Publications

YearTitleFirst AuthorJournalDOI
2018Facing Global Change: The Millennium Challenge for Plant ScientistsBassoNew Phytologisthttps://doi.org/10.1111/nph.15376
2026Genomic Approaches to Accelerate American Chestnut RestorationWestbrookSciencehttps://doi.org/10.1126/science.adw3225
2026Population Genomics of Pseudocercospora griseola Reveals New Groups in the Middle American Clade and the Presence of the Endophytic Bacterium Achromobacter xylosoxidansSerrato-DiazPhytopathologyhttps://doi.org/10.1094/PHYTO-09-24-0302-R
2026Allosteric Prediction Via Convolutional Neural Networks and Protein Structural and Dynamical FeaturesRajeshwarBiophysical Journalhttps://doi.org/10.1016/j.bpj.2025.12.011
2026Genetic and Epigenetic Signatures of in Response to Abiotic StressesLiPlant Stresshttps://doi.org/10.1016/j.stress.2026.101228
2026Genomic Signatures in Variovorax Enabling Colonization of the Populus EndosphereBealsmSystemshttps://doi.org/10.1128/msystems.01605-25
2025Utilizing Plant Synthetic Biology to Accelerate Plant-Microbe Interactions ResearchYangBioDesign Researchhttps://doi.org/10.1016/j.bidere.2025.100007
2025Pseudomonas aeruginosa Adhesion and Biofilm Formation on Poly(L-Lysine)-Tethered Hydrogels: Synergistic Effect of Substrate Stiffness and Positive Charge DensityWangLangmuirhttps://doi.org/10.1021/acs.langmuir.5c02709
2025The Microbiologist's Guide to MetaproteomicsVan Den BosscheiMetahttps://doi.org/10.1002/imt2.70031
2025LipoCLEAN: A Machine Learning Filter to Improve Untargeted Lipid Identification ConfidenceTavisAnalytical Chemistryhttps://doi.org/10.1021/acs.analchem.4c04040
2025RefAHL: A Curated Quorum Sensing Reference Linking Diverse LuxI-Type Signal Synthases with Their Acyl-Homoserine Lactone ProductsSchaeferMicrobiology Resource Announcementshttps://doi.org/10.1128/mra.00407-25
2025Predicting Receptor-Ligand Pairing Preferences in Plant-Microbe Interfaces Via Molecular Dynamics and Machine LearningPratesComputational and Structural Biotechnology Journalhttps://doi.org/10.1016/j.csbj.2025.06.029
2025Time-Series RNAMetabarcoding of the Active Populus tremuloides Root Microbiome Reveals Hidden Temporal Dynamics and Dormant Core MembersNashmSystemshttps://doi.org/10.1128/msystems.00285-25
2025Dual-Mycorrhizal Colonization Is Determined by Plant Age and Host Identity in Two Species of PopulusNashMycorrhizahttps://doi.org/10.1007/s00572-025-01215-6
2025BONCAT-Live for Isolation and Cultivation of Active Environmental BacteriaMulaymBiohttps://doi.org/10.1128/mbio.02389-25
2025To Immunity and Beyond: The Central Role of Jasmonate Signalling in Beneficial Root-Microbe-Environment InteractionsMarques-GalvezNew Phytologisthttps://doi.org/10.1111/nph.70446
2025Comparative Transcriptomics Uncovers Poplar and Fungal Genetic Determinants of Ectomycorrhizal CompatibilityMarques-GalvezThe Plant Journalhttps://doi.org/10.1111/tpj.70352
2025Woody Plant Transformation: Current Status, Challenges, and Future PerspectivesMaharjanPlantshttps://doi.org/10.3390/plants14223420
2025Poplar Transformation with Variable Explant Sources to Maximize Transformation EfficiencyLuScientific Reportshttps://doi.org/10.1038/s41598-024-81235-y
2025Eucalyptus grandis MYB-Like and RAN-Like Zinc Finger Proteins Display Dual Roles in Regulating Plant Immunity and Symbiosis PathwaysHillPhysiologia Plantarumhttps://doi.org/10.1111/ppl.70454
2025A Novel Bacterial Protein Family That Catalyses Nitrous Oxide ReductionHeNaturehttps://doi.org/10.1038/s41586-025-09401-4
2025Controlling Matric Potential in Microfluidics to Examine Microbial Dynamics in Unsaturated Porous MediaFranklinSoil Biology and Biochemistryhttps://doi.org/10.1016/j.soilbio.2025.109916
2025Fungal EndophytesCosnerCurrent Biologyhttps://doi.org/10.1016/j.cub.2025.08.058
2025Catabolic Pathway Acquisition by Rhizosphere Bacteria Readily Enables Growth with a Root Exudate Component but Does Not Affect Root ColonizationChristelmBiohttps://doi.org/10.1128/mbio.03016-24
2025Complete Genome Sequences of Five Variovorax Strains Isolated from the Populus Rhizosphere and EndosphereBealsMicrobiology Resource Announcementshttps://doi.org/10.1128/mra.00990-25
2025Quorum Sensing Modulates Microbial Community Structure through Regulation of Secondary MetabolitesArmesmSpherehttps://doi.org/10.1128/msphere.01050-24
2025Dynamic Rhizodeposition in the Woody Perennial Populus trichocarpaAppidiPlant, Cell & Environmenthttps://doi.org/10.1111/pce.70004
2025Unraveling Bacterial Adaptation Strategies in the Microbiome Shaped by the Chemical Environment of the Plant RhizosphereAppidiPhytobiomes Journalhttps://doi.org/10.1094/Pbiomes-08-24-0081-R
2024AtDGCRr14L Contributes to Salt-Stress Tolerance Via Regulating Pre-mRNA Splicing in ArabidopsisXieThe Plant Journalhttps://doi.org/10.1111/tpj.17136
2024Formation of a Constructed Microbial Community in a Nutrient-Rich Environment Indicates Bacterial Interspecific CompetitionWangmSystemshttps://doi.org/10.1128/msystems.00006-24
2024Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-Free SystemSwordScientific Reportshttps://doi.org/10.1038/s41598-024-61376-w
2024Genetic Underpinnings of Arthropod Community Distributions in Populus trichocarpaSimonNew Phytologisthttps://doi.org/10.1111/nph.19660
2024Divide and Conquer: Using Rhizovision Explorer to Aggregate Data from Multiple Root Scans Using Image Concatenation and Statistical MethodsSeethepalliNew Phytologisthttps://doi.org/10.1111/nph.20151
2024Fungal Elemental Profiling Unleashed through Rapid Laser-Induced Breakdown Spectroscopy (LIBS)RushmSystemshttps://doi.org/10.1128/msystems.00919-24
2024Complete Genome Sequence of sp. Strain Populi, an Actinobacterium Isolated from Populus trichocarpa RhizospherePodarMicrobiology Resource Announcementshttps://doi.org/10.1128/mra.00851-24
2024Decoding the Chemical Language of Suillus Fungi: Genome Mining and Untargeted Metabolomics Uncover Terpene Chemical DiversityMudbharimSystemshttps://doi.org/10.1128/msystems.01225-23
2024Populus MYC2 Orchestrates Root Transcriptional Reprogramming of Defence Pathway to Impair Laccaria bicolor Ectomycorrhizal DevelopmentMarques-GalvezNew Phytologisthttps://doi.org/10.1111/nph.19609
2024A Small Secreted Protein Serves as a Plant-Derived Effector Mediating Symbiosis between Populus and Laccaria bicolorLiuHorticulture Researchhttps://doi.org/10.1093/hr/uhae232
2024Biotechnology and Genomic Approaches to Mitigating Disease Impacts on Forest HealthLeBoldusAnnual Review of Phytopathologyhttps://doi.org/10.1146/annurev-phyto-021622-114434
2024Ant Handling Changes Myrmecochore Seed Coat Microbiomes and Alters Diversity of Seed-Borne Plant Pathogenic FungiLashFunctional Ecologyhttps://doi.org/10.1111/1365-2435.14517
2024Complete Genome Sequence of Luteolibacter sp. Strain Populi, a Member of Phylum Verrucomicrobiota Isolated from the Populus trichocarpa RhizosphereImaiMicrobiology Resource Announcementshttps://doi.org/10.1128/mra.00801-24
2024Monitoring the Impact of Confinement on Hyphal Penetration and Fungal BehaviorGuoPLoS Onehttps://doi.org/10.1371/journal.pone.0312855
2024Microbial Colonisation Rewires the Composition and Content of Poplar Root Exudates, Root and Shoot MetabolomesFracchiaMicrobiomehttps://doi.org/10.1186/s40168-024-01888-9
2024From Microbes to Microbiomes: Applications for Plant Health and Sustainable AgricultureBeattiePhytopathologyhttps://doi.org/10.1094/PHYTO-02-24-0054-KC
2024Seasonality and Longer-Term Development Generate Temporal Dynamics in the Populus MicrobiomeArgiroffmSystemshttps://doi.org/10.1128/msystems.00886-23
2023CRISPR/Cas9-Based Gene Activation and Base Editing in PopulusYaoHorticulture Researchhttps://doi.org/10.1093/hr/uhad085
2023DNA Hypomethylation of the Host Tree Impairs Interaction with Mutualistic Ectomycorrhizal FungusVigneaudNew Phytologisthttps://doi.org/10.1111/nph.18734
2023A mini-TGA Protein Modulates Gene Expression through Heterogeneous Association with Transcription FactorsTomazPlant Physiologyhttps://doi.org/10.1093/plphys/kiac579
2023A Mesorhizobium japonicum Quorum Sensing Circuit That Involves Three Linked Genes and an Unusual Acyl-Homoserine Lactone SignalSuomBiohttps://doi.org/10.1128/mbio.01010-23
2023Lectin Receptor-Like Kinase Signaling during Engineered Ectomycorrhiza ColonizationShresthaCellshttps://doi.org/10.3390/cells12071082
2023Unraveling the Functional Dark Matter through Global MetagenomicsPavlopoulosNaturehttps://doi.org/10.1038/s41586-023-06583-7
2023Plant Myo-Inositol Transport Influences Bacterial Colonization PhenotypesO'BanionCurrent Biologyhttps://doi.org/10.1016/j.cub.2023.06.057
2023A Rapid Assay for Assessing Bacterial Effects on Arabidopsis ThermotoleranceLeePlant Methodshttps://doi.org/10.1186/s13007-023-01022-0
2023Climatic Clustering and Longitudinal Analysis with Impacts on Food, Bioenergy, and PandemicsLagergrenPhytobiomes Journalhttps://doi.org/10.1094/pbiomes-02-22-0007-r
2023Signatures of Prescribed Fire in the Microbial Communities of Cornus florida Are Largely Undetectable Five Months Post-FireKapoorPeerJhttps://doi.org/10.7717/peerj.15822
2023A Glimpse into the Fungal Metabolomic Abyss: Novel Network Analysis Reveals Relationships between Exogenous Compounds and Their OutputsGopalakrishnan MeenaPNAS Nexushttps://doi.org/10.1093/pnasnexus/pgad322
2023Differences in Spore Size and Atmospheric Survival Shape Stark Contrasts in the Dispersal Dynamics of Two Closely Related Fungal PathogensGolanFungal Ecologyhttps://doi.org/10.1016/j.funeco.2023.101298
2023Investigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter SystemDinglasanACS Synthetic Biologyhttps://doi.org/10.1021/acssynbio.2c00658
2023Rewiring Cell-Free Metabolic Flux in E. coli Lysates Using a Block-Push-Pull ApproachDinglasanSynthetic Biologyhttps://doi.org/10.1093/synbio/ysad007
2023Ectomycorrhizal Symbiosis Prepares Its Host Locally and Systemically for Abiotic Cue Signalingde Freitas PereiraThe Plant Journalhttps://doi.org/10.1111/tpj.16465
2023Mechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas-Rahnella Co-CultureDahalMetaboliteshttps://doi.org/10.3390/metabo13020140
2023Exploring the Role of Plant Lysin Motif Receptor-Like Kinases in Regulating Plant-Microbe Interactions in the Bioenergy Crop PopulusCopeComputational and Structural Biotechnology Journalhttps://doi.org/10.1016/j.csbj.2022.12.052
2023Microstructural and Rheological Transitions in Bacterial BiofilmsCharltonAdvanced Sciencehttps://doi.org/10.1002/advs.202207373
2022The Ectomycorrhizal Basidiomycete Laccaria bicolor Releases a GH28 Polygalacturonase That Plays a Key Role in Symbiosis Establishment.ZhangNew Phytologisthttps://doi.org/10.1111/nph.17940
2022In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass SpectrometryWaltonJournal of the American Society for Mass Spectrometryhttps://doi.org/10.1021/jasms.2c00081
2022Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and DevelopmentVillalobos SolisFrontiers in Fungal Biologyhttps://doi.org/10.3389/ffunb.2022.808578
2022Meta-Omics-Aided Isolation of an Elusive Anaerobic Arsenic-Methylating Soil BacteriumViacavaISME Journalhttps://doi.org/10.1038/s41396-022-01220-z
2022Lipo-Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial GrowthRushmSystemshttps://doi.org/10.1128/msystems.01052-22
2022Mycorrhiza-Induced Mycocypins of Laccaria bicolor Are Potent Protease Inhibitors with Nematotoxic and Collembola Antifeedant ActivityPlettEnvironmental Microbiologyhttps://doi.org/10.1111/1462-2920.16115
2022Benchmarking Second and Third-Generation Sequencing Platforms for Microbial MetagenomicsMeslierScientific Datahttps://doi.org/10.1038/s41597-022-01762-z
2022Evolutionary Transition to the Ectomycorrhizal Habit in the Genomes of a Hyperdiverse Lineage of Mushroom-Forming FungiLooneyNew Phytologisthttps://doi.org/10.1111/nph.17892
2022Biological and Molecular Components for Genetically Engineering Biosensors in PlantsLiuBioDesign Researchhttps://doi.org/10.34133/2022/9863496
2022Diversity and Conservation of Plant Small Secreted Proteins Associated with Arbuscular Mycorrhizal SymbiosisHuHorticulture Researchhttps://doi.org/10.1093/hr/uhac043
2022Abscisic Acid Supports Colonization of Eucalyptus grandis Roots by the Mutualistic Ectomycorrhizal Fungus Pisolithus microcarpusHillNew Phytologisthttps://doi.org/10.1111/nph.17825
2022Precision Genome Editing in Plants Using Gene Targeting and Prime Editing: Existing and Emerging StrategiesHassanBiotechnology Journalhttps://doi.org/10.1002/biot.202100673
2022Quantifying Biofilm Propagation on Chemically Modified SurfacesHalstedBiofilmhttps://doi.org/10.1016/j.bioflm.2022.100088
2022Relationships between Sphaerulina musiva Infection and the Populus Microbiome and MetabolomeDovemSystemshttps://doi.org/10.1128/msystems.00120-22
2022The Promises, Challenges, and Opportunities of Omics for Studying the Plant HolobiontCarperMicroorganismshttps://doi.org/10.3390/microorganisms10102013
2022Phylogenetic Conservatism of Mycoparasitism and Its Contribution to Pathogen AntagonismBargeMolecular Ecologyhttps://doi.org/10.1111/mec.16436
2022Hotspots of Root-Exuded Amino Acids Are Created within a Rhizosphere-on-a-ChipAufrechtLab Chiphttps://doi.org/10.1039/d1lc00705j
2022Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate SystemAppidiMolecular Plant-Microbe Interactionshttps://doi.org/10.1094/MPMI-01-22-0011-TA
2021The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpaYatesGenome Biology and Evolutionhttps://doi.org/10.1093/gbe/evab198
2021Climate-Driven Divergence in Plant-Microbiome Interactions Generates Range-Wide Variation in Bud Break PhenologyWareCommunications Biologyhttps://doi.org/10.1038/s42003-021-02244-5
2021Formation, Characterization and Modeling of Emergent Synthetic Microbial CommunitiesWangComputational and Structural Biotechnology Journalhttps://doi.org/10.1016/j.csbj.2021.03.034
2021Quantitative Resistance Linked to Late EffectorsVeneault-FourreyNew Phytologisthttps://doi.org/10.1111/nph.17462
2021Phylogenetic Diversity of 200+ Isolates of the Ectomycorrhizal Fungus Cenococcum geophilum Associated with Populus trichocarpa Soils in the Pacific Northwest, USA and Comparison to Globally Distributed RepresentativesVelezPLoS Onehttps://doi.org/10.1371/journal.pone.0231367
2021Metaproteomics Reveals Insights into Microbial Structure, Interactions, and Dynamic Regulation in Defined Communities as They Respond to Environmental DisturbanceShresthaBMC Microbiologyhttps://doi.org/10.1186/s12866-021-02370-4
2021Small RNAs at the Interface of the Plant-Fungal InteractionsSawyerFungal Genomics & Biologyhttps://www.longdom.org/open-access/small-rnas-at-the-interface-of-the-plantfungal-interactions-61113.html
2021A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolorRuytinxMicroorganismshttps://doi.org/10.3390/microorganisms9122612
2021Bioprospecting Trichoderma: A Systematic Roadmap to Screen Genomes and Natural Products for Biocontrol ApplicationsRushFrontiers in Fungal Biologyhttps://doi.org/10.3389/ffunb.2021.716511
2021Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase DiversityRuiz-DuenasMolecular Biology and Evolutionhttps://doi.org/10.1093/molbev/msaa301
2021Towards Engineering Ectomycorrhization into Switchgrass Bioenergy Crops Via a Lectin Receptor-Like KinaseQiaoPlant Biotechnology Journalhttps://doi.org/10.1111/pbi.13671
2021Spatially Co-Registered Wide-Field Nonlinear Optical Imaging of Living and Complex Biosystems in a Total Internal Reflection GeometryPremadasaAnalysthttps://doi.org/10.1039/d1an00129a
2021Intra-Species Genetic Variability Drives Carbon Metabolism and Symbiotic Host Interactions in the Ectomycorrhizal Fungus Pisolithus microcarpusPlettEnvironmental Microbiologyhttps://doi.org/10.1111/1462-2920.15320
2021Image-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis LeavesPavicicPlantshttps://doi.org/10.3390/plants10010158
2021Genetic Determinants of Endophytism in the Arabidopsis Root MycobiomeMesnyNature Communicationshttps://doi.org/10.1038/s41467-021-27479-y
2021Desert Truffle Genomes Reveal Their Reproductive Modes and New Insights into Plant-Fungal Interaction and Ectendomycorrhizal LifestyleMarques-GalvezNew Phytologisthttps://doi.org/10.1111/nph.17044
2021Structural Basis for a Bacterial Pip System Plant Effector Recognition ProteinLuoProceedings of the National Academy of Sciences, USAhttps://doi.org/10.1073/pnas.2019462118
2021Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root FungiLiaoFrontiers in Microbiologyhttps://doi.org/10.3389/fmicb.2021.680267
2021Metabolomic Patterns of Septoria Canker Resistant and Susceptible Populus trichocarpa Genotypes 24 Hours PostinoculationLenzPhytopathologyhttps://doi.org/10.1094/PHYTO-02-21-0053-R
2021amPEPpy 1.0: A Portable and Accurate Antimicrobial Peptide Prediction ToolLawrenceBioinformaticshttps://doi.org/10.1093/bioinformatics/btaa917
2021ALD1 Accumulation in Arabidopsis Epidermal Plastids Confers Local and Non-Autonomous Disease ResistanceJiangJournal of Experimental Botanyhttps://doi.org/10.1093/jxb/eraa609
2021Advances and Perspectives in Discovery and Functional Analysis of Small Secreted Proteins in PlantsHuHorticulture Researchhttps://doi.org/10.1038/s41438-021-00570-7
2021Characterization of Terpene Biosynthesis in Melaleuca quinquenervia and Ecological Consequences of Terpene Accumulation during Myrtle Rust InfectionHsiehPlant-Environment Interactionshttps://doi.org/10.1002/pei3.10056
2021Construct Design for CRISPR/Cas-Based Genome Editing in PlantsHassanTrends in Plant Sciencehttps://doi.org/10.1016/j.tplants.2021.06.015
2021A Lysate Proteome Engineering Strategy for Enhancing Cell-Free Metabolite ProductionGarciaMetabolic Engineering Communicationshttps://doi.org/10.1016/j.mec.2021.e00162
2021A k-mer Based Approach for Classifying Viruses without Taxonomy Identifies Viral Associations in Human Autism and Plant MicrobiomesGarciaComputational and Structural Biotechnology Journalhttps://doi.org/10.1016/j.csbj.2021.10.029
2021Colonization of Naive Roots from Populus tremula x alba Involves Successive Waves of Fungi and Bacteria with Different Trophic AbilitiesFracchiaApplied and Environmental Microbiologyhttps://doi.org/10.1128/AEM.02541-20
2021Microevolution in the Pansecondary Metabolome of Aspergillus flavus and Its Potential Macroevolutionary Implications for Filamentous FungiDrottProceedings of the National Academy of Sciences, USAhttps://doi.org/10.1073/pnas.2021683118
2021Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic FactorsDovemSpherettps://doi.org/10.1128/mSphere.01316-20
2021Fire Alters Plant Microbiome Assembly Patterns: Integrating the Plant and Soil Microbial Response to DisturbanceDoveNew Phytologisthttps://doi.org/10.1111/nph.17248
2021Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-Based Cell-Free SystemsDinglasanJournal of Visualized Experimentshttps://doi.org/10.3791/62852
2021Role of Reactive Oxygen Species and Hormones in Plant Responses to Temperature ChangesDevireddyInternational Journal of Molecular Scienceshttps://doi.org/10.3390/ijms22168843
2021Cryptic Genetic Structure and Copy-Number Variation in the Ubiquitous Forest Symbiotic Fungus Cenococcum geophilumDauphinEnvironmental Microbiologyhttps://doi.org/10.1111/1462-2920.15752
2021Plant-Microbe Interactions: From Genes to Ecosystems Using as a Model SystemCreggerPhytobiomes Journalhttps://doi.org/10.1094/Pbiomes-01-20-0009-Fi
2021Cultivating the Bacterial Microbiota of Populus RootsCarpermSystemshttps://doi.org/10.1128/mSystems.01306-20
2021Identification of a Diguanylate Cyclase Expressed in the Presence of Plants and Its Application for Discovering Candidate Gene Products Involved in Plant Colonization by Pantoea sp. YR343BiblePLoS Onehttps://doi.org/10.1371/journal.pone.0248607
2020Insight into a Highly Polymorphic Endophyte Isolated from the Roots of the Halophytic Seepweed Suaeda salsa: Laburnicola rhizohalophila sp. nov. (Didymosphaeriaceae, Pleosporales)YuanFungal Biologyhttps://doi.org/10.1016/j.funbio.2019.10.001
2020Transcriptional Regulation of Drought Response in Arabidopsis and Woody PlantsYaoFrontiers in Plant Sciencehttps://doi.org/10.3389/fpls.2020.572137
2020Plant Biosystems Design Research Roadmap 1.0YangBioDesign Researchhttps://doi.org/10.34133/2020/8051764
2020Arabidopsis C-Terminal Binding Protein ANGUSTIFOLIA Modulates Transcriptional Co-Regulation of MYB46 and WRKY33XieNew Phytologisthttps://doi.org/10.1111/nph.16826
2020A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe InteractionsVillalobos SolisMolecular Plant-Microbe Interactionhttps://doi.org/10.1094/MPMI-04-20-0082-TA
2020A Carotenoid-Deficient Mutant of the Plant-Associated Microbe Pantoea sp. YR343 Displays an Altered Membrane ProteomeVijaya KumarScientific Reportshttps://doi.org/10.1038/s41598-020-71672-w
2020Plant Hosts Modify Belowground Microbial Community Response to Extreme DroughtVeachmSystemshttps://doi.org/10.1128/mSystems.00092-20
2020Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell SurfaceSunFrontiers in Plant Sciencehttps://doi.org/10.3389/fpls.2020.596301
2020Can Exascale Computing and Explainable Artificial Intelligence Applied to Plant Biology Deliver on the United Nations Sustainable Development Goals?StreichCurrent Opinion in Biotechnologyhttps://doi.org/10.1016/j.copbio.2020.01.010
2020Outbreak of Septoria Canker Caused by Sphaerulina musiva on Populus trichocarpa in Eastern OregonSondreliPlant Diseasehttps://doi.org/10.1094/Pdis-03-20-0494-Pdn
2020Host Plant Genetic Control of Associated Fungal and Insect Species in a Populus Hybrid CrossSimonEcology and Evolutionhttps://doi.org/10.1002/ece3.6266
2020Isolation, Characterization, and Pathogenicity of Two Pseudomonas syringae Pathovars from Populus trichocarpa SeedsSaint-VincentMicroorganismshttps://doi.org/10.3390/microorganisms8081137
2020Lipo-Chitooligosaccharides as Regulatory Signals of Fungal Growth and DevelopmentRushNature Communicationshttps://doi.org/10.1038/s41467-020-17615-5
2020Complete Genome Sequence of Starkeya sp. Strain ORNL1, a Soil Alphaproteobacterium Isolated from the Rhizosphere of Populus deltoidesPodar Microbiology Resource Announcementshttps://doi.org/10.1128/MRA.00644-20
2020Complete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides RhizospherePodarMicrobiology Resource Announcementshttps://doi.org/10.1128/MRA.00617-20
2020Mycorrhizal Effector PaMISSP10b Alters Polyamine Biosynthesis in Eucalyptus Root Cells and Promotes Root ColonizationPlettNew Phytologisthttps://doi.org/10.1111/nph.16759
2020Draft Genome Sequence of Larkinella sp. Strain Bk230, Isolated from Populus deltoides RootsPelletierMicrobiology Resource Announcementshttps://doi.org/10.1128/MRA.00159-20
2020Regional Differences in the Structure of Juglans nigra Phytobiome Reflect Geographical Differences in Thousand Cankers Disease SeverityOnufrakPhytobiomes Journalhttps://doi.org/10.1094/Pbiomes-05-20-0044-R
2020A Nitrogenase-Like Enzyme System Catalyzes Methionine, Ethylene, and Methane BiogenesisNorthSciencehttps://doi.org/10.1126/science.abb6310
2020Ectomycorrhizal Fungal Diversity Interacts with Soil Nutrients to Predict Plant Growth Despite Weak Plant-Soil FeedbacksNashPlant and Soilhttps://doi.org/10.1007/s11104-020-04616-y
2020Targeted Growth Medium Dropouts Promote Aromatic Compound Synthesis in Crude E. coli Cell-Free SystemsMohrACS Synthetic Biologyhttps://doi.org/10.1021/acssynbio.9b00524
2020Large-Scale Genome Sequencing of Mycorrhizal Fungi Provides Insights into the Early Evolution of Symbiotic TraitsMiyauchiNature Communicationshttps://doi.org/10.1038/s41467-020-18795-w
2020Impacts of Soil Microbiome Variations on Root Colonization by Fungi and Bacteria and on the Metabolome of Populus tremula x albaMangeot-PeterPhytobiomes Journalhttps://doi.org/10.1094/Pbiomes-08-19-0042-R
2020Reconfiguring Plant Metabolism for Biodegradable Plastic ProductionLuBioDesign Researchhttps://doi.org/10.34133/2020/9078303
2020Plasticity of Phymatotrichopsis omnivora Infection Strategies Is Dependent on Host and Nonhost Plant ResponsesKankanalaPlant, Cell & Environmenthttps://doi.org/10.1111/pce.13721
2020The Small Secreted Effector Protein MiSSP7.6 of Laccaria bicolor Is Required for the Establishment of Ectomycorrhizal SymbiosisKangEnvironmental Microbiologyhttps://doi.org/10.1111/1462-2920.14959
2020Plant Biosystems Design for a Carbon-Neutral BioeconomyKalluriFrontiers in Plant Sciencehttps://doi.org/10.34133/2020/7914051
2020Prime Editing Technology and Its Prospects for Future Applications in Plant Biology ResearchHassanBioDesign Researchhttps://doi.org/10.34133/2020/9350905
2020P Finder: Genomic and Metagenomic Annotation of RNase P RNA GeneEllisBMC Genomicshttps://doi.org/10.1186/s12864-020-6615-z
2020Microbiome Variation across Two Hemlock Species with Hemlock Woolly Adelgid InfestationDoveFrontiers in Microbiologyhttps://doi.org/10.3389/fmicb.2020.01528
2020The Mutualism Effector MiSSP7 of Laccaria bicolor Alters the Interactions between the Poplar JAZ6 Protein and Its Associated ProteinsDaguerreScientific Reportshttps://doi.org/10.1038/s41598-020-76832-6
2020Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillusCasarrubiaFrontiers in Microbiologyhttps://doi.org/10.3389/fmicb.2020.00341
2020Draft Genome Sequence of Tumebacillus sp. Strain Bk434, Isolated from the Roots of Eastern CottonwoodCarperMicrobiology Resource Announcementshttps://doi.org/10.1128/MRA.00351-20
2020DISCo-Microbe: Design of an Identifiable Synthetic Community of MicrobesCarperPeerJhttps://doi.org/10.7717/peerj.8534
2020In Situ Chemical Monitoring and Imaging of Contents within Microfluidic Devices Having a Porous Membrane Wall Using Liquid Microjunction Surface Sampling Probe Mass SpectrometryCahillJournal of the American Society for Mass Spectrometryhttps://doi.org/10.1021/jasms.9b00093
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2015Evolving Insights to Understanding MycorrhizasDickieNew Phytologisthttps://doi.org/10.1111/nph.13290
2015Phosphorylation of RACK1 in PlantsChenPlant Signaling & Behaviorhttps://doi.org/10.1080/15592324.2015.1022013
2015Arabidopsis AZI1 Family Proteins Mediate Signal Mobilization for Systemic Defence PrimingCecchiniNature Communicationshttps://doi.org/10.1038/ncomms8658
2015ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in ArabidopsisCecchiniMolecular Plant-Microbe Interactionshttps://doi.org/10.1094/MPMI-06-14-0187-R
2014Single Cell Swimming Dynamics of Listeria monocytogenes Using a Nanoporous Microfluidic PlatformWrightLab Chiphttps://doi.org/10.1039/c3lc51138c
2014MIDAS: A Database-Searching Algorithm for Metabolite Identification in MetabolomicsWangAnalytical Chemistryhttps://doi.org/10.1021/ac5014783
2014Genomic and Transcriptomic Analysis of Laccaria bicolor CAZome Reveals Insights into Polysaccharides Remodelling during Symbiosis EstablishmentVeneault-FourreyFungal Genetics and Biologyhttps://doi.org/10.1016/j.fgb.2014.08.007
2014Evaluation and Validation of De Novo and Hybrid Assembly Techniques to Derive High-Quality Genome SequencesUtturkarBioinformaticshttps://doi.org/10.1093/bioinformatics/btu391
2014Populus trichocarpa and Populus deltoides Exhibit Different Metabolomic Responses to Colonization by the Symbiotic Fungus Laccaria bicolorTschaplinskiMolecular Plant-Microbe Interactionshttps://doi.org/10.1094/MPMI-09-13-0286-R
2014Ethylene and Jasmonic Acid Act as Negative Modulators during Mutualistic Symbiosis between Laccaria bicolor and Populus RootsPlettNew Phytologisthttps://doi.org/10.1111/nph.12655
2014Effector MiSSP7 of the Mutualistic Fungus Laccaria bicolor Stabilizes the Populus JAZ6 Protein and Represses Jasmonic Acid (JA) Responsive GenesPlettProceedings of the National Academy of Sciences, USAhttps://doi.org/10.1073/pnas.1322671111
2014Transgenic American Chestnuts Show Enhanced Blight Resistance and Transmit the Trait to T1 ProgenyNewhousePlant Sciencehttps://doi.org/10.1016/j.plantsci.2014.04.004
2014Strigolactone-Regulated Proteins Revealed by ITRAQ-Based Quantitative Proteomics in ArabidopsisLiJournal of Proteome Researchhttps://doi.org/10.1021/pr400925t
2014Quality Scores for 32,000 GenomeLandStandards in Genomic Scienceshttps://doi.org/10.1186/1944-3277-9-20
2014Newly Identified Helper Bacteria Stimulate Ectomycorrhizal Formation in PopulusLabbeFrontiers in Plant Sciencehttps://doi.org/10.3389/fpls.2014.00579
2014Fungal Biology: Compiling Genomes and Exploiting ThemLabbeNew Phytologisthttps://doi.org/10.1111/nph.12891
2014Expanding Genomics of Mycorrhizal SymbiosisKuoFrontiers in Microbiologyhttps://doi.org/10.3389/fmicb.2014.00582
2014Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions between Bacteria and PlantsKarpinetsMolecular Plant-Microbe Interactionshttps://doi.org/10.1094/MPMI-12-13-0368-R
2014Selective Herbivory by an Invasive Cyprinid, the Rudd Scardinius erythrophthalmusKapuscinskiFreshwater Biologyhttps://doi.org/10.1111/fwb.12433
2014Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8DeveauGenome Announcementshttps://doi.org/10.1128/genomeA.01152-13
2014Characterization of MORE AXILLARY GROWTH Genes in PopulusCzarneckiPLoS Onehttps://doi.org/10.1371/journal.pone.0102757
2014Comparison of Single-Molecule Sequencing and Hybrid Approaches for Finishing the Genome of Clostridium autoethanogenum and Analysis of CRISPR Systems in Industrial Relevant ClostridiaBrownBiotechnology for Biofuelshttps://doi.org/10.1186/1754-6834-7-40
2014Plant Host and Soil Origin Influence Fungal and Bacterial Assemblages in the Roots of Woody PlantsBonitoMolecular Ecologyhttps://doi.org/10.1111/mec.12821
2013Evolutionary Analyses of Non-Family Genes in PlantsYePlant Journalhttps://doi.org/10.1111/tpj.12073
2013Sipros/ProRata: A Versatile Informatics System for Quantitative Community ProteomicsWangBioinformaticshttps://doi.org/10.1093/bioinformatics/btt329
2013Heterotrimeric G Protein Signalling in the Plant KingdomUranoOpen Biologyhttps://doi.org/10.1098/rsob.120186
2013Microbe-Independent Entry of Oomycete RxLR Effectors and Fungal RxLR-Like Effectors into Plant and Animal Cells Is Specific and ReproducibleTylerMolecular Plant-Microbe Interactionshttps://doi.org/10.1094/MPMI-02-13-0051-IA
2013Identification, Characterization of an AP2/ERF Transcription Factor That Promotes Adventitious, Lateral Root Formation in PopulusTrupianoPlantahttps://doi.org/10.1007/s00425-013-1890-4
2013Genome of an Arbuscular Mycorrhizal Fungus Provides Insight into the Oldest Plant SymbiosisTisserantProceedings of the National Academy of Sciences, USAhttps://doi.org/10.1073/pnas.1313452110
2013Involvement of Auxin Pathways in Modulating Root Architecture during Beneficial Plant-Microorganism InteractionsSukumarPlant, Cell & Environmenthttps://doi.org/10.1111/pce.12036
2013Comparative Metagenomic and rRNA Microbial Diversity Characterization Using Archaeal and Bacterial Synthetic CommunitiesShakyaEnvironmental Microbiologyhttps://doi.org/10.1111/1462-2920.12086
2013A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides TreesShakyaPLoS Onehttps://doi.org/10.1371/journal.pone.0076382
2013Mycorrhizas and New Phytologist: Une Vraie Histoire D'AmourSelosseNew Phytologisthttps://doi.org/10.1111/nph.12545
2013LuxR- and LuxI-Type Quorum-Sensing Circuits Are Prevalent in Members of the Populus deltoides MicrobiomeSchaeferApplied and Environmental Microbiologyhttps://doi.org/10.1128/AEM.01417-13
2013Inside Arbuscular Mycorrhizal Roots-Molecular Probes to Understand the SymbiosisRuzickaPlant Genomehttps://doi.org/10.3835/plantgenome2012.06.0007
2013Temperature-Dependent Shade Avoidance Involves the Receptor-Like Kinase ERECTAPatelThe Plant Journalhttps://doi.org/10.1111/tpj.12088
2013Genome Anchored QTLs for Biomass Productivity in Hybrid Populus Grown under Contrasting EnvironmentsMucheroPLoS Onehttps://doi.org/10.1371/journal.pone.0054468
2013Lectin-Functionalized Poly(Glycidyl Methacrylate)-Block-Poly(Vinyldimethyl Azlactone) Surface Scaffolds for High Avidity Microbial CaptureHansenBiomacromoleculeshttps://doi.org/10.1021/bm4011358
2013New North American Truffles (Tuber spp.) and Their Ectomycorrhizal AssociationsGuevara Mycologiahttps://doi.org/10.3852/12-087
2013A Dual Role of Strigolactones in Phosphate Acquisition and Utilization in PlantsCzarneckiInternational Journal of Molecular Medicinehttps://doi.org/10.3390/ijms14047681
2013Leaf Endophytes and Populus Genotype Affect Severity of Damage from the Necrotrophic Leaf Pathogen, Drepanopeziza populiBusbyEcospherehttps://doi.org/10.1890/Es13-00127.1
2012Pseudomonas fluorescens Induces Strain-Dependent and Strain-Independent Host Plant Responses in Defense Networks, Primary Metabolism, Photosynthesis, and FitnessWestonMolecular Plant-Microbe Interactionshttps://doi.org/10.1094/MPMI-09-11-0253
2012Secretome of the Free-Living Mycelium from the Ectomycorrhizal Basidiomycete Laccaria bicolorVincentJournal of Proteome Researchhttps://doi.org/10.1021/pr200895f
2012The Transcriptome of the Arbuscular Mycorrhizal Fungus Glomus intraradices (Daom 197198) Reveals Functional Tradeoffs in an Obligate SymbiontTisserantNew Phytologisthttps://doi.org/10.1111/j.1469-8137.2011.03948.x
2012The M. truncatula SUNN Gene Is Expressed in Vascular Tissue, Similarly to RDN1, Consistent with the Role of These Nodulation Regulation Genes in Long Distance SignalingSchnabelPlant Signaling & Behaviorhttps://doi.org/10.4161/psb.7.1.18491
2012Poplar Root Exudates Contain Compounds That Induce the Expression of MiSSP7 in Laccaria bicolorPlettPlant Signaling & Behaviorhttps://doi.org/10.4161/psb.7.1.18357
2012Phylogenetic, Genomic Organization and Expression Analysis of Hydrophobin Genes in the Ectomycorrhizal Basidiomycete Laccaria bicolorPlettFungal Genetics and Biologyhttps://doi.org/10.1016/j.fgb.2012.01.002
2012Enhancing a Pathway-Genome Database (PGDB) to Capture Subcellular Localization of Metabolites and Enzymes: The Nucleotide-Sugar Biosynthetic Pathways of Populus trichocarpaNagDatabasehttps://doi.org/10.1093/database/bas013
2012Monodisperse Alginate Microgel Formation in a Three-Dimensional Microfluidic Droplet GeneratorLianBiomicrofluidicshttps://doi.org/10.1063/1.4765337
2012Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap VelosLiJournal of Proteome Researchhttps://doi.org/10.1021/pr200748h
2012Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators Crp and ArcaLeuzeGene Regulation and Systems Biologyhttps://doi.org/10.4137/GRSB.S9357
2012Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolorLabbePLoS Onehttps://doi.org/10.1371/journal.pone.0040197
2012Initial Characterization of Shade Avoidance Response Suggests Functional Diversity between Populus Phytochrome B GenesKarveNew Phytologist.https://doi.org/10.1111/j.1469-8137.2012.04288.x
2012Analyzing Large Biological Datasets with Association NetworksKarpinetsNucleic Acids Researchhttps://doi.org/10.1093/nar/gks403
2012The Importance of Individuals: Intraspecific Diversity of Mycorrhizal Plants and Fungi in EcosystemsJohnsonNew Phytologisthttps://doi.org/10.1111/j.1469-8137.2012.04087.x
2012Gene and Translation Initiation Site Prediction in Metagenomic SequencesHyattBioinformaticshttps://doi.org/10.1093/bioinformatics/bts429
2012Photoautotrophic Symbiont and Geography Are Major Factors Affecting Highly Structured and Diverse Bacterial Communities in the Lichen MicrobiomeHodkinsonEnvironmental Microbiologyhttps://doi.org/10.1111/j.1462-2920.2011.02560.x
2012Highly Efficient Isolation of Populus Mesophyll Protoplasts and Its Application in Transient Expression AssaysGuoPLoS Onehttps://doi.org/10.1371/journal.pone.0044908
2012Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides.BrownJournal of Bacteriologyhttps://doi.org/10.1128/JB.01243-12
2012Draft Genome Sequence of Rhizobium sp. Strain Pdo1-076, a Bacterium Isolated from Populus deltoides.BrownJournal of Bacteriologyhttps://doi.org/10.1128/JB.00198-12
2011Genomic Aspects of Research Involving Polyploid PlantsYangPlant Cell Tissue and Organ Culturehttps://doi.org/10.1007/s11240-010-9826-1
2011Discovery and Annotation of Small Proteins Using Genomics, Proteomics, and Computational ApproachesYangGenome Researchhttps://doi.org/10.1101/gr.109280.110
2011Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial EnvironmentsWisniewski-DyePLoS Geneticshttps://doi.org/10.1371/journal.pgen.1002430
2011Comparative Physiology and Transcriptional Networks Underlying the Heat Shock Response in Populus trichocarpa, Arabidopsis thaliana and Glycine maxWestonPlant, Cell and Environmenthttps://doi.org/10.1111/j.1365-3040.2011.02347.x
2011Mutualistic Interactions on a Knife-Edge between Saprotrophy and PathogenesisVeneault-FourreyCurrent Opinion in Plant Biologyhttps://doi.org/10.1016/j.pbi.2011.03.022
2011Lifestyle Lessons from Ectomycorrhizal Fungal GenomesPlettTrends in Geneticshttps://doi.org/10.1016/j.tig.2010.10.005
2011Measuring Dissociation Rate Constants of Protein Complexes through Subunit Exchange: Experimental Design and Theoretical ModelingPanPLoS Onehttps://doi.org/10.1371/journal.pone.0028827
2011Sequencing the Fungal Tree of LifeMartinNew Phytologisthttps://doi.org/10.1111/j.1469-8137.2011.03688.x
2011Structure and Expression Profile of the Phosphate Pht1 Transporter Gene Family in Mycorrhizal Populus trichocarpaLoth-PeredaPlant Physiologyhttps://doi.org/10.1104/pp.111.180646
2011Survey and Analysis of Simple Sequence Repeats in the Laccaria bicolor Genome, with Development of Microsatellite MarkersLabbeCurrent Geneticshttps://doi.org/10.1007/s00294-010-0328-9
2011Identification of Quantitative Trait Loci Affecting Ectomycorrhizal Symbiosis in an Interspecific F1 Poplar Cross and Differential Expression of Genes in Ectomycorrhizas of the Two Parents: Populus deltoides and Populus trichocarpaLabbeTree Genetics & Genomeshttps://doi.org/10.1007/s11295-010-0361-3
2011Abscisic Acid Receptors: Past, Present and FutureGuoJournal of Integrative Plant Biologyhttps://doi.org/10.1111/j.1744-7909.2011.01044.x
2011Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil TypesGottelApplied and Environmental Microbiologyhttps://doi.org/10.1128/AEM.05255-11
2011Characterization of Cell Surface and Extracellular Matrix Remodeling of Azospirillum brasilense Chemotaxis-Like 1 Signal Transduction Pathway Mutants by Atomic Force MicroscopyEdwardsFEMS Microbiology Lettershttps://doi.org/10.1111/j.1574-6968.2010.02156.x
2011Bacterial immobilization for imaging by Atomic Force MicroscopyAllisonJournal of Visualized Experimentshttps://doi.org/10.3791/2880
2010Apoplast Proteome Reveals That Extracellular Matrix Contributes to Multistress Response in PoplarPechanovaBMC Genomicshttps://doi.org/10.1186/1471-2164-11-674
2010CAZymes Analysis Toolkit (CAT): Web Service for Searching and Analyzing Carbohydrate-Active Enzymes in a Newly Sequenced Organism Using CAZy DatabaseParkGlycobiologyhttps://doi.org/10.1093/glycob/cwq106
2010Biosynthesis and Emission of Insect-Induced Methyl Salicylate and Methyl Benzoate from RiceZhaoPlant Physiology and Biochemistryhttps://doi.org/10.1016/j.plaphy.2010.01.023
2010Shewanella Knowledgebase: Integration of the Experimental Data and Computational Predictions Suggests a Biological Role for Transcription of Intergenic RegionsKarpinetsDatabasehttps://doi.org/10.1093/database/baq012