Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation)

The sterol-binding activity of PATHOGENESIS-RELATED PROTEIN 1 reveals the mode of action of an antimicrobial protein

(2017) Jordi Gamir et al.   PLANT JOURNAL

Expression profiling in Pinus radiata infected with Fusarium circinatum

(2017) Angela Carrasco et al.   Tree Genetics & Genomes

De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

(2017) Daniel Blande et al.   Scientific Data

Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization

(2016) Andrew S. Fister et al.   BMC GENOMICS

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure

(2016) Camilla Beate Hill et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Erik A. Visser et al.   BMC GENOMICS

Management of Fusarium diseases affecting conifers

(2015) Thomas R. Gordon et al.   CROP PROTECTION

Identification of protein coding regions in RNA transcripts

(2015) Shiyuyun Tang et al.   NUCLEIC ACIDS RESEARCH

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

Plant PRRs and the Activation of Innate Immune Signaling

(2014) Alberto P. Macho et al.   MOLECULAR CELL

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Development and commercialisation of the Pinus patula × P. tecunumanii hybrid in response to the threat of Fusarium circinatum

(2014) A. Kanzler et al.   NEW FORESTS

Tree immunity: growing old without antibodies

(2014) Peri A. Tobias et al.   TRENDS IN PLANT SCIENCE

MAPK Cascades in Plant Disease Resistance Signaling

(2013) Xiangzong Meng et al.   Annual Review of Phytopathology

Systemic Acquired Resistance: Turning Local Infection into Global Defense

(2013) Zheng Qing Fu et al.   Annual Review of Plant Biology

Plant Immunity to Necrotrophs

(2012) Tesfaye Mengiste   Annual Review of Phytopathology

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

(2012) Limin Fu 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Reactive oxygen species and their role in plant defence and cell wall metabolism

(2012) Jose A. O’Brien et al.   PLANTA

Hormonal Modulation of Plant Immunity

(2011) Corné M.J. Pieterse et al.   Annual Review of Cell and Developmental Biology

Hormone Crosstalk in Plant Disease and Defense: More Than Just JASMONATE-SALICYLATE Antagonism

(2011) Alexandre Robert-Seilaniantz et al.   Annual Review of Phytopathology

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

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

Selection of Pinus spp. in South Africa for tolerance to infection by the pitch canker fungus

(2011) R. G. Mitchell et al.   NEW FORESTS

Expression and β-glucan binding properties of Scots pine (Pinus sylvestris L.) antimicrobial protein (Sp-AMP)

(2011) Sanjeewani Sooriyaarachchi et al.   PLANT MOLECULAR BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Primitive Defence: The MiAMP1 Antimicrobial Peptide Family

(2009) John M. Manners   PLANT MOLECULAR BIOLOGY REPORTER

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

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

Germin and Germin-like Proteins: Evolution, Structure, and Function

(2008) Jim M. Dunwell et al.   CRITICAL REVIEWS IN PLANT SCIENCES

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS