Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes

Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

(2018) Aristóteles Góes-Neto et al.   PeerJ

Network-based approaches for analysis of complex biological systems

(2016) Deborah Chasman et al.   CURRENT OPINION IN BIOTECHNOLOGY

Can a Network Approach Resolve How Adaptive vs Nonadaptive Plasticity Impacts Evolutionary Trajectories?

(2016) Eva K. Fischer et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Characterization of an AGAMOUS gene expressed throughout development of the fleshy fruit-like structure produced by Ginkgo biloba around its seeds

(2015) Alessandro Lovisetto et al.   BMC EVOLUTIONARY BIOLOGY

What are the Evolutionary Origins of Mitochondria? A Complex Network Approach

(2015) Daniel S. Carvalho et al.   PLoS One

Which Phylogenetic Networks are Merely Trees with Additional Arcs?

(2015) Andrew R. Francis et al.   SYSTEMATIC BIOLOGY

Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis

(2015) Katherine C. H. Amrine et al.   PLoS One

Parallel Recruitment of Multiple Genes into C4 Photosynthesis

(2013) Pascal-Antoine Christin et al.   Genome Biology and Evolution

MADSreloaded: evolution of theAGAMOUSsubfamily genes

(2013) Ludovico Dreni et al.   NEW PHYTOLOGIST

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

(2012) James C. Schnable et al.   Genome Biology and Evolution

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Gene family evolution in green plants with emphasis on the origination and evolution ofArabidopsis thalianagenes

(2012) Ya-Long Guo   PLANT JOURNAL

Positional orthology: putting genomic evolutionary relationships into context

(2011) C. N. Dewey   BRIEFINGS IN BIOINFORMATICS

Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints

(2011) Michaël Bekaert et al.   PLANT CELL

Detecting Network Communities: An Application to Phylogenetic Analysis

(2011) Roberto F. S. Andrade et al.   PLoS Computational Biology

Comparative protein analysis of the chitin metabolic pathway in extant organisms: A complex network approach

(2010) Aristóteles Góes-Neto et al.   BIOSYSTEMS

Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development

(2010) I. L. Pan et al.   JOURNAL OF EXPERIMENTAL BOTANY

A new bioinformatics analysis tools framework at EMBL-EBI

(2010) M. Goujon et al.   NUCLEIC ACIDS RESEARCH

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

IDENTIFICATION OF COMMUNITY STRUCTURE IN NETWORKS USING HIGHER ORDER NEIGHBORHOOD CONCEPTS

(2009) ROBERTO F. S. ANDRADE et al.   INTERNATIONAL JOURNAL OF BIFURCATION AND CHAOS

Translational Biology: From Arabidopsis Flowers to Grass Inflorescence Architecture

(2009) B. E. Thompson et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Understanding biological functions through molecular networks

(2008) Jing-Dong Jackie Han   CELL RESEARCH

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT