Datasets archived at AspGD

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  • Colabardini AC, et al. (2013) Functional Characterization of Aspergillus nidulans ypkA, a Homologue of the Mammalian Kinase SGK. PLoS One 8(3):e57630.
  • de Souza WR, et al. (2013) The influence of Aspergillus niger transcription factors AraR and XlnR in the gene expression during growth in D-xylose, L-arabinose and steam-exploded sugarcane bagasse. Fungal Genet Biol. 2013 Jul 26.
  • Kawauchi M, et al. (2013) Fungus-Specific Sirtuin HstD Coordinates Secondary Metabolism and Development through Control of LaeA. Eukaryot Cell 12(8):1087-96.
  • Novodvorska M, et al. (2013) Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing. BMC Genomics 14:246.
  • Wiedner SD, et al. (2013) Disparate Proteome Responses of Pathogenic and Nonpathogenic Aspergilli to Human Serum Measured by Activity-Based Protein Profiling (ABPP). Mol Cell Proteomics 12(7):1791-805.
  • Barker BM, et al. (2012) Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter. BMC Genomics 13:62.
  • Carberry S, et al. (2012) Gliotoxin effects on fungal growth: Mechanisms and exploitation. Fungal Genet Biol 49(4):302-12.
  • Carvalho ND, et al. (2012) Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress. BMC Genomics 13(1):350.
  • Delmas S, et al. (2012) Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing. PLoS Genet 8(8):e1002875.
  • Hagag S, et al. (2012) Transcriptional and Proteomic Analysis of the Aspergillus fumigatus DeltaprtT Protease-Deficient Mutant. PLoS One 7(4):e33604.
  • Iwashita K. (2012) Unpublished A. oryzae RNA-Seq data from the laboratory of Dr. K. Iwashita.
    Unpublished data supplied to AspGD by Dr. K. Iwashita.
  • Nishida H. (2012) Conservation of nucleosome positions in duplicated and orthologous gene pairs. ScientificWorldJournal 2012:298174.
  • Ogawa M, et al. (2012) ManR, a novel Zn(II)(2)Cys(6) transcriptional activator, controls the beta-mannan utilization system in Aspergillus oryzae. Fungal Genet Biol 49(12):987-95.
  • Sibthorp C, Caddick MX. (2012) Unpublished A. nidulans RNA-Seq data from the laboratory of Mark X. Caddick.
    Unpublished data supplied to AspGD by Dr. Mark X. Caddick.
  • Wartenberg D, et al. (2012) Proteome analysis of the farnesol-induced stress response in Aspergillus nidulans-The role of a putative dehydrin. J Proteomics. 2012 May 23. [Epub ahead of print].
  • Zhao G, et al. (2012) Comparative proteome analysis of Aspergillus oryzae 3.042 and A. oryzae 100-8 strains: Towards the production of different soy sauce flavors. J Proteomics 75(13):3914-24.
  • Blatzer M, et al. (2011) SREBP coordinates iron and ergosterol homeostasis to mediate triazole drug and hypoxia responses in the human fungal pathogen Aspergillus fumigatus. PLoS Genet. 2011 Dec;7(12):e1002374. Epub 2011 Dec 1.
  • Cagas SE, et al. (2011) The Proteomic Signature of Aspergillus fumigatus During Early Development. Mol Cell Proteomics. 2011 Nov;10(11):M111.010108. Epub 2011 Aug 8.
  • Cagas SE, et al. (2011) Profiling the Aspergillus fumigatus proteome in response to caspofungin. Antimicrob Agents Chemother. 2011 Jan;55(1):146-54. Epub 2010 Oct 25.
  • de Bekker C, et al. (2011) Single cell transcriptomics of neighboring hyphae of Aspergillus niger. Genome Biol. 2011 Aug 4;12(8):R71.
  • Gautam P, et al. (2011) Transcriptomic and proteomic profile of Aspergillus fumigatus on exposure to artemisinin. Mycopathologia. 2011 Nov;172(5):331-46. Epub 2011 Jul 14.
  • Hartmann T, et al. (2011) Oligopeptide transport and regulation of extracellular proteolysis are required for growth of Aspergillus fumigatus on complex substrates but not for virulence. Mol Microbiol. 2011 Nov;82(4):917-35. doi: 10.1111/j.1365-2958.2011.07868.x. Epub 2011 Oct 24.
  • JCVI (2011) Large-Scale Sequencing of A. fumigatus strains at JCVI.
    Unpublished data supplied to AspGD by Natalie Fedorova, JCVI, and described in more detail here. Data files in VCF, BAM, or GFF format, and the reference sequence used in the alignments, are available from AspGD via the Downloads link.
  • Mela F, et al. (2011) Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger. ISME J. 2011 Sep;5(9):1494-504. doi: 10.1038/ismej.2011.29. Epub 2011 May 26.
  • Morton CO, et al. (2011) The temporal dynamics of differential gene expression in Aspergillus fumigatus interacting with human immature dendritic cells in vitro. PLoS One. 2011 Jan 14;6(1):e16016.
  • Ohno A, et al. (2011) A carrier fusion significantly induces unfolded protein response in heterologous protein production by Aspergillus oryzae. Appl Microbiol Biotechnol. 2011 Dec;92(6):1197-206. Epub 2011 Aug 7.
  • Oosthuizen JL, et al. (2011) Dual organism transcriptomics of airway epithelial cells interacting with conidia of Aspergillus fumigatus. PLoS One. 2011;6(5):e20527. Epub 2011 May 31.
  • Pusztahelyi T, et al. (2011) Comparison of transcriptional and translational changes caused by long-term menadione exposure in Aspergillus nidulans. Fungal Genet Biol. 2011 Feb;48(2):92-103. Epub 2010 Aug 24.
  • Ruger-Herreros C, et al. (2011) Regulation of conidiation by light in Aspergillus nidulans. Genetics. 2011 Aug;188(4):809-22. Epub 2011 May 30.
  • Sharon H, et al. (2011) PrtT-regulated proteins secreted by Aspergillus fumigatus activate MAPK signaling in exposed A549 lung cells leading to necrotic cell death. PLoS One. 2011 Mar 11;6(3):e17509.
  • Albrecht D, et al. (2010) Integrative analysis of the heat shock response in Aspergillus fumigatus. BMC Genomics. 2010 Jan 15;11:32.
  • Gehrke A, et al. (2010) Heptahelical receptors GprC and GprD of Aspergillus fumigatus are essential regulators of colony growth, hyphal morphogenesis, and virulence. Appl Environ Microbiol. 2010 Jun;76(12):3989-98. Epub 2010 Apr 23.
  • Jorgensen TR, et al. (2010) Transcriptomic insights into the physiology of Aspergillus niger approaching a specific growth rate of zero. Appl Environ Microbiol. 2010 Aug;76(16):5344-55. Epub 2010 Jun 18.
  • Liu H, et al. (2010) Aspergillus fumigatus AcuM regulates both iron acquisition and gluconeogenesis. Mol Microbiol. 2010 Nov;78(4):1038-54. Epub 2010 Sep 27.
  • Masuo S, et al. (2010) Global gene expression analysis of Aspergillus nidulans reveals metabolic shift and transcription suppression under hypoxia. Mol Genet Genomics 284(6):415-424.
  • Nahlik K, et al. (2010) The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development. Mol Microbiol. 2010 Nov;78(4):964-79. Epub 2010 Sep 27.
  • Schinko T, et al. (2010) Transcriptome analysis of nitrate assimilation in Aspergillus nidulans reveals connections to nitric oxide metabolism. Mol Microbiol. 2010 Nov;78(3):720-38. Epub 2010 Sep 27.
  • Terabayashi Y, et al. (2010) Identification and characterization of genes responsible for biosynthesis of kojic acid, an industrially important compound from Aspergillus oryzae. Fungal Genet Biol. 2010 Dec;47(12):953-61. Epub 2010 Sep 16.
  • van den Berg RA, et al. (2010) Identification of modules in Aspergillus niger by gene co-expression network analysis. Fungal Genet Biol. 2010 Jun;47(6):539-50. Epub 2010 Mar 27.
  • Wang B, et al. (2010) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res. 2010 Aug;38(15):5075-87. Epub 2010 Apr 14.
    This publicly available A. oryzae RNA-Seq dataset comprises eight experiments. Paired-end RNA-sequencing (RNA-Seq), using the Illumina platform, was conducted on polyadenylated-enriched mRNA isolated from four different culture conditions. Data were downloaded from NCBI: and data files in BAM or FASTQ format are available from AspGD via the Downloads link.
  • Do JH, et al. (2009) Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model. BMC Genomics. 2009 Jul 8;10:306.
  • Hagiwara D, et al. (2009) Transcriptional profiling for Aspergillus nidulans HogA MAPK signaling pathway in response to fludioxonil and osmotic stress. Fungal Genet Biol. 2009 Nov;46(11):868-78. Epub 2009 Jul 22.
  • Jorgensen TR, et al. (2009) Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway. BMC Genomics. 2009 Jan 23;10:44.
  • Malavazi I, et al. (2009) Phenotypic analysis of genes whose mRNA accumulation is dependent on calcineurin in Aspergillus fumigatus. Fungal Genet Biol. 2009 Oct;46(10):791-802. Epub 2009 Jun 30.
  • Martens-Uzunova ES, et al. (2009) Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics. Fungal Genet Biol. 2009 Mar;46 Suppl 1:S170-S179.
  • Panagiotou G, et al. (2009) Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools. Appl Environ Microbiol 75(7):2212-20.
  • Sakamoto K, et al. (2009) Aspergillus oryzae atfA controls conidial germination and stress tolerance. Fungal Genet Biol. 2009 Dec;46(12):887-97. Epub 2009 Sep 19.
  • Salazar M, et al. (2009) Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Mol Genet Genomics 282(6):571-86.
  • Schroeckh V, et al. (2009) Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans. Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14558-63. Epub 2009 Aug 6.
  • Twumasi-Boateng K, et al. (2009) Transcriptional profiling identifies a role for BrlA in the response to nitrogen depletion and for StuA in the regulation of secondary metabolite clusters in Aspergillus fumigatus. Eukaryot Cell. 2009 Jan;8(1):104-15. Epub 2008 Nov 21.
  • van der Veen D, et al. (2009) Analysis of variance components reveals the contribution of sample processing to transcript variation. Appl Environ Microbiol. 2009 Apr;75(8):2414-22. Epub 2009 Feb 20.
  • Andersen MR, et al. (2008) A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4387-92. Epub 2008 Mar 10.
  • Bhabhra R, et al. (2008) Impaired ribosome biogenesis disrupts the integration between morphogenesis and nuclear duplication during the germination of Aspergillus fumigatus. Eukaryot Cell. 2008 Apr;7(4):575-83. Epub 2008 Feb 22.
  • deGouvea PF, et al. (2008) Functional characterization of the Aspergillus fumigatus PHO80 homologue. Fungal Genet Biol. 2008 Jul;45(7):1135-46. Epub 2008 Apr 8.
  • Hagiwara D, et al. (2008) Functional analysis of C2H2 zinc finger transcription factor CrzA involved in calcium signaling in Aspergillus nidulans. Curr Genet 54(6):325-38.
  • McDonagh A, et al. (2008) Sub-telomere directed gene expression during initiation of invasive aspergillosis. PLoS Pathog. 2008 Sep 12;4(9):e1000154.
  • Sakamoto K, et al. (2008) Aspergillus oryzae atfB encodes a transcription factor required for stress tolerance in conidia. Fungal Genet Biol. 2008 Jun;45(6):922-32. Epub 2008 Mar 25.
  • Savoldi M, et al. (2008) Farnesol induces the transcriptional accumulation of the Aspergillus nidulans Apoptosis-Inducing Factor (AIF)-like mitochondrial oxidoreductase. Mol Microbiol 70(1):44-59.
  • Schrettl M, et al. (2008) SreA-mediated iron regulation in Aspergillus fumigatus. Mol Microbiol. 2008 Oct;70(1):27-43. Epub 2008 Aug 21.
  • Sugui JA, et al. (2008) Genes differentially expressed in conidia and hyphae of Aspergillus fumigatus upon exposure to human neutrophils. PLoS One. 2008 Jul 9;3(7):e2655.
  • Yuan XL, et al. (2008) Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles. Mol Genet Genomics. 2008 Jun;279(6):545-61.
  • Breakspear A, et al. (2007) Aspergillus nidulans conidiation genes dewA, fluG, and stuA are differentially regulated in early vegetative growth. Eukaryot Cell. 2007 Sep;6(9):1697-700. Epub 2007 Jul 13.
  • Guillemette T, et al. (2007) Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger. BMC Genomics. 2007 Jun 11;8:158.
  • Malavazi I, et al. (2007) Transcriptome analysis of the Aspergillus nidulans AtmA (ATM, Ataxia- Telangiectasia mutated) null mutant. Mol Microbiol 66(1):74-99.
  • Meyer V, et al. (2007) Survival in the presence of antifungals: genome-wide expression profiling of Aspergillus niger in response to sublethal concentrations of caspofungin and fenpropimorph. J Biol Chem. 2007 Nov 9;282(45):32935-48. Epub 2007 Sep 5.
  • da Silva Ferreira ME, et al. (2006) Transcriptome analysis of Aspergillus fumigatus exposed to voriconazole. Curr Genet. 2006 Jul;50(1):32-44. Epub 2006 Apr 19.
  • David H, et al. (2006) Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans. Genome Biol 2006;7(11):R108.
  • Malavazi I, et al. (2006) Transcriptome analysis of Aspergillus nidulans exposed to camptothecin-induced DNA damage. Eukaryot Cell. 2006 Oct;5(10):1688-704.
  • Masai K, et al. (2006) Square-plate culture method allows detection of differential gene expression and screening of novel, region-specific genes in Aspergillus oryzae. Appl Microbiol Biotechnol. 2006 Aug;71(6):881-91. Epub 2006 May 18.
  • Pocsi I, et al. (2005) Comparison of gene expression signatures of diamide, H2O2 and menadione exposed Aspergillus nidulans cultures--linking genome-wide transcriptional changes to cellular physiology. BMC Genomics. 2005 Dec 20;6:182.
  • Ray A, et al. (2004) Negative subtraction hybridization: an efficient method to isolate large numbers of condition-specific cDNAs. BMC Genomics. 2004 Mar 29;5(1):22.

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