TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors

Improved specificity of TALE-based genome editing using an expanded RVD repertoire

(2015) Jeffrey C Miller et al.   NATURE METHODS

Genetic engineering of theXa10promoter for broad-spectrum and durable resistance toXanthomonas oryzaepv.oryzae

(2015) Xuan Zeng et al.   PLANT BIOTECHNOLOGY JOURNAL

A TALE of Transposition: Tn 3 -Like Transposons Play a Major Role in the Spread of Pathogenicity Determinants of Xanthomonas citri and Other Xanthomonads

(2015) Rafael Marini Ferreira et al.   mBio

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

Identification of putative TAL effector targets of the citrus canker pathogens shows functional convergence underlying disease development and defense response

(2014) Andre LA Pereira et al.   BMC GENOMICS

Complete decoding of TAL effectors for DNA recognition

(2014) Junjiao Yang et al.   CELL RESEARCH

TAL effectors - pathogen strategies and plant resistance engineering

(2014) Jens Boch et al.   NEW PHYTOLOGIST

Modes of TAL effector-mediated repression

(2014) Jeannette Werner et al.   NUCLEIC ACIDS RESEARCH

The Rice TAL Effector-Dependent Resistance Protein XA10 Triggers Cell Death and Calcium Depletion in the Endoplasmic Reticulum

(2014) D. Tian et al.   PLANT CELL

From dead leaf, to new life: TAL effectors as tools for synthetic biology

(2014) Orlando de Lange et al.   PLANT JOURNAL

Lateral organ boundaries 1 is a disease susceptibility gene for citrus bacterial canker disease

(2014) Y. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A TAL effector repeat architecture for frameshift binding

(2014) Annekatrin Richter et al.   Nature Communications

Code-Assisted Discovery of TAL Effector Targets in Bacterial Leaf Streak of Rice Reveals Contrast with Bacterial Blight and a Novel Susceptibility Gene

(2014) Raul A. Cernadas et al.   PLoS Pathogens

Rapid and Efficient Protocols for Throughput Extraction of High Quality Plasmid DNA from Strains of Xanthomonas axonopodis pv malvacearum and Escherichia coli

(2013) P. K. Chakrabarty et al.   JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Five phylogenetically close riceSWEETgenes confer TAL effector-mediated susceptibility toXanthomonas oryzaepv.oryzae

(2013) Jana Streubel et al.   NEW PHYTOLOGIST

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Analysis of Xanthomonas oryzae pv. oryzicola Population in Mali and Burkina Faso Reveals a High Level of Genetic and Pathogenic Diversity

(2013) I. Wonni et al.   PHYTOPATHOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Artificial repressors for controlling gene expression in bacteria

(2012) Mark C. Politz et al.   CHEMICAL COMMUNICATIONS

TAL effectors: function, structure, engineering and applications

(2012) Amanda Nga-Sze Mak et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

High-efficiency TALEN-based gene editing produces disease-resistant rice

(2012) Ting Li et al.   NATURE BIOTECHNOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Addition of transcription activator-like effector binding sites to a pathogen strain-specific rice bacterial blight resistance gene makes it effective against additional strains and against bacterial leaf streak

(2012) Aaron W. Hummel et al.   NEW PHYTOLOGIST

TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction

(2012) Erin L. Doyle et al.   NUCLEIC ACIDS RESEARCH

Gene silencing using the recessive rice bacterial blight resistance gene xa13 as a new paradigm in plant breeding

(2012) Changyan Li et al.   PLANT CELL REPORTS

Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology

(2012) Benjamin A. Blount et al.   PLoS One

Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

(2012) D. Deng et al.   SCIENCE

Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates

(2012) Steven P. Lund et al.   Statistical Applications in Genetics and Molecular Biology

How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

(2012) Xiaoqing Yu et al.   BioData Mining

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.

(2011) A. J. Bogdanove et al.   JOURNAL OF BACTERIOLOGY

Colonization of Rice Leaf Blades by an African Strain of Xanthomonas oryzae pv. oryzae Depends on a New TAL Effector That Induces the Rice Nodulin-3 Os11N3 Gene

(2011) Yanhua Yu et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function

(2010) Jens Boch et al.   Annual Review of Phytopathology

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Promoter elements of rice susceptibility genes are bound and activated by specific TAL effectors from the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae

(2010) Patrick Römer et al.   NEW PHYTOLOGIST

Rice xa13 Recessive Resistance to Bacterial Blight Is Defeated by Induction of the Disease Susceptibility Gene Os-11N3

(2010) G. Antony et al.   PLANT CELL

First Report of Bacterial Leaf Streak Caused by Xanthomonas oryzae pv. oryzicola on Rice in Burkina Faso

(2010) I. Wonni et al.   PLANT DISEASE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

BRAT: bisulfite-treated reads analysis tool

(2009) Elena Y. Harris et al.   BIOINFORMATICS

Pathogen-Induced Expressional Loss of Function is the Key Factor in Race-Specific Bacterial Resistance Conferred by a Recessive R Gene xa13 in Rice

(2009) Meng Yuan et al.   PLANT AND CELL PHYSIOLOGY

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

(2008) Steven L Salzberg et al.   BMC GENOMICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY