Genomic structure predicts metabolite dynamics in microbial communities

Reconfiguration of metabolic fluxes in Pseudomonas putida as a response to sub-lethal oxidative stress

(2021) Pablo I. Nikel et al.   ISME Journal

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

(2021) Thomas Sakoparnig et al.   eLife

Evolution of generalists by phenotypic plasticity

(2020) David T. Fraebel et al.   iScience

Complete genome sequence of Paracoccus denitrificans ATCC 19367 and its denitrification characteristics

(2019) yuanyuan Si et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Predictive genomic traits for bacterial growth in culture versus actual growth in soil

(2019) Junhui Li et al.   ISME Journal

Massively parallel screening of synthetic microbial communities

(2019) Jared Kehe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism

(2019) Andrew F. Schober et al.   Cell Reports

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

(2019) Charles J. Norsigian et al.   Nature Protocols

High-order interactions distort the functional landscape of microbial consortia

(2019) Alicia Sanchez-Gorostiaga et al.   PLOS BIOLOGY

Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community

(2019) Harry Mickalide et al.   Cell Systems

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

(2018) Gregory L. Medlock et al.   Cell Systems

Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy

(2017) Pawel Lycus et al.   ISME Journal

The nitrogen cycle

(2016) Lisa Y. Stein et al.   CURRENT BIOLOGY

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates

(2016) Elin E Lilja et al.   ISME Journal

The P aracoccus denitrificans NarK-like nitrate and nitrite transporters-probing nitrate uptake and nitrate/nitrite exchange mechanisms

(2016) Alan D. Goddard et al.   MOLECULAR MICROBIOLOGY

A Lab Assembled Microcontroller-Based Sensor Module for Continuous Oxygen Measurement in Portable Hypoxia Chambers

(2016) Saroj P. Mathupala et al.   PLoS One

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

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

(2016) Karthik Anantharaman et al.   Nature Communications

Microbial interactions lead to rapid micro-scale successions on model marine particles

(2016) Manoshi S. Datta et al.   Nature Communications

phylosignal: an R package to measure, test, and explore the phylogenetic signal

(2016) François Keck et al.   Ecology and Evolution

Constrained Allocation Flux Balance Analysis

(2016) Matteo Mori et al.   PLoS Computational Biology

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

High taxonomic variability despite stable functional structure across microbial communities

(2016) Stilianos Louca et al.   Nature Ecology & Evolution

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

(2015) Brian J. Vaccaro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies

(2015) Matthew Perisin et al.   ISME Journal

Statistical learning and selective inference

(2015) Jonathan Taylor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Automated adaptive inference of phenomenological dynamical models

(2015) Bryan C. Daniels et al.   Nature Communications

Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent

(2015) Andy Phaiboun et al.   PLoS Computational Biology

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Mapping the stereotyped behaviour of freely moving fruit flies

(2014) G. J. Berman et al.   Journal of the Royal Society Interface

The Multifaceted Role of the Intestinal Microbiota in Colon Cancer

(2014) Thergiory Irrazábal et al.   MOLECULAR CELL

Persistent gut microbiota immaturity in malnourished Bangladeshi children

(2014) Sathish Subramanian et al.   NATURE

Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions

(2014) Daniel R. H. Graf et al.   PLoS One

Microbial ecology of denitrification in biological wastewater treatment

(2014) Huijie Lu et al.   WATER RESEARCH

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations

(2012) O. X. Cordero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Denitrification in Gram-positive bacteria: an underexplored trait

(2011) Ines Verbaendert et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

Ecological and evolutionary factors underlying global and local assembly of denitrifier communities

(2010) Christopher M Jones et al.   ISME Journal

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The Evolution and Future of Earth’s Nitrogen Cycle

(2010) Donald E. Canfield et al.   SCIENCE

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Physiological Roles of Two Dissimilatory Nitrate Reductases in the Deep-Sea DenitrifierPseudomonassp. Strain MT-1

(2009) Eriko IKEDA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Compensatory periplasmic nitrate reductase activity supports anaerobic growth of Pseudomonas aeruginosa PAO1 in the absence of membrane nitrate reductase

(2009) Nadine E. Van Alst et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Genome streamlining and the elemental costs of growth

(2009) Dag O. Hessen et al.   TRENDS IN ECOLOGY & EVOLUTION

Scaling laws in functional genome content across prokaryotic clades and lifestyles

(2009) Nacho Molina et al.   TRENDS IN GENETICS

Phylogenetic Analysis of Nitrite, Nitric Oxide, and Nitrous Oxide Respiratory Enzymes Reveal a Complex Evolutionary History for Denitrification

(2008) Christopher M. Jones et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interdependence of two NarK domains in a fused nitrate/nitrite transporter

(2008) Alan D. Goddard et al.   MOLECULAR MICROBIOLOGY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

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