A. Andrianopoulos and M. Hynes, Cloning and analysis of the positively acting regulatory gene amdR from Aspergillus nidulans., Molecular and Cellular Biology, vol.8, issue.8, pp.3532-3541, 1988.
DOI : 10.1128/MCB.8.8.3532

S. Baker and J. Bennett, An overview of the genus Aspergillus The aspergilli: genomics, medical applications, biotechnology, and research methods, pp.3-13, 2008.

A. Beauvais, An extracellular matrix glues together the aerial-grown hyphae of Aspergillus fumigatus, Cellular Microbiology, vol.15, issue.6, pp.1588-1600, 2007.
DOI : 10.1016/S0960-9822(99)80019-0

J. Bennett and M. Klich, Mycotoxins, Clinical Microbiology Reviews, vol.16, issue.3, pp.497-516, 2003.
DOI : 10.1128/CMR.16.3.497-516.2003

G. Bienert and T. Jahn, Major Intrinsic Proteins and Arsenic Transport in Plants: New Players and Their Potential Role, Adv. Exp. Med. Biol, vol.679, pp.111-125, 2010.
DOI : 10.1007/978-1-4419-6315-4_9

V. Bruno, Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq, Genome Research, vol.20, issue.10, pp.1451-1458, 2010.
DOI : 10.1101/gr.109553.110

S. Bruns, Functional genomic profiling of Aspergillus fumigatus biofilm reveals enhanced production of the mycotoxin gliotoxin, PROTEOMICS, vol.47, issue.17, pp.3097-3107, 2010.
DOI : 10.1080/13693780802609604

M. Cook and M. Tyers, Size control goes global, Current Opinion in Biotechnology, vol.18, issue.4, pp.341-350, 2007.
DOI : 10.1016/j.copbio.2007.07.006

A. Decottignies, ATPase and Multidrug Transport Activities of the Overexpressed Yeast ABC Protein Yor1p, Journal of Biological Chemistry, vol.1327, issue.20, pp.12612-12622, 1998.
DOI : 10.1016/S0005-2736(97)00050-3

P. De-groot, The Cell Wall of the Human Pathogen Candida glabrata: Differential Incorporation of Novel Adhesin-Like Wall Proteins, Eukaryotic Cell, vol.7, issue.11, pp.1951-1964, 2008.
DOI : 10.1128/EC.00284-08

D. Denning and W. Hope, Therapy for fungal diseases: opportunities and priorities, Trends in Microbiology, vol.18, issue.5, pp.195-204, 2010.
DOI : 10.1016/j.tim.2010.02.004

J. Dennis, I. Nabi, and M. Demetriou, Metabolism, Cell Surface Organization, and Disease, Cell, vol.139, issue.7, pp.1229-1241, 2009.
DOI : 10.1016/j.cell.2009.12.008
URL : https://doi.org/10.1016/j.cell.2009.12.008

A. Dranginis, J. Rauceo, J. Coronado, and P. Lipke, A Biochemical Guide to Yeast Adhesins: Glycoproteins for Social and Antisocial Occasions, Microbiology and Molecular Biology Reviews, vol.71, issue.2, pp.282-294, 2007.
DOI : 10.1128/MMBR.00037-06
URL : http://mmbr.asm.org/content/71/2/282.full.pdf

N. Dunkel, A Gain-of-Function Mutation in the Transcription Factor Upc2p Causes Upregulation of Ergosterol Biosynthesis Genes and Increased Fluconazole Resistance in a Clinical Candida albicans Isolate, Eukaryotic Cell, vol.7, issue.7, pp.1180-1190, 2008.
DOI : 10.1128/EC.00103-08

W. Dunne and J. , Bacterial Adhesion: Seen Any Good Biofilms Lately?, Clinical Microbiology Reviews, vol.15, issue.2, pp.155-166, 2002.
DOI : 10.1128/CMR.15.2.155-166.2002
URL : http://cmr.asm.org/content/15/2/155.full.pdf

N. Fedorova, Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus, PLoS Genetics, vol.141, issue.4, p.1000046, 2008.
DOI : 10.1371/journal.pgen.1000046.s018

T. Fontaine, Cell wall ??1-3glucans induce the aggregation of germinating conidia of Aspergillus fumigatus, Fungal Genetics and Biology, vol.47, issue.8, pp.707-712, 2010.
DOI : 10.1016/j.fgb.2010.04.006

D. Geiser, The current status of species recognition and identification in Aspergillus, Studies in Mycology, vol.59, pp.1-10, 2007.
DOI : 10.3114/sim.2007.59.01

J. Gibbons, Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics, Molecular Biology and Evolution, vol.18, issue.5, pp.2731-2744, 2009.
DOI : 10.1101/gr.074492.107
URL : https://academic.oup.com/mbe/article-pdf/26/12/2731/13639986/msp188.pdf

F. Gravelat, MedA governs adherence, host cell interactions and virulence, Cellular Microbiology, vol.5, issue.4, pp.473-488, 2010.
DOI : 10.1016/S0926-6593(66)80120-0
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1462-5822.2009.01408.x/pdf

V. Grosse and S. Krappmann, The Asexual Pathogen Aspergillus fumigatus Expresses Functional Determinants of Aspergillus nidulans Sexual Development, Eukaryotic Cell, vol.7, issue.10, pp.1724-1732, 2008.
DOI : 10.1128/EC.00157-08

C. Hittinger, M. Johnston, J. Tossberg, and A. Rokas, Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life, Proceedings of the National Academy of Sciences, vol.9, issue.3, pp.1476-1481, 2010.
DOI : 10.1186/1471-2105-9-128

A. Iovdijova and V. Bencko, Potential risk of exposure to selected xenobiotic residues and their fate in the food chain?part I: classification of xenobiotics, Ann. Agric. Environ. Med, vol.17, pp.183-192, 2010.

M. Jansen, D. Winde, J. Pronk, and J. , Hxt-Carrier-Mediated Glucose Efflux upon Exposure of Saccharomyces cerevisiae to Excess Maltose, Applied and Environmental Microbiology, vol.68, issue.9, pp.4259-4265, 2002.
DOI : 10.1128/AEM.68.9.4259-4265.2002

H. Jiang and W. Wong, SeqMap: mapping massive amount of oligonucleotides to the genome, Bioinformatics, vol.14, issue.8, pp.2395-2396, 2008.
DOI : 10.1261/rna.1070208

M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000.
DOI : 10.1093/nar/28.1.27

N. Keller, G. Turner, and J. Bennett, Fungal secondary metabolism ??? from biochemistry to genomics, Nature Reviews Microbiology, vol.70, issue.12, pp.937-947, 2005.
DOI : 10.1038/nature04300

C. Lamarre, Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia, BMC Genomics, vol.9, issue.1, p.417, 2008.
DOI : 10.1186/1471-2164-9-417

J. Latge, Aspergillus fumigatus and aspergillosis, Clin. Microbiol. Rev, vol.12, pp.310-350, 1999.
DOI : 10.1128/9781555815523

J. Latge and W. Steinbach, Aspergillus fumigatus and aspergillosis, p.569, 2009.
DOI : 10.1128/9781555815523

R. Lints, M. Davis, and M. Hynes, The positively acting amdA gene of Aspergillus nidulans encodes a protein with two C2H2 zinc-finger motifs, Molecular Microbiology, vol.5, issue.5, pp.965-975, 1995.
DOI : 10.1101/gad.5.4.670

S. Maiya, A. Grundmann, S. Li, and G. Turner, The Fumitremorgin Gene Cluster of Aspergillus fumigatus: Identification of a Gene Encoding Brevianamide F Synthetase, ChemBioChem, vol.42, issue.7, pp.1062-1069, 2006.
DOI : 10.1016/j.fgb.2004.10.002

S. Maiya, A. Grundmann, X. Li, S. Li, and G. Turner, Identification of a Hybrid PKS/NRPS Required for Pseurotin A Biosynthesis in the Human PathogenAspergillus fumigatus, ChemBioChem, vol.19, issue.14, pp.1736-1743, 2007.
DOI : 10.1248/cpb.19.1739

A. Mari and E. Scala, Allergome: a unifying platform, Arb. Paul Ehrlich Inst. Bundesamt Sera Impfstoffe Frankf. A. M, pp.29-39, 2006.

L. Martinez and A. Casadevall, Cryptococcus neoformans Biofilm Formation Depends on Surface Support and Carbon Source and Reduces Fungal Cell Susceptibility to Heat, Cold, and UV Light, Applied and Environmental Microbiology, vol.73, issue.14, pp.4592-4601, 2007.
DOI : 10.1128/AEM.02506-06
URL : http://aem.asm.org/content/73/14/4592.full.pdf

A. Mcdonagh, Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis, PLoS Pathogens, vol.25, issue.9, p.1000154, 2008.
DOI : 10.1371/journal.ppat.1000154.s016

E. Mellado, A New Aspergillus fumigatus Resistance Mechanism Conferring In Vitro Cross-Resistance to Azole Antifungals Involves a Combination of cyp51A Alterations, Antimicrobial Agents and Chemotherapy, vol.51, issue.6, pp.1897-1904, 2007.
DOI : 10.1128/AAC.01092-06

I. Meneau and D. Sanglard, isolates, Medical Mycology, vol.47, issue.s1, pp.307-311, 2005.
DOI : 10.1128/AAC.48.2.568-574.2004

A. Mortazavi, B. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nature Methods, vol.14, issue.7, pp.621-628, 2008.
DOI : 10.1128/MCB.14.3.1647

E. Mowat, J. Butcher, C. Williams, and G. Ramage, P630 Aspergillus fumigatus biofilms are refractory to antifungal challenge, International Journal of Antimicrobial Agents, vol.29, pp.147-148, 2007.
DOI : 10.1016/S0924-8579(07)70472-7

E. Mowat, Phase-dependent antifungal activity against Asper- Biofilm Transcriptome of A, 2008.

E. Mowat, C. Williams, B. Jones, S. Mcchlery, and G. Ramage, mycetoma development: is this a biofilm?, Medical Mycology, vol.98, issue.1, pp.120-126, 2009.
DOI : 10.1016/j.tripleo.2003.12.035

H. Mulder, M. Saloheimo, M. Penttila, and S. Madrid, The transcription factor HACA mediates the unfolded protein response in Aspergillus niger , and up-regulates its own transcription, Molecular Genetics and Genomics, vol.271, issue.2, pp.130-140, 2004.
DOI : 10.1007/s00438-003-0965-5

F. Muller, M. Seidler, and A. Beauvais, biofilms in the clinical setting, Medical Mycology, vol.12, issue.S1, pp.96-100, 2011.
DOI : 10.1128/IAI.73.9.5420-5425.2005

U. Nagalakshmi, The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing, Science, vol.265, issue.12, pp.1344-1349, 2008.
DOI : 10.1146/annurev.micro.59.031805.133833

A. Nascimento, Multiple Resistance Mechanisms among Aspergillus fumigatus Mutants with High-Level Resistance to Itraconazole, Antimicrobial Agents and Chemotherapy, vol.47, issue.5, pp.1719-1726, 2003.
DOI : 10.1128/AAC.47.5.1719-1726.2003
URL : http://aac.asm.org/content/47/5/1719.full.pdf

J. Nett, H. Sanchez, M. Cain, and D. Andes, Biofilm Resistance Due to Drug???Sequestering Matrix Glucan, The Journal of Infectious Diseases, vol.202, issue.1, pp.171-175, 2010.
DOI : 10.1086/651200
URL : https://academic.oup.com/jid/article-pdf/202/1/171/18061894/202-1-171.pdf

W. Nierman, Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus, Nature, vol.33, issue.suppl. 1, pp.1151-1156, 2005.
DOI : 10.1016/j.fgb.2003.12.003

S. Paris, Conidial Hydrophobins of Aspergillus fumigatus, Applied and Environmental Microbiology, vol.69, issue.3, pp.1581-1588, 2003.
DOI : 10.1128/AEM.69.3.1581-1588.2003

R. Pattison and A. Amtmann, N-glycan production in the endoplasmic reticulum of plants, Trends in Plant Science, vol.14, issue.2, pp.92-99, 2009.
DOI : 10.1016/j.tplants.2008.11.008

R. Perrin, Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA, PLoS Pathogens, vol.34, issue.4, p.50, 2007.
DOI : 10.1371/journal.ppat.0030050.st003

R. Pitts, D. Rinker, P. Jones, A. Rokas, and L. Zwiebel, Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding, BMC Genomics, vol.17, issue.01, p.271, 2011.
DOI : 10.1093/jmedent/17.1.54

R. Rajendran, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.5, 2011.
DOI : 10.1128/AAC.01189-10

Q. Ren, K. Chen, and I. Paulsen, TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels, Nucleic Acids Research, vol.35, issue.Database, pp.274-279, 2007.
DOI : 10.1093/nar/gkl925
URL : https://academic.oup.com/nar/article-pdf/35/suppl_1/D274/3871210/gkl925.pdf

A. Ruepp, The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes, Nucleic Acids Research, vol.32, issue.18, pp.5539-5545, 2004.
DOI : 10.1093/nar/gkh894

M. Seidler, S. Salvenmoser, and F. Muller, Aspergillus fumigatus Forms Biofilms with Reduced Antifungal Drug Susceptibility on Bronchial Epithelial Cells, Antimicrobial Agents and Chemotherapy, vol.52, issue.11, pp.4130-4136, 2008.
DOI : 10.1128/AAC.00234-08
URL : http://aac.asm.org/content/52/11/4130.full.pdf

J. Slaven, Increased expression of a novel Aspergillus fumigatus ABC transporter gene, atrF, in the presence of itraconazole in an itraconazole resistant clinical isolate, Fungal Genetics and Biology, vol.36, issue.3, pp.199-206, 2002.
DOI : 10.1016/S1087-1845(02)00016-6

E. Snelders, Emergence of Azole Resistance in Aspergillus fumigatus and Spread of a Single Resistance Mechanism, PLoS Medicine, vol.347, issue.11, p.219, 2008.
DOI : 10.1371/journal.pmed.0050219.sd003

R. Sokal and F. Rohlf, Biometry: the principles and practice of statistics in biological research, 1995.

F. Soriani, Functional characterization of the Aspergillus fumigatus CRZ1 homologue, CrzA, Molecular Microbiology, vol.258, issue.6, pp.1274-1291, 2008.
DOI : 10.1128/EC.4.4.703-715.2005

G. Soto and S. Hultgren, Bacterial adhesins: common themes and variations in architecture and assembly, J. Bacteriol, vol.181, pp.1059-1071, 1999.

A. Strittmatter, S. Irniger, and G. Braus, Induction of jlbA mRNA synthesis for a putative bZIP protein of Aspergillus nidulans by amino acid starvation, Curr. Genet, vol.39, pp.327-334, 2001.

M. Sunde, A. Kwan, M. Templeton, R. Beever, and J. Mackay, Structural analysis of hydrophobins, Micron, vol.39, issue.7, pp.773-784, 2008.
DOI : 10.1016/j.micron.2007.08.003

F. Tekaia and J. Latge, Aspergillus fumigatus: saprophyte or pathogen?, Current Opinion in Microbiology, vol.8, issue.4, pp.385-392, 2005.
DOI : 10.1016/j.mib.2005.06.017

N. Thau, Rodletless mutants of Aspergillus fumigatus, Infect. Immun, vol.62, pp.4380-4388, 1994.

M. Tobin, R. Peery, and P. Skatrud, Genes encoding multiple drug resistance-like proteins in Aspergillus fumigatus and Aspergillus flavus, Gene, vol.200, issue.1-2, pp.11-23, 1997.
DOI : 10.1016/S0378-1119(97)00281-3

T. Udeigwe, P. Eze, J. Teboh, and M. Stietiya, Application, chemistry, and environmental implications of contaminant-immobilization amendments on agricultural soil and water quality, Environment International, vol.37, issue.1, pp.258-267, 2011.
DOI : 10.1016/j.envint.2010.08.008

S. Upadhyay, Identification and characterization of a laminin-binding protein of Aspergillus fumigatus: extracellular thaumatin domain protein (AfCalAp), Journal of Medical Microbiology, vol.68, issue.6, pp.714-722, 2009.
DOI : 10.1128/IAI.68.6.3377-3384.2000

M. Vallim, K. Miller, and B. Miller, Aspergillus SteA (Sterile12-like) is a homeodomain-C2/H2-Zn+2 finger transcription factor required for sexual reproduction, Molecular Microbiology, vol.153, issue.2, pp.290-301, 2000.
DOI : 10.1101/gad.7.8.1584

G. Vediyappan and T. Rossignol, Interaction of Candida albicans Biofilms with Antifungals: Transcriptional Response and Binding of Antifungals to Beta-Glucans, Antimicrobial Agents and Chemotherapy, vol.54, issue.5, pp.2096-2111, 2010.
DOI : 10.1128/AAC.01638-09
URL : https://hal.archives-ouvertes.fr/pasteur-01524688

K. Verstrepen and F. Klis, Flocculation, adhesion and biofilm formation in yeasts, Molecular Microbiology, vol.15, issue.1, pp.5-15, 2006.
DOI : 10.1101/gr.1024903
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05072.x/pdf

K. Vienken, M. Scherer, and R. Fischer, The Zn(II)2Cys6 Putative Aspergillus nidulans Transcription Factor Repressor of Sexual Development Inhibits Sexual Development Under Low-Carbon Conditions and in Submersed Culture, Genetics, vol.169, issue.2, pp.619-630, 2005.
DOI : 10.1534/genetics.104.030767

Z. Wang, M. Gerstein, and M. Snyder, RNA-Seq: a revolutionary tool for transcriptomics, Nature Reviews Genetics, vol.328, issue.1, pp.57-63, 2009.
DOI : 10.1038/nrg2484
URL : http://europepmc.org/articles/pmc2949280?pdf=render

T. Ward, J. Bielawski, H. Kistler, E. Sullivan, O. Donnell et al., Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium, Proceedings of the National Academy of Sciences, vol.68, issue.5, pp.9278-9283, 2002.
DOI : 10.1128/AEM.68.5.2148-2154.2002

B. Wilhelm, Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution, Nature, vol.376, issue.7199, pp.1239-1243, 2008.
DOI : 10.1091/mbc.01-10-0507