NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

(2012) R. Carr et al.   BIOINFORMATICS

Network-based approaches for linking metabolism with environment

(2012) Sarath Janga et al.   GENOME BIOLOGY

Ecosystems biology of microbial metabolism

(2011) Niels Klitgord et al.   CURRENT OPINION IN BIOTECHNOLOGY

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

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

(2010) S. Chaffron et al.   GENOME RESEARCH

Emergent cooperation in microbial metabolism

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

The large-scale organization of the bacterial network of ecological co-occurrence interactions

(2010) Shiri Freilich et al.   NUCLEIC ACIDS RESEARCH

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species

(2010) Shiri Freilich et al.   PLoS Computational Biology

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

(2009) Bas E. Dutilh et al.   BIOINFORMATICS

Topological Signatures of Species Interactions in Metabolic Networks

(2009) Elhanan Borenstein et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Applications of genome-scale metabolic reconstructions

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

Metagenomics reveals our incomplete knowledge of global diversity

(2008) M. Pignatelli et al.   BIOINFORMATICS

Metabolic innovations towards the human lineage

(2008) Shiri Freilich et al.   BMC EVOLUTIONARY BIOLOGY

Reconstruction of biochemical networks in microorganisms

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

The evolution of modularity in bacterial metabolic networks

(2008) A. Kreimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An environmental perspective on metabolism

(2007) Thomas Handorf et al.   JOURNAL OF THEORETICAL BIOLOGY