A Functional Phylogenomic View of the Seed Plants

Using whole genome presence/absence data to untangle function in 12 Drosophila genomes

(2014) Jeffrey A. Rosenfeld et al.   FLY

C4 eudicots are not younger than C4 monocots

(2011) Pascal-Antoine Christin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants

(2010) Cédric Finet et al.   CURRENT BIOLOGY

Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

(2010) Angélica Cibrián-Jaramillo et al.   Genome Biology and Evolution

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics

(2010) B. Zhong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Control of female gamete formation by a small RNA pathway in Arabidopsis

(2010) Vianey Olmedo-Monfil et al.   NATURE

Small RNA Makes Its Move

(2010) R. Martienssen   SCIENCE

Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

(2010) J. Gordon Burleigh et al.   SYSTEMATIC BIOLOGY

Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

(2009) J Gordon Burleigh et al.   BMC EVOLUTIONARY BIOLOGY

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny

(2009) Thomas Werner Anthony Braukmann et al.   CURRENT GENETICS

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

(2009) Rebecca A. Mosher et al.   NATURE

VirtualPlant: A Software Platform to Support Systems Biology Research

(2009) M. S. Katari et al.   PLANT PHYSIOLOGY

Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data

(2008) Sarah Mathews   AMERICAN JOURNAL OF BOTANY

The meaning of Darwin's “abominable mystery”

(2008) William E. Friedman   AMERICAN JOURNAL OF BOTANY

The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates

(2008) Skip R McCoy et al.   BMC EVOLUTIONARY BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

(2008) R. D. Morin et al.   GENOME RESEARCH

Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling

(2008) Yanis Bouchenak-Khelladi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

(2008) A. Stamatakis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gene-Specific Signatures of Elevated Non-Synonymous Substitution Rates Correlate Poorly across the Plasmodium Genus

(2008) Gareth D. Weedall et al.   PLoS One

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY