Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil

Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system

(2017) Zhou Li et al.   ENVIRONMENTAL MICROBIOLOGY

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

(2016) Viktor Jonsson et al.   BMC GENOMICS

Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies

(2016) Cosmin Lazar et al.   JOURNAL OF PROTEOME RESEARCH

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

(2016) Noriko A. Cassman et al.   Scientific Reports

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

(2016) Cristina N. Butterfield et al.   PeerJ

Advanced Solvent Based Methods for Molecular Characterization of Soil Organic Matter by High-Resolution Mass Spectrometry

(2015) Malak M. Tfaily et al.   ANALYTICAL CHEMISTRY

Seasonal changes in soil organic matter after a decade of nutrient addition in a lowland tropical forest

(2015) Benjamin L. Turner et al.   BIOGEOCHEMISTRY

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

The application of ecological stoichiometry to plant–microbial–soil organic matter transformations

(2015) Sophie Zechmeister-Boltenstern et al.   ECOLOGICAL MONOGRAPHS

Fine-root responses to fertilization reveal multiple nutrient limitation in a lowland tropical forest

(2015) Nina Wurzburger et al.   ECOLOGY

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

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

Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis

(2015) Ben O Oyserman et al.   ISME Journal

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

(2015) Jenni Hultman et al.   NATURE

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Soil organic phosphorus transformations along a coastal dune chronosequence under New Zealand temperate rain forest

(2014) Benjamin L. Turner et al.   BIOGEOCHEMISTRY

Omega: an Overlap-graph de novo Assembler for Metagenomics

(2014) Bahlul Haider et al.   BIOINFORMATICS

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

(2014) Juanjuan Chai et al.   BMC EVOLUTIONARY BIOLOGY

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

(2014) Annika C Mosier et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments

(2014) Richard A. Hurt et al.   PLoS One

The response of microbial biomass and hydrolytic enzymes to a decade of nitrogen, phosphorus, and potassium addition in a lowland tropical rain forest

(2013) Benjamin L. Turner et al.   BIOGEOCHEMISTRY

Sipros/ProRata: a versatile informatics system for quantitative community proteomics

(2013) Yingfeng Wang et al.   BIOINFORMATICS

Species-specific responses of foliar nutrients to long-term nitrogen and phosphorus additions in a lowland tropical forest

(2013) Jordan R. Mayor et al.   JOURNAL OF ECOLOGY

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Seasonal Changes and Treatment Effects on Soil Inorganic Nutrients Following a Decade of Fertilizer Addition in a Lowland Tropical Forest

(2013) Benjamin L. Turner et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms

(2012) Alexander Tveit et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Potassium, phosphorus, or nitrogen limit root allocation, tree growth, or litter production in a lowland tropical forest

(2011) S. Joseph Wright et al.   ECOLOGY

Tropical tree seedling growth responses to nitrogen, phosphorus and potassium addition

(2011) Louis S. Santiago et al.   JOURNAL OF ECOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Effects of phosphorus addition on soil microbial biomass and community composition in three forest types in tropical China

(2011) Lei Liu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil organic phosphorus in lowland tropical rain forests

(2010) Benjamin L. Turner et al.   BIOGEOCHEMISTRY

Identification of β-propeller phytase-encoding genes in culturable Paenibacillus and Bacillus spp. from the rhizosphere of pasture plants on volcanic soils

(2010) Milko A. Jorquera et al.   FEMS MICROBIOLOGY ECOLOGY

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

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

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Resource partitioning for soil phosphorus: a hypothesis

(2008) Benjamin L. Turner   JOURNAL OF ECOLOGY