A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen
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Title
A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen
Authors
Keywords
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Journal
eLife
Volume 9, Issue -, Pages -
Publisher
eLife Sciences Publications, Ltd
Online
2020-12-18
DOI
10.7554/elife.62208
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Note: Only part of the references are listed.- SciPy 1.0: fundamental algorithms for scientific computing in Python
- (2020) Pauli Virtanen et al. NATURE METHODS
- Loss of centromere function drives karyotype evolution in closely related Malassezia species
- (2020) Sundar Ram Sankaranarayanan et al. eLife
- The elusive structure of centro-chromatin: molecular order or dynamic heterogenetity?
- (2020) Harsh Nagpal et al. JOURNAL OF MOLECULAR BIOLOGY
- Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium
- (2020) Michael F. Seidl et al. mBio
- SignalP 5.0 improves signal peptide predictions using deep neural networks
- (2019) José Juan Almagro Armenteros et al. NATURE BIOTECHNOLOGY
- Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum
- (2019) Ayako Tsushima et al. Genome Biology and Evolution
- Sequencing Disparity in the Genomic Era
- (2019) Kyle T David et al. MOLECULAR BIOLOGY AND EVOLUTION
- Destabilization of chromosome structure by histone H3 lysine 27 methylation
- (2019) Mareike Möller et al. PLoS Genetics
- The ENCODE Blacklist: Identification of Problematic Regions of the Genome
- (2019) Haley M. Amemiya et al. Scientific Reports
- Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus
- (2019) Zhao Peng et al. PLoS Genetics
- Receptor-Like Cytoplasmic Kinases: Central Players in Plant Receptor Kinase–Mediated Signaling
- (2018) Xiangxiu Liang et al. Annual Review of Plant Biology
- Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss
- (2018) Xiaoqian Shi-Kunne et al. ENVIRONMENTAL MICROBIOLOGY
- Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0
- (2018) Jana Sperschneider et al. MOLECULAR PLANT PATHOLOGY
- Heterochromatin: Guardian of the Genome
- (2018) Aniek Janssen et al. Annual Review of Cell and Developmental Biology
- Extraordinary Genome Instability and Widespread Chromosome Rearrangements During Vegetative Growth
- (2018) Mareike Möller et al. GENETICS
- Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
- (2018) Anish Dattani et al. GENOME RESEARCH
- Verticillium dahliaeLysM effectors differentially contribute to virulence on plant hosts
- (2017) Anja Kombrink et al. MOLECULAR PLANT PATHOLOGY
- Widespread adenine N6-methylation of active genes in fungi
- (2017) Stephen J Mondo et al. NATURE GENETICS
- Evolution and genome architecture in fungal plant pathogens
- (2017) Mareike Möller et al. NATURE REVIEWS MICROBIOLOGY
- Regulation and Role of Fungal Secondary Metabolites
- (2016) Juliane Macheleidt et al. Annual Review of Genetics
- Knock-down of the methyltransferase Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi
- (2016) Lena Studt et al. ENVIRONMENTAL MICROBIOLOGY
- Mind the gap; seven reasons to close fragmented genome assemblies
- (2016) Bart P.H.J. Thomma et al. FUNGAL GENETICS AND BIOLOGY
- A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi
- (2016) Julien Y. Dutheil et al. Genome Biology and Evolution
- Neurosporachromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3
- (2016) Jonathan M. Galazka et al. GENOME RESEARCH
- Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen
- (2016) Luigi Faino et al. GENOME RESEARCH
- Near-optimal probabilistic RNA-seq quantification
- (2016) Nicolas L Bray et al. NATURE BIOTECHNOLOGY
- Normal chromosome conformation depends on subtelomeric facultative heterochromatin inNeurospora crassa
- (2016) Andrew D. Klocko et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens
- (2016) Michael F. Seidl et al. PLoS Pathogens
- VSEARCH: a versatile open source tool for metagenomics
- (2016) Torbjørn Rognes et al. PeerJ
- Understanding Plant Immunity as a Surveillance System to Detect Invasion
- (2015) David E. Cook et al. Annual Review of Phytopathology
- PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R
- (2015) Jan Grau et al. BIOINFORMATICS
- Product Binding Enforces the Genomic Specificity of a Yeast Polycomb Repressive Complex
- (2015) Phillip A. Dumesic et al. CELL
- The Role of Chromosome Domains in Shaping the Functional Genome
- (2015) Tom Sexton et al. CELL
- The two-speed genomes of filamentous pathogens: waltz with plants
- (2015) Suomeng Dong et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- How eukaryotic filamentous pathogens evade plant recognition
- (2015) Ely Oliveira-Garcia et al. CURRENT OPINION IN MICROBIOLOGY
- Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin
- (2015) Kirsty Jamieson et al. GENOME RESEARCH
- Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
- (2015) Luigi Faino et al. mBio
- Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes
- (2015) Klaas Schotanus et al. Epigenetics & Chromatin
- Building Predictive Models inRUsing thecaretPackage
- (2015) Max Kuhn Journal of Statistical Software
- FactoMineR: AnRPackage for Multivariate Analysis
- (2015) Sébastien Lê et al. Journal of Statistical Software
- The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets
- (2015) Takaya Saito et al. PLoS One
- Sex or no sex: Evolutionary adaptation occurs regardless
- (2014) Michael F. Seidl et al. BIOESSAYS
- Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte-plant symbiosis
- (2014) Tetsuya Chujo et al. MOLECULAR MICROBIOLOGY
- PASTEC: An Automatic Transposable Element Classification Tool
- (2014) Claire Hoede et al. PLoS One
- H3K27me and PRC2 transmit a memory of repression across generations and during development
- (2014) L. J. Gaydos et al. SCIENCE
- Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans
- (2014) Jessica L. Soyer et al. PLoS Genetics
- “One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
- (2014) Marc Bailly-Bechet et al. Mobile DNA
- Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen
- (2013) R. de Jonge et al. GENOME RESEARCH
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
- (2013) Jason D Buenrostro et al. NATURE METHODS
- MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
- (2013) M. S. Campbell et al. PLANT PHYSIOLOGY
- Software for Computing and Annotating Genomic Ranges
- (2013) Michael Lawrence et al. PLoS Computational Biology
- The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters
- (2013) Lanelle R. Connolly et al. PLoS Genetics
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification
- (2012) Stefan G Amyotte et al. BMC GENOMICS
- Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
- (2012) Tom Sexton et al. CELL
- Centromeres of filamentous fungi
- (2012) Kristina M. Smith et al. CHROMOSOME RESEARCH
- Dynamic regulation of Polycomb group activity during plant development
- (2012) Marian Bemer et al. CURRENT OPINION IN PLANT BIOLOGY
- Genome evolution in filamentous plant pathogens: why bigger can be better
- (2012) Sylvain Raffaele et al. NATURE REVIEWS MICROBIOLOGY
- Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing
- (2012) R. de Jonge et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
- (2012) Günter P. Wagner et al. THEORY IN BIOSCIENCES
- ‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes
- (2012) Matthew D. Schultz et al. TRENDS IN GENETICS
- pROC: an open-source package for R and S+ to analyze and compare ROC curves
- (2011) Xavier Robin et al. BMC BIOINFORMATICS
- The NumPy Array: A Structure for Efficient Numerical Computation
- (2011) Stéfan van der Walt et al. COMPUTING IN SCIENCE & ENGINEERING
- Heterochromatin Is Required for Normal Distribution of Neurospora crassa CenH3
- (2011) K. M. Smith et al. MOLECULAR AND CELLULAR BIOLOGY
- Mapping and analysis of chromatin state dynamics in nine human cell types
- (2011) Jason Ernst et al. NATURE
- The Polycomb complex PRC2 and its mark in life
- (2011) Raphaël Margueron et al. NATURE
- Considering Transposable Element Diversification in De Novo Annotation Approaches
- (2011) Timothée Flutre et al. PLoS One
- Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
- (2011) Thierry Rouxel et al. Nature Communications
- Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis
- (2011) Stephen B. Goodwin et al. PLoS Genetics
- Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens
- (2011) Steven J. Klosterman et al. PLoS Pathogens
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
- (2010) N. C. Riddle et al. GENOME RESEARCH
- Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
- (2010) Li-Jun Ma et al. NATURE
- Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage
- (2010) S. Raffaele et al. SCIENCE
- Linking the emergence of fungal plant diseases with ecological speciation
- (2010) Tatiana Giraud et al. TRENDS IN ECOLOGY & EVOLUTION
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- BSMAP: whole genome bisulfite sequence MAPping program
- (2009) Yuanxin Xi et al. BMC BIOINFORMATICS
- Finding the fifth base: Genome-wide sequencing of cytosine methylation
- (2009) R. Lister et al. GENOME RESEARCH
- Fine-grained annotation and classification of de novo predicted LTR retrotransposons
- (2009) Sascha Steinbiss et al. NUCLEIC ACIDS RESEARCH
- LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
- (2008) David Ellinghaus et al. BMC BIOINFORMATICS
- Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi
- (2008) Rasmus JN Frandsen et al. BMC MOLECULAR BIOLOGY
- Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa
- (2008) Z. A. Lewis et al. GENOME RESEARCH
- Direct Interaction between DNA Methyltransferase DIM-2 and HP1 Is Required for DNA Methylation in Neurospora crassa
- (2008) S. Honda et al. MOLECULAR AND CELLULAR BIOLOGY
- Heterochromatin and RNAi Are Required to Establish CENP-A Chromatin at Centromeres
- (2008) H. D. Folco et al. SCIENCE
- The Parasexual Cycle in Candida albicans Provides an Alternative Pathway to Meiosis for the Formation of Recombinant Strains
- (2008) Anja Forche et al. PLOS BIOLOGY
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