Effector gene silencing mediated by histone methylation underpins host adaptation in an oomycete plant pathogen

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

(2018) Marina Pais et al.   BMC EVOLUTIONARY BIOLOGY

Evidence for intragenic recombination and selective sweep in an effector gene of Phytophthora infestans

(2018) Lina Yang et al.   Evolutionary Applications

WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update

(2018) Jia Ye et al.   NUCLEIC ACIDS RESEARCH

The 25–26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous Genes

(2017) Jinbu Jia et al.   Frontiers in Microbiology

Cladosporium fulvum Effectors: Weapons in the Arms Race with Tomato

(2016) Pierre J.G.M. de Wit   Annual Review of Phytopathology

Strain Specific Factors Control Effector Gene Silencing in Phytophthora sojae

(2016) Sirjana Devi Shrestha et al.   PLoS One

Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization

(2016) Julia I. Qüesta et al.   SCIENCE

Improved Placement of Multi-mapping Small RNAs

(2016) Nathan R. Johnson et al.   G3-Genes Genomes Genetics

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

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

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth

(2015) Evelina Y. Basenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Klaas Schotanus et al.   Epigenetics & Chromatin

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

(2014) Tetsuya Chujo et al.   MOLECULAR MICROBIOLOGY

Antifungal drug resistance evoked via RNAi-dependent epimutations

(2014) Silvia Calo et al.   NATURE

What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory

(2014) Philipp A. Steffen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Epigenetic control of effectors in plant pathogens

(2014) Mark Gijzen et al.   Frontiers in Plant Science

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

(2013) Noah Fahlgren et al.   PLoS One

Epigenetics and the evolution of virulence

(2013) Takao Kasuga et al.   TRENDS IN MICROBIOLOGY

Transgenerational gene silencing causes gain of virulence in a plant pathogen

(2013) Dinah Qutob et al.   Nature Communications

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

Chromosomal Copy Number Variation, Selection and Uneven Rates of Recombination Reveal Cryptic Genome Diversity Linked to Pathogenicity

(2013) Rhys A. Farrer et al.   PLoS Genetics

Mechanisms and Evolution of Virulence in Oomycetes

(2012) Rays H.Y. Jiang et al.   Annual Review of Phytopathology

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans

(2012) Ramesh R. Vetukuri et al.   PLoS One

Genome Structure and Reproductive Behaviour Influence the Evolutionary Potential of a Fungal Phytopathogen

(2012) Guillaume Daverdin et al.   PLoS Pathogens

Evidence for involvement of Dicer-like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans

(2011) RAMESH R. VETUKURI et al.   MOLECULAR PLANT PATHOLOGY

Analysis of polymorphism and transcription of the effector gene Avr1b in Phytophthora sojae isolates from China virulent to Rps1b

(2011) LINKAI CUI et al.   MOLECULAR PLANT PATHOLOGY

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

(2011) Yufeng Wu et al.   PLANT CELL

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Origin of the polycomb repressive complex 2 and gene silencing by an E(z) homolog in the unicellular alga Chlamydomonas

(2010) Scott Shaver et al.   Epigenetics

Distribution, Pathotypes, and Metalaxyl Sensitivity of Phytophthora sojae from Heilongjiang and Fujian Provinces in China

(2010) Linkai Cui et al.   PLANT DISEASE

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

(2010) Eric M. Mendenhall et al.   PLoS Genetics

Copy Number Variation and Transcriptional Polymorphisms of Phytophthora sojae RXLR Effector Genes Avr1a and Avr3a

(2009) Dinah Qutob et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Polycomb complexes and epigenetic states

(2008) Yuri B Schwartz et al.   CURRENT OPINION IN CELL BIOLOGY

Internuclear gene silencing in Phytophthora infestans is established through chromatin remodelling

(2008) P. van West et al.   MICROBIOLOGY-SGM

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH