Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications

Noncoding RNAs, Emerging Regulators in Root Endosymbioses

(2016) Christine Lelandais-Brière et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

(2016) Alexander J. Westermann et al.   NATURE

Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility

(2016) Febé E. Meyer et al.   Frontiers in Plant Science

Genome-Enabled Analysis of Plant-Pathogen Migration

(2015) Erica M. Goss   Annual Review of Phytopathology

Molecular identification and virulence analysis of AVR genes in rice blast pathogen, Magnaporthe oryzae from Eastern India

(2015) Jahangir Imam et al.   EUPHYTICA

When plants brace for the emerging pathogens

(2015) Biswapriya B. Misra et al.   PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY

Dual RNA Sequencing Reveals the Expression of Unique Transcriptomic Signatures in Lipopolysaccharide-Induced BV-2 Microglial Cells

(2015) Amitabh Das et al.   PLoS One

Phytopathogen emergence in the genomics era

(2015) Elisha Thynne et al.   TRENDS IN PLANT SCIENCE

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

(2015) Abirami Ramalingam et al.   Frontiers in Plant Science

The Pathogen-Host Interactions database (PHI-base): additions and future developments

(2014) Martin Urban et al.   NUCLEIC ACIDS RESEARCH

Understanding and engineering beneficial plant-microbe interactions: plant growth promotion in energy crops

(2014) Kerrie Farrar et al.   PLANT BIOTECHNOLOGY JOURNAL

Transposon Mutagenesis of the Plant-Associated Bacillus amyloliquefaciens ssp. plantarum FZB42 Revealed That the nfrA and RBAM17410 Genes Are Involved in Plant-Microbe-Interactions

(2014) Anto Budiharjo et al.   PLoS One

Agrobacterium tumefaciens responses to plant-derived signaling molecules

(2014) Sujatha Subramoni et al.   Frontiers in Plant Science

Analysis of plant microbe interactions in the era of next generation sequencing technologies

(2014) Claudia Knief   Frontiers in Plant Science

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

The Role of Prophage in Plant-Pathogenic Bacteria

(2013) Alessandro M. Varani et al.   Annual Review of Phytopathology

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Systemic signaling during plant defense

(2013) Aardra Kachroo et al.   CURRENT OPINION IN PLANT BIOLOGY

Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers

(2013) Jahangir Imam et al.   EUPHYTICA

Plant innate immunity: An updated insight into defense mechanism

(2013) Mehanathan Muthamilarasan et al.   JOURNAL OF BIOSCIENCES

On the front line: structural insights into plant–pathogen interactions

(2013) Lennart Wirthmueller et al.   NATURE REVIEWS MICROBIOLOGY

Ensembl Genomes 2013: scaling up access to genome-wide data

(2013) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Population Structure and Pathotype Diversity of the Wheat Blast PathogenMagnaporthe oryzae25 Years After Its Emergence in Brazil

(2013) João L. Nunes Maciel et al.   PHYTOPATHOLOGY

Deployment of theBurkholderia glumaetype III secretion system as an efficient tool for translocating pathogen effectors to monocot cells

(2013) Shailendra Sharma et al.   PLANT JOURNAL

The INs and OUTs of pattern recognition receptors at the cell surface

(2012) Martina Beck et al.   CURRENT OPINION IN PLANT BIOLOGY

Ecosystem transformation by emerging infectious disease: loss of large tanoak from California forests

(2012) Richard C. Cobb et al.   JOURNAL OF ECOLOGY

Frontiers in metabolic reconstruction and modeling of plant genomes

(2012) S. M. D. Seaver et al.   JOURNAL OF EXPERIMENTAL BOTANY

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

Dual RNA-seq of pathogen and host

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

Genome evolution in filamentous plant pathogens: why bigger can be better

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

One world, many pathogens!

(2012) Kerry O. Britton et al.   NEW PHYTOLOGIST

A Really Useful Pathogen,Agrobacterium tumefaciens

(2012)   PLANT CELL

Are we ready for genome-scale modeling in plants?

(2012) Eva Collakova et al.   PLANT SCIENCE

Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species

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

Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals

(2012) X. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

(2012) R. de Jonge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent advances in tomato functional genomics: utilization of VIGS

(2012) Pranav Pankaj Sahu et al.   PROTOPLASMA

Emergence of the sudden oak death pathogen Phytophthora ramorum

(2012) Niklaus J. Grünwald et al.   TRENDS IN MICROBIOLOGY

Acid-Induced Type VI Secretion System Is Regulated by ExoR-ChvG/ChvI Signaling Cascade in Agrobacterium tumefaciens

(2012) Chih-Feng Wu et al.   PLoS Pathogens

A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

(2012) Eva H. Stukenbrock et al.   PLoS Pathogens

Leveraging Proteomics to Understand Plant–Microbe Interactions

(2012) Dhileepkumar Jayaraman et al.   Frontiers in Plant Science

The Rules of Engagement in the Legume-Rhizobial Symbiosis

(2011) Giles E.D. Oldroyd et al.   Annual Review of Genetics

Roles of Arbuscular Mycorrhizas in Plant Nutrition and Growth: New Paradigms from Cellular to Ecosystem Scales

(2011) Sally E. Smith et al.   Annual Review of Plant Biology

An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism

(2011) Eleftherios Pilalis et al.   BIOTECHNOLOGY AND BIOENGINEERING

De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes

(2011) Matthew G Links et al.   BMC GENOMICS

The evolution of metabolic networks of E. coli

(2011) David J Baumler et al.   BMC Systems Biology

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

(2011) Ottar Rolfsson et al.   BMC Systems Biology

Chalara fraxinea is an invasive pathogen in France

(2011) Claude Husson et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Adaptive potential of ash (Fraxinus excelsior) populations against the novel emerging pathogen Hymenoscyphus pseudoalbidus

(2011) Erik Dahl Kjaer et al.   Evolutionary Applications

The Integrity of the Periplasmic Domain of the VirA Sensor Kinase Is Critical for Optimal Coordination of the Virulence Signal Response in Agrobacterium tumefaciens

(2011) G. R. Nair et al.   JOURNAL OF BACTERIOLOGY

Plasmodiophora brassicae: a review of an emerging pathogen of the Canadian canola (Brassica napus) crop

(2011) SHEAU-FANG HWANG et al.   MOLECULAR PLANT PATHOLOGY

A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors inMelampsora larici-populina(Poplar Leaf Rust)

(2011) Stéphane Hacquard et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

GenBank

(2011) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Combined Noninvasive Imaging and Modeling Approaches Reveal Metabolic Compartmentation in the Barley Endosperm

(2011) Hardy Rolletschek et al.   PLANT CELL

Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: flux variability analysis in relation to 13C metabolic flux analysis

(2011) Jordan Hay et al.   PLANT JOURNAL

Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos

(2011) Jordan Hay et al.   PLANT JOURNAL

Dickeya species: an emerging problem for potato production in Europe

(2011) I. K. Toth et al.   PLANT PATHOLOGY

Descendants of Primed Arabidopsis Plants Exhibit Resistance to Biotic Stress

(2011) A. Slaughter et al.   PLANT PHYSIOLOGY

Next-Generation Systemic Acquired Resistance

(2011) E. Luna et al.   PLANT PHYSIOLOGY

Proteomic changes in grape embryogenic callus in response to Agrobacterium tumefaciens-mediated transformation

(2011) Fengxia Zhao et al.   PLANT SCIENCE

The Plant Pathogen Phytophthora andina Emerged via Hybridization of an Unknown Phytophthora Species and the Irish Potato Famine Pathogen, P. infestans

(2011) Erica M. Goss et al.   PLoS One

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

(2011) Rajib Saha et al.   PLoS One

Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

(2011) T. A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

(2011) Joelle Amselem et al.   PLoS Genetics

Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus

(2011) Taisei Kikuchi et al.   PLoS Pathogens

Biofuel production improvement with genome-scale models: The role of cell composition

(2010) Ryan S. Senger   Biotechnology Journal

Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans

(2010) Sylvain Raffaele et al.   BMC GENOMICS

Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions

(2010) A. Pinzon et al.   BRIEFINGS IN BIOINFORMATICS

Biotechnological concepts for improving plant innate immunity

(2010) Andrea A Gust et al.   CURRENT OPINION IN BIOTECHNOLOGY

Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response

(2010) Michal Jaskiewicz et al.   EMBO REPORTS

Use of genome-scale metabolic models for understanding microbial physiology

(2010) Liming Liu et al.   FEBS LETTERS

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

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

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

Emerging Complexity in Reactive Oxygen Species Production and Signaling during the Response of Plants to Pathogens

(2010) T. Vellosillo et al.   PLANT PHYSIOLOGY

C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

Changes in antioxidant systems in soybean as affected by Sclerotinia sclerotiorum (Lib.) de Bary

(2010) Djordje Malenčić et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome

(2010) L. Baxter et al.   SCIENCE

Pathogenesis, parasitism and mutualism in the trophic space of microbe–plant interactions

(2010) Adrian C. Newton et al.   TRENDS IN MICROBIOLOGY

Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis

(2010) Paola Bonfante et al.   Nature Communications

The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions

(2009) Trudy Torto-Alalibo et al.   BMC MICROBIOLOGY

MAPK cascade signalling networks in plant defence

(2009) Andrea Pitzschke et al.   CURRENT OPINION IN PLANT BIOLOGY

Host small RNAs are big contributors to plant innate immunity

(2009) Chellappan Padmanabhan et al.   CURRENT OPINION IN PLANT BIOLOGY

Molecular Basis of ChvE Function in Sugar Binding, Sugar Utilization, and Virulence in Agrobacterium tumefaciens

(2009) F. He et al.   JOURNAL OF BACTERIOLOGY

Capturing the essence of a metabolic network: A flux balance analysis approach

(2009) Ettore Murabito et al.   JOURNAL OF THEORETICAL BIOLOGY

Towards the automated engineering of a synthetic genome

(2009) Javier Carrera et al.   Molecular BioSystems

Geographic limits of a clonal population of wheat yellow rust in the Mediterranean region

(2009) B. BAHRI et al.   MOLECULAR ECOLOGY

Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato crops

(2009) INGE M. HANSSEN et al.   MOLECULAR PLANT PATHOLOGY

Emerging Concepts in Effector Biology of Plant-Associated Organisms

(2009) Saskia A. Hogenhout et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Association Genetics Reveals Three Novel Avirulence Genes from the Rice Blast Fungal Pathogen Magnaporthe oryzae

(2009) K. Yoshida et al.   PLANT CELL

Agrobacterium tumefaciens Promotes Tumor Induction by Modulating Pathogen Defense in Arabidopsis thaliana

(2009) C.-W. Lee et al.   PLANT CELL

A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties

(2009) M. G. Poolman et al.   PLANT PHYSIOLOGY

Innate Immunity in Plants: An Arms Race Between Pattern Recognition Receptors in Plants and Effectors in Microbial Pathogens

(2009) T. Boller et al.   SCIENCE

Against the grain: safeguarding rice from rice blast disease

(2009) Pari Skamnioti et al.   TRENDS IN BIOTECHNOLOGY

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

(2008) Steven L Salzberg et al.   BMC GENOMICS

Comparative transcriptome analysis ofAgrobacterium tumefaciensin response to plant signal salicylic acid, indole-3-acetic acid and γ-amino butyric acid reveals signalling cross-talk andAgrobacterium-plant co-evolution

(2008) Ze-Chun Yuan et al.   CELLULAR MICROBIOLOGY

Post-transcriptional RNA silencing in plant–microbe interactions: a touch of robustness and versatility

(2008) Olivier Voinnet   CURRENT OPINION IN PLANT BIOLOGY

Biotech crops: technologies, achievements and prospects

(2008) M. A. Y. Akhond et al.   EUPHYTICA

Ramularia collo-cygni: the biology of an emerging pathogen of barley

(2008) Dale R. Walters et al.   FEMS MICROBIOLOGY LETTERS

Speciation in fungi

(2008) Tatiana Giraud et al.   FUNGAL GENETICS AND BIOLOGY

The secretome of the maize pathogen Ustilago maydis

(2008) Olaf Mueller et al.   FUNGAL GENETICS AND BIOLOGY

Genome-scale modeling ofSynechocystissp. PCC 6803 and prediction of pathway insertion

(2008) Pengcheng Fu   JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY

Comparative proteomic studies of root–microbe interactions

(2008) Ulrike Mathesius   Journal of Proteomics

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Plant-microbe and plant-insect interactions meet common grounds

(2008) Peer M. Schenk et al.   NEW PHYTOLOGIST

From Guard to Decoy: A New Model for Perception of Plant Pathogen Effectors

(2008) R. A.L. van der Hoorn et al.   PLANT CELL

Flux Balance Analysis of Barley Seeds: A Computational Approach to Study Systemic Properties of Central Metabolism

(2008) E. Grafahrend-Belau et al.   PLANT PHYSIOLOGY

Recognition of the Hyaloperonospora parasitica effector ATR13 triggers resistance against oomycete, bacterial, and viral pathogens

(2008) M. C. Rentel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA