Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Haplotype-phased genome assembly of virulent Phythophthora ramorum isolate ND886 facilitated by long-read sequencing reveals effector polymorphisms and copy number variation

(2019) Mathu Malar C et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Draft assembly of Phytopthora capsici from long-read sequencing uncovers complexity

(2019) Chenming Cui et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

(2018) Marina Pais et al.   BMC EVOLUTIONARY BIOLOGY

SvABA: genome-wide detection of structural variants and indels by local assembly

(2018) Jeremiah A. Wala et al.   GENOME RESEARCH

Populations of Phytophthora rubi Show Little Differentiation and High Rates of Migration Among States in the Western United States

(2018) Javier F. Tabima et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

(2018) Andrew D. Armitage et al.   PLoS One

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Whole Genome Sequences of the Raspberry and Strawberry Pathogens Phytophthora rubi and P. fragariae

(2017) Javier F. Tabima et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

ApoplastP : prediction of effectors and plant proteins in the apoplast using machine learning

(2017) Jana Sperschneider et al.   NEW PHYTOLOGIST

Identification of pathogenicity-related genes inFusarium oxysporumf. sp.cepae

(2016) Andrew Taylor et al.   MOLECULAR PLANT PATHOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

The Use of Arbuscular Mycorrhizal Fungi to Improve Strawberry Production in Coir Substrate

(2016) Louisa Robinson Boyer et al.   Frontiers in Plant Science

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Identification of Transcription Factor Genes and Their Correlation with the High Diversity of Stramenopiles

(2014) Francisco Javier Buitrago-Flórez et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

(2013) Y. Liao et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

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

Deletion of the Phytophthora sojae Avirulence Gene Avr1d Causes Gain of Virulence on Rps1d

(2013) Ren Na et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The Phytophthora sojae Avr1d Gene Encodes an RxLR-dEER Effector with Presence and Absence Polymorphisms Among Pathogen Strains

(2013) Weixiao Yin et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Transgenerational gene silencing causes gain of virulence in a plant pathogen

(2013) Dinah Qutob et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Detection of Bacterial 16S rRNA and Identification of Four Clinically Important Bacteria by Real-Time PCR

(2012) Robert J. Clifford et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Transcriptional Programming and Functional Interactions within thePhytophthora sojaeRXLR Effector Repertoire

(2011) Qunqing Wang et al.   PLANT CELL

Sequence Variants of the Phytophthora sojae RXLR Effector Avr3a/5 Are Differentially Recognized by Rps3a and Rps5 in Soybean

(2011) Suomeng Dong et al.   PLoS One

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Copy Number Variation and Transcriptional Polymorphisms of Phytophthora sojae RXLR Effector Genes Avr1a and Avr3a

(2009) Dinah Qutob et al.   PLoS One

The Phytophthora sojae Avirulence Locus Avr3c Encodes a Multi-Copy RXLR Effector with Sequence Polymorphisms among Pathogen Strains

(2009) Suomeng Dong et al.   PLoS One

Internuclear gene silencing in Phytophthora infestans is established through chromatin remodelling

(2008) P. van West et al.   MICROBIOLOGY-SGM

The Phytophthora infestans Avirulence Gene Avr4 Encodes an RXLR-dEER Effector

(2008) Pieter M. J. A. van Poppel et al.   MOLECULAR PLANT-MICROBE INTERACTIONS