Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Secondary metabolism in Trichoderma – Chemistry meets genomics

(2016) Susanne Zeilinger et al.   Fungal Biology Reviews

Impact of the omic technologies for understanding the modes of action of biological control agents against plant pathogens

(2015) Sebastien Massart et al.   BIOCONTROL

Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica

(2015) Konstantia Gkarmiri et al.   BMC GENOMICS

Fungal invasion of the rhizosphere microbiome

(2015) Emilie Chapelle et al.   ISME Journal

The Effect of Phylogenetically Different Bacteria on the Fitness of Pseudomonas fluorescens in Sand Microcosms

(2015) Olaf Tyc et al.   PLoS One

Resilience of the Natural Phyllosphere Microbiota of the Grapevine to Chemical and Biological Pesticides

(2014) Michele Perazzolli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum

(2014) Andrei Steindorff et al.   BMC GENOMICS

Bacillus subtilisattachment toAspergillus nigerhyphae results in mutually altered metabolism

(2014) Isabelle Benoit et al.   ENVIRONMENTAL MICROBIOLOGY

Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria

(2014) Aurélie Deveau et al.   MICROBIAL ECOLOGY

Transcriptional responses of the bacterial antagonistSerratia plymuthicato the fungal phytopathogenRhizoctonia solani

(2014) Saraswoti Neupane et al.   Environmental Microbiology Reports

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters

(2013) Christopher Sibthorp et al.   BMC GENOMICS

Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism

(2013) Lea Atanasova et al.   BMC GENOMICS

Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation

(2013) Ji Young Jung et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

High throughput sequencing methods and analysis for microbiome research

(2013) Julia M. Di Bella et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System

(2013) Cassandra Collins et al.   JOURNAL OF PROTEOME RESEARCH

Transcriptomics of the Rice Blast Fungus Magnaporthe oryzae in Response to the Bacterial Antagonist Lysobacter enzymogenes Reveals Candidate Fungal Defense Response Genes

(2013) Sandra M. Mathioni et al.   PLoS One

A Metatranscriptomic Approach to the Identification of Microbiota Associated with the Ant Formica exsecta

(2013) Helena Johansson et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

(2012) Marco Falda et al.   BMC BIOINFORMATICS

Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes

(2012) Michele Perazzolli et al.   BMC GENOMICS

Draft Genome Sequence of Salt-Tolerant Yeast Debaryomyces hansenii var. hansenii MTCC 234

(2012) Shailesh Kumar et al.   EUKARYOTIC CELL

Identification of a Hypochlorite-specific Transcription Factor fromEscherichia coli

(2012) Katharina M. Gebendorfer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Studying trophic interactions between a plant pathogen and two different antagonistic microorganisms using a 13C-labeled compound and isotope ratio mass spectrometry

(2012) Alberto Pellegrini et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Identification of Mycoparasitism-Related Genes in Trichoderma atroviride

(2011) Barbara Reithner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger

(2011) Francesca Mela et al.   ISME Journal

Secondary metabolism in Trichoderma - a genomic perspective

(2011) P. K. Mukherjee et al.   MICROBIOLOGY-SGM

Secrets of the subterranean pathosystem of Armillaria

(2011) KENDRA BAUMGARTNER et al.   MOLECULAR PLANT PATHOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Inferring dispersal patterns of the generalist root fungus Armillaria mellea

(2011) Renaud Travadon et al.   NEW PHYTOLOGIST

iPath2.0: interactive pathway explorer

(2011) Takuji Yamada et al.   NUCLEIC ACIDS RESEARCH

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

(2011) Christian P Kubicek et al.   GENOME BIOLOGY

Translational Research onTrichoderma: From 'Omics to the Field

(2010) Matteo Lorito et al.   Annual Review of Phytopathology

Armillaria melleaInduces a Set of Defense Genes in Grapevine Roots and One of Them Codifies a Protein with Antifungal Activity

(2010) Michele Perazzolli et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments

(2010) Paul J. Janssen et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey

(2009) Verena Seidl et al.   BMC GENOMICS

Inter-kingdom encounters: recent advances in molecular bacterium–fungus interactions

(2009) Mika T. Tarkka et al.   CURRENT GENETICS

Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats

(2009) Rashid Nazir et al.   FEMS MICROBIOLOGY ECOLOGY

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

(2009) V. Barbe et al.   MICROBIOLOGY-SGM

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data

(2009) J. M. Ruijter et al.   NUCLEIC ACIDS RESEARCH

Impact of the biocontrol agent Trichoderma atroviride SC1 on soil microbial communities of a vineyard in northern Italy

(2009) Federica Savazzini et al.   SOIL BIOLOGY & BIOCHEMISTRY

The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571

(2008) Kyung-Bum Lee et al.   BMC GENOMICS

Ecophysiological requirements and survival of aTrichoderma atrovirideisolate with biocontrol potential

(2008) Claudia Maria Oliveira Longa et al.   JOURNAL OF BASIC MICROBIOLOGY

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

(2008) Marco A van den Berg et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescens Pf29Arp

(2008) M. Barret et al.   NEW PHYTOLOGIST