2021
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2020
(2020) Constructing a yeast to express the largest cellulosome complex on the cell surface.
Proc Natl Acad Sci U S A 117(5), 2385-2394.
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(2020) Identification of a gene encoding the last step of the L-rhamnose catabolic pathway in Aspergillus niger revealed the inducer of the pathway regulator.
Microbiol Res 234, 126426.
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(2020) Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen.
Phytopathology , PHYTO12190478A.
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(2020) Narnaviruses: novel players in fungal-bacterial symbioses.
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(2020) The architecture of metabolism maximizes biosynthetic diversity in the largest class of fungi.
Mol Biol Evol .
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(2020) The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi.
Mol Biol Evol 37(10), 2838-2856.
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(2020) 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.
Stud Mycol 96, 141-153.
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(2020) A comparative genomics study of 23 Aspergillus species from section Flavi.
Nat Commun 11(1), 1106.
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(2020) Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi.
New Phytol .
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(2020) Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle.
New Phytol .
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(2020) Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.
Nature Communications 11(1).
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(2020) Conserved white rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus.
DNA Res .
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(2020) Unique genomic traits for cold adaptation in Naganishia vishniacii, a polyextremophile yeast isolated from Antarctica.
FEMS Yeast Res .
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(2020) Synthetic hybrids of six yeast species.
Nat Commun 11(1), 2085.
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(2020) Intra-species genetic variability drives carbon metabolism and symbiotic host interactions in the ectomycorrhizal fungus Pisolithus microcarpus.
Environ Microbiol .
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(2020) Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships.
Syst Biol 69(1), 17-37.
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(2020) Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity.
Mol Biol Evol .
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(2020) Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.
Life (Basel) 10(12).
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(2020) Comparative genomics of pyrophilous fungi reveals a link between fire events and developmental genes.
Environ Microbiol .
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(2020) Production of Fungal Mycelia in a Temperate Coniferous Forest Shows Distinct Seasonal Patterns.
J Fungi (Basel) 6(4).
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(2020) Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose.
Biotechnol Biofuels 13, 69.
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(2020) Draft Genome Assemblies of Ionic Liquid-Resistant Yarrowia lipolytica PO1f and Its Superior Evolved Strain, YlCW001.
Microbiol Resour Announc 9(9).
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(2020) The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus.
Proc Natl Acad Sci U S A 117(11), 6003-6013.
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2019
(2019) Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae.
New Phytol .
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(2019) Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae.
New Phytol .
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(2019) Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants.
BMC Biol 17(1), 88.
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(2019) Broad-specificity GH131 beta-glucanases are a hallmark of Fungi and Oomycetes that colonise plants.
Environ Microbiol .
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(2019) Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers.
Environ Microbiol .
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(2019) An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots.
Plant Cell Environ .
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(2019) Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass.
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(2019) Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails.
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(2019) Draft Genome Sequence of the Ectomycorrhizal Ascomycete Sphaerosporella brunnea.
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(2019) Diversity of cytosine methylation across the fungal tree of life.
Nat Ecol Evol 3(3), 479-490.
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(2019) Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens.
Microbiol Resour Announc 8(18).
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(2019) Glucose-mediated repression of plant biomass utilization in the white-rot fungus Dichomitus squalens.
Appl Environ Microbiol .
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(2019) Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens.
J Biotechnol .
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(2019) Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).
Mol Phylogenet Evol 133, 152-163.
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(2019) Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases.
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(2019) Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases.
J Biol Chem 294(45), 17117-17130.
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(2019) Phyllosticta citricarpa and sister species of global importance to Citrus.
Mol Plant Pathol 20(12), 1619-1635.
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(2019) Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium.
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(2019) Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network.
BMC Genomics 20(1), 853.
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(2019) Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.
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(2019) Evolution and comparative genomics of the most common Trichoderma species.
BMC Genomics 20(1), 485.
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(2019) Genomic characterization of carbapenem-resistant Shewanella algae isolated from Asian hard clam (Meretrix lusoria).
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(2019) Fungal Endophytes of Populus trichocarpa Alter Host Phenotype, Gene Expression, and Rhizobiome Composition.
Mol Plant Microbe Interact 32(7), 853-864.
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(2019) Comparative Genomics and Transcriptomics to Analyze Fruiting Body Development in Filamentous Ascomycetes.
Genetics .
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(2019) Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina.
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(2019) Early Diverging Fungus Mucor circinelloides Lacks Centromeric Histone CENP-A and Displays a Mosaic of Point and Regional Centromeres.
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(2019) Mitovirus and Mitochondrial Coding Sequences from Basal Fungus Entomophthora muscae.
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(2019) Tracking of enzymatic biomass deconstruction by fungal secretomes highlights markers of lignocellulose recalcitrance.
Biotechnol Biofuels 12, 76.
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(2019) Inorganic nitrogen availability alters Eucalyptus grandis receptivity to the ectomycorrhizal fungus Pisolithus albus but not symbiotic nitrogen transfer.
New Phytol .
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(2019) Diverse members of the Xylariales lack canonical mating-type regions.
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(2019) Megaphylogeny resolves global patterns of mushroom evolution.
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(2019) Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi.
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2018
(2018) The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.
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(2018) Leveraging single-cell genomics to expand the fungal tree of life.
Nat Microbiol .
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(2018) Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases.
G3 (Bethesda) 8(10), 3311-3319.
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(2018) The fungus that came in from the cold: dry rot's pre-adapted ability to invade buildings.
ISME J 12(3), 791-801.
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(2018) Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails.
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(2018) Litter chemistry influences decomposition through activity of specific microbial functional guilds.
Ecological Monographs 88(3), 429-444.
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(2018) An analysis of codon bias in six red yeast species.
Yeast .
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(2018) Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships.
Fungal Biol Biotechnol 5, 12.
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(2018) High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.
New Phytol .
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(2018) Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides.
Elife 7.
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(2018) Dichomitus squalens partially tailors its molecular responses to the composition of solid wood.
Environ Microbiol .
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(2018) Dichomitus squalens partially tailors its molecular responses to the composition of solid wood.
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(2018) Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum.
Front Microbiol 9, 141.
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(2018) Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.
PLoS Genet 14(4), e1007322.
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(2018) Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance.
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(2018) The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet.
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(2018) Phylogenetic and Phylogenomic Definition of Rhizopus Species.
G3 (Bethesda) 8(6), 2007-2018.
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(2018) Multi-omic analyses of extensively decayed Pinus contorta reveal expression of diverse array of lignocellulose degrading enzymes.
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(2018) Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes.
Applied and Environmental Microbiology 84(20), 14.
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(2018) Broad genomic sampling reveals a smut pathogenic ancestry of the fungal clade Ustilaginomycotina.
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(2018) Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species.
Proc Natl Acad Sci U S A 115(4), E753-E761.
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(2018) Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi.
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(2018) Evolutionary instability of CUG-Leu in the genetic code of budding yeasts.
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(2018) Earth BioGenome Project: Sequencing life for the future of life.
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(2018) Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates.
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(2018) Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors.
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(2018) Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga.
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(2018) Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.
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(2018) Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass.
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(2018) Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle.
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(2018) Coniella lustricola, a new species from submerged detritus.
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(2018) Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts.
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(2018) Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales).
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(2018) Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion.
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(2018) Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.
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(2018) Genetic dissection of interspecific differences in yeast thermotolerance.
Nat Genet 50(11), 1501-1504.
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Genome Res 28(4), 569-580.
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(2018) Substrate-Specific Differential Gene Expression and RNA editing in the Brown Rot Fungus Fomitopsis pinicola.
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(2018) Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies.
Genome Biol Evol 10(12), 3250-3261.
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2017
(2017) Phylogenetics and Phylogenomics of Rust Fungi.
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(2017) Population genomics of picophytoplankton unveils novel chromosome hypervariability.
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(2017) Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales.
BMC Genomics 18(1), 883.
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(2017) Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments.
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(2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.
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(2017) The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation.
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(2017) Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas.
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(2017) Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress.
PLoS Biol 15(12), e2004050.
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(2017) Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12.
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(2017) A parts list for fungal cellulosomes revealed by comparative genomics.
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(2017) A parts list for fungal cellulosomes revealed by comparative genomics.
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(2017) Draft Genome Sequence of Coniochaeta ligniaria NRRL 30616, a Lignocellulolytic Fungus for Bioabatement of Inhibitors in Plant Biomass Hydrolysates.
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(2017) Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: a case study using the lichen-forming genus Peltigera section Polydactylon.
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(2017) Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen -forming genus Peltigera section Polydactylon.
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(2017) FunGAP: Fungal Genome Annotation Pipeline Using Evidence-based Gene Model Evaluation.
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(2017) FunGAP: Fungal Genome Annotation Pipeline Using Evidence-based Gene Model Evaluation.
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(2017) Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.
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(2017) Widespread adenine N6-methylation of active genes in fungi.
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(2017) Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi.
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(2017) Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi.
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(2017) Widespread adenine N6-methylation of active genes in fungi.
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(2017) Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus.
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(2017) Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus.
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(2017) Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution.
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(2017) The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi.
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(2017) The homothallic mating-type locus of the conifer needle endophyte Phialocephala scopiformis DAOMC 229536 (order Helotiales).
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(2017) The homothallic mating-type locus of the conifer needle endophyte Phialocephala scopiformis DAOMC 229536 (order Helotiales).
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(2017) The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex.
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(2017) The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa.
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(2017) Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens.
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(2017) A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism.
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(2017) A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism.
PLoS Genet 13(5), e1006737.
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2016
(2016) Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus.
Environ Microbiol .
10.1111/1462-2920.13360
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(2016) Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control.
PLoS Genet 12(8), e1005876.
10.1371/journal.pgen.1005876
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(2016) Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles.
PLoS Genet 12(6), e1006108.
10.1371/journal.pgen.1006108
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(2016) Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.
Curr Biol .
10.1016/j.cub.2016.04.038
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(2016) Draft Genome Sequence of Microdochium bolleyi, a Dark Septate Fungal Endophyte of Beach Grass.
Genome Announc 4(2).
10.1128/genomeA.00270-16
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(2016) The genome of Xylona heveae provides a window into fungal endophytism.
Fungal Biol 120(1), 26-42.
10.1016/j.funbio.2015.10.002
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(2016) The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete.
Fungal Biol 120(8), 961-74.
10.1016/j.funbio.2016.05.003
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(2016) Genetics of mating in members of the Chaetomiaceae as revealed by experimental and genomic characterization of reproduction in Myceliophthora heterothallica.
Fungal Genet Biol 86, 9-19.
10.1016/j.fgb.2015.11.007
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(2016) Lipid metabolic changes in an early divergent fungus govern the establishment of a mutualistic symbiosis with endobacteria.
Proc Natl Acad Sci U S A 113(52), 15102-15107.
10.1073/pnas.1615148113
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(2016) Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2.
Genome Announc 4(5).
10.1128/genomeA.00976-16
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(2016) Visual Comparative Omics of Fungi for Plant Biomass Deconstruction.
Front Microbiol 7, 1335.
10.3389/fmicb.2016.01335
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(2016) Ochratoxin A production by Penicillium thymicola.
Fungal Biol 120(8), 1041-9.
10.1016/j.funbio.2016.04.002
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(2016) Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum.
Nat Commun 7, 12662.
10.1038/ncomms12662
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(2016) Comparative genomics of biotechnologically important yeasts.
Proc Natl Acad Sci U S A .
10.1073/pnas.1603941113
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(2016) Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes.
Science .
10.1126/science.aad1431
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(2016) Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi.
Anaerobe 38, 39-46.
10.1016/j.anaerobe.2015.11.008
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(2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.
Mycologia 108(5), 1028-1046.
10.3852/16-042
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(2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.
Mycologia 108(5), 1028-1046.
10.3852/16-042
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(2016) Full Genome of Phialocephala scopiformis DAOMC 229536, a Fungal Endophyte of Spruce Producing the Potent Anti-Insectan Compound Rugulosin.
Genome Announc 4(1).
10.1128/genomeA.01768-15
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(2016) Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.
PLoS One 11(7), e0155839.
10.1371/journal.pone.0155839
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(2016) Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi.
PLoS One 11(7), e0157844.
10.1371/journal.pone.0157844
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2015
(2015) Draft Genome Sequence of Neurospora crassa Strain FGSC 73.
Genome Announc 3(2).
10.1128/genomeA.00074-15
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(2015) Genetic isolation between two recently diverged populations of a symbiotic fungus.
Mol Ecol .
10.1111/mec.13132
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(2015) Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.
Genome Biol Evol 7(6), 1590-601.
10.1093/gbe/evv090
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(2015) Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus.
Biotechnol Biofuels 8, 216.
10.1186/s13068-015-0407-8
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(2015) Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus.
Biotechnol Biofuels 8, 216.
10.1186/s13068-015-0407-8
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(2015) Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.
Proc Natl Acad Sci U S A 112(11), 3451-6.
10.1073/pnas.1424293112
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(2015) Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis.
New Phytol .
10.1111/nph.13546
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(2015) Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.
Front Microbiol 6, 978.
10.3389/fmicb.2015.00978
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(2015) Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii.
Fungal Genet Biol 76, 78-92.
10.1016/j.fgb.2015.02.002
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(2015) Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.
PLoS One 10(7), e0132628.
10.1371/journal.pone.0132628
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(2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists (vol 47, pg 410, 2015).
Nature Genetics 47(4), 410-415.
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(2015) Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists (vol 47, pg 410, 2015).
Nature Genetics 47(4), 410-415.
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(2015) Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems.
MBio 6(4).
10.1128/mBio.00918-15
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(2015) Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype.
BMC Genomics 16, 326.
10.1186/s12864-015-1526-0
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(2015) Genome sequence of a white rot fungus Schizopora paradoxa KUC8140 for wood decay and mycoremediation.
J Biotechnol 211, 42-43.
10.1016/j.jbiotec.2015.06.426
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(2015) Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea.
PLoS One 10(10), e0141586.
10.1371/journal.pone.0141586
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(2015) Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities.
Mol Biol Evol .
10.1093/molbev/msv337
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(2015) Identification of a Novel Nematotoxic Protein by Challenging the Model Mushroom Coprinopsis cinerea with a Fungivorous Nematode.
G3 (Bethesda) 6(1), 87-98.
10.1534/g3.115.023069
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(2015) The Mutualist Laccaria bicolor Expresses a Core Gene Regulon During the Colonization of Diverse Host Plants and a Variable Regulon to Counteract Host-Specific Defenses.
Mol Plant Microbe Interact 28(3), 261-73.
10.1094/MPMI-05-14-0129-FI
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(2015) Degradation of Bunker C Fuel Oil by White-Rot Fungi in Sawdust Cultures Suggests Potential Applications in Bioremediation.
PLoS One 10(6), e0130381.
10.1371/journal.pone.0130381
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2014
(2014) Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita.
New Phytol .
10.1111/nph.13140
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(2014) Transcriptional responses of the Bdtf1-deletion mutant to the phytoalexin brassinin in the necrotrophic fungus Alternaria brassicicola.
Molecules 19(8), 10717-32.
10.3390/molecules190810717
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(2014) Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius.
Int J Food Microbiol 179, 10-7.
10.1016/j.ijfoodmicro.2014.03.013
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(2014) Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species.
BMC Genomics 15, 549.
10.1186/1471-2164-15-549
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(2014) MycoCosm portal: gearing up for 1000 fungal genomes.
Nucleic Acids Res 42(Database issue), D699-704.
10.1093/nar/gkt1183
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(2014) Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi.
Genome Biol Evol 6(7), 1564-78.
10.1093/gbe/evu121
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(2014) Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood.
PLoS Genet 10(12), e1004759.
10.1371/journal.pgen.1004759
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(2014) Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood.
PLoS Genet 10(12), e1004759.
10.1371/journal.pgen.1004759
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(2014) Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.
Proc Natl Acad Sci U S A 111(48), 16995-7002.
10.1073/pnas.1418963111
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(2014) Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum.
Nat Commun 5, 3745.
10.1038/ncomms4745
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(2014) Expanding genomics of mycorrhizal symbiosis.
Front Microbiol 5, 582.
10.3389/fmicb.2014.00582
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(2014) Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts.
Nat Commun 5, 4471.
10.1038/ncomms5471
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(2014) The genome portal of the Department of Energy Joint Genome Institute: 2014 updates.
Nucleic Acids Res 42(Database issue), D26-31.
10.1093/nar/gkt1069
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(2014) Genomics of wood-degrading fungi.
Fungal Genet Biol .
10.1016/j.fgb.2014.05.001
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(2014) The phytoalexin camalexin induces fundamental changes in the proteome of Alternaria brassicicola different from those caused by brassinin.
Fungal Biol 118(1), 83-93.
10.1016/j.funbio.2013.11.005
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(2014) Duplications and losses in gene families of rust pathogens highlight putative effectors.
Front Plant Sci 5, 299.
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(2014) The mutualist Laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defenses.
Mol Plant Microbe Interact .
10.1094/MPMI-05-14-0129-FI
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(2014) Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.
Proc Natl Acad Sci U S A 111(27), 9923-8.
10.1073/pnas.1400592111
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(2014) Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass.
Appl Environ Microbiol 80(2), 540-54.
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(2014) Draft Genome Sequence of a Rare Smut Relative, Tilletiaria anomala UBC 951.
Genome Announc 2(3).
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(2014) Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae.
New Phytol 202(2), 554-64.
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(2014) Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production.
Genome Biol Evol 6(9), 2557-66.
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2013
(2013) Fungal genomes mining to discover novel sterol esterases and lipases as catalysts.
BMC Genomics 14, 712.
10.1186/1471-2164-14-712
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(2013) Phylogenetic and Phylogenomic overview of the Polyporales.
Mycologia .
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(2013) Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives.
Genome Announc 1(3).
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(2013) Fungal-specific transcription factor AbPf2 activates pathogenicity in Alternaria brassicicola.
Plant J 75(3), 498-514.
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(2013) Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.
PLoS Genet 9(1), e1003233.
10.1371/journal.pgen.1003233
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(2013) The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens.
ISME J 7(7), 1333-43.
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(2013) Comparative Genomics Analysis of Trichoderma reesei Strains .
Industrial Biotechnology 9(6), 352-367.
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(2013) Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence.
G3 (Bethesda) 3(1), 41-63.
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(2013) Pan genome of the phytoplankton Emiliania underpins its global distribution.
Nature 499(7457), 209-13.
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(2013) Insights into bilaterian evolution from three spiralian genomes.
Nature 493(7433), 526-531.
Doi 10.1038/Nature11696
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(2013) Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora.
Mycologia 105(6), 1445-55.
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(2013) Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.
Proc Natl Acad Sci U S A 110(50), 20117-22.
10.1073/pnas.1313452110
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2012
(2012) Phylogenomic analysis of polyketide synthase-encoding genes in Trichoderma.
Microbiology 158(Pt 1), 147-54.
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(2012) Harnessing glycosylation to improve cellulase activity.
Curr Opin Biotechnol 23(3), 338-45.
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(2012) The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.
Genome Biol 13(5), R39.
10.1186/gb-2012-13-5-r39
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(2012) Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola.
PLoS Pathog 8(10), e1002974.
10.1371/journal.ppat.1002974
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(2012) Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.
Nature 492(7427), 59-65.
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(2012) The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry.
PLoS Genet 8(11).
Artn E1003088Doi 10.1371/Journal.Pgen.1003088
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(2012) Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.
Proceedings of the National Academy of Sciences of the United States of America 109(14), 5458-5463.
DOI 10.1073/pnas.1119912109
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(2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.
Science 336(6089), 1715-9.
10.1126/science.1221748
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(2012) The genome portal of the Department of Energy Joint Genome Institute.
Nucleic Acids Res 40(Database issue), D26-32.
10.1093/nar/gkr947
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(2012) Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.
Mol Plant Microbe Interact 25(10), 1350-60.
10.1094/MPMI-02-12-0028-R
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(2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.
Proc Natl Acad Sci U S A 109(43), 17501-6.
10.1073/pnas.1206847109
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(2012) Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.
PLoS Pathog 8(12), e1003037.
10.1371/journal.ppat.1003037
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(2012) Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen.
New Phytologist 194(4), 1001-1013.
DOI 10.1111/j.1469-8137.2012.04128.x
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(2012) The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction.
Fungal Genet Biol 49(3), 217-26.
10.1016/j.fgb.2012.01.007
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(2012) The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties.
International Journal of Food Microbiology 157(2), 202-209.
DOI 10.1016/j.ijfoodmicro.2012.05.008
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(2012) Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolor.
Fungal Genetics and Biology 49(3), 199-209.
DOI 10.1016/j.fgb.2012.01.002
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(2012) The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry.
Environmental Microbiology 14(6), 1477-1487.
DOI 10.1111/j.1462-2920.2012.02736.x
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(2012) A versatile toolkit for high throughput functional genomics with Trichoderma reesei.
Biotechnol Biofuels 5(1), 1.
10.1186/1754-6834-5-1
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(2012) A Zinc-Finger-Family Transcription Factor, AbVf19, Is Required for the Induction of a Gene Subset Important for Virulence in Alternaria brassicicola.
Molecular Plant-Microbe Interactions 25(4), 443-452.
Doi 10.1094/Mpmi-10-11-0275
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(2012) Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.
Bmc Genomics 13.
Artn 444
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(2012) Mapping N-Linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry.
Journal of Proteome Research 11(1), 143-156.
Doi 10.1021/Pr200916k
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2011
(2011) Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.
Genome Res 21(6), 885-97.
10.1101/gr.112169.110
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(2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
Science 332(6032), 960-3.
10.1126/science.1203810
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(2011) Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris.
Nat Biotechnol 29(10), 922-7.
10.1038/nbt.1976
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(2011) The Ecoresponsive Genome of Daphnia pulex.
Science 331(6017), 555-561.
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(2011) Trichoderma: the genomics of opportunistic success.
Nat Rev Microbiol 9(10), 749-59.
10.1038/nrmicro2637
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(2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi.
Proc Natl Acad Sci U S A 108(22), 9166-71.
10.1073/pnas.1019315108
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(2011) The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi.
Science 333(6043), 762-5.
10.1126/science.1205411
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(2011) Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.
Genetics 189(1), 55-69.
10.1534/genetics.111.130690
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(2011) Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.
Proceedings of the National Academy of Sciences of the United States of America 108(11), 4352-4357.
DOI 10.1073/pnas.1016106108
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(2011) Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.
Plos Genetics 7(6).
ARTN e1002070
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(2011) Fueling the future with fungal genomics.
Mycology 2(3), 192-209.
10.1080/21501203.2011.584577
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(2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.
Nat Genet 43(5), 476-81.
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(2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.
Genome Biology 12(4).
Artn R40
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(2011) Sequencing the fungal tree of life.
New Phytol 190(4), 818-21.
10.1111/j.1469-8137.2011.03688.x
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(2011) Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa.
G3 (Bethesda) 1(4), 303-16.
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(2011) Novel hydrophobins from Trichoderma define a new hydrophobin subclass: protein properties, evolution, regulation and processing.
J Mol Evol 72(4), 339-51.
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(2011) The GC-Rich Mitochondrial and Plastid Genomes of the Green Alga Coccomyxa Give Insight into the Evolution of Organelle DNA Nucleotide Landscape.
Plos One 6(8).
ARTN e23624
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(2011) Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.
Genome Biol 12(2), R20.
10.1186/gb-2011-12-2-r20
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(2011) Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species.
Appl Environ Microbiol 77(13), 4499-507.
10.1128/AEM.00508-11
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(2011) Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.
Proc Natl Acad Sci U S A 108(32), 13212-7.
10.1073/pnas.1103039108
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2010
(2010) The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex.
Plant Cell 22(9), 2943-55.
10.1105/tpc.110.076406
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(2010) The genome of Naegleria gruberi illuminates early eukaryotic versatility.
Cell 140(5), 631-42.
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(2010) The genome of the Western clawed frog Xenopus tropicalis.
Science 328(5978), 633-6.
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(2010) Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides.
Nucleic Acids Res 38(16), 5535-41.
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(2010) Genome sequence of the model mushroom Schizophyllum commune.
Nat Biotechnol 28(9), 957-63.
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(2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.
Science 329(5988), 223-6.
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(2010) Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens phakopsora pachyrhizi and p. meibomiae.
Mycologia 102(4), 887-97.
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(2010) Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium.
Appl Environ Microbiol 76(11), 3599-610.
10.1128/AEM.00058-10
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(2010) Laccase and its role in production of extracellular reactive oxygen species during wood decay by the brown rot basidiomycete Postia placenta.
Appl Environ Microbiol 76(7), 2091-7.
10.1128/AEM.02929-09
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2009
(2009) The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion.
Plos Genetics 5(8).
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(2009) Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing.
Proceedings of the National Academy of Sciences of the United States of America 106(38), 16151-16156.
DOI 10.1073/pnas.0905848106
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(2009) Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion.
Proc Natl Acad Sci U S A 106(6), 1954-9.
10.1073/pnas.0809575106
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(2009) The Sorghum bicolor genome and the diversification of grasses.
Nature 457(7229), 551-6.
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(2009) Telomere organization in the ligninolytic basidiomycete Pleurotus ostreatus.
Appl Environ Microbiol 75(5), 1427-36.
10.1128/AEM.01889-08
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(2009) Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey.
BMC Genomics 10, 567.
10.1186/1471-2164-10-567
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(2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.
Science 324(5924), 268-72.
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(2009) Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger.
Bmc Genomics 10.
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(2009) Proteomics for validation of automated gene model predictions.
Methods Mol Biol 492, 447-52.
10.1007/978-1-59745-493-3_27
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2008
(2008) Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth.
BMC Genomics 9, 523.
10.1186/1471-2164-9-523
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(2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes.
Nature 456(7219), 239-44.
10.1038/nature07410
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(2008) High-resolution metagenomics targets specific functional types in complex microbial communities.
Nature Biotechnology 26(9), 1029-1034.
Doi 10.1038/Nbt.1488
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(2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
Nature 451(7180), 783-788.
Doi 10.1038/Nature06617
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(2008) A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies.
New Phytol 180(2), 316-28.
10.1111/j.1469-8137.2008.02614.x
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(2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.
Nature 452(7183), 88-U7.
Doi 10.1038/Nature06556
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(2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).
Nat Biotechnol 26(5), 553-60.
10.1038/nbt1403
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(2008) The amphioxus genome and the evolution of the chordate karyotype.
Nature 453(7198), 1064-71.
10.1038/nature06967
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(2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
Science 319(5859), 64-69.
DOI 10.1126/science.1150646
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(2008) The Trichoplax genome and the nature of placozoans.
Nature 454(7207), 955-60.
10.1038/nature07191
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(2008) Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola.
Fungal Genet Biol 45(5), 628-37.
10.1016/j.fgb.2007.12.005
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2007
(2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis.
Nat Biotechnol 25(3), 319-26.
10.1038/nbt1290
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(2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.
Nature Methods 4(6), 495-500.
Doi 10.1038/Nmeth1043
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(2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Science 318(5848), 245-251.
Doi 10.1126/Science.1143609
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(2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.
Proceedings of the National Academy of Sciences of the United States of America 104(18), 7705-7710.
Doi 10.1073/Pnas.0611046104
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(2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
Science 317(5834), 86-94.
10.1126/science.1139158
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2006
(2006) Aspergillus niger genomics: Past, present and into the future.
Medical Mycology 44, S17-S21.
Doi 10.1080/13693780600921037
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(2006) Comparative genomics of the lactic acid bacteria.
Proc Natl Acad Sci U S A 103(42), 15611-6.
10.1073/pnas.0607117103
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(2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Science 313(5793), 1596-1604.
Doi 10.1126/Science.1128691
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(2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.
Science 313(5791), 1261-1266.
Doi 10.1126/Science.1128796
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(2006) Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins.
Fungal Genetics and Biology 43(5), 343-356.
Doi 10.1016/J.Fgb.2006.01.003
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2004
(2004) The sequence and analysis of duplication-rich human chromosome 16.
Nature 432(7020), 988-94.
10.1038/nature03187
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(2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.
Nature Biotechnology 22(6), 695-700.
10.1038/nbt967
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(2004) The DNA sequence and comparative analysis of human chromosome 5.
Nature 431(7006), 268-74.
10.1038/nature02919
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