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Publications – 2017
Atractiella rhizophila sp. nov., an endorrhizal fungus isolated from the Populus root microbiome
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Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer
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Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens
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The Identification of Phytohormone Receptor Homologs in Early Diverging Fungi Suggests a Role for Plant Sensing in Land Colonization by Fungi
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Diverse Plant-Associated Pleosporalean Fungi from Saline Areas:
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The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation
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Network Metamodeling: Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network Topology
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Populus trichocarpa encodes small, effector-like secreted proteins that are highly induces during mutualistic symbiosis
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Characterization of a novel, ubiquitous fungal endophyte from the rhizosphere and root endosphere of Populus trees
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Publications – 2016
A carotenoid-deficient mutant in Pantoea sp. YR343, a bacteria isolated from the rhizosphere of Populus deltoides, is defective in root colonization
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Two poplar-associated bacterial isolates induce additive favorable responses in a constructed plant-microbiome system
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Transgenic soybean overexpressing GmSAMT1 exhibits resistance to multiple-HG types of soybean cyst nematode Heterodera glycines
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Isolating a functionally relevant guild of fungi from the Populus rhizosphere.
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Characterization of DWARF14 genes in Populus
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While-you-wait proteins? Producing biomolecules at the point of need.
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Chapter Five: The Sphagnum Genome Project: A new model for ecological and evolutionary genomics
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The Sphagnum microbiome: new insights from an ancient plant lineage.
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Enrichment of root endophytic bacteria from Populus deltoides and single-cell genomics analysis
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A LuxR homolog in a Cottonwood tree endophyte that activates gene expression in response to a plant signal or specific peptides.
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Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to withstand Salinity.
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Down-regulation of KORRIGAN-like endo-β-1,4-glucanase genes impacts
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Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
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Unearthing the roots of ectomycorrhizal symbioses
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Poplar PtabZIP1 positively regulates lateral root formation and flavonoid synthesis and enhance biomass growth under drought.
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Root bacterial endophytes alter plant phenotype, but not physiology
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Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray
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Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas
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ß-glucan unmasking in some Candida albicans mutants correlates with increases in cell wall surface roughness and decreases in cell wall elasticity
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Fungal and plant gene expression in the Tulasnella calospora–Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas
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Molecular Mycorrhizal Symbiosis
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Integrated Proteomics and Metabolomics Suggests Symbiotic Metabolism and Multimodal Regulation in a Fungal-Endobacterial System
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A New Method for Qualitative Multiscale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy
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Genome-wide analysis of lectin receptorlike kinases in Populus
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Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
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Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution
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Signaling pathways driving the development of ectomycorrhizal symbiosis
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Harnessing mycorrhizal genomics for biological insights
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The evolution of the mycorrhizal lifestyles – a genomic perspective
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Mycorrhiza helper bacteria
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Ecologically Different Fungi Affect Arabidopsis Development: Contribution of Soluble and Volatile Compounds
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Publications – 2015
Prospects and challenges for fungal metatranscriptomics of complex communities
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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
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The mutualist Laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defenses
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Insights from 20 years of bacterial genome sequencing
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3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics.
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ALD1 regulates the basal immune components and early inducible defense responses in Arabidopsis.
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Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomychorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome
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Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylinddrosporum and its involvement in ectomycorrhizal symbiosis.
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Development of the Poplar-Laccaria bicolor ectomycorrhiza Modifies Root Auxin Metabolism, Signaling, and Response.
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Reconsidering mutualistic plant-fungal interactions through the lens of effector biology
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Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry
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PanFP: Pangenome-based functional profiles for microbial communities.
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Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment
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Diversity of Pseudomonas genomes, including Populus-associated isolates, as revealed by comparative genome analysis.
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Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors
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Phosphorylation of RACK1 in plants
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Sequence data for Clostridium autoehanogenum using three generations of sequencing technologies
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Microstencils to generate defined, multi-species patterns of bacteria
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The Small Ethylene Response Factor ERF96 is Involved in the Regulation of the Abscisic Acid Response in Arabidopsis
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Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere
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Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins
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Publications – 2014
Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas
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Extreme diversification of the mating type-high-mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungus
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Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus roots
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Genome resequencing in Populus. Revealing large-scale genome variation and implications on specialized-trait genomes.
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Populus trichocarpa and Populus deltoides Exhibit Different Metabolomic Responses to Colonization by the Symbiotic fungus Laccaria bicolor
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Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions between Bacteria and Plants
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Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia
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Transgenic American chestnuts show enhanced blight resistance and transmit the trait to T1 progeny.
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Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and
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Characterization of MORE AXILLARY GROWTH Genes in Populus
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Duplications and losses in gene families of rust pathogens highlight putative effectors.
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Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.
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Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts
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Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences
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Selective herbivory by an invasive cyprinid, the rudd Scardinius erythrophthalmus
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MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics
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Towards a holistic understanding of the beneficial interactions across the Populus microbiome
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Quality scores for 32,000 genomes
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Strigolactone-Regulated Proteins Revealed by iTRAQ-Based Quantitative Proteomics in Arabidopsis
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Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment
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Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host–microbiome interactions on understanding ecosystem function
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Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus
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Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants
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Fungal biology: compiling genomes and exploiting them
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Publications – 2013
Genome Anchored QTLs for Biomass Production in Hybrid Populus Grown Under Contrasting Environments
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Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
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LuxR- and LuxI-type quorum sensing circuits are prevalent in members of the Populus deltoides microbiome
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Identification, characterization of an AP2/ERF transcriptiion factor that promotes adventitious, lateral root formation in Populus.
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Sipros/ProRata: a versatile informatics system for quantitative community proteomics
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Inside arbuscular mycorrhizal roots-Molecular probes to understand the symbiosis
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Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments.
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Who is controlling whom within ectomycorrhiza symbiosis: insights from genomic and functional analyses
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Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-Like effectors into plant and animal cells is specific and reproducible.
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New insights into ectomycorrhizal symbiosis evolution and function
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Heterotrimeric G protein signaling in the plant kingdom
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A Dual Role of Strigolactones in Phosphate Acquisition and Utilization in Plants
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Repeated Elements in Filamentous Fungi with a Focus on Wood-Decay Fungi
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Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis
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Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus
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Mycorrhizas and New Phytologist: une vraie historie d’amour
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The Ecological Genomics of Fungi
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Lectin-functionalized poly(glycidyl methacrylate)-block-poly(vinyldimethyl azlactone) surface scaffolds for high avidity microbial capture
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Single cell swimming dynamics of Listeria monocytogenes using a nanoporous microfluidic platform
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A Multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.
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Atomic Force Microscope Controlled Topographical Imaging and Proximal Probe Thermal Desorption/Ionization Mass Spectrometry Imaging
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Evolutionary analyses of non-family genes in plants
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Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi
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Publications – 2012
Analyzing large biological datasets with association networks
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Pseudomonas fluorescens Induces Strain-Dependent and Strain-Independent Host Plant Responses
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Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome.
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Secretome of the Free-living Mycelium from the Ectomycorrhizal Basidiomycete Laccaria bicolor
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Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa
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Poplar root exudates contain compounds that induce the expression of MiSSP7 in Laccaria bicolor
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The M. truncatula SUNN gene is expressed in vascular tissue, similarly to RDN1, consistent with the role of these nodulation regulation genes in long distance signaling
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Highly Efficient Isolation of Populus Mesophyll Protoplasts and Its Application in Transient Expression Assays
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New North American truffles (Tuber spp.) and their ectomycorrhizal associations
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Gene and translation initiation site prediction in metagenomic sequences
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Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor
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Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes
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Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides
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Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA
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System-wide Studies of N-Lysine Acetylation in Rhodopseudomonas palustris Reveal Substrate Specificity of Protein Acetyltransferases
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Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoides
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Phylogenetic, genomic organization and expression analysis of hydrophobin genes in the ectomycorrhizal basidiomycete Laccaria bicolor
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Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos
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Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator
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Involvement of auxin pathways in modulating root architecture during beneficial plant-
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Temperature-Dependent Shade Avoidance Involves the Receptor-Like Kinase ERECTA
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Sequencing the fungal tree of life
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The importance of individuals: intraspecific diversity of mycorrhizal plants and fungi in ecosystems. -Tansley review-
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The AINTEGUMENTA LIKE1 homeotic transcription factor PtAIL1 controls the formation of adventitious root primordia in Poplar.
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Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
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Ten years of genomics for ectomycorrhizal fungi: what have we achieved and where are we headed?
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Molecular Interactions in Mycorrhizal Development
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Communication Between Plant, Ectomycorrhizal
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Communication between plant, ectomycorrhizal fungi and helper bacteria.
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De-constructing a mutualist: How the molecular blueprints of model symbiotic fungi are changing our understanding of mutualism.
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Signaling in ectomycorrhizal symbiosis
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Publications – 2011
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
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Abscisic acid receptors: past, present and future
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A Secreted Effector Protein of Laccaria bicolor is Required for Symbiosis Development
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Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max
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Characterization of cell surface and extracellular matrix remodeling of Azospirillum brasilense chemotaxis-like 1 signal transduction pathway mutants by atomic force microscopy.
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Identification of quantitiative trait loci affecting ectomycorrhizal symbiosis in an interspecific F1 poplar cross and differentail expression of genes in ectomycorrhizas of the two parents: Populus deltoides and Populus trichocarpa.
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Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes.
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Bacterial Immobilization for Imaging by Atomic Force Microscopy
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Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers
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Mutualistic interactions on a knife-edge between saprotrophy and pathogenesis.
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Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.
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Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments
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The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont
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Measuring Dissociation Rate Constants of Protein Complexes Through Subunit Exchanges: Experimental Design and Theoretical Modeling
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Tapping Genomics to Unravel Ectomycorrhizal Symbiosis
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Structure and Expression Profile of the Phosphate Pht1 Transporter Gene Family in Mycorrhizal Populus trichocarpa
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Mutualistic Effectors: Architects of Symbiosis
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Innovative biological solutions to challenges in sustainable biofuels production.
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Publications – 2010
CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database
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Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar
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Biosynthesis and emission of insect-induced methyl salicylate and methyl benzoate from rice.
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Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions
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