Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

Microbiome and infectivity studies reveal complex polyspecies tree disease in Acute Oak Decline

(2017) Sandra Denman et al.   ISME Journal

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Acute Oak Decline and Agrilus biguttatus: The Co-Occurrence of Stem Bleeding and D-Shaped Emergence Holes in Great Britain

(2017) Nathan Brown et al.   Forests

How holobionts get sick—toward a unifying scheme of disease

(2017) Silvio D. Pitlik et al.   Microbiome

Forest disturbance across the conterminous United States from 1985–2012: The emerging dominance of forest decline

(2016) Warren B. Cohen et al.   FOREST ECOLOGY AND MANAGEMENT

Rapid identification of bacteria associated with Acute Oak Decline by high-resolution melt analysis

(2016) C. Brady et al.   LETTERS IN APPLIED MICROBIOLOGY

Isolation studies reveal a shift in the cultivable microbiome of oak affected with Acute Oak Decline

(2016) Sandra Denman et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Networking in the Plant Microbiome

(2016) Marcel G. A. van der Heijden et al.   PLOS BIOLOGY

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

How eukaryotic filamentous pathogens evade plant recognition

(2015) Ely Oliveira-Garcia et al.   CURRENT OPINION IN MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease

(2015) Roberto Buonaurio et al.   Frontiers in Plant Science

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

A review of Agrilus biguttatus in UK forests and its relationship with acute oak decline

(2014) N. Brown et al.   FORESTRY

A description of the symptoms of Acute Oak Decline in Britain and a comparative review on causes of similar disorders on oak in Europe

(2014) S. Denman et al.   FORESTRY

Towards a holistic understanding of the beneficial interactions across thePopulusmicrobiome

(2014) Stéphane Hacquard et al.   NEW PHYTOLOGIST

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics

(2014) Muriel Vayssier-Taussat et al.   Frontiers in Cellular and Infection Microbiology

Unraveling the plant microbiome: looking back and future perspectives

(2014) Gabriele Berg et al.   Frontiers in Microbiology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Changes in the proteome and water state in bark and xylem of Hydrangea paniculata during loss of freezing tolerance

(2013) Majken Pagter et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

PlantGSEA: a gene set enrichment analysis toolkit for plant community

(2013) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

The Role of Secretion Systems and Small Molecules in Soft-RotEnterobacteriaceaePathogenicity

(2012) Amy Charkowski et al.   Annual Review of Phytopathology

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Sizing up metatranscriptomics

(2012) Mary Ann Moran et al.   ISME Journal

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak

(2010) Saneyoshi Ueno et al.   BMC GENOMICS

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Primary Metabolism and Plant Defense—Fuel for the Fire

(2009) Melvin D. Bolton   MOLECULAR PLANT-MICROBE INTERACTIONS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

New tools for discovering and characterizing microbial diversity

(2008) Erick Cardenas et al.   CURRENT OPINION IN BIOTECHNOLOGY