De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms

Transcriptomic Analysis of Drought Stress Responses in Ammopiptanthus mongolicus Leaves Using the RNA-Seq Technique

(2015) Fei Gao et al.   PLoS One

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

De Novo Transcriptome Assembly from Inflorescence of Orchis italica: Analysis of Coding and Non-Coding Transcripts

(2014) Sofia De Paolo et al.   PLoS One

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

(2013) Rajinder Singh et al.   NATURE

RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo Assembly for Subsequent Functional Genomics Approaches

(2013) Haikuo Fan et al.   PLoS One

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

(2012) Michael R. McKain et al.   AMERICAN JOURNAL OF BOTANY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

Towards the genetic architecture of seed lipid biosynthesis and accumulation in Arabidopsis thaliana

(2011) C M O'Neill et al.   HEREDITY

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

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales

(2010) Tao Shi et al.   ANNALS OF BOTANY

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Low genetic variation detected within the widespread mangrove species Nypa fruticans (Palmae) from Southeast Asia

(2009) Shuguang Jian et al.   AQUATIC BOTANY

Regulation of HSD1 in Seeds of Arabidopsis thaliana

(2009) Sébastien Baud et al.   PLANT AND CELL PHYSIOLOGY

The frequency of polyploid speciation in vascular plants

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

The flowering world: a tale of duplications

(2009) Yves Van de Peer et al.   TRENDS IN PLANT SCIENCE

The Pentatricopeptide Repeat Protein PPR5 Stabilizes a Specific tRNA Precursor in Maize Chloroplasts

(2008) S. Beick et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2008) S. A. Smith et al.   SCIENCE