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

Network-based approaches for linking metabolism with environment

(2012) Sarath Janga et al.   GENOME BIOLOGY

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

(2011) E. E. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

Systems approaches to microbial communities and their functioning

(2010) Wilfred FM Röling et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata

(2010) Ludovic Cottret et al.   PLoS Computational Biology

Topological Signatures of Species Interactions in Metabolic Networks

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

Metabolic-network-driven analysis of bacterial ecological strategies

(2009) Shiri Freilich et al.   GENOME BIOLOGY

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