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Biofuels"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B59","doi-asserted-by":"crossref","first-page":"579","DOI":"10.3389\/fpls.2015.00579","article-title":"Candidate effector proteins of the necrotrophic apple canker pathogen Valsa mali can suppress BAX-induced PCD,","volume":"6","author":"Li","year":"2015","journal-title":"Front Plant Sci"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B60","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1111\/nph.13544","article-title":"Genome sequence of Valsa canker pathogens uncovers a potential adaptation of colonization of woody bark,","volume":"208","author":"Yin","year":"2015","journal-title":"New Phytol"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B61","doi-asserted-by":"crossref","first-page":"1002869","DOI":"10.1371\/journal.pgen.1002869","article-title":"Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae,","volume":"8","author":"Xue","year":"2012","journal-title":"PLoS Genet"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B62","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1093\/bioinformatics\/btu023","article-title":"Exploring genome characteristics and sequence quality without a reference,","volume":"30","author":"Simpson","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B63","doi-asserted-by":"crossref","first-page":"e1003998","DOI":"10.1371\/journal.pcbi.1003998","article-title":"Extensive error in the number of genes inferred from draft genome assemblies,","volume":"10","author":"Denton","year":"2014","journal-title":"PLoS Comput. Biol"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B64","doi-asserted-by":"crossref","first-page":"3849","DOI":"10.1038\/ncomms4849","article-title":"Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics,","volume":"5","author":"Zhang","year":"2014","journal-title":"Nat. Commun"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B65","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.funbio.2011.11.010","article-title":"Genetic and pathogenic diversity of Neofusicoccum parvum in new Zealand vineyards,","volume":"116","author":"Baskarathevan","year":"2012","journal-title":"Fungal Biol"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B66","doi-asserted-by":"crossref","first-page":"e23534","DOI":"10.1038\/srep23534","article-title":"dbPAF: an integrative database of protein phosphorylation in animals and fungi,","volume":"6","author":"Ullah","year":"2016","journal-title":"Sci. Rep."},{"key":"key\n\t\t\t\t20180328144612_dsx040-B67","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1111\/j.1364-3703.2009.00579.x","article-title":"The role of mitogen activated protein (MAP) kinase signalling components and the Ste12 transcription factor in germination and pathogenicity of Botrytis cinerea,","volume":"11","author":"Schamber","year":"2010","journal-title":"Mol. Plant Pathol."},{"key":"key\n\t\t\t\t20180328144612_dsx040-B68","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1016\/j.fgb.2009.06.001","article-title":"MAP kinase signalling pathway components and targets conserved between the distantly related plant pathogenic fungi Mycosphaerella graminicola and Magnaporthe grisea,","volume":"46","author":"Kramer","year":"2009","journal-title":"Fungal Genet. Biol."},{"key":"key\n\t\t\t\t20180328144612_dsx040-B69","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1089\/ars.2012.5062","article-title":"Virulence regulation of phytopathogenic fungi by pH,","volume":"19","author":"Alkan","year":"2013","journal-title":"Antioxid. Redox Signal"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B70","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1094\/MPMI-18-0602","article-title":"Functional analysis of the cytochrome P450 monooxygenase gene bcbot1 of Botrytis cinerea indicates that botrydial is a strain-specific virulence factor,","volume":"18","author":"Siewers","year":"2005","journal-title":"Mol. Plant Microbe Interact"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B71","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1038\/nature04332","article-title":"Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus","volume":"438","author":"Nierman","year":"2005","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B72","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/j.pmpp.2010.06.007","article-title":"Inhibitory effects of polypeptides secreted by the grapevine pathogens Phaeomoniella chlamydospora and Phaeoacremonium aleophilum on plant cell activities,","volume":"74","author":"Luini","year":"2010","journal-title":"Physiol. Mol. Plant Pathol."},{"key":"key\n\t\t\t\t20180328144612_dsx040-B73","doi-asserted-by":"crossref","first-page":"e0156392","DOI":"10.1371\/journal.pone.0156392","article-title":"pH regulation of electrogenic sugar\/H+ symport in MFS sugar permeases,","volume":"1111","author":"Bazzone","year":"2016","journal-title":"PLoS ONE"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B74","first-page":"1","article-title":"MFS transportome of the human pathogenic yeast Candida albicans,","volume":"99","author":"Gaur","year":"2008","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B75","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1104\/pp.111.176347","article-title":"Analysis of two in planta expressed LysM effector homologs from the fungus Mycosphaerella graminicola reveals novel functional properties and varying contributions to virulence on wheat,","volume":"156","author":"Marshall","year":"2011","journal-title":"Plant Physiol"},{"key":"key\n\t\t\t\t20180328144612_dsx040-B76","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1094\/MPMI-06-12-0154-R","article-title":"In planta effector competition assays detect Hyaloperonospora arabidopsidis effectors that contribute to virulence and localize to different plant subcellular compartments,","volume":"26","author":"Badel","year":"2013","journal-title":"Mol. 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