genetics, 10 (7). pp. 2131-2140.

Mousavi-Derazmahalleh, M., Bayer, P.E., Hane, J.K., Valliyodan, B., Nguyen, H.T., Nelson, M.N., Erskine, W., Varshney, R.K.ORCID: 0000-0002-4562-9131, Papa, R. and Edwards, D. (2018) Adapting legume crops to climate change using genomic approaches. Plant, Cell & Environment, 42 (1). pp. 6-19.

Williams, A.H., Sharma, M., Thatcher, L.F., Azam, S., Hane, J.K., Sperschneider, J., Kidd, B.N., Anderson, J.P., Ghosh, R., Garg, G., Lichtenzveig, J., Kistler, H.C., Shea, T., Young, S., Buck, S-A.G., Kamphuis, L.G., Saxena, R., Pande, S., Ma, L-J, Varshney, R.K.ORCID: 0000-0002-4562-9131 and Singh, K.B. (2016) Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics, 17 (1). Art. 191.

Varshney, R.K.ORCID: 0000-0002-4562-9131, Song, C., Saxena, R.K., Azam, S., Yu, S., Sharpe, A.G., Cannon, S., Baek, J., Rosen, B.D., Tar'an, B., Millan, T., Zhang, X., Ramsay, L.D., Iwata, A., Wang, Y., Nelson, W., Farmer, A.D., Gaur, P.M., Soderlund, C., Penmetsa, R.V., Xu, C., Bharti, A.K., He, W., Winter, P., Zhao, S., Hane, J.K., Carrasquilla-Garcia, N., Condie, J.A., Upadhyaya, H.D., Luo, M-C, Thudi, M., Gowda, C.L.L., Singh, N.P., Lichtenzveig, J., Gali, K.K., Rubio, J., Nadarajan, N., Dolezel, J., Bansal, K.C., Xu, X., Edwards, D., Zhang, G., Kahl, G., Gil, J., Singh, K.B., Datta, S.K., Jackson, S.A., Wang, J. and Cook, D.R. (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology, 31 (3). pp. 240-246.

Rouxel, T., Grandaubert, J., Hane, J.K., Hoede, C., van de Wouw, A.P., Couloux, A., Dominguez, V., Anthouard, V., Bally, P., Bourras, S., Cozijnsen, A.J., Ciuffetti, L.M., Degrave, A., Dilmaghani, A., Duret, L., Fudal, I., Goodwin, S.B., Gout, L., Glaser, N., Linglin, J., Kema, G.H.J., Lapalu, N., Lawrence, C.B., May, K., Meyer, M., Ollivier, B., Poulain, Julie, Schoch, Conrad L., Simon, A., Spatafora, J.W., Stachowiak, A., Turgeon, B.G., Tyler, B.M., Vincent, D., Weissenbach, J., Amselem, J., Quesneville, H., Oliver, R.P., Wincker, P., Balesdent, M-H. and Howlett, B.J. (2011) Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nature Communications, 2 (1). p. 202.

Goodwin, S.B., Ben M'Barek, S., Dhillon, B., Wittenberg, A.H.J., Crane, C.F., Hane, J.K., Foster, A.J., Van der Lee, T.A.J., Grimwood, J., Aerts, A., Antoniw, J., Bailey, A., Bluhm, B., Bowler, J., Bristow, J., van der Burgt, A., Canto-Canché, B., Churchill, A.C.L., Conde-Ferràez, L., Cools, H.J., Coutinho, P.M., Csukai, M., Dehal, P., De Wit, P., Donzelli, B., van de Geest, H.C., van Ham, R.C.H.J., Hammond-Kosack, K.E., Henrissat, B., Kilian, A., Kobayashi, A.K., Koopmann, E., Kourmpetis, Y., Kuzniar, A., Lindquist, E., Lombard, V., Maliepaard, C., Martins, N., Mehrabi, R., Nap, J.P.H., Ponomarenko, A., Rudd, J.J., Salamov, A., Schmutz, J., Schouten, H., Shapiro, H., Stergiopoulos, I., Torriani, S.F.F., Tu, H., de Vries, R.P., Waalwijk, C., Ware, S.B., Wiebenga, A., Zwiers, L-H, Oliver, R.P., Grigoriev, I.V. and Kema, G.H.J. (2011) Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis. PLoS Genetics, 7 (6). e1002070.

Ipcho, S.V.S., Hane, J.K., Antoni, E.A., AHREN, D., Henrissat, B., Friesen, T.L., Solomon, P.S. and Oliver, R.P. (2011) Transcriptome analysis of Stagonospora nodorum: gene models, effectors, metabolism and pantothenate dispensability. Molecular Plant Pathology, 13 (6). pp. 531-545.

Ellwood, S.R., Liu, Z.H., Syme, R.A., Lai, Z.B., Hane, J.K., Keiper, F., Moffat, C.S., Oliver, R.P. and Friesen, T.L. (2011) A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres. Genome Biology, 11 (11). Art. No. R109 2010.

Hane, J.K., Rouxel, T., Howlett, B.J., Kema, G.H.J., Goodwin, S.B. and Oliver, R.P. (2011) A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biology, 12 (5). R45.

van de Wouw, A.P., Cozijnsen, A.J., Hane, J.K., Brunner, P.C., McDonald, B.A., Oliver, R.P. and Howlett, B.J. (2010) Evolution of linked avirulence effectors in Leptosphaeria maculans is affected by genomic environment and exposure to resistance genes in host plants. PLoS Pathogens, 6 (11). e1001180.

Hane, J.K. and Oliver, R.P. (2010) In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes. BMC Genomics, 11 (1). p. 655.

Antoni, E.A., Rybak, K., Tucker, M.A., Hane, J.K., Solomon, P.S., Drenth, A., Shankar, M. and Oliver, R.P. (2010) Ubiquity of ToxA and absence of ToxB in Australian populations of Pyrenophora tritici-repentis. Australasian Plant Pathology, 39 (1). pp. 63-68.

Bringans, S., Hane, J.K., Casey, T., Tan, K-C, Lipscombe, R., Solomon, P.S. and Oliver, R.P. (2009) Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum. BMC Bioinformatics, 10 (1). p. 301.

Ellwood, S.R., Phan, H.T.T., Jordan, M., Hane, J.K., Torres, A.M., Avila, C.M., Cruz-Izquierdo, S. and Oliver, R.P. (2008) Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris. BMC Genomics, 9 (1). p. 380.

Hane, J.K. and Oliver, R.P. (2008) RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences. BMC Bioinformatics, 9 (1). p. 478.

Solomon, P.S., Ipcho, S.V.S., Hane, J.K., Tan, K.C. and Oliver, R.P. (2008) A quantitative PCR approach to determine gene copy number. Fungal Genetics Reports, 55 . pp. 5-8.

Hane, J.K., Lowe, R.G.T., Solomon, P.S., Tan, K.C., Schoch, C.L., Spatafora, J.W., Crous, P.W., Kodira, C., Birren, B.W., Galagan, J.E., Torriani, S.F.F., McDonald, B.A. and Oliver, R.P. (2007) Dothideomycete Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum. The Plant Cell, 19 (11). pp. 3347-3368.

Phan, H.T.T., Ellwood, S.R., Hane, J.K., Ford, R., Materne, M. and Oliver, R.P. (2007) Extensive macrosynteny between Medicago truncatula and Lens culinaris ssp. culinaris. Theoretical and Applied Genetics, 114 (3). pp. 549-558.

Nelson, M.N., Phan, H.T.T., Ellwood, S.R., Moolhuijzen, P.M., Hane, J.K., Williams, A., O'Lone, C.E., Fosu-Nyarko, J., Scobie, M., Cakir, M., Jones, M.G.K.ORCID: 0000-0001-5002-0227, Bellgard, M., Książkiewicz, M., Wolko, B., Barker, S., Oliver, R.P. and Cowling, W.A. (2006) The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula. Theoretical and Applied Genetics, 113 (2). pp. 225-238.

Conference Paper

Nelson, M., Phan, H., Ellwood, S., Moolhuijzen, P., Lone, C., Williams, A., Hane, J., Buirchell, B., Bellgard, M. and Cowling, W. (2005) Genetic mapping of domestication traits in narrow leafed lupin (lupinus angustifolius): Using synteny to search for candidate genes in Medicago truncatula. In: 2nd Australian Model Legume Workshop, 5-8 April 2005, Perth, Western Australia

Phan, H., Elwood, S., Moolhuijzen, P., Williams, A., Hane, J., Ford, R., Bellgard, M. and Oliver, R. (2005) Genomic synteny in legumes: Application to crop breeding. In: 2nd Australian Model Legume Workshop, 5 - 8 April 2005, Rottnest Island, Western Australia

Conference Item

van de Wouw, A.P., Cozijnsen, A.J., Hane, J., Brunner, P.C., McDonald, B.A., Oliver, R.P. and Howlett, B.J. (2010) Deletions, repeat-induced point mutations and amino acid substitutions drive evolution of linked effectors in a fungal plant pathogen. In: OzBio, 26 September - 1 October, Melbourne, Australia.

Ipcho, S.V.S., Hane, J.K., Solomon, P.S. and Oliver, R.P. (2008) Dissecting the infection machinery of Stagonospora nodorum using DNA microarrays. In: 9th International Congress of Plant Pathology ICPP 2008, 24 - 29, Torino, Italy.

Oliver, R.P., Solomon, P.S., Hane, J., Ferguson-Hunt, M., McDonald, B.A., Faris, J. and Friesen, T.L. (2008) Multiple host-specific toxins, lateral gene transfer and gene loss in the evolution of cereal Pleosporalean Pathogens. In: International Conference on Biotic Plant Interactions, 27 - 29 March, Brisbane, Australia.

Oliver, R.P., Solomon, P.S., Hane, J., Ferguson-Hunt, M., McDonald, B.A., Faris, J. and Friesen, T.L. (2008) Multiple host-specific toxins, lateral gene transfer and gene loss in the evolution of cereal Pleosporalean Pathogens. In: 9th International Congress of Plant Pathology ICPP 2008, 24 - 29, Torino, Italy.

Oliver, R.P., Solomon, P.S., Hane, J.K., Tan, K.C., Lowe, R.G.T., Waters, O.D.C., Stukenbrock, E.H., McDonald, B.A. and Friesen, T.L. (2007) Fungal proteins, metabolites and signalling pathways controlling the interaction between wheat and Stagonospora nodorum. In: XIII International Congress on Molecular Plant-Microbe Interactions, 21 - 27 July, Sorrento, Italy.

Oliver, R.P., Solomon, P.S., Hane, J., Stukenbrock, E.H., McDonald, B.A., Liu, Z., Faris, J.D. and Friesen, T.L. (2007) Interspecific transfer of host-specific toxin genes in Stagonospora nodorum. In: XXIV Fungal Genetics Conference, 20 - 25 March, Pacific Grove, California, USA.

Nelson, M., Phan, H., Ellwood, S., Moolhuijzen, P., Bellgard, M., Hane, J., Williams, A., Fosu-Nyarko, J., Wolko, B., Ksiarkiewicz, M., Cakir, M., Jones, M.ORCID: 0000-0001-5002-0227, Scobie, M., O'Lone, C., Barker, S., Oliver, R. and Cowling, W. (2006) The first gene-based map of narrow-leafed lupin - location of domestication genes and conserved synteny with Medicago truncatula. In: Crop Updates 2006: Lupins and Pulses, 15 - 16 February 2006, The Burswood International Resort, Perth.

Book Chapter

Hane, J.K., Williams, A.H. and Oliver, R.P. (2011) Genomic and comparative analysis of the Class Dothideomycetes. In: Pöggeler, S. and Wöstemeyer, J., (eds.) The Mycota, XIV: Evolution of Fungi and Fungal-Like Organisms. Springer, pp. 205-229.


Hane, James (2011) Bioinformatic genome analysis of the necrotrophic wheat-pathogenic fungus Phaeosphaeria nodorum and related Dothideomycete fungi. PhD thesis, Murdoch University.

This list was generated on Sat Jan 28 16:41:52 2023 UTC.