Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

(2018) Lamprinos Frantzeskakis et al.   BMC GENOMICS

The fine balance between mutualism and antagonism in the Epichloë festucae –grass symbiotic interaction

(2018) Barry Scott et al.   CURRENT OPINION IN PLANT BIOLOGY

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

Widespread adenine N6-methylation of active genes in fungi

(2017) Stephen J Mondo et al.   NATURE GENETICS

Form and function of topologically associating genomic domains in budding yeast

(2017) Umut Eser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Epichloë festucae antifungal protein has activity against the plant pathogen Sclerotinia homoeocarpa, the causal agent of dollar spot disease

(2017) Zipeng Tian et al.   Scientific Reports

OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes

(2016) Alison C. Testa et al.   Genome Biology and Evolution

A gapless genome sequence of the fungusBotrytis cinerea

(2016) Jan A. L. Van Kan et al.   MOLECULAR PLANT PATHOLOGY

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts et al.   NUCLEIC ACIDS RESEARCH

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

On TADs and LADs: Spatial Control Over Gene Expression

(2016) Adriana Gonzalez-Sandoval et al.   TRENDS IN GENETICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

HiCdat: a fast and easy-to-use Hi-C data analysis tool

(2015) Marc W. Schmid et al.   BMC BIOINFORMATICS

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

The two-speed genomes of filamentous pathogens: waltz with plants

(2015) Suomeng Dong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism inEpichloëspp.

(2015) Carla J. Eaton et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Accurate identification of centromere locations in yeast genomes using Hi-C

(2015) N. Varoquaux et al.   NUCLEIC ACIDS RESEARCH

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

The 3D folding of metazoan genomes correlates with the association of similar repetitive elements

(2015) Axel Cournac et al.   NUCLEIC ACIDS RESEARCH

Endophytic Epichloë species and their grass hosts: from evolution to applications

(2015) Kari Saikkonen et al.   PLANT MOLECULAR BIOLOGY

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

(2015) Luigi Faino et al.   mBio

MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis

(2015) Kieu Thi Minh Pham et al.   PLoS Genetics

Models of chromosome structure

(2014) Mario Nicodemi et al.   CURRENT OPINION IN CELL BIOLOGY

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

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

(2014) Tetsuya Chujo et al.   MOLECULAR MICROBIOLOGY

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

(2014) Takeshi Mizuguchi et al.   NATURE

Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure

(2014) Ralph S. Grand et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

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

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

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum

(2013) Sarah M Schmidt et al.   BMC GENOMICS

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

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

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci

(2013) Christopher L. Schardl et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Transcription factories: genetic programming in three dimensions

(2012) Lucas Brandon Edelman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Fungal endophytes of grasses

(2012) Aiko Tanaka et al.   CURRENT OPINION IN PLANT BIOLOGY

New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

(2012) Lijuan Wei et al.   Molecular Plant

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Abundant Degenerate Miniature Inverted-Repeat Transposable Elements in Genomes of Epichloid Fungal Endophytes of Grasses

(2011) Damien J. Fleetwood et al.   Genome Biology and Evolution

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

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

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Disruption of Signaling in a Fungal-Grass Symbiosis Leads to Pathogenesis

(2010) C. J. Eaton et al.   PLANT PHYSIOLOGY

What triggers grass endophytes to switch from mutualism to pathogenism?

(2010) Carla J. Eaton et al.   PLANT SCIENCE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Target site selection by the mariner-like element, Mos1

(2009) Gwénaelle Crénès et al.   GENETICA

Effects of endophytic fungi on some drought tolerance mechanisms of tall fescue in a hydroponics culture

(2009) F. Bayat et al.   RUSSIAN JOURNAL OF PLANT PHYSIOLOGY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Repeat induced point mutation in two asexual fungi, Aspergillus niger and Penicillium chrysogenum

(2008) Ilka Braumann et al.   CURRENT GENETICS

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

(2008) C. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA