Genome‐scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae

Niclosamide Blocks Rice Leaf Blight by Inhibiting Biofilm Formation of Xanthomonas oryzae

(2018) Sunil Kumar Sahu et al.   Frontiers in Plant Science

A Genome-Scale Metabolic Reconstruction of Phytophthora infestans With the Integration of Transcriptional Data Reveals the Key Metabolic Patterns Involved in the Interaction of Its Host

(2018) David Botero et al.   Frontiers in Genetics

BioModels: expanding horizons to include more modelling approaches and formats

(2017) Mihai Glont et al.   NUCLEIC ACIDS RESEARCH

RNAi as an emerging approach to control Fusarium head blight disease and mycotoxin contamination in cereals

(2017) Ana Karla Machado et al.   PEST MANAGEMENT SCIENCE

Advances on plant-pathogen interactions from molecular toward systems biology perspectives

(2017) Rémi Peyraud et al.   PLANT JOURNAL

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection

(2017) Michael Zimmermann et al.   mSystems

Biosynthesis of xanthan gum by Xanthomonas campestris LRELP-1 using kitchen waste as the sole substrate

(2016) Panyu Li et al.   CARBOHYDRATE POLYMERS

The RpfB-Dependent Quorum Sensing Signal Turnover System Is Required for Adaptation and Virulence in Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae

(2016) Xing-Yu Wang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The infectious intracellular lifestyle of Salmonella enterica relies on the adaptation to nutritional conditions within the Salmonella-containing vacuole

(2016) Lautaro Diacovich et al.   Virulence

Identification of Pectin Degrading Enzymes Secreted by Xanthomonas oryzae pv. oryzae and Determination of Their Role in Virulence on Rice

(2016) Lavanya Tayi et al.   PLoS One

Phytohormone-mediated interkingdom signaling shapes the outcome of rice-Xanthomonas oryzae pv. oryzae interactions

(2015) Jing Xu et al.   BMC PLANT BIOLOGY

Methyl 3-Hydroxymyristate, a Diffusible Signal MediatingphcQuorum Sensing inRalstonia solanacearum

(2015) Kenji Kai et al.   CHEMBIOCHEM

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data

(2014) Ankit Gupta et al.   PLoS One

Lysobacter enzymogenes Uses Two Distinct Cell-Cell Signaling Systems for Differential Regulation of Secondary-Metabolite Biosynthesis and Colony Morphology

(2013) Guoliang Qian et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100

(2013) Sarah Schatschneider et al.   JOURNAL OF BIOTECHNOLOGY

The Rice Bacterial PathogenXanthomonas oryzaepv.oryzaeProduces 3-Hydroxybenzoic Acid and 4-Hydroxybenzoic Acid via XanB2 for Use in Xanthomonadin, Ubiquinone, and Exopolysaccharide Biosynthesis

(2013) Lian Zhou et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Secretome analysis of the rice bacteriumXanthomonas oryzae(Xoo) using in vitro and in planta systems

(2013) Yiming Wang et al.   PROTEOMICS

The xylem as battleground for plant hosts and vascular wilt pathogens

(2013) Koste A. Yadeta et al.   Frontiers in Plant Science

Genome subtraction for the identification of potential antimicrobial targets in Xanthomonas oryzae pv. oryzae PXO99A pathogenic to rice

(2013) V. Keshri et al.   3 Biotech

Software applications for flux balance analysis

(2012) M. Lakshmanan et al.   BRIEFINGS IN BIOINFORMATICS

Alternative cardiolipin synthase Cls1 compensates for stalled Cls2 function inStaphylococcus aureusunder conditions of acute acid stress

(2012) Ryosuke L. Ohniwa et al.   FEMS MICROBIOLOGY LETTERS

The Entner-Doudoroff Pathway Is Obligatory for Gluconate Utilization and Contributes to the Pathogenicity of Vibrio cholerae

(2012) T. Patra et al.   JOURNAL OF BACTERIOLOGY

Structural Basis of Substrate Binding Specificity Revealed by the Crystal Structures of Polyamine Receptors SpuD and SpuE from Pseudomonas aeruginosa

(2012) Donghui Wu et al.   JOURNAL OF MOLECULAR BIOLOGY

The diffusible factor synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways

(2012) Lian Zhou et al.   MOLECULAR MICROBIOLOGY

Atypical Regulation of Virulence-Associated Functions by a Diffusible Signal Factor in Xanthomonas oryzae pv. oryzae

(2012) Rikky Rai et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Polyamines Are Required for Virulence in Salmonella enterica Serovar Typhimurium

(2012) Lotte Jelsbak et al.   PLoS One

A Comparison of Computational Methods for Identifying Virulence Factors

(2012) Lu-Lu Zheng et al.   PLoS One

Genomic Analysis of Xanthomonas oryzae Isolates from Rice Grown in the United States Reveals Substantial Divergence from Known X. oryzae Pathovars

(2011) L. R. Triplett et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Pathogenomics of Xanthomonas: understanding bacterium–plant interactions

(2011) Robert P. Ryan et al.   NATURE REVIEWS MICROBIOLOGY

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae produces multiple DSF-family signals in regulation of virulence factor production

(2010) Ya-Wen He et al.   BMC MICROBIOLOGY

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Polyamines are required for the expression of key Hms proteins important for Yersinia pestis biofilm formation

(2010) Brian W. Wortham et al.   ENVIRONMENTAL MICROBIOLOGY

Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae

(2010) Theodore R. Sana et al.   Metabolomics

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Cardiolipin and the osmotic stress responses of bacteria

(2009) Tatyana Romantsov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

New genes of Xanthomonas citri subsp. citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library

(2009) Marcelo L Laia et al.   BMC MICROBIOLOGY

Virulence analysis and gene expression profiling of the pigment-deficient mutant ofXanthomonas oryzaepathovaroryzae

(2009) Young-Jin Park et al.   FEMS MICROBIOLOGY LETTERS

The xrvA gene of Xanthomonas oryzae pv. oryzae, encoding an H-NS-like protein, regulates virulence in rice

(2009) J.-X. Feng et al.   MICROBIOLOGY-SGM

Glycogen contributes to the environmental persistence and transmission of Vibrio cholerae

(2009) Lori Bourassa et al.   MOLECULAR MICROBIOLOGY

A Cell Wall-Degrading Esterase of Xanthomonas oryzae Requires a Unique Substrate Recognition Module for Pathogenesis on Rice

(2009) G. Aparna et al.   PLANT CELL

Endogenous Nitric Oxide Protects Bacteria Against a Wide Spectrum of Antibiotics

(2009) I. Gusarov et al.   SCIENCE

Discovery of virulence factors of pathogenic bacteria

(2008) Hsing-Ju Wu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Glycogen and Maltose Utilization by Escherichia coli O157:H7 in the Mouse Intestine

(2008) S. A. Jones et al.   INFECTION AND IMMUNITY

Genome-wide identification of pathogenicity genes inXanthomonas oryzaepv.oryzaeby transposon mutagenesis

(2008) J. C. Wang et al.   PLANT PATHOLOGY