Regulation of Cellulase and Hemicellulase Gene Expression in Fungi, Current Genomics, vol.14, issue.4, pp.230-249, 2013. ,
DOI : 10.2174/1389202911314040002
HTSeq--a Python framework to work with high-throughput sequencing data, Encyclopedia of Information Science and Technology Khosrow-Pour: Information Resources Management Association), pp.166-169, 2014. ,
DOI : 10.1093/bioinformatics/btu638
Delignification by Wood-Decay Fungi, Annual Review of Phytopathology, vol.29, issue.1, pp.381-398, 1991. ,
DOI : 10.1146/annurev.py.29.090191.002121
Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus, Biotechnology for Biofuels, vol.9, issue.1, p.216, 2015. ,
DOI : 10.1186/1475-2859-9-58
URL : https://hal.archives-ouvertes.fr/hal-01439025
Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis, BMC Genomics, vol.13, issue.1, pp.57-67, 2012. ,
DOI : 10.1351/pac198759020257
URL : https://hal.archives-ouvertes.fr/hal-01001052
Laccase is essential for lignin degradation by the white-rot fungus Pycnoporus cinnabarinus, FEBS Lett, vol.40797, pp.89-92, 1997. ,
DOI : 10.1016/s0014-5793(97)00301-3
URL : http://onlinelibrary.wiley.com/doi/10.1016/S0014-5793(97)00301-3/pdf
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes, Science, vol.147, issue.1, pp.1715-1719, 2012. ,
DOI : 10.1086/337577
URL : https://hal.archives-ouvertes.fr/hal-01268324
Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii, Fungal Genetics and Biology, vol.76, pp.78-92, 2015. ,
DOI : 10.1016/j.fgb.2015.02.002
MycoCosm portal: gearing up for 1000 fungal genomes, Nucleic Acids Research, vol.42, issue.D1, pp.699-704, 1183. ,
DOI : 10.1093/nar/gkt1183
URL : https://academic.oup.com/nar/article-pdf/42/D1/D699/3619942/gkt1183.pdf
Carbohydrate-binding domains: multiplicity of biological roles, Applied Microbiology and Biotechnology, vol.88, issue.5, pp.1241-1249, 2010. ,
DOI : 10.1128/jb.169.4.1564-1570.1987
Fungal delignification of lignocellulosic biomass improves the saccharification of cellulosics, Biodegradation, vol.60, issue.1, pp.797-804, 2011. ,
DOI : 10.1016/j.ibiod.2007.02.003
Fungal aryl-alcohol oxidase: a peroxide-producing flavoenzyme involved in lignin degradation, Applied Microbiology and Biotechnology, vol.338, issue.4, 2012. ,
DOI : 10.1016/j.gene.2004.04.025
Temporal Alterations in the Secretome of the Selective Ligninolytic Fungus Ceriporiopsis subvermispora during Growth on Aspen Wood Reveal This Organism's Strategy for Degrading Lignocellulose, Applied and Environmental Microbiology, vol.80, issue.7, pp.2062-2070, 1128. ,
DOI : 10.1128/AEM.03652-13
Copper radical oxidases and related extracellular oxidoreductases of wood-decay Agaricomycetes, Fungal Genetics and Biology, vol.72, 2014. ,
DOI : 10.1016/j.fgb.2014.05.011
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Self-organized formation of topologically correct feature maps WGCNA: an R package for weighted correlation network analysis, Genome Biol. Biol. Cybern. BMC Bioinformatics, vol.14, issue.9, pp.59-69559, 1186. ,
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R, Bioinformatics, vol.24, issue.5, pp.719-720, 2008. ,
DOI : 10.1093/bioinformatics/btm563
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes, Biotechnology for Biofuels, vol.6, issue.1, pp.41-51, 2013. ,
DOI : 10.1186/1471-2148-12-186
URL : https://hal.archives-ouvertes.fr/hal-01268121
The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown, BMC Genomics, vol.15, issue.1, pp.486-496, 2014. ,
DOI : 10.1186/1471-2164-15-486
URL : https://hal.archives-ouvertes.fr/hal-01204353
Least squares quantization in PCM, IEEE Transactions on Information Theory, vol.28, issue.2, pp.129-137, 1982. ,
DOI : 10.1109/TIT.1982.1056489
URL : http://www.cs.toronto.edu/~roweis/csc2515-2006/readings/lloyd57.pdf
Peculiarities of Pycnoporus species for applications in biotechnology, Applied Microbiology and Biotechnology, vol.112, issue.103, pp.1129-1149, 2011. ,
DOI : 10.1016/S0269-7491(00)00136-6
The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Research, vol.42, issue.D1, pp.490-495, 2014. ,
DOI : 10.1093/nar/gkt1178
Some methods for classification and analysis of multivariate observations, Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability, pp.281-297, 1967. ,
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi, Proceedings of the National Academy of Sciences, vol.111, issue.27, pp.9923-9928, 2013. ,
DOI : 10.1128/jb.169.5.2195-2201.1987
URL : https://hal.archives-ouvertes.fr/hal-01578657
Model-based clustering for RNA-seq data A global genome segmentation method for exploration of epigenetic patterns, Bioinformatics PLoS ONE, vol.30, issue.7, pp.197-205, 2012. ,
Introduction to Data Mining, 2014. ,
Self-and Super-organising Maps in R: the kohonen package Analysis of whole transcriptome sequencing data: workflow and software, J. Stat. Softw. Genomics Inform, vol.13, pp.119-125, 2007. ,