Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

Zygotes segregate entire parental genomes in distinct blastomere lineages causing cleavage-stage chimerism and mixoploidy

(2016) Aspasia Destouni et al.   GENOME RESEARCH

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nonadaptive Amino Acid Convergence Rates Decrease over Time

(2015) Richard A. Goldstein et al.   MOLECULAR BIOLOGY AND EVOLUTION

High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba

(2015) Lorenzo Carretero-Paulet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptome and Genome Size Analysis of the Venus Flytrap

(2015) Michael Krogh Jensen et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

Characterization and heterologous expression of a PR-1 protein from traps of the carnivorous plant Nepenthes mirabilis

(2014) Franziska Buch et al.   PHYTOCHEMISTRY

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

(2014) F. Denoeud et al.   SCIENCE

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

Secreted major Venus flytrap chitinase enables digestion of Arthropod prey

(2013) Paulina Paszota et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

TCC: an R package for comparing tag count data with robust normalization strategies

(2013) Jianqiang Sun et al.   BMC BIOINFORMATICS

The Dionaea muscipula Ammonium Channel DmAMT1 Provides NH4+ Uptake Associated with Venus Flytrap’s Prey Digestion

(2013) Sönke Scherzer et al.   CURRENT BIOLOGY

Biomechanics of plant–insect interactions

(2013) Heather M Whitney et al.   CURRENT OPINION IN PLANT BIOLOGY

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

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

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

S-like ribonuclease gene expression in carnivorous plants

(2013) Emi Nishimura et al.   PLANTA

Glucan-rich diet is digested and taken up by the carnivorous sundew (Drosera rotundifolia L.): implication for a novel role of plant β-1,3-glucanases

(2013) Jaroslav Michalko et al.   PLANTA

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth

(2012) Franziska Buch et al.   ANNALS OF BOTANY

Proteomic analysis of secreted protein induced by a component of prey in pitcher fluid of the carnivorous plant Nepenthes alata

(2012) Naoya Hatano et al.   Journal of Proteomics

The Protein Composition of the Digestive Fluid from the Venus Flytrap Sheds Light on Prey Digestion Mechanisms

(2012) Waltraud X. Schulze et al.   MOLECULAR & CELLULAR PROTEOMICS

Molecular and Functional Evolution of Class I Chitinases for Plant Carnivory in the Caryophyllales

(2012) T. Renner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees

(2012) Yi-Chieh Wu et al.   SYSTEMATIC BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Quite a few reasons for calling carnivores ‘the most wonderful plants in the world’

(2011) Elżbieta Król et al.   ANNALS OF BOTANY

BadiRate: estimating family turnover rates by likelihood-based methods

(2011) P. Librado et al.   BIOINFORMATICS

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

(2011) Diego Darriba et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

A Cysteine Endopeptidase (“Dionain”) Is Involved in the Digestive Fluid ofDionaea muscipula(Venus’s Fly-trap)

(2011) Kenji TAKAHASHI et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

(2011) Botond Sipos et al.   BMC BIOINFORMATICS

Transcriptome Analysis of Sarracenia, an Insectivorous Plant

(2011) A. Srivastava et al.   DNA RESEARCH

Functional characterization of a class III acid endochitinase from the traps of the carnivorous pitcher plant genus, Nepenthes

(2011) Sandy Rottloff et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

The age and diversification of the angiosperms re-revisited

(2010) Charles D. Bell et al.   AMERICAN JOURNAL OF BOTANY

Traps of carnivorous pitcher plants as a habitat: composition of the fluid, biodiversity and mutualistic activities

(2010) Wolfram Adlassnig et al.   ANNALS OF BOTANY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

(2010) M. D. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Energetics and the evolution of carnivorous plants—Darwin's ‘most wonderful plants in the world’

(2009) Aaron M. Ellison et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evidence for an ancient adaptive episode of convergent molecular evolution

(2009) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteome Analysis of Pitcher Fluid of the Carnivorous PlantNepenthes alata

(2008) Naoya Hatano et al.   JOURNAL OF PROTEOME RESEARCH

Identification of the Wax Ester Synthase/Acyl-Coenzyme A:Diacylglycerol Acyltransferase WSD1 Required for Stem Wax Ester Biosynthesis in Arabidopsis

(2008) F. Li et al.   PLANT PHYSIOLOGY

Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes

(2007) Pawel Michalak   GENOMICS