Diversification of the C-TERMINALLY ENCODED PEPTIDE (CEP) gene family in angiosperms, and evolution of plant-family specific CEP genes

An improved genome release (version Mt4.0) for the model legume Medicago truncatula

(2014) Haibao Tang et al.   BMC GENOMICS

Bioinformatic and phylogenetic analysis of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) and the CLE-LIKE signal peptide genes in the Pinophyta

(2014) Timothy J Strabala et al.   BMC PLANT BIOLOGY

The Transcriptome of Nacobbus aberrans Reveals Insights into the Evolution of Sedentary Endoparasitism in Plant-Parasitic Nematodes

(2014) Sebastian Eves-van den Akker et al.   Genome Biology and Evolution

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)

(2013) Peng Zhou et al.   BMC BIOINFORMATICS

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

(2013) Tiina Särkinen et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionarily conserved CLE peptide signaling in plant development, symbiosis, and parasitism

(2013) Kaori Miyawaki et al.   CURRENT OPINION IN PLANT BIOLOGY

Solution NMR studies of the plant peptide hormone CEP inform function

(2013) Benjamin G. Bobay et al.   FEBS LETTERS

Allelic diversity and molecular characterization of puroindoline genes in five diploid species of the Aegilops genus

(2013) Susana Cuesta et al.   JOURNAL OF EXPERIMENTAL BOTANY

Message in a bottle: small signalling peptide outputs during growth and development

(2013) Nathan Czyzewicz et al.   JOURNAL OF EXPERIMENTAL BOTANY

CEP genes regulate root and shoot development in response to environmental cues and are specific to seed plants

(2013) Christina Delay et al.   JOURNAL OF EXPERIMENTAL BOTANY

The peptide-encoding CEP1 gene modulates lateral root and nodule numbers in Medicago truncatula

(2013) N. Imin et al.   JOURNAL OF EXPERIMENTAL BOTANY

The CEP family in land plants: evolutionary analyses, expression studies, and role in Arabidopsis shoot development

(2013) Ianto Roberts et al.   JOURNAL OF EXPERIMENTAL BOTANY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

(2013) S. Cheng et al.   PLANT CELL

Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella

(2013) S. Chamala et al.   SCIENCE

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

(2012) Philippe Lemey et al.   BIOINFORMATICS

A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica

(2012) Neeraja M Krishnan et al.   BMC GENOMICS

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

(2012) Aureliano Bombarely et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

CLE Signaling Systems During Plant Development and Nematode Infection

(2012) S. Kiyohara et al.   PLANT AND CELL PHYSIOLOGY

Patterns and Evolution of Nucleotide Landscapes in Seed Plants

(2012) Laurana Serres-Giardi et al.   PLANT CELL

Transcriptional and Functional Classification of the GOLVEN/ROOT GROWTH FACTOR/CLE-Like Signaling Peptides Reveals Their Role in Lateral Root and Hair Formation

(2012) A. Fernandez et al.   PLANT PHYSIOLOGY

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Secreted Kinase Phosphorylates Extracellular Proteins That Regulate Biomineralization

(2012) V. S. Tagliabracci et al.   SCIENCE

Recent progress in research on small post-translationally modified peptide signals in plants

(2011) Yoshikatsu Matsubayashi   GENES TO CELLS

Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

(2011) Hiroaki Sakai et al.   Genome Biology and Evolution

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

(2010) Bastian Schäferhoff et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) Cédric Finet et al.   CURRENT BIOLOGY

Low-complexity sequences and single amino acid repeats: not just “junk” peptide sequences

(2010) Wilfried Haerty et al.   GENOME

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Post-Translational Modifications in Secreted Peptide Hormones in Plants

(2010) Y. Matsubayashi   PLANT AND CELL PHYSIOLOGY

Noncanonical Translation Initiation of the Arabidopsis Flowering Time and Alternative Polyadenylation Regulator FCA

(2010) G. G. Simpson et al.   PLANT CELL

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana

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

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): New insights from phylogenetic analyses of low-copy nuclear genes

(2009) M. Rousseau-Gueutin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Defensin-like polypeptide LUREs are pollen tube attractants secreted from synergid cells

(2009) Satohiro Okuda et al.   NATURE

Participation of Leaky Ribosome Scanning in Protein Dual Targeting by Alternative Translation Initiation in Higher Plants

(2009) Y. Wamboldt et al.   PLANT CELL

Bioinformatic analysis of the CLE signaling peptide family

(2008) Karsten Oelkers et al.   BMC PLANT BIOLOGY

Keep Your Fingers Off My DNA: Protein–Protein Interactions Mediated by C2H2 Zinc Finger Domains

(2008) Kathryn J. Brayer et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

(2008) J. S.S. Ammiraju et al.   PLANT CELL

Identification of a biologically active, small, secreted peptide in Arabidopsis byin silicogene screening, followed by LC-MS-based structure analysis

(2008) Kentaro Ohyama et al.   PLANT JOURNAL