Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

(2014) J. L. Wegrzyn et al.   GENETICS

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola

(2013) Jun-Jun Liu et al.   BMC GENOMICS

Characterisation of the wheat (triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat

(2013) Youko Oono et al.   BMC GENOMICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Transcriptome resources and functional characterization of monoterpene synthases for two host species of the mountain pine beetle, lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana)

(2013) Dawn E Hall et al.   BMC PLANT BIOLOGY

WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance

(2013) Naoki Yokotani et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Pfam: the protein families database

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

De novoassembly of maritime pine transcriptome: implications for forest breeding and biotechnology

(2013) Javier Canales et al.   PLANT BIOTECHNOLOGY JOURNAL

Comparative analysis of de novo transcriptome assembly

(2013) Kaitlin Clarke et al.   Science China-Life Sciences

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

(2012) Nathalie Pavy et al.   BMC BIOLOGY

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

(2012) Nicole Gruenheit et al.   BMC GENOMICS

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

(2012) Jialei Duan et al.   BMC GENOMICS

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

Uniform standards for genome databases in forest and fruit trees

(2012) J. L. Wegrzyn et al.   Tree Genetics & Genomes

Gebiss: an ImageJ plugin for the specification of ground truth and the performance evaluation of 3d segmentation algorithms

(2011) Janos Kriston-Vizi et al.   BMC BIOINFORMATICS

EuroPineDB: a high-coverage web database for maritime pine transcriptome

(2011) Noé Fernández-Pozo et al.   BMC GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform

(2011) M. Van Bel et al.   PLANT PHYSIOLOGY

A White Spruce Gene Catalog for Conifer Genome Analyses

(2011) Philippe Rigault et al.   PLANT PHYSIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

Pitch canker caused byFusarium circinatum– a growing threat to pine plantations and forests worldwide

(2008) M. J. Wingfield et al.   AUSTRALASIAN PLANT PATHOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS