Simultaneous Transcriptome Analysis of Sorghum and Bipolaris sorghicola by Using RNA-seq in Combination with De Novo Transcriptome Assembly

The Unfolded Protein Response in Secretory Cell Function

(2012) Kristin A. Moore et al.   Annual Review of Genetics

Plant Innate Immunity: Perception of Conserved Microbial Signatures

(2012) Benjamin Schwessinger et al.   Annual Review of Plant Biology

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-Bipolaris sorghicola interaction

(2012) Hiroshi Mizuno et al.   BMC PLANT BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Over-expression of rice leucine-rich repeat protein results in activation of defense response, thereby enhancing resistance to bacterial soft rot in Chinese cabbage

(2012) Young Ho Park et al.   PLANT CELL REPORTS

Simultaneous RNA-Seq Analysis of a Mixed Transcriptome of Rice and Blast Fungus Interaction

(2012) Yoshihiro Kawahara et al.   PLoS One

CDPKs in immune and stress signaling

(2012) Marie Boudsocq et al.   TRENDS IN PLANT SCIENCE

Fungal enzyme sets for plant polysaccharide degradation

(2011) Joost van den Brink et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

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

The cross-pathway control system regulates production of the secondary metabolite toxin, sirodesmin PL, in the ascomycete, Leptosphaeria maculans

(2011) Candace E Elliott et al.   BMC MICROBIOLOGY

Rice Hypersensitive Induced Reaction Protein 1 (OsHIR1) associates with plasma membrane and triggers hypersensitive cell death

(2011) Liang Zhou et al.   BMC PLANT BIOLOGY

A rice calcium-dependent protein kinase is expressed in cortical root cells during the presymbiotic phase of the arbuscular mycorrhizal symbiosis

(2011) Lidia Campos-Soriano et al.   BMC PLANT BIOLOGY

Protein kinase signaling networks in plant innate immunity

(2011) Guillaume Tena et al.   CURRENT OPINION IN PLANT BIOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rice WRKY45 plays important roles in fungal and bacterial disease resistance

(2011) MASAKI SHIMONO et al.   MOLECULAR PLANT PATHOLOGY

Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence

(2011) AMANDINE DELTEIL et al.   MOLECULAR PLANT PATHOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Expression of the rice CDPK-7 in sorghum: molecular and phenotypic analyses

(2011) Tejinder Kumar Mall et al.   PLANT MOLECULAR BIOLOGY

Positional cloning of ds1, the target leaf spot resistance gene against Bipolaris sorghicola in sorghum

(2011) Hiroyuki Kawahigashi et al.   THEORETICAL AND APPLIED GENETICS

Getting the Most from the Host: How Pathogens Force Plants to Cooperate in Disease

(2010) Sophie Hok et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The Hypersensitive Induced Reaction and Leucine-Rich Repeat Proteins Regulate Plant Cell Death Associated with Disease and Plant Immunity

(2010) Hyong Woo Choi et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Plant immunity: towards an integrated view of plant–pathogen interactions

(2010) Peter N. Dodds et al.   NATURE REVIEWS GENETICS

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Enhanced disease resistance in transgenic carrot (Daucus carota L.) plants over-expressing a rice cationic peroxidase

(2010) O. Wally et al.   PLANTA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Receptor-mediated signalling in plants: molecular patterns and programmes

(2009) M. Tor et al.   JOURNAL OF EXPERIMENTAL BOTANY

Analysis of Transcriptome Changes Induced by Ptr ToxA in Wheat Provides Insights into the Mechanisms of Plant Susceptibility

(2009) Iovanna Pandelova et al.   Molecular Plant

Roadmap for future research on plant pathogen effectors

(2009) JAMES R. ALFANO   MOLECULAR PLANT PATHOLOGY

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

PlnTFDB: updated content and new features of the plant transcription factor database

(2009) Paulino Pérez-Rodríguez et al.   NUCLEIC ACIDS RESEARCH

A novel simple extracellular leucine-rich repeat (eLRR) domain protein from rice (OsLRR1) enters the endosomal pathway and interacts with the hypersensitive-induced reaction protein 1 (OsHIR1)

(2009) LIANG ZHOU et al.   PLANT CELL AND ENVIRONMENT

The Role of WRKY Transcription Factors in Plant Immunity

(2009) S. P. Pandey et al.   PLANT PHYSIOLOGY

Fungal LysM effectors: extinguishers of host immunity?

(2009) Ronnie de Jonge et al.   TRENDS IN MICROBIOLOGY

A Role for the Unfolded Protein Response (UPR) in Virulence and Antifungal Susceptibility in Aspergillus fumigatus

(2009) Daryl L. Richie et al.   PLoS Pathogens

Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in Medicago truncatula

(2008) Marina A Naoumkina et al.   BMC PLANT BIOLOGY

Unique aspects of the grass cell wall

(2008) J VOGEL   CURRENT OPINION IN PLANT BIOLOGY

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

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

Specific functions of individual class III peroxidase genes

(2008) C. Cosio et al.   JOURNAL OF EXPERIMENTAL BOTANY

A class III peroxidase specifically expressed in pathogen-attacked barley epidermis contributes to basal resistance

(2008) ANNIKA JOHRDE et al.   MOLECULAR PLANT PATHOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

PeroxiBase: a database with new tools for peroxidase family classification

(2008) D. Koua et al.   NUCLEIC ACIDS RESEARCH

Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis

(2008) Gunther Doehlemann et al.   PLANT JOURNAL

Isolation and identification of two genes encoding leucine-rich repeat (LRR) proteins differentially responsive to pathogen attack and salt stress in tobacco

(2008) Zhao-Shi Xu et al.   PLANT SCIENCE