Orchidstra 2.0—A Transcriptomics Resource for the Orchid Family

Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification

(2015) John V. Freudenstein et al.   ANNALS OF BOTANY

An updated classification of Orchidaceae

(2015) Mark W. Chase et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

OryzaGenome: Genome Diversity Database of WildOryzaSpecies

(2015) Hajime Ohyanagi et al.   PLANT AND CELL PHYSIOLOGY

TheVignaGenome Server, ‘VigGS’: A Genomic Knowledge Base of the GenusVignaBased on High-Quality, Annotated Genome Sequence of the Azuki Bean,Vigna angularis(Willd.) Ohwi & Ohashi

(2015) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice

(2015) Yoshihiro Kawahara et al.   PLANT AND CELL PHYSIOLOGY

CANTATAdb: A Collection of Plant Long Non-Coding RNAs

(2015) Michał W. Szcześniak et al.   PLANT AND CELL PHYSIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)

(2014) Xiaolan Rao et al.   BMC GENOMICS

The velamen protects photosynthetic orchid roots against UV-B damage, and a large dated phylogeny implies multiple gains and losses of this function during the Cenozoic

(2014) Guillaume Chomicki et al.   NEW PHYTOLOGIST

De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB

(2014) Koichiro Aya et al.   PLANT AND CELL PHYSIOLOGY

Deep Sequencing-Based Analysis of the Cymbidium ensifolium Floral Transcriptome

(2014) Xiaobai Li et al.   PLoS One

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

(2014) Sofia De Paolo et al.   PLoS One

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development

(2013) Jianxia Zhang et al.   BMC GENOMICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

OrchidBase 2.0: Comprehensive Collection of Orchidaceae Floral Transcriptomes

(2013) Wen-Chieh Tsai et al.   PLANT AND CELL PHYSIOLOGY

Orchidstra: An Integrated Orchid Functional Genomics Database

(2013) Chun-lin Su et al.   PLANT AND CELL PHYSIOLOGY

Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite

(2013) Ya-Ting Chao et al.   PLANT MOLECULAR BIOLOGY

Transcriptome and Proteome Data Reveal Candidate Genes for Pollinator Attraction in Sexually Deceptive Orchids

(2013) Khalid E. M. Sedeek et al.   PLoS One

A Modified ABCDE Model of Flowering in Orchids Based on Gene Expression Profiling Studies of the Moth Orchid Phalaenopsis aphrodite

(2013) Chun-lin Su et al.   PLoS One

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

De Novo Assembly of Expressed Transcripts and Global Analysis of the Phalaenopsis aphrodite Transcriptome

(2011) Chun-lin Su et al.   PLANT AND CELL PHYSIOLOGY

Characterization of Oncidium ‘Gower Ramsey’ Transcriptomes using 454 GS-FLX Pyrosequencing and Their Application to the Identification of Genes Associated with Flowering Time

(2011) Yu-Yun Chang et al.   PLANT AND CELL PHYSIOLOGY

Genome size diversity in orchids: consequences and evolution

(2009) I. J. Leitch et al.   ANNALS OF BOTANY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Natural polyploidy in Vanilla planifolia (Orchidaceae)

(2008) Séverine Bory et al.   GENOME