A single bacterial genus maintains root growth in a complex microbiome

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

(2020) Thorsten Thiergart et al.   Nature Ecology & Evolution

Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere

(2019) Charlotte I. Carlström et al.   Nature Ecology & Evolution

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response

(2019) Omri M. Finkel et al.   PLOS BIOLOGY

Chemical hijacking of auxin signaling with an engineered auxin–TIR1 pair

(2018) Naoyuki Uchida et al.   Nature Chemical Biology

Assembly and ecological function of the root microbiome across angiosperm plant species

(2018) Connor R. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of synthetic bacterial communities for predictable plant phenotypes

(2018) Sur Herrera Paredes et al.   PLOS BIOLOGY

Bacterial Production of Indole Related Compounds Reveals Their Role in Association Between Duckweeds and Endophytes

(2018) Sarah Gilbert et al.   Frontiers in Chemistry

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

Local Auxin Biosynthesis Is a Key Regulator of Plant Development

(2018) Javier Brumos et al.   DEVELOPMENTAL CELL

Root microbiota drive direct integration of phosphate stress and immunity

(2017) Gabriel Castrillo et al.   NATURE

Genomic features of bacterial adaptation to plants

(2017) Asaf Levy et al.   NATURE GENETICS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

A high resolution map of theArabidopsis thalianadevelopmental transcriptome based on RNA-seq profiling

(2016) Anna V. Klepikova et al.   PLANT JOURNAL

Bacteria and fungi controlling plant growth by manipulating auxin: Balance between development and defense

(2015) Jutta Ludwig-Müller   JOURNAL OF PLANT PHYSIOLOGY

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MT-Toolbox: improved amplicon sequencing using molecule tags

(2014) Scott M Yourstone et al.   BMC BIOINFORMATICS

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

The rhizobacterium Variovorax paradoxus 5C-2, containing ACC deaminase, promotes growth and development of Arabidopsis thaliana via an ethylene-dependent pathway

(2013) Lin Chen et al.   JOURNAL OF EXPERIMENTAL BOTANY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular Mechanisms of Ethylene–Auxin Interaction

(2013) Linda Robles et al.   Molecular Plant

Quorum Sensing and Indole-3-Acetic Acid Degradation Play a Role in Colonization and Plant Growth Promotion of Arabidopsis thaliana by Burkholderia phytofirmans PsJN

(2013) Ana Zúñiga et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Anaerobic Metabolism of Indoleacetate

(2012) C. Ebenau-Jehle et al.   JOURNAL OF BACTERIOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas Evades Immune Recognition of Flagellin in Both Mammals and Plants

(2011) Bart W. Bardoel et al.   PLoS Pathogens

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Salicylic acid deficiency in NahG transgenic lines and sid2 mutants increases seed yield in the annual plant Arabidopsis thaliana

(2009) M. E. Abreu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Emerging Concepts in Effector Biology of Plant-Associated Organisms

(2009) Saskia A. Hogenhout et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Discovery of a bacterial gene cluster for catabolism of the plant hormone indole 3-acetic acid

(2008) Johan H.J. Leveau et al.   FEMS MICROBIOLOGY ECOLOGY

An allelic exchange system for compliant genetic manipulation of the select agents Burkholderia pseudomallei and Burkholderia mallei

(2008) Mohamad A. Hamad et al.   GENE

Molecular communication in the rhizosphere

(2008) Denis Faure et al.   PLANT AND SOIL