Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

Genes on B chromosomes: Old questions revisited with new tools

(2015) Ali M. Banaei-Moghaddam et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Product Binding Enforces the Genomic Specificity of a Yeast Polycomb Repressive Complex

(2015) Phillip A. Dumesic et al.   CELL

Chromatin analyses of Zymoseptoria tritici : Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq)

(2015) Jessica L. Soyer et al.   FUNGAL GENETICS AND BIOLOGY

Sequential de novo centromere formation and inactivation on a chromosomal fragment in maize

(2015) Yalin Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements

(2015) Jonathan Grandaubert et al.   G3-Genes Genomes Genetics

The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola

(2015) Braham Dhillon et al.   BMC GENOMICS

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

Variability of chromosome structure in pathogenic fungi—of ‘ends and odds’

(2014) Jonathan M Galazka et al.   CURRENT OPINION IN MICROBIOLOGY

Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs

(2014) Ronny Kellner et al.   Genome Biology and Evolution

Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

(2014) Suhua Feng et al.   MOLECULAR CELL

Redundant Mechanisms to Form Silent Chromatin at Pericentromeric Regions Rely on BEND3 and DNA Methylation

(2014) Nehmé Saksouk et al.   MOLECULAR CELL

Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte-plant symbiosis

(2014) Tetsuya Chujo et al.   MOLECULAR MICROBIOLOGY

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

(2014) Takeshi Mizuguchi et al.   NATURE

Novel Telomere-Anchored PCR Approach for Studying Sexual Stage Telomeres in Aspergillus nidulans

(2014) Nengding Wang et al.   PLoS One

Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans

(2014) Jessica L. Soyer et al.   PLoS Genetics

Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant

(2013) W. C. Earnshaw et al.   CHROMOSOME RESEARCH

Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans

(2013) J. Thakur et al.   GENOME RESEARCH

Maize centromeres expand and adopt a uniform size in the genetic background of oat

(2013) K. Wang et al.   GENOME RESEARCH

The dispensable chromosome ofLeptosphaeria maculansshelters an effector gene conferring avirulence towardsBrassica rapa

(2013) Marie-Hélène Balesdent et al.   NEW PHYTOLOGIST

Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

(2013) I. Makarevitch et al.   PLANT CELL

Transcriptional Reprogramming of Wheat and the Hemibiotrophic Pathogen Septoria tritici during Two Phases of the Compatible Interaction

(2013) Fen Yang et al.   PLoS One

De novo centromere formation on a chromosome fragment in maize

(2013) S. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regional control of histone H3 lysine 27 methylation in Neurospora

(2013) K. Jamieson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stepwise Evolution of Essential Centromere Function in a Drosophila Neogene

(2013) B. D. Ross et al.   SCIENCE

Ordered Kinetochore Assembly in the Human-Pathogenic Basidiomycetous Yeast Cryptococcus neoformans

(2013) L. Kozubowski et al.   mBio

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

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

(2013) Daniel Croll et al.   PLoS Genetics

Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

(2013) Philipp Wiemann et al.   PLoS Pathogens

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Neocentromeres and epigenetically inherited features of centromeres

(2012) Laura S. Burrack et al.   CHROMOSOME RESEARCH

Centromeres of filamentous fungi

(2012) Kristina M. Smith et al.   CHROMOSOME RESEARCH

Microevolution of Cryptococcus neoformans Driven by Massive Tandem Gene Amplification

(2012) E. W. L. Chow et al.   MOLECULAR BIOLOGY AND EVOLUTION

Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation

(2012) Shinji Honda et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loss of the DNA Methyltransferase MET1 Induces H3K9 Hypermethylation at PcG Target Genes and Redistribution of H3K27 Trimethylation to Transposons in Arabidopsis thaliana

(2012) Angelique Deleris et al.   PLoS Genetics

Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion

(2012) Thierry Cheutin et al.   PLoS Genetics

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

Diversity in Requirement of Genetic and Epigenetic Factors for Centromere Function in Fungi

(2011) Babhrubahan Roy et al.   EUKARYOTIC CELL

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

(2011) E. H. Stukenbrock et al.   GENOME RESEARCH

Heterochromatin Is Required for Normal Distribution of Neurospora crassa CenH3

(2011) K. M. Smith et al.   MOLECULAR AND CELLULAR BIOLOGY

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

(2010) Chris A. Brown et al.   CURRENT BIOLOGY

Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore

(2010) Jan H Bergmann et al.   EMBO JOURNAL

Accidental Amplification and Inactivation of a Methyltransferase Gene Eliminates Cytosine Methylation in Mycosphaerella graminicola

(2010) Braham Dhillon et al.   GENETICS

Broad chromosomal domains of histone modification patterns in C. elegans

(2010) T. Liu et al.   GENOME RESEARCH

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

(2010) Eva H. Stukenbrock et al.   PLoS Genetics

Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase

(2010) Amnon Koren et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Tools for Fungal Proteomics: Multifunctional Neurospora Vectors for Gene Replacement, Protein Expression and Protein Purification

(2009) S. Honda et al.   GENETICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Meiosis Drives Extraordinary Genome Plasticity in the Haploid Fungal Plant Pathogen Mycosphaerella graminicola

(2009) Alexander H. J. Wittenberg et al.   PLoS One

Neocentromeres Form Efficiently at Multiple Possible Loci in Candida albicans

(2009) Carrie Ketel et al.   PLoS Genetics

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

Histone modifications associated with both A and B chromosomes of maize

(2008) Weiwei Jin et al.   CHROMOSOME RESEARCH

Characterization of Chromosome Ends in the Filamentous Fungus Neurospora crassa

(2008) C. Wu et al.   GENETICS

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

(2008) Z. A. Lewis et al.   GENOME RESEARCH

Heterochromatin and RNAi Are Required to Establish CENP-A Chromatin at Centromeres

(2008) H. D. Folco et al.   SCIENCE

Heterochromatin Integrity Affects Chromosome Reorganization After Centromere Dysfunction

(2008) K. Ishii et al.   SCIENCE

The fungus Neurospora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9

(2008) Kristina M Smith et al.   Epigenetics & Chromatin

Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus

(2008) Natalie D. Fedorova et al.   PLoS Genetics