Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

Enhanced Control of Cucumber Wilt Disease by Bacillus amyloliquefaciens SQR9 by Altering the Regulation of Its DegU Phosphorylation

(2014) Z. Xu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

From environmental signals to regulators: Modulation of biofilm development in Gram-positive bacteria

(2014) Eisha Mhatre et al.   JOURNAL OF BASIC MICROBIOLOGY

De-coupling of root–microbiome associations followed by antagonist inoculation improves rhizosphere soil suppressiveness

(2013) Meihua Qiu et al.   BIOLOGY AND FERTILITY OF SOILS

Application of Natural Blends of Phytochemicals Derived from the Root Exudates ofArabidopsisto the Soil Reveal That Phenolic-related Compounds Predominantly Modulate the Soil Microbiome

(2013) Dayakar V. Badri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Sticking together: building a biofilm the Bacillus subtilis way

(2013) Hera Vlamakis et al.   NATURE REVIEWS MICROBIOLOGY

IslandViewer update: improved genomic island discovery and visualization

(2013) Bhavjinder K. Dhillon et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

Effects of different plant root exudates and their organic acid components on chemotaxis, biofilm formation and colonization by beneficial rhizosphere-associated bacterial strains

(2013) Nan Zhang et al.   PLANT AND SOIL

Bacillus subtilis biofilm induction by plant polysaccharides

(2013) P. B. Beauregard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of Bacillomycin D in Bacillus amyloliquefaciens SQR9 to Antifungal Activity and Biofilm Formation

(2012) Zhihui Xu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced root colonization and biocontrol activity of Bacillus amyloliquefaciens SQR9 by abrB gene disruption

(2012) Jun Weng et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Application of bio-organic fertilizer can control Fusarium wilt of cucumber plants by regulating microbial community of rhizosphere soil

(2012) Meihua Qiu et al.   BIOLOGY AND FERTILITY OF SOILS

Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates

(2012) Ben Fan et al.   BMC MICROBIOLOGY

Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyteAzoarcussp. strain BH72

(2012) Teja Shidore et al.   ENVIRONMENTAL MICROBIOLOGY

Biocontrol of tomato wilt disease byBacillus subtilisisolates from natural environments depends on conserved genes mediating biofilm formation

(2012) Yun Chen et al.   ENVIRONMENTAL MICROBIOLOGY

The Complete Genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 Contains a Gene Cluster for Nonribosomal Synthesis of Iturin A

(2012) J. Blom et al.   JOURNAL OF BACTERIOLOGY

The Genome of Plant Growth-Promoting Bacillus amyloliquefaciens subsp. plantarum Strain YAU B9601-Y2 Contains a Gene Cluster for Mersacidin Synthesis

(2012) K. Hao et al.   JOURNAL OF BACTERIOLOGY

SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of σD in Bacillus subtilis

(2012) Loralyn M. Cozy et al.   MOLECULAR MICROBIOLOGY

A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants

(2012) Yun Chen et al.   MOLECULAR MICROBIOLOGY

Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi

(2012) S. T. Coradetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins

(2012) E. A. Znameroski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacillus subtilis SQR 9 can control Fusarium wilt in cucumber by colonizing plant roots

(2011) Yun Cao et al.   BIOLOGY AND FERTILITY OF SOILS

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

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture

(2011) Alejandro Pérez-García et al.   CURRENT OPINION IN BIOTECHNOLOGY

LuxS Mediates Iron-Dependent Biofilm Formation, Competence, and Fratricide in Streptococcus pneumoniae

(2011) Claudia Trappetti et al.   INFECTION AND IMMUNITY

Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42

(2011) Christian Rückert et al.   JOURNAL OF BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

A new bioorganic fertilizer can effectively control banana wilt by strong colonization with Bacillus subtilis N11

(2011) Nan Zhang et al.   PLANT AND SOIL

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics

(2011) Vinoy K Ramachandran et al.   GENOME BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Identification of Up-regulated Genes of Bacillus amyloliquefaciens B55 During the Early Stage of Direct Surface Contact with Rice R109 Root

(2010) Jun Liu et al.   CURRENT MICROBIOLOGY

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons

(2010) R. Borriss et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

(2010) Amrita Pati et al.   NATURE METHODS

Plant-Growth-Promoting Rhizobacteria

(2009) Ben Lugtenberg et al.   Annual Review of Microbiology

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Rhizosphere chemical dialogues: plant–microbe interactions

(2009) Dayakar V Badri et al.   CURRENT OPINION IN BIOTECHNOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Structure and Complexity of a Bacterial Transcriptome

(2009) K. D. Passalacqua et al.   JOURNAL OF BACTERIOLOGY

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Regulation and function of root exudates

(2009) DAYAKAR V. BADRI et al.   PLANT CELL AND ENVIRONMENT

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

(2009) Stéphane Compant et al.   SOIL BIOLOGY & BIOCHEMISTRY

Global Gene Expression Profiles Suggest an Important Role for Nutrient Acquisition in Early Pathogenesis in a Plant Model of Pseudomonas aeruginosa Infection

(2008) T. L. Weir et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Control of cell fate by the formation of an architecturally complex bacterial community

(2008) H. Vlamakis et al.   GENES & DEVELOPMENT

Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens

(2008) X.H. Chen et al.   JOURNAL OF BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Root-Secreted Malic Acid Recruits Beneficial Soil Bacteria

(2008) T. Rudrappa et al.   PLANT PHYSIOLOGY

Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis

(2008) D. Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacillus lipopeptides: versatile weapons for plant disease biocontrol

(2008) Marc Ongena et al.   TRENDS IN MICROBIOLOGY