Genome-wide DNA methylation and transcriptomic profiles in the lifestyle strategies and asexual development of the forest fungal pathogen Heterobasidion parviporum

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

(2018) Zhen Zeng et al.   BMC GENOMICS

Global DNA Methylation in the Chestnut Blight Fungus Cryphonectria parasitica and Genome-Wide Changes in DNA Methylation Accompanied with Sectorization

(2018) Kum-Kang So et al.   Frontiers in Plant Science

Differential DNA methylation may contribute to temporal and spatial regulation of gene expression and the development of mycelia and conidia in entomopathogenic fungus Metarhizium robertsii

(2017) Wanzhen Li et al.   Fungal Biology

DEAD box RNA helicases crucial regulators of gene expression and oncogenesis

(2016) Mrinal Kanti Ghosh   Frontiers in Bioscience-Landmark

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Analysis of DNA Methyltransferase Gene Family in Fungi: A Focus on Basidiomycota

(2016) Ruirui Huang et al.   Frontiers in Plant Science

Genome wide transcriptome profiling of Fusarium oxysporum f sp. ciceris conidial germination reveals new insights into infection-related genes

(2016) Mamta Sharma et al.   Scientific Reports

Histone H3K4 methylation regulates hyphal growth, secondary metabolism and multiple stress responses inFusarium graminearum

(2015) Ye Liu et al.   ENVIRONMENTAL MICROBIOLOGY

Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense

(2015) Yingjie Zhu et al.   Scientific Reports

Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae

(2015) Junhyun Jeon et al.   Scientific Reports

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

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

Single Base-Resolution Methylome of the Dizygotic Sheep

(2015) Yangzi Wang et al.   PLoS One

Protein Kinases in Plant-Pathogenic Fungi: Conserved Regulators of Infection

(2014) David Turrà et al.   Annual Review of Phytopathology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments

(2014) Egor Dolzhenko et al.   BMC BIOINFORMATICS

Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

(2014) Johanna Rytioja et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Secret lifestyles of Neurospora crassa

(2014) Hsiao-Che Kuo et al.   Scientific Reports

A study on the distribution of 37 well conserved families of C2H2 zinc finger genes in eukaryotes

(2013) Arun Seetharam et al.   BMC GENOMICS

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Comparative pathobiology of Heterobasidion annosum during challenge on Pinus sylvestris and Arabidopsis roots: an analysis of defensin gene expression in two pathosystems

(2013) Emad Jaber et al.   PLANTA

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

(2013) Alaguraj Veluchamy et al.   Nature Communications

The COMPASS Family of Histone H3K4 Methylases: Mechanisms of Regulation in Development and Disease Pathogenesis

(2012) Ali Shilatifard   Annual Review of Biochemistry

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome evolution in filamentous plant pathogens: why bigger can be better

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

(2012) Åke Olson et al.   NEW PHYTOLOGIST

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Conservation and divergence of DNA methylation in eukaryotes

(2011) Zhixi Su et al.   Epigenetics

Cdc42/Rho GTPases in fungi: variations on a common theme

(2011) Steven D. Harris   MOLECULAR MICROBIOLOGY

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

DNA methylation regulates phenotype-dependent transcriptional activity in Candida albicans

(2011) P. K. Mishra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and function of WD40 domain proteins

(2011) Chao Xu et al.   Protein & Cell

Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex

(2010) Assaf Zemach et al.   CURRENT BIOLOGY

A Genetic Engineering Solution to the “Arginine Conversion Problem” in Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)

(2010) Claudia C. Bicho et al.   MOLECULAR & CELLULAR PROTEOMICS

The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development

(2010) Krystyna Nahlik et al.   MOLECULAR MICROBIOLOGY

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Lessons from Fungal F-Box Proteins

(2009) Wilfried Jonkers et al.   EUKARYOTIC CELL

An operational definition of epigenetics

(2009) S. L. Berger et al.   GENES & DEVELOPMENT

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Transcription factors in fungi

(2008) Ekaterina Shelest   FEMS MICROBIOLOGY LETTERS