Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

(2018) Alexander Crits-Christoph et al.   NATURE

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon

(2018) Evan P. Starr et al.   Microbiome

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

(2018) Kateryna Zhalnina et al.   Nature Microbiology

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

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

(2018) Qiuming Yao et al.   Nature Ecology & Evolution

Phylogenetically conserved resource partitioning in the coastal microbial loop

(2017) Samuel Bryson et al.   ISME Journal

Genomic features of bacterial adaptation to plants

(2017) Asaf Levy et al.   NATURE GENETICS

Stable isotope probing of carbon flow in the plant holobiont

(2016) Feth el Zahar Haichar et al.   CURRENT OPINION IN BIOTECHNOLOGY

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

(2016) Freya Mosbæk et al.   ISME Journal

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

(2016) Jeffrey J. Marlow et al.   Frontiers in Microbiology

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

(2016) Cristina N. Butterfield et al.   PeerJ

Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

(2016) Samuel Bryson et al.   mSystems

XoxFencoding an alternative methanol dehydrogenase is widespread in coastal marine environments

(2015) Martin Taubert et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

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

(2015) S. L. Lebeis et al.   SCIENCE

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

15N- and2H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity

(2014) Nicholas B. Justice et al.   ENVIRONMENTAL MICROBIOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

(2014) Zhou Li et al.   Nature Communications

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

(2014) Emilie E. L. Muller et al.   Nature Communications

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Structure and Functions of the Bacterial Microbiota of Plants

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

AmphoraNet: The webserver implementation of the AMPHORA2 metagenomic workflow suite

(2013) Csaba Kerepesi et al.   GENE

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

Modularity of methylotrophy, revisited

(2011) Ludmila Chistoserdova   ENVIRONMENTAL MICROBIOLOGY

Evolution of cytokinin biosynthesis and degradation

(2011) I. Frebort et al.   JOURNAL OF EXPERIMENTAL BOTANY

Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities

(2011) Chongle Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

(2010) Sarah M Sowell et al.   ISME Journal

Functional investigation of methanol dehydrogenase-like protein XoxF in Methylobacterium extorquens AM1

(2010) S. Schmidt et al.   MICROBIOLOGY-SGM

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2

(2010) B. Drigo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Expanding World of Methylotrophic Metabolism

(2009) Ludmila Chistoserdova et al.   Annual Review of Microbiology

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Carbon flow in the rhizosphere: carbon trading at the soil–root interface

(2009) D. L. Jones et al.   PLANT AND SOIL

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

(2009) N. Delmotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial quorum sensing and nitrogen cycling in rhizosphere soil

(2008) Kristen M. DeAngelis et al.   FEMS MICROBIOLOGY ECOLOGY

Plant host habitat and root exudates shape soil bacterial community structure

(2008) Feth el Zahar Haichar et al.   ISME Journal

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY