Transient dynamics of competitive exclusion in microbial communities

Calibration and analysis of genome-based models for microbial ecology

(2015) Stilianos Louca et al.   eLife

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

(2014) Inka Vanwonterghem et al.   ISME Journal

Gene-centric approach to integrating environmental genomics and biogeochemical models

(2014) Daniel C. Reed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

(2014) A. K. Hawley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Clarifying the regulation of NO/N2O production in Nitrosomonas europaea during anoxic–oxic transition via flux balance analysis of a metabolic network model

(2014) Octavio Perez-Garcia et al.   WATER RESEARCH

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

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

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

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu et al.   PLoS Computational Biology

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

(2013) William R. Harcombe et al.   PLoS Computational Biology

General and rare bacterial taxa demonstrating different temporal dynamic patterns in an activated sludge bioreactor

(2012) Taek-Seung Kim et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Geomicrobial Kinetics: Extrapolating Laboratory Studies to Natural Environments

(2012) Qusheng Jin et al.   GEOMICROBIOLOGY JOURNAL

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Bacteriophage ecology in environmental biotechnology processes

(2011) Orr H Shapiro et al.   CURRENT OPINION IN BIOTECHNOLOGY

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

(2011) Aline Frossard et al.   ISME Journal

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

(2011) Tancredi Caruso et al.   ISME Journal

Inherent and apparent traits in microbial nutrient uptake

(2011) DL Aksnes et al.   MARINE ECOLOGY PROGRESS SERIES

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Bacterial community dynamics in a functionally stable pilot-scale wastewater treatment plant

(2010) Xiaohui Wang et al.   BIORESOURCE TECHNOLOGY

Metagenomics and the Units of Biological Organization

(2010) W. Ford Doolittle et al.   BIOSCIENCE

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Combined niche and neutral effects in a microbial wastewater treatment community

(2010) I. D. Ofiteru et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Towards functional molecular fingerprints

(2009) Maxime Dumont et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia

(2009) Elena Zaikova et al.   ENVIRONMENTAL MICROBIOLOGY

Optimal uptake kinetics: physiological acclimation explains the pattern of nitrate uptake by phytoplankton in the ocean

(2009) SL Smith et al.   MARINE ECOLOGY PROGRESS SERIES

Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation

(2009) Adam L. Meadows et al.   METABOLIC ENGINEERING

Nonrandom Assembly of Bacterial Populations in Activated Sludge Flocs

(2009) Joaquín M. Ayarza et al.   MICROBIAL ECOLOGY

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

The inoculum effect on the ammonia-oxidizing bacterial communities in parallel sequential batch reactors

(2009) Lieven Wittebolle et al.   WATER RESEARCH

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Predicting biological system objectives de novo from internal state measurements

(2008) Erwin P Gianchandani et al.   BMC BIOINFORMATICS

The Microbial Engines That Drive Earth's Biogeochemical Cycles

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