Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

(2017) Bing Feng et al.   Scientific Reports

Phylogeny of metabolic networks: A spectral graph theoretical approach

(2015) Krishanu Deyasi et al.   JOURNAL OF BIOSCIENCES

New Approach for Phylogenetic Tree Recovery Based on Genome-Scale Metabolic Networks

(2014) Daniel Gamermann et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Long-term phenotypic evolution of bacteria

(2014) Germán Plata et al.   NATURE

Automation on the Generation of Genome-Scale Metabolic Models

(2012) R. Reyes et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes

(2012) Christof Winter et al.   PLoS Computational Biology

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life

(2010) E. Kurt Lienau et al.   CLADISTICS

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?

(2009) Stefano Allesina et al.   PLoS Computational Biology

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY