Design of synthetic bacterial communities for predictable plant phenotypes

Root microbiota drive direct integration of phosphate stress and immunity

(2017) Gabriel Castrillo et al.   NATURE

Improving phosphorus use efficiency: a complex trait with emerging opportunities

(2017) Sigrid Heuer et al.   PLANT JOURNAL

The highly buffered Arabidopsis immune signaling network conceals the functions of its components

(2017) Rachel A. Hillmer et al.   PLoS Genetics

Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent

(2016) Kei Hiruma et al.   CELL

Evaluation of different approaches to describe the sorption and desorption of phosphorus in soils on experimental data

(2016) Caroline van der Salm et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root

(2016) D. Ristova et al.   Science Signaling

From the Lab to the Farm: An Industrial Perspective of Plant Beneficial Microorganisms

(2016) J. Jacob Parnell et al.   Frontiers in Plant Science

Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root

(2016) D. Ristova et al.   Science Signaling

Individual Members of the Microbiota Disproportionately Modulate Host Innate Immune Responses

(2015) Annah S. Rolig et al.   Cell Host & Microbe

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

Non-targeted profiling of semi-polar metabolites in Arabidopsis root exudates uncovers a role for coumarin secretion and lignification during the local response to phosphate limitation

(2015) Jörg Ziegler et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differentiating phosphate-dependent and phosphate-independent systemic phosphate-starvation response networks in Arabidopsis thaliana through the application of phosphite

(2015) Ricarda Jost et al.   JOURNAL OF EXPERIMENTAL BOTANY

The EXS Domain of PHO1 Participates in the Response of Shoots to Phosphate Deficiency via a Root-to-Shoot Signal

(2015) Stefanie Wege et al.   PLANT PHYSIOLOGY

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

(2015) S. L. Lebeis et al.   SCIENCE

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

(2014) S. Anders et al.   BIOINFORMATICS

MT-Toolbox: improved amplicon sequencing using molecule tags

(2014) Scott M Yourstone et al.   BMC BIOINFORMATICS

Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

(2014) J. J. Faith et al.   Science Translational Medicine

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

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

PlantGSEA: a gene set enrichment analysis toolkit for plant community

(2013) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

Identification of Downstream Components of Ubiquitin-Conjugating Enzyme PHOSPHATE2 by Quantitative Membrane Proteomics in Arabidopsis Roots

(2013) T.-K. Huang et al.   PLANT CELL

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

(2013) Jeremy J. Minty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

Root Nodulation: A Paradigm for How Plant-Microbe Symbiosis Influences Host Developmental Pathways

(2011) Guilhem J. Desbrosses et al.   Cell Host & Microbe

Soil Microorganisms Mediating Phosphorus Availability Update on Microbial Phosphorus

(2011) A. E. Richardson et al.   PLANT PHYSIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Uncoupling phosphate deficiency from its major effects on growth and transcriptome via PHO1 expression in Arabidopsis

(2010) Hatem Rouached et al.   PLANT JOURNAL

Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women

(2010) Oliver Fiehn et al.   PLoS One

Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil

(2010) Kathryn G. Eilers et al.   SOIL BIOLOGY & BIOCHEMISTRY

A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis

(2010) Regla Bustos et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quality control for plant metabolomics: reporting MSI-compliant studies

(2008) Oliver Fiehn et al.   PLANT JOURNAL

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE