Published in Nat Biotechnol on January 28, 2007
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res (2007) 3.84
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet (2008) 3.23
Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud Mycol (2011) 2.71
The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol (2008) 2.43
Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet (2011) 2.35
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Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol (2011) 2.15
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Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One (2011) 1.43
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Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger. BMC Genomics (2007) 1.35
Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genet (2012) 1.35
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Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nat Commun (2012) 1.30
Chemical induction of silent biosynthetic pathway transcription in Aspergillus niger. J Ind Microbiol Biotechnol (2009) 1.30
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Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles. Mol Genet Genomics (2008) 1.28
Spatial differentiation in the vegetative mycelium of Aspergillus niger. Eukaryot Cell (2007) 1.25
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An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J Bacteriol (2011) 1.24
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Comparative characterization of fungal anthracenone and naphthacenedione biosynthetic pathways reveals an α-hydroxylation-dependent Claisen-like cyclization catalyzed by a dimanganese thioesterase. J Am Chem Soc (2011) 1.22
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Dissecting colony development of Neurospora crassa using mRNA profiling and comparative genomics approaches. Eukaryot Cell (2008) 1.21
Strategies for mining fungal natural products. J Ind Microbiol Biotechnol (2013) 1.21
Fungal sex and pathogenesis. Clin Microbiol Rev (2010) 1.16
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics (2008) 1.15
A novel screening method for cell wall mutants in Aspergillus niger identifies UDP-galactopyranose mutase as an important protein in fungal cell wall biosynthesis. Genetics (2008) 1.15
Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger. BMC Genomics (2013) 1.14
Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PLoS One (2013) 1.12
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res (2008) 1.12
New insight into the ochratoxin A biosynthetic pathway through deletion of a nonribosomal peptide synthetase gene in Aspergillus carbonarius. Appl Environ Microbiol (2012) 1.12
Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level. BMC Genomics (2011) 1.10
Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger. ISME J (2011) 1.10
The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate. Microb Cell Fact (2010) 1.10
A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations. Mol Microbiol (2013) 1.10
Transcriptomic insights into the physiology of Aspergillus niger approaching a specific growth rate of zero. Appl Environ Microbiol (2010) 1.09
A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol (2011) 1.08
Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway. BMC Genomics (2009) 1.07
Systemic analysis of the response of Aspergillus niger to ambient pH. Genome Biol (2009) 1.07
Repeat induced point mutation in two asexual fungi, Aspergillus niger and Penicillium chrysogenum. Curr Genet (2008) 1.05
Ochratoxin a: general overview and actual molecular status. Toxins (Basel) (2010) 1.05
Secondary metabolite profiling, growth profiles and other tools for species recognition and important Aspergillus mycotoxins. Stud Mycol (2007) 1.05
Aspergillus genomes and the Aspergillus cloud. Nucleic Acids Res (2008) 1.05
Genome sequence of the white koji mold Aspergillus kawachii IFO 4308, used for brewing the Japanese distilled spirit shochu. Eukaryot Cell (2011) 1.04
Evolution and diversity of a fungal self/nonself recognition locus. PLoS One (2010) 1.03
Activation of the dormant secondary metabolite production by introducing gentamicin-resistance in a marine-derived Penicillium purpurogenum G59. Mar Drugs (2012) 1.02
Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production. BMC Genomics (2009) 1.02
Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone. Fungal Genet Biol (2010) 1.02
Fumonisin and ochratoxin production in industrial Aspergillus niger strains. PLoS One (2011) 1.01
Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans. J Ind Microbiol Biotechnol (2013) 1.00
Aegerolysins: structure, function, and putative biological role. Protein Sci (2009) 0.99
Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics. Genome Biol (2007) 0.99
Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing. BMC Genomics (2013) 0.99
Characterization of a silent azaphilone gene cluster from Aspergillus niger ATCC 1015 reveals a hydroxylation-mediated pyran-ring formation. Chem Biol (2012) 0.99
The carbon starvation response of Aspergillus niger during submerged cultivation: insights from the transcriptome and secretome. BMC Genomics (2012) 0.98
Analysis of regulation of pentose utilisation in Aspergillus niger reveals evolutionary adaptations in Eurotiales. Stud Mycol (2011) 0.97
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics (2009) 0.97
CADRE: the Central Aspergillus Data REpository 2012. Nucleic Acids Res (2011) 0.97
Germination of conidia of Aspergillus niger is accompanied by major changes in RNA profiles. Stud Mycol (2012) 0.97
Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev (2014) 0.97
Identification and characterization of a novel diterpene gene cluster in Aspergillus nidulans. PLoS One (2012) 0.96
What can comparative genomics tell us about species concepts in the genus Aspergillus? Stud Mycol (2007) 0.96
Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse. Biotechnol Biofuels (2011) 0.96
Effects of a defective ERAD pathway on growth and heterologous protein production in Aspergillus niger. Appl Microbiol Biotechnol (2010) 0.95
The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger. Fungal Genet Biol (2014) 0.94
The function and evolution of the Aspergillus genome. Trends Microbiol (2012) 0.94
Application of the Saccharomyces cerevisiae FLP/FRT recombination system in filamentous fungi for marker recycling and construction of knockout strains devoid of heterologous genes. Appl Environ Microbiol (2010) 0.94
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data. BMC Genomics (2010) 0.94
The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics (2014) 0.94
Presence and functionality of mating type genes in the supposedly asexual filamentous fungus Aspergillus oryzae. Appl Environ Microbiol (2012) 0.94
Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst Biol (2009) 0.93
Terminal amino acids disturb xylanase thermostability and activity. J Biol Chem (2011) 0.93
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics. BMC Genomics (2008) 0.92
Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose. PLoS One (2011) 0.92
The genome of an industrial workhorse. Nat Biotechnol (2007) 0.92
Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics. Eukaryot Cell (2009) 0.92
Single cell transcriptomics of neighboring hyphae of Aspergillus niger. Genome Biol (2011) 0.92
Hydrophobins from Aspergillus species cannot be clearly divided into two classes. BMC Res Notes (2010) 0.91
A broader role for AmyR in Aspergillus niger: regulation of the utilisation of D-glucose or D-galactose containing oligo- and polysaccharides. Appl Microbiol Biotechnol (2011) 0.91
The Penicillium chrysogenum extracellular proteome. Conversion from a food-rotting strain to a versatile cell factory for white biotechnology. Mol Cell Proteomics (2010) 0.91
Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain. Mol Genet Genomics (2008) 0.91
Comparative genomics and transcriptomics analyses reveal divergent lifestyle features of nematode endoparasitic fungus Hirsutella minnesotensis. Genome Biol Evol (2014) 0.91
Genome sequence of Aspergillus luchuensis NBRC 4314. DNA Res (2016) 0.90
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res (2008) 27.83
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
Live or let die: the cell's response to p53. Nat Rev Cancer (2002) 15.06
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res (2013) 10.24
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Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science (2013) 8.81
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res (2004) 8.79
The genome of the kinetoplastid parasite, Leishmania major. Science (2005) 8.64
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature (2005) 7.74
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res (2003) 7.22
X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell (2006) 7.17
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
An evolving hierarchical family classification for glycosyltransferases. J Mol Biol (2003) 6.48
Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell (2006) 6.42
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27
Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature (2013) 6.07
Structure and function in rhodopsin: high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible N-acetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc Natl Acad Sci U S A (2002) 5.91
Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature (2009) 5.90
The amsterdam declaration on fungal nomenclature. IMA Fungus (2011) 5.86
Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5.79
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature (2010) 5.79
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature (2006) 5.52
Genome sequencing and analysis of Aspergillus oryzae. Nature (2005) 5.47
Functional genomic hypothesis generation and experimentation by a robot scientist. Nature (2004) 5.41
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol (2008) 5.38
The automation of science. Science (2009) 5.34
Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet (2012) 5.28
Fungal secondary metabolism - from biochemistry to genomics. Nat Rev Microbiol (2005) 5.27
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol (2008) 5.19
The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science (2012) 4.93
Total knee arthroplasty volume, utilization, and outcomes among Medicare beneficiaries, 1991-2010. JAMA (2012) 4.89
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol (2004) 4.85
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics (2003) 4.49
Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A (2005) 4.40
Improved response to disasters and outbreaks by tracking population movements with mobile phone network data: a post-earthquake geospatial study in Haiti. PLoS Med (2011) 4.38
Availability of consumer prices from US hospitals for a common surgical procedure. JAMA Intern Med (2013) 4.35
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med (2011) 4.24
Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Eng Des Sel (2006) 4.13
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A (2009) 4.09
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (2009) 4.05
A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc Natl Acad Sci U S A (2007) 4.04
Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A (2009) 4.03
Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol (2011) 3.97
A community-driven global reconstruction of human metabolism. Nat Biotechnol (2013) 3.89
The G(0)/G(1) switch gene 2 regulates adipose lipolysis through association with adipose triglyceride lipase. Cell Metab (2010) 3.61
A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol (2003) 3.57
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet (2011) 3.52
High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol (2003) 3.48
The PEDANT genome database. Nucleic Acids Res (2003) 3.47
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res (2004) 3.44
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A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol (2004) 3.32
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels (2013) 3.30
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Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet (2008) 3.23
Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol (2008) 3.16
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A complex barcode underlies the heterogeneous response of p53 to stress. Nat Rev Mol Cell Biol (2008) 3.13
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Predictors of resistance to preoperative trastuzumab and vinorelbine for HER2-positive early breast cancer. Clin Cancer Res (2007) 3.08