2022
(2022) Phenotype to genotype in Neurospora crassa: Association of the scumbo phenotype with mutations in the gene encoding ceramide C9-methyltransferase.
Current Research in Microbial Sciences 3, 100117.
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(2022) Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis.
G3 (Bethesda, Md.) .
10.1093/g3journal/jkac061
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(2022) Detailed analysis of the D-galactose catabolic pathways in Aspergillus niger reveals complexity at both metabolic and regulatory level.
Fungal Genetics and Biology 159, 103670.
10.1016/j.fgb.2022.103670
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(2022) Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis.
STAR Protocols 3(1), 100968.
10.1016/j.xpro.2021.100968
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(2022) Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes.
New Phytologist 233(3), 1317-1330.
10.1111/nph.17873
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(2022) Unraveling the regulation of sugar beet pulp utilization in the industrially relevant fungus Aspergillus niger.
iScience 25(4), 104065.
10.1016/j.isci.2022.104065
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(2022) Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales).
Microbiology Resource Announcements 11(2), e00995-21.
10.1128/mra.00995-21
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(2022) Abscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpus.
New Phytologist 233(2), 966-982.
10.1111/nph.17825
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(2022) The Earth BioGenome Project 2020: Starting the clock.
Proceedings of the National Academy of Sciences 119(4), e2115635118.
10.1073/pnas.2115635118
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(2022) Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom‐forming fungi.
New Phytologist .
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(2022) GalR, GalX and AraR co‐regulate d‐galactose and l‐arabinose utilization in Aspergillus nidulans.
Microbial Biotechnology .
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(2022) Genome Sequence and Analysis of the Flavinogenic Yeast Candida membranifaciens IST 626.
Journal of Fungi 8(3), 254.
10.3390/jof8030254
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(2022) Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina.
Genome Biology and Evolution 14(1), evab279.
10.1093/gbe/evab279
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(2022) Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures.
Molecular Ecology 31(7), 1963-1979.
10.1111/mec.16369
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(2022) An optimized ChIP‐Seq framework for profiling histone modifications in Chromochloris zofingiensis.
Plant Direct 6(3), e392.
10.1002/pld3.392
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(2022) Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species.
Journal of Fungi 8(3), 311.
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(2022) Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.
Molecular Biology and Evolution 39(2), msab372.
10.1093/molbev/msab372
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(2022) The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis.
Proceedings of the National Academy of Sciences 119(3), e2103527119.
10.1073/pnas.2103527119
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(2022) Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales.
New Phytologist 233(3), 1383-1400.
10.1111/nph.17858
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2021
(2021) The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold.
Plos Pathogens 17(2), 36.
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(2021) Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates.
Biotechnology for Biofuels 14(1), 234.
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(2021) Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi.
Scientific Reports 11(1), 12.
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(2021) Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity.
Microbial Biotechnology , 13.
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(2021) The Melampsora americana population on Salix purpurea in the Great Lakes region is highly diverse with a contributory influence of clonality.
Phytopathology .
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(2021) Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum.
Environmental Microbiology .
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(2021) Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens.
New Phytologist .
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(2021) The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi.
Proceedings of the National Academy of Sciences 118(26), e2025689118.
10.1073/pnas.2025689118
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(2021) PhycoCosm, a comparative algal genomics resource.
Nucleic Acids Res 49(D1), D1004-D1011.
10.1093/nar/gkaa898
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(2021) Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme.
G3: Genes, Genomes, Genetics , jkab398.
10.1093/g3journal/jkab398
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(2021) Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.
Environmental Microbiology , 17.
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(2021) Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation.
IMA Fungus 12(1).
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(2021) Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica.
Journal of Fungi 7(10), 854.
10.3390/jof7100854
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(2021) Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing.
mSphere 6(5), e00564-21.
10.1128/mSphere.00564-21
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(2021) DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus.
Proceedings of the National Academy of Sciences 118(13), e2009501118.
10.1073/pnas.2009501118
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(2021) IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains.
Proceedings of the National Academy of Sciences of the United States of America 118(4), 9.
10.1073/pnas.2010003118
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(2021) Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides.
Frontiers in Bioengineering and Biotechnology 8, 16.
10.3389/fbioe.2020.612832
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(2021) Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass.
Biotechnology for Biofuels 14(1).
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(2021) Symbiotic nitrogen fixation in the reproductive structures of a basidiomycete fungus.
Current Biology 31(17), 3905-3914.e6.
10.1016/j.cub.2021.06.033
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(2021) Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi.
Frontiers in Microbiology 12, 680267.
10.3389/fmicb.2021.680267
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(2021) Annotated genome sequence of the high-biomass-producing yellow-green alga tribonema minus.
Microbiology Resource Announcements 10(24).
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(2021) Metabolic Modeling of Fungi.
Encyclopedia of Mycology , 394-405.
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(2021) Genetic determinants of endophytism in the Arabidopsis root mycobiome.
Nature Communications 12(1), 7227.
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(2021) RNA-editing in Basidiomycota, revisited.
ISME Communications 1(1), 70.
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(2021) Draft Genome Sequences of the Black Truffles Tuber brumale Vittad. and Tuber indicum Cook & Massee.
Microbiology Resource Announcements 10(4), 3.
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(2021) Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom.
Scientific Reports 11(1).
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(2021) A multiomic approach to understand how pleurotus eryngii transforms non-woody lignocellulosic material.
Journal of Fungi 7(6).
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(2021) CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner.
The Cell Surface 7, 100050.
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(2021) Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus aureobasidium pullulansto identify potential biocontrol genes.
Microbial Cell 8(8).
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(2021) Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357.
G3: Genes, Genomes, Genetics 11(8).
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(2021) A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction.
Frontiers in Fungal Biology 2(29).
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(2021) Anaerobic gut fungi are an untapped reservoir of natural products.
Proceedings of the National Academy of Sciences of the United States of America 118(18).
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(2021) Discovery of photosynthesis genes through whole-genome sequencing of acetaterequiring mutants of Chlamydomonas reinhardtii.
PLoS Genetics 17(9).
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(2021) Exploring proteomes of robust yarrowia lipolytica isolates cultivated in biomass hydrolysate reveals key processes impacting mixed sugar utilization, lipid accumulation, and degradation.
mSystems 6(4).
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(2021) Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus.
mSystems 6(1), e00002-21.
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(2021) Mechanisms of Manganese(II) Oxidation by Filamentous Ascomycete Fungi Vary With Species and Time as a Function of Secretome Composition.
Frontiers in Microbiology 12, 19.
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(2021) Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes.
Journal of Advanced Research .
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(2021) RNA-Seq-based high-resolution linkage map reveals the genetic architecture of fruiting body development in shiitake mushroom, Lentinula edodes.
Computational and Structural Biotechnology Journal 19, 1641-1653.
10.1016/j.csbj.2021.03.016
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(2021) RNA-Seq-based high-resolution linkage map reveals the genetic architecture of fruiting body development in shiitake mushroom, Lentinula edodes.
Computational and Structural Biotechnology Journal 19, 1641-1653.
10.1016/j.csbj.2021.03.016
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(2021) Genome-wide role of codon usage on transcription and identification of potential regulators.
Proceedings of the National Academy of Sciences of the United States of America 118(6), 11.
10.1073/pnas.2022590118
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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.
10.1073/pnas.1916529117
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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.
10.1016/j.micres.2020.126426
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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.
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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.
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(2019) Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).
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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.
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(2019) Comparative Genomics and Transcriptomics to Analyze Fruiting Body Development in Filamentous Ascomycetes.
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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.
Viruses 11(4).
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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.
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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) 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.
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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.
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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.
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(2018) An analysis of codon bias in six red yeast species.
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(2018) Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships.
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(2018) High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.
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(2018) Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides.
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(2018) Dichomitus squalens partially tailors its molecular responses to the composition of solid wood.
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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.
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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.
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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.
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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.
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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.
Sci Rep 8(1), 6321.
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(2018) Evolutionary instability of CUG-Leu in the genetic code of budding yeasts.
Nat Commun 9(1), 1887.
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(2018) Earth BioGenome Project: Sequencing life for the future of life.
Proc Natl Acad Sci U S A 115(17), 4325-4333.
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(2018) Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates.
New Phytol 218(1), 54-65.
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(2018) Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors.
Front Microbiol 9, 276.
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(2018) Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga.
Genome Announc 6(14).
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(2018) Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli.
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(2018) Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists.
New Phytol 217(3), 1213-1229.
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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.
Biotechnol Biofuels 11, 201.
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(2018) Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle.
Genome Announc 6(25).
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(2018) Coniella lustricola, a new species from submerged detritus.
Mycological Progress 17(1-2), 191-203.
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(2018) Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts.
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(2018) Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts.
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(2018) Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication.
Scientific Reports 8, 12.
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(2018) Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales).
Frontiers in Microbiology 9(3058), 21.
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(2018) Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion.
Mycologia 110(2), 316-324.
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(2018) Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.
Nat Genet .
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(2018) Genetic dissection of interspecific differences in yeast thermotolerance.
Nat Genet 50(11), 1501-1504.
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(2018) Genome-reconstruction for eukaryotes from complex natural microbial communities.
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.
Appl Environ Microbiol 84(16).
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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.
Adv Genet 100, 267-307.
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(2017) Population genomics of picophytoplankton unveils novel chromosome hypervariability.
Sci Adv 3(7), e1700239.
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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.
Biotechnol Biofuels 10, 35.
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(2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.
Genome Biol 18(1), 28.
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(2017) The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation.
Environ Microbiol 19(3), 1338-1354.
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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.
New Phytol 213(1), 365-379.
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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.
Nat Microbiol 2, 17087.
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(2017) A parts list for fungal cellulosomes revealed by comparative genomics.
Nat Microbiol 2, 17087.
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(2017) Draft Genome Sequence of Coniochaeta ligniaria NRRL 30616, a Lignocellulolytic Fungus for Bioabatement of Inhibitors in Plant Biomass Hydrolysates.
Genome Announc 5(4).
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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.
Nature 541(7638), 536-540.
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(2017) Widespread adenine N6-methylation of active genes in fungi.
Nat Genet 49(6), 964-968.
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(2017) Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi.
Nat Commun 8(1), 1843.
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(2017) Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi.
Nat Commun 8(1), 1843.
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(2017) Widespread adenine N6-methylation of active genes in fungi.
Nat Genet 49(6), 964-968.
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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.
G3 (Bethesda) 7(6), 1775-1789.
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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) Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.
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(2017) The homothallic mating-type locus of the conifer needle endophyte Phialocephala scopiformis DAOMC 229536 (order Helotiales).
Fungal Biol 121(12), 1011-1024.
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(2017) The homothallic mating-type locus of the conifer needle endophyte Phialocephala scopiformis DAOMC 229536 (order Helotiales).
Fungal Biol 121(12), 1011-1024.
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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) Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria.
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(2017) The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies.
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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) 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.
Environ Microbiol .
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(2017) Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels.
Appl Microbiol Biotechnol 101(6), 2603-2618.
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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.
10.1371/journal.pgen.1006737
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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.
10.1371/journal.pgen.1006737
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2016
(2016) Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus.
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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 .
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(2016) Draft Genome Sequence of Microdochium bolleyi, a Dark Septate Fungal Endophyte of Beach Grass.
Genome Announc 4(2).
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(2016) The genome of Xylona heveae provides a window into fungal endophytism.
Fungal Biol 120(1), 26-42.
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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.
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(2016) Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2.
Genome Announc 4(5).
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(2016) Visual Comparative Omics of Fungi for Plant Biomass Deconstruction.
Front Microbiol 7, 1335.
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(2016) Ochratoxin A production by Penicillium thymicola.
Fungal Biol 120(8), 1041-9.
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(2016) Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum.
Nat Commun 7, 12662.
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(2016) Comparative genomics of biotechnologically important yeasts.
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(2016) Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes.
Science .
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(2016) Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi.
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(2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.
Mycologia 108(5), 1028-1046.
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(2016) A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.
Mycologia 108(5), 1028-1046.
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(2016) Full Genome of Phialocephala scopiformis DAOMC 229536, a Fungal Endophyte of Spruce Producing the Potent Anti-Insectan Compound Rugulosin.
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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.
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2015
(2015) Draft Genome Sequence of Neurospora crassa Strain FGSC 73.
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(2015) Genetic isolation between two recently diverged populations of a symbiotic fungus.
Mol Ecol .
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Genome Biol Evol 7(6), 1590-601.
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(2015) Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus.
Biotechnol Biofuels 8, 216.
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(2015) Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus.
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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.
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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 .
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(2015) Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.
Front Microbiol 6, 978.
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(2015) Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii.
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(2015) Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.
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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.
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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.
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(2015) Genome sequence of a white rot fungus Schizopora paradoxa KUC8140 for wood decay and mycoremediation.
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(2015) Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea.
PLoS One 10(10), e0141586.
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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 .
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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.
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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 .
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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.
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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.
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(2014) MycoCosm portal: gearing up for 1000 fungal genomes.
Nucleic Acids Res 42(Database issue), D699-704.
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(2014) Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi.
Genome Biol Evol 6(7), 1564-78.
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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.
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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.
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(2014) Genomic adaptations of the halophilic Dead Sea filamentous fungus Eurotium rubrum.
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(2014) Draft Genome Sequence of a Rare Smut Relative, Tilletiaria anomala UBC 951.
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(2014) Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae.
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(2014) Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production.
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(2013) Fungal genomes mining to discover novel sterol esterases and lipases as catalysts.
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(2013) The central role of selenium in the biochemistry and ecology of the harmful pelagophyte, Aureococcus anophagefferens.
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(2013) Pan genome of the phytoplankton Emiliania underpins its global distribution.
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(2013) Insights into bilaterian evolution from three spiralian genomes.
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2012
(2012) Phylogenomic analysis of polyketide synthase-encoding genes in Trichoderma.
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Genome Biol 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.
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(2012) Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.
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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.
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(2012) Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.
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(2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.
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(2012) The genome portal of the Department of Energy Joint Genome Institute.
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(2012) Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.
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(2012) The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction.
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(2012) The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties.
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(2012) Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolor.
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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.
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Bmc Genomics 13.
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(2011) Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.
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(2011) Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.
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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.
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(2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis.
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