James K Hane

James K Hane

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James K Hane

James K Hane

Publications by authors named "James K Hane"

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"CATAStrophy," a Genome-Informed Trophic Classification of Filamentous Plant Pathogens - How Many Different Types of Filamentous Plant Pathogens Are There?

Front Microbiol 2019 21;10:3088. Epub 2020 Jan 21.

Laboratory of Phytopathology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands.

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http://dx.doi.org/10.3389/fmicb.2019.03088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986263PMC
January 2020

Adapting legume crops to climate change using genomic approaches.

Plant Cell Environ 2019 01 13;42(1):6-19. Epub 2018 Jun 13.

School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia.

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http://dx.doi.org/10.1111/pce.13203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334278PMC
January 2019

Bioinformatic prediction of plant-pathogenicity effector proteins of fungi.

Curr Opin Microbiol 2018 12 22;46:43-49. Epub 2018 Feb 22.

Centre for Crop and Disease Management, Curtin University, Kent Street, Bentley, WA 6102, Australia; Curtin Institute for Computation, Curtin University, Kent Street, Bentley, WA 6102, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.mib.2018.01.017DOI Listing
December 2018

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin.

Theor Appl Genet 2018 Dec 17;131(12):2543-2554. Epub 2018 Sep 17.

UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.

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http://dx.doi.org/10.1007/s00122-018-3171-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6244526PMC
December 2018

Pan-Parastagonospora Comparative Genome Analysis-Effector Prediction and Genome Evolution.

Genome Biol Evol 2018 09 1;10(9):2443-2457. Epub 2018 Sep 1.

Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia.

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http://dx.doi.org/10.1093/gbe/evy192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6152946PMC
September 2018

Correction to: Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity.

BMC Genomics 2018 09 13;19(1):673. Epub 2018 Sep 13.

Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia.

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http://dx.doi.org/10.1186/s12864-018-5059-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6136185PMC
September 2018

Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi.

Mol Plant Microbe Interact 2018 08 28;31(8):779-788. Epub 2018 Jun 28.

1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and.

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https://apsjournals.apsnet.org/doi/10.1094/MPMI-06-17-0135-F
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http://dx.doi.org/10.1094/MPMI-06-17-0135-FIDOI Listing
August 2018

Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin.

Theor Appl Genet 2018 Apr 20;131(4):887-901. Epub 2018 Jan 20.

UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.

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http://dx.doi.org/10.1007/s00122-017-3045-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852200PMC
April 2018

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity.

BMC Genomics 2018 Apr 23;19(1):279. Epub 2018 Apr 23.

Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia.

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http://dx.doi.org/10.1186/s12864-018-4680-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5913888PMC
April 2018

Mass-spectrometry data for Rhizoctonia solani proteins produced during infection of wheat and vegetative growth.

Data Brief 2016 Sep 27;8:267-71. Epub 2016 May 27.

CSIRO Agriculture, Floreat, Western Australia; The University of Western Australia Institute of Agriculture, Crawley, Western Australia.

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https://linkinghub.elsevier.com/retrieve/pii/S23523409163033
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http://dx.doi.org/10.1016/j.dib.2016.05.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4906030PMC
September 2016

OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes.

Genome Biol Evol 2016 07 3;8(6):2044-64. Epub 2016 Jul 3.

Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Perth, Australia Curtin Institute for Computation, Curtin University, Perth, Australia.

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http://dx.doi.org/10.1093/gbe/evw121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943192PMC
July 2016

The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress.

PLoS One 2015 18;10(5):e0126978. Epub 2015 May 18.

CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Wembley, Western Australia, Australia; The Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126978PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4436139PMC
April 2016

Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts.

Mol Cell Proteomics 2016 Apr 25;15(4):1188-203. Epub 2016 Jan 25.

From the ‡CSIRO Agriculture, Floreat, Western Australia; §The University of Western Australia Institute of Agriculture, Crawley, Western Australia;

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http://dx.doi.org/10.1074/mcp.M115.054502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824849PMC
April 2016

Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici.

G3 (Bethesda) 2016 04 7;6(4):779-91. Epub 2016 Apr 7.

Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia 2601

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http://dx.doi.org/10.1534/g3.115.025197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825649PMC
April 2016

Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors.

Front Plant Sci 2015 23;6:1168. Epub 2015 Dec 23.

CSIRO Agriculture, Black Mountain Laboratories Canberra, ACT, Australia.

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http://dx.doi.org/10.3389/fpls.2015.01168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4688413PMC
January 2016

Next-generation re-sequencing as a tool for rapid bioinformatic screening of presence and absence of genes and accessory chromosomes across isolates of Zymoseptoria tritici.

Fungal Genet Biol 2015 Jun;79:71-5

CCDM Bioinformatics, Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia; Curtin Institute for Computation, Curtin University, Perth, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.fgb.2015.04.012DOI Listing
June 2015

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.

BMC Genomics 2015 Mar 11;16:170. Epub 2015 Mar 11.

Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Bentley, WA, 6102, Australia.

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http://dx.doi.org/10.1186/s12864-015-1344-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4363200PMC
March 2015

Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers.

Plant Biotechnol J 2015 Jan 24;13(1):14-25. Epub 2014 Jul 24.

CSIRO Plant Industry, Wembley, WA, Australia; The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.

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http://dx.doi.org/10.1111/pbi.12229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309465PMC
January 2015

The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species.

BMC Genomics 2014 Aug 7;15:660. Epub 2014 Aug 7.

Graham Centre for Agricultural Innovation, School of Agricultural and Wine Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga 2650, NSW, Australia.

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http://www.biomedcentral.com/content/pdf/1471-2164-15-660.pd
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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-15-660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133081PMC
August 2014

Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8.

PLoS Genet 2014 May 8;10(5):e1004281. Epub 2014 May 8.

Molecular Plant Pathology and Crop Genomics Laboratory, Centre for Environment and Life Sciences, Division of Plant Industry, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia; The University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia.

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http://dx.doi.org/10.1371/journal.pgen.1004281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014442PMC
May 2014

A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi.

BMC Genomics 2013 Nov 20;14:807. Epub 2013 Nov 20.

Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Centre for Environment and Life Sciences, Perth, Western Australia, Australia.

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http://dx.doi.org/10.1186/1471-2164-14-807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914424PMC
November 2013

Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery.

G3 (Bethesda) 2013 Jun 21;3(6):959-69. Epub 2013 Jun 21.

Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Department of Environment and Agriculture, Bentley WA 6845, Australia.

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http://dx.doi.org/10.1534/g3.112.004994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689807PMC
June 2013

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi.

Genome Biol 2011 24;12(5):R45. Epub 2011 May 24.

Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth, 6845, Australia.

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http://dx.doi.org/10.1186/gb-2011-12-5-r45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219968PMC
February 2012

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 2011 Oct 21;12:521. Epub 2011 Oct 21.

Plant Industry, Commonwealth Scientific and Industrial Research Organisation, Private Bag No, 5, Wembley WA 6913, Australia.

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http://dx.doi.org/10.1186/1471-2164-12-521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206524PMC
October 2011

A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres.

Genome Biol 2010 10;11(11):R109. Epub 2010 Nov 10.

Department of Environment and Agriculture, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia.

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http://dx.doi.org/10.1186/gb-2010-11-11-r109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156948PMC
June 2011

In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.

BMC Genomics 2010 Nov 24;11:655. Epub 2010 Nov 24.

Faculty of Health Sciences, Murdoch University, Perth, Western Australia, 6150, Australia.

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http://dx.doi.org/10.1186/1471-2164-11-655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017866PMC
November 2010

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.

BMC Bioinformatics 2008 Nov 12;9:478. Epub 2008 Nov 12.

Australian Centre for Necrotrophic Fungal Pathogens, Faculty of Health Sciences, Murdoch University, Murdoch, Australia.

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http://dx.doi.org/10.1186/1471-2105-9-478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621366PMC
November 2008

Extensive macrosynteny between Medicago truncatula and Lens culinaris ssp. culinaris.

Theor Appl Genet 2007 Feb 22;114(3):549-58. Epub 2006 Nov 22.

Australian Centre for Nectrotropic Fungal Pathogens, State Agricultural Biotechnology Centre, Department of Health Sciences, Murdoch University, Perth, WA 6150, Australia.

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http://dx.doi.org/10.1007/s00122-006-0455-3DOI Listing
February 2007