Dynamic transcriptome profiling of Bean Common Mosaic Virus (BCMV) infection in Common Bean (Phaseolus vulgaris L.)

Transcriptional slippage in the positive-sense RNA virus family Potyviridae

(2015) A. Olspert et al.   EMBO REPORTS

RNA Polymerase Slippage as a Mechanism for the Production of Frameshift Gene Products in Plant Viruses of the Potyviridae Family

(2015) Bernardo Rodamilans et al.   JOURNAL OF VIROLOGY

Bean common mosaic virus Isolate Exhibits a Novel Pathogenicity Profile in Common Bean, Overcoming the bc-3 Resistance Allele Coding for the Mutated eIF4E Translation Initiation Factor

(2015) Xue Feng et al.   PHYTOPATHOLOGY

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions inBrachypodium distachyon

(2015) Kranthi K. Mandadi et al.   PLANT CELL

Capsicum annuum transcription factor WRKYa positively regulates defense response upon TMV infection and is a substrate of CaMK1 and CaMK2

(2015) Sung Un Huh et al.   Scientific Reports

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis

(2014) Feng Ding et al.   BMC GENOMICS

Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

(2014) Vikas Belamkar et al.   BMC GENOMICS

Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis

(2014) Young-Ju Kwon et al.   BMC PLANT BIOLOGY

Achievements and Challenges in Legume Breeding for Pest and Disease Resistance

(2014) Diego Rubiales et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Differential gene transcript accumulation in peas in response to powdery mildew (Erysiphe pisi) attack

(2014) E. Barilli et al.   EUPHYTICA

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Recombinants of Bean common mosaic virus (BCMV) and Genetic Determinants of BCMV Involved in Overcoming Resistance in Common Bean

(2014) Xue Feng et al.   PHYTOPATHOLOGY

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

(2014) Yanting Shen et al.   PLANT CELL

Occurrence and Characterization of Bean common mosaic virus Strain NL1 in Iowa

(2014) K. Martin et al.   PLANT DISEASE

Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens

(2014) C.-Y. Chang et al.   PLANT PHYSIOLOGY

Deep Sequencing–Based Transcriptome Profiling Reveals Comprehensive Insights into the Responses of Nicotiana benthamiana to Beet necrotic yellow vein virus Infections Containing or Lacking RNA4

(2014) Huiyan Fan et al.   PLoS One

Multiple Different Defense Mechanisms Are Activated in the Young Transgenic Tobacco Plants Which Express the Full Length Genome of the Tobacco Mosaic Virus, and Are Resistant against this Virus

(2014) Balaji Jada et al.   PLoS One

Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk

(2014) Christos Kissoudis et al.   Frontiers in Plant Science

Sensing the environment: key roles of membrane-localized kinases in plant perception and response to abiotic stress

(2013) Yuriko Osakabe et al.   JOURNAL OF EXPERIMENTAL BOTANY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

(2013) D. Staiger et al.   PLANT CELL

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

Comparative Transcriptome Profiling of a Resistant vs. Susceptible Tomato (Solanum lycopersicum) Cultivar in Response to Infection by Tomato Yellow Leaf Curl Virus

(2013) Tianzi Chen et al.   PLoS One

Relationship between gene responses and symptoms induced by Rice grassy stunt virus

(2013) Kouji Satoh et al.   Frontiers in Microbiology

MYB transcription factor genes as regulators for plant responses: an overview

(2013) Supriya Ambawat et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Post-translational regulation of WRKY transcription factors in plant immunity

(2012) Nobuaki Ishihama et al.   CURRENT OPINION IN PLANT BIOLOGY

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

The interaction of plant biotic and abiotic stresses: from genes to the field

(2012) N. J. Atkinson et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Transcriptome Analysis of Nicotiana tabacum Infected by Cucumber mosaic virus during Systemic Symptom Development

(2012) Jie Lu et al.   PLoS One

NAC proteins: regulation and role in stress tolerance

(2012) Swati Puranik et al.   TRENDS IN PLANT SCIENCE

Identification of differentially expressed genes induced by Bamboo mosaic virus infection in Nicotiana benthamiana by cDNA-amplified fragment length polymorphism

(2011) Shun-Fang Cheng et al.   BMC PLANT BIOLOGY

Expression of coordinately regulated defence response genes and analysis of their role in disease resistance in Medicago truncatula

(2011) DEBORAH A. SAMAC et al.   MOLECULAR PLANT PATHOLOGY

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of NAC transcription factor family in rice

(2010) Mohammed Nuruzzaman et al.   GENE

Immunological detection of bean common mosaic virus in French bean (Phaseolus vulgaris L.) leaves

(2010) Poonam Verma et al.   INDIAN JOURNAL OF MICROBIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

An Induced Mutation in Tomato eIF4E Leads to Immunity to Two Potyviruses

(2010) Florence Piron et al.   PLoS One

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors

(2009) Keiichi Mochida et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Potyviral resistance derived from cultivars ofPhaseolus vulgariscarryingbc-3is associated with the homozygotic presence of a mutatedeIF4Eallele

(2009) MASOUD NADERPOUR et al.   MOLECULAR PLANT PATHOLOGY

Genome-Wide Analysis of Differentially Expressed Genes During the Early Stages of Tomato Infection by a Potyvirus

(2009) Poliane Alfenas-Zerbini et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

An overlapping essential gene in the Potyviridae

(2008) B. Y.-W. Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA