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(2021) Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi.
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(2021) Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity.
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(2021) PhycoCosm, a comparative algal genomics resource.
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(2021) Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay.
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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.
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(2021) IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains.
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(2021) Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides.
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(2021) Draft Genome Sequences of the Black Truffles Tuber brumale Vittad. and Tuber indicum Cook & Massee.
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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.
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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) 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.
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2020
(2020) Constructing a yeast to express the largest cellulosome complex on the cell surface.
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(2020) Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen.
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(2020) The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi.
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(2020) A comparative genomics study of 23 Aspergillus species from section Flavi.
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(2020) Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits.
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(2020) Conserved white rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus.
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(2020) Unique genomic traits for cold adaptation in Naganishia vishniacii, a polyextremophile yeast isolated from Antarctica.
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(2020) Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships.
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(2020) Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity.
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(2020) Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES.
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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.
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(2020) Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose.
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(2020) Draft Genome Assemblies of Ionic Liquid-Resistant Yarrowia lipolytica PO1f and Its Superior Evolved Strain, YlCW001.
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2019
(2019) Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae.
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(2019) Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae.
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(2019) Broad-specificity GH131 beta-glucanases are a hallmark of Fungi and Oomycetes that colonise plants.
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(2019) Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers.
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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 Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens.
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(2019) Glucose-mediated repression of plant biomass utilization in the white-rot fungus Dichomitus squalens.
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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) 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.
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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) 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) Inorganic nitrogen availability alters Eucalyptus grandis receptivity to the ectomycorrhizal fungus Pisolithus albus but not symbiotic nitrogen transfer.
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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) Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases.
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(2018) High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.
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(2018) Dichomitus squalens partially tailors its molecular responses to the composition of solid wood.
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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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(2017) The homothallic mating-type locus of the conifer needle endophyte Phialocephala scopiformis DAOMC 229536 (order Helotiales).
Fungal Biol 121(12), 1011-1024.
10.1016/j.funbio.2017.08.007
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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.
10.1016/j.funbio.2017.08.007
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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.
Fungal Biol 121(3), 212-221.
10.1016/j.funbio.2016.11.007
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(2017) Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria.
Nat Ecol Evol 1(12), 1931-1941.
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(2017) The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies.
Microbiol Spectr 5(5).
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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.
Biotechnol Biofuels 10, 149.
10.1186/s13068-017-0807-z
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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.
Biotechnol Biofuels 10, 149.
10.1186/s13068-017-0807-z
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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.
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.
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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.
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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.
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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.
Genome Announc 4(1).
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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.
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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) Draft Genome Sequence of Neurospora crassa Strain FGSC 73.
Genome Announc 3(2).
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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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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.
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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) 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) Genome sequence of a white rot fungus Schizopora paradoxa KUC8140 for wood decay and mycoremediation.
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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.
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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.
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PLoS Genet 10(12), e1004759.
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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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(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.
International Journal of Food Microbiology 157(2), 202-209.
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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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2011
(2011) Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.
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(2011) The Ecoresponsive Genome of Daphnia pulex.
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Proceedings of the National Academy of Sciences of the United States of America 108(11), 4352-4357.
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(2011) Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.
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(2009) The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion.
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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.
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(2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
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(2008) The amphioxus genome and the evolution of the chordate karyotype.
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(2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
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(2008) The Trichoplax genome and the nature of placozoans.
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2007
(2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis.
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(2007) The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.
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(2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
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2006
(2006) Aspergillus niger genomics: Past, present and into the future.
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2004
(2004) The sequence and analysis of duplication-rich human chromosome 16.
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(2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.
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