A road map for the development of community systems (CoSy) biology

Intercellular Nanotubes Mediate Bacterial Communication

(2011) Gyanendra P. Dubey et al.   CELL

Transcript amplification from single bacterium for transcriptome analysis

(2011) Y. Kang et al.   GENOME RESEARCH

RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture

(2011) Adam Z Rosenthal et al.   ISME Journal

Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions

(2011) Christopher P Belnap et al.   ISME Journal

Microbial laboratory evolution in the era of genome-scale science

(2011) T. M. Conrad et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Imaging mass spectrometry in microbiology

(2011) Jeramie D. Watrous et al.   NATURE REVIEWS MICROBIOLOGY

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

When microbial conversations get physical

(2011) Gemma Reguera   TRENDS IN MICROBIOLOGY

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Close Interspecies Interactions between Prokaryotes from Sulfureous Environments

(2011) Johannes Müller et al.   Frontiers in Microbiology

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

Construction and optimization of synthetic pathways in metabolic engineering

(2010) Dokyun Na et al.   CURRENT OPINION IN MICROBIOLOGY

Bioturbation and the role of microniches for sulfate reduction in coastal marine sediments

(2010) Victoria J. Bertics et al.   ENVIRONMENTAL MICROBIOLOGY

Structural and operational complexity of the Geobacter sulfurreducens genome

(2010) Y. Qiu et al.   GENOME RESEARCH

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

The Future of microbial metagenomics (or is ignorance bliss?)

(2010) Jack A Gilbert et al.   ISME Journal

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

Electric currents couple spatially separated biogeochemical processes in marine sediment

(2010) Lars Peter Nielsen et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Laboratory evolution of glutathione biosynthesis reveals natural compensatory pathways

(2010) Karthik Veeravalli et al.   Nature Chemical Biology

Messy biology and the origins of evolutionary innovations

(2010) Dan S Tawfik   Nature Chemical Biology

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

(2010) Radhakrishnan Mahadevan et al.   NATURE REVIEWS MICROBIOLOGY

Rapid evolution of stability and productivity at the origin of a microbial mutualism

(2010) K. L. Hillesland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria

(2010) Z. M. Summers et al.   SCIENCE

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Metabolic systems biology

(2009) Bernhard Palsson   FEBS LETTERS

Central Role of the Cell in Microbial Ecology

(2009) K. Zengler   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Snowdrift game dynamics and facultative cheating in yeast

(2009) Jeff Gore et al.   NATURE

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

Automatic policing of biochemical annotations using genomic correlations

(2009) Tzu-Lin Hsiao et al.   Nature Chemical Biology

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

Coupling a genome-scale metabolic model with a reactive transport model to describein situuranium bioremediation

(2009) Timothy D. Scheibe et al.   Microbial Biotechnology

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

(2008) Ainslie E.F. Little et al.   Annual Review of Microbiology

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Defined spatial structure stabilizes a synthetic multispecies bacterial community

(2008) H. J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans

(2008) Mircea Podar et al.   GENOME BIOLOGY