Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires

(2013) Vikas Kumar et al.   PLoS One

Plastome sequences of two New World bamboos-Arundinaria gigantea and Cryptochloa strictiflora (Poaceae)-extend phylogenomic understanding of Bambusoideae

(2012) Sean V. Burke et al.   AMERICAN JOURNAL OF BOTANY

Applications of next-generation sequencing in plant biology

(2012) Ashley N. Egan et al.   AMERICAN JOURNAL OF BOTANY

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

(2012) Emmanuel Buschiazzo et al.   BMC EVOLUTIONARY BIOLOGY

The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families

(2012) M. M. Pentony et al.   Genome Biology and Evolution

Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

(2012) Sabrina Simon et al.   Genome Biology and Evolution

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Using nuclear gene data for plant phylogenetics: Progress and prospects

(2012) Elizabeth A. Zimmer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

An A/ENTH Domain-Containing Protein Functions as an Adaptor for Clathrin-Coated Vesicles on the Growing Cell Plate in Arabidopsis Root Cells

(2012) K. Song et al.   PLANT PHYSIOLOGY

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants

(2012) Ruth E. Timme et al.   PLoS One

Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing

(2012) Ming Chen et al.   PLoS One

De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)

(2012) Xue-Mei Zhang et al.   PLoS One

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Folate Biosynthesis, Turnover, and Transport in Plants

(2011) Andrew D. Hanson et al.   Annual Review of Plant Biology

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life

(2011) Lothar Wissler et al.   BMC EVOLUTIONARY BIOLOGY

Genome-wide analysis of rice and Arabidopsis identifies two glyoxalase genes that are highly expressed in abiotic stresses

(2011) Ananda Mustafiz et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Homologous pairing and the role of pairing centers in meiosis

(2011) J.-H. Tsai et al.   JOURNAL OF CELL SCIENCE

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

(2011) Edgar M. Medina et al.   JOURNAL OF MOLECULAR EVOLUTION

Biotic Stress-Responsive Rice Proteome: An Overview

(2011) Yiming Wang et al.   JOURNAL OF PLANT BIOLOGY

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Consistent Phylogenetic Backbone for the Fungi

(2011) I. Ebersberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplasts

(2011) Zhi-Qiang Wu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins

(2011)   NEW PHYTOLOGIST

The RNA recognition motif protein RBM11 is a novel tissue-specific splicing regulator

(2011) Simona Pedrotti et al.   NUCLEIC ACIDS RESEARCH

Generation and analysis of expressed sequence tags from a normalized cDNA library of young leaf from Ma bamboo (Dendrocalamus latiflorus Munro)

(2011) Z. M. Gao et al.   PLANT CELL REPORTS

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

(2011) Yun-Jie Zhang et al.   PLoS One

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae)

(2010) Jerrold I. Davis et al.   AMERICAN JOURNAL OF BOTANY

Pleiotropy, plasticity, and the evolution of plant abiotic stress tolerance

(2010) David L. Des Marais et al.   Annals of the New York Academy of Sciences

Characterization of plant eukaryotic translation initiation factor 6 (eIF6) genes: The essential role in embryogenesis and their differential expression in Arabidopsis and rice

(2010) Yuki Kato et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Signatures of selection in loci governing major colour patterns in Heliconius butterflies and related species

(2010) Grace C Wu et al.   BMC EVOLUTIONARY BIOLOGY

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences

(2010) Zhenhua Peng et al.   BMC PLANT BIOLOGY

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

(2010) T. I. Gossmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interpopulation patterns of divergence and selection across the transcriptome of the copepod Tigriopus californicus

(2010) FELIPE S. BARRETO et al.   MOLECULAR ECOLOGY

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

(2010) Jerome C. Regier et al.   NATURE

Differential contributions of ribosomal protein genes to Arabidopsis thaliana leaf development

(2010) Gorou Horiguchi et al.   PLANT JOURNAL

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA recognition motifs involved in nuclear import of RNA-binding proteins

(2010) Alejandro Cassola et al.   RNA Biology

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

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

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Plant molecular stress responses face climate change

(2010) Ishita Ahuja et al.   TRENDS IN PLANT SCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger 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

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Modifications of RNA polymerase II are pivotal in regulating gene expression states

(2009) Emily Brookes et al.   EMBO REPORTS

Sequence and expression analysis of the C3HC4-type RING finger gene family in rice

(2009) Ke Ma et al.   GENE

The Evolution of Meiosis From Mitosis

(2009) A. S. Wilkins et al.   GENETICS

Evolutionary Insights on C4 Photosynthetic Subtypes in Grasses from Genomics and Phylogenetics

(2009) Pascal-Antoine Christin et al.   Genome Biology and Evolution

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

(2009) Adrian Schneider et al.   Genome Biology and Evolution

Positively Selected Disease Response Orthologous Gene Sets in the Cereals Identified Using Sorghum bicolor L. Moench Expression Profiles and Comparative Genomics

(2009) A. Zamora et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data

(2009) Jose Eduardo de la Torre-Bárcena et al.   PLoS One

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

(2009) Xiyin Wang et al.   GENOME BIOLOGY

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

(2008) Andrzej T. Wierzbicki et al.   CELL

RNA recognition motifs: boring? Not quite

(2008) Antoine Cléry et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The age of the grasses and clusters of origins of C4photosynthesis

(2008) ALBERTO VICENTINI et al.   GLOBAL CHANGE BIOLOGY

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

(2008) Sarawood Sungkaew et al.   JOURNAL OF PLANT RESEARCH

Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts

(2008) Y. Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Salt stress alleviation in transgenic Vigna mungo L. Hepper (blackgram) by overexpression of the glyoxalase I gene using a novel Cestrum yellow leaf curling virus (CmYLCV) promoter

(2008) Prasanna Bhomkar et al.   MOLECULAR BREEDING

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

Dated historical biogeography of the temperate Loliinae (Poaceae, Pooideae) grasses in the northern and southern hemispheres

(2007) Luis A. Inda et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION