Land-plant Phylogenomic and Pomegranate Transcriptomic Analyses Reveal an Evolutionary Scenario of CYP75 Genes Subsequent to Whole Genome Duplications

Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice

(2018) Kaifa Wei et al.   BMC GENOMICS

The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology

(2018) Zhaohe Yuan et al.   PLANT BIOTECHNOLOGY JOURNAL

Functional Analysis of the FZF1 Genes of Saccharomyces uvarum

(2018) Xiaozhen Liu et al.   Frontiers in Microbiology

Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants

(2017) Hugues Renault et al.   MOLECULAR BIOLOGY AND EVOLUTION

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing the genome of the most recent common ancestor of flowering plants

(2017) Florent Murat et al.   NATURE GENETICS

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

(2016) Kazutaka Katoh et al.   BIOINFORMATICS

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

(2016) Nicolas Devos et al.   NEW PHYTOLOGIST

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Genome-wide analysis of the lignin toolbox ofEucalyptus grandis

(2015) Victor Carocha et al.   NEW PHYTOLOGIST

Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales

(2015) Samuel F. Brockington et al.   NEW PHYTOLOGIST

Multiple evolution of flavonoid 3′,5′-hydroxylase

(2015) Christian Seitz et al.   PLANTA

Polyploidy: adaptation to the genomic environment

(2014) Jesse D. Hollister   NEW PHYTOLOGIST

Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

(2013) Susana Magallón et al.   AMERICAN JOURNAL OF BOTANY

Fossil Records in the Lythraceae

(2013) Shirley A. Graham   BOTANICAL REVIEW

Evolution of the Cation Chloride Cotransporter Family: Ancient Origins, Gene Losses, and Subfunctionalization through Duplication

(2013) Anna-Maria Hartmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Homospermidine Synthase in the Convolvulaceae: A Story of Gene Duplication, Gene Loss, and Periods of Various Selection Pressures

(2013) E. Kaltenegger et al.   PLANT CELL

Estimating divergence times in large molecular phylogenies

(2012) K. Tamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Duplication and Loss in a MADS Box Gene Transcription Factor Circuit

(2011) Hae-Lim Lee et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Recent advances on the regulation of anthocyanin synthesis in reproductive organs

(2011) Katia Petroni et al.   PLANT SCIENCE

Jane: a new tool for the cophylogeny reconstruction problem

(2010) Chris Conow et al.   Algorithms for Molecular Biology

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice

(2009) C. Zou et al.   PLANT PHYSIOLOGY