Publications

Year	Title	First Author	Journal	DOI
2015	Sphagnum Physiology in the Context of Changing Climate: Emergent Influences of Genomics, Modelling and Host-Microbiome Interactions on Understanding Ecosystem Function	Weston	Plant, Cell & Environment	https://doi.org/10.1111/pce.12458
2015	3-Way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics	Weighill	PLoS Computational Biology	https://doi.org/10.1371/journal.pcbi.1004079
2015	The Small Ethylene Response Factor Erf96 Is Involved in the Regulation of the Abscisic Acid Response in Arabidopsis	Wang	Frontiers in Plant Science	https://doi.org/10.3389/fpls.2015.01064
2015	Development of the Poplar-Laccaria bicolor Ectomycorrhiza Modifies Root Auxin Metabolism, Signaling, and Response	Vayssieres	Plant Physiology	ttps://doi.org/10.1104/pp.114.255620
2015	Mycorrhizal Ecology and Evolution: The Past, the Present, and the Future	van der Heijden	New Phytologist	https://doi.org/10.1111/nph.13288
2015	Sequence Data for Clostridium autoethanogenum Using Three Generations of Sequencing Technologies	Utturkar	Scientific Data	https://doi.org/10.1038/sdata.2015.14
2015	Microstencils to Generate Defined, Multi-Species Patterns of Bacteria	Timm	Biomicrofluidics	https://doi.org/10.1063/1.4935938
2015	Metabolic Functions of Pseudomonas fluorescensPopulus deltoides Depend on Rhizosphere or Endosphere Isolation Compartment	Timm	Frontiers in Microbiology	https://doi.org/10.3389/fmicb.2015.01118
2015	Functional Guild Classification Predicts the Enzymatic Role of Fungi in Litter and Soil Biogeochemistry	Talbot	Soil Biology and Biochemistry	https://doi.org/10.1016/j.soilbio.2015.05.006
2015	Computational Ranking of Yerba Mate Small Molecules Based on Their Predicted Contribution to Antibacterial Activity against Methicillin-Resistant Staphylococcus aureus	Rempe	PLoS One	https://doi.org/10.1371/journal.pone.0123925
2015	Metagenome Sequence of Elaphomyces granulatus from Sporocarp Tissue Reveals Ascomycota Ectomycorrhizal Fingerprints of Genome Expansion and a Proteobacteria-Rich Microbiome	Quandt	Environmental Microbiology	https://doi.org/10.1111/1462-2920.12840
2015	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	Plett	Molecular Plant-Microbe Interactions	https://doi.org/10.1094/MPMI-05-14-0129-FI
2015	Reconsidering Mutualistic Plant-Fungal Interactions through the Lens of Effector Biology	Plett	Current Opinion in Plant Biology	https://doi.org/10.1016/j.pbi.2015.06.001
2015	Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins	Pellegrin	Frontiers in Microbiology	https://doi.org/10.3389/fmicb.2015.01278
2015	High-Resolution Genetic Mapping of Allelic Variants Associated with Cell Wall Chemistry in Populus	Muchero	BMC Genomics	https://doi.org/10.1186/s12864-015-1215-z
2015	Insights from 20 Years of Bacterial Genome Sequencing	Land	Functional & Integrative Genomics	https://doi.org/10.1007/s10142-015-0433-4
2015	Prospects and Challenges for Fungal Metatranscriptomics of Complex Communities	Kuske	Fungal Ecology	https://doi.org/10.1016/j.funeco.2014.12.005
2015	Convergent Losses of Decay Mechanisms and Rapid Turnover of Symbiosis Genes in Mycorrhizal Mutualists	Kohler	Nature Genetics	https://doi.org/10.1038/ng.3223
2015	Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere	Klingeman	Genome Announcements	https://doi.org/10.1128/genomeA.01344-15
2015	PanFP: Pangenome-Based Functional Profiles for Microbial Communities	Jun	BMC Research Notes	https://doi.org/10.1186/s13104-015-1462-8
2015	Towards a Holistic Understanding of the Beneficial Interactions across the Populus Microbiome	Hacquard	New Phytologist	https://doi.org/10.1111/nph.13133
2015	Comparative Genomics, Proteomics and Transcriptomics Give New Insight into the Exoproteome of the Basidiomycete Hebeloma cylindrosporum and Its Involvement in Ectomycorrhizal Symbiosis	Dore	New Phytologist	https://doi.org/10.1111/nph.13546
2015	Evolving Insights to Understanding Mycorrhizas	Dickie	New Phytologist	https://doi.org/10.1111/nph.13290
2015	Phosphorylation of RACK1 in Plants	Chen	Plant Signaling & Behavior	https://doi.org/10.1080/15592324.2015.1022013
2015	Arabidopsis AZI1 Family Proteins Mediate Signal Mobilization for Systemic Defence Priming	Cecchini	Nature Communications	https://doi.org/10.1038/ncomms8658
2015	ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in Arabidopsis	Cecchini	Molecular Plant-Microbe Interactions	https://doi.org/10.1094/MPMI-06-14-0187-R
2014	Single Cell Swimming Dynamics of Listeria monocytogenes Using a Nanoporous Microfluidic Platform	Wright	Lab Chip	https://doi.org/10.1039/c3lc51138c
2014	MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics	Wang	Analytical Chemistry	https://doi.org/10.1021/ac5014783
2014	Genomic and Transcriptomic Analysis of Laccaria bicolor CAZome Reveals Insights into Polysaccharides Remodelling during Symbiosis Establishment	Veneault-Fourrey	Fungal Genetics and Biology	https://doi.org/10.1016/j.fgb.2014.08.007
2014	Evaluation and Validation of De Novo and Hybrid Assembly Techniques to Derive High-Quality Genome Sequences	Utturkar	Bioinformatics	https://doi.org/10.1093/bioinformatics/btu391
2014	Populus trichocarpa and Populus deltoides Exhibit Different Metabolomic Responses to Colonization by the Symbiotic Fungus Laccaria bicolor	Tschaplinski	Molecular Plant-Microbe Interactions	https://doi.org/10.1094/MPMI-09-13-0286-R
2014	Extensive Sampling of Basidiomycete Genomes Demonstrates Inadequacy of the White-Rot/Brown-Rot Paradigm for Wood Decay Fungi	Riley	Proceedings of the National Academy of Sciences, USA	https://doi.org/10.1073/pnas.1400592111
2014	Extreme Diversification of the Mating Type-High-Mobility Group (MATA-HMG) Gene Family in a Plant-Associated Arbuscular Mycorrhizal Fungus	Riley	New Phytologist	https://doi.org/10.1111/nph.12462
2014	Ethylene and Jasmonic Acid Act as Negative Modulators during Mutualistic Symbiosis between Laccaria bicolor and Populus Roots	Plett	New Phytologist	https://doi.org/10.1111/nph.12655
2014	Effector MiSSP7 of the Mutualistic Fungus Laccaria bicolor Stabilizes the Populus JAZ6 Protein and Represses Jasmonic Acid (JA) Responsive Genes	Plett	Proceedings of the National Academy of Sciences, USA	https://doi.org/10.1073/pnas.1322671111
2014	Duplications and Losses in Gene Families of Rust Pathogens Highlight Putative Effectors	Pendleton	Frontiers in Plant Science	https://doi.org/10.3389/fpls.2014.00299
2014	Transgenic American Chestnuts Show Enhanced Blight Resistance and Transmit the Trait to T1 Progeny	Newhouse	Plant Science	https://doi.org/10.1016/j.plantsci.2014.04.004
2014	Latent Homology and Convergent Regulatory Evolution Underlies the Repeated Emergence of Yeasts	Nagy	Nature Communications	https://doi.org/10.1038/ncomms5471
2014	Strigolactone-Regulated Proteins Revealed by ITRAQ-Based Quantitative Proteomics in Arabidopsis	Li	Journal of Proteome Research	https://doi.org/10.1021/pr400925t
2014	Quality Scores for 32,000 Genome	Land	Standards in Genomic Sciences	https://doi.org/10.1186/1944-3277-9-20
2014	Newly Identified Helper Bacteria Stimulate Ectomycorrhizal Formation in Populus	Labbe	Frontiers in Plant Science	https://doi.org/10.3389/fpls.2014.00579
2014	Fungal Biology: Compiling Genomes and Exploiting Them	Labbe	New Phytologist	https://doi.org/10.1111/nph.12891
2014	Expanding Genomics of Mycorrhizal Symbiosis	Kuo	Frontiers in Microbiology	https://doi.org/10.3389/fmicb.2014.00582
2014	Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions between Bacteria and Plants	Karpinets	Molecular Plant-Microbe Interactions	https://doi.org/10.1094/MPMI-12-13-0368-R
2014	Selective Herbivory by an Invasive Cyprinid, the Rudd Scardinius erythrophthalmus	Kapuscinski	Freshwater Biology	https://doi.org/10.1111/fwb.12433
2014	Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8	Deveau	Genome Announcements	https://doi.org/10.1128/genomeA.01152-13
2014	Characterization of MORE AXILLARY GROWTH Genes in Populus	Czarnecki	PLoS One	https://doi.org/10.1371/journal.pone.0102757
2014	Comparison of Single-Molecule Sequencing and Hybrid Approaches for Finishing the Genome of Clostridium autoethanogenum and Analysis of CRISPR Systems in Industrial Relevant Clostridia	Brown	Biotechnology for Biofuels	https://doi.org/10.1186/1754-6834-7-40
2014	Plant Host and Soil Origin Influence Fungal and Bacterial Assemblages in the Roots of Woody Plants	Bonito	Molecular Ecology	https://doi.org/10.1111/mec.12821
2013	Evolutionary Analyses of Non-Family Genes in Plants	Ye	Plant Journal	https://doi.org/10.1111/tpj.12073
2013	Sipros/ProRata: A Versatile Informatics System for Quantitative Community Proteomics	Wang	Bioinformatics	https://doi.org/10.1093/bioinformatics/btt329
2013	Heterotrimeric G Protein Signalling in the Plant Kingdom	Urano	Open Biology	https://doi.org/10.1098/rsob.120186
2013	Microbe-Independent Entry of Oomycete RxLR Effectors and Fungal RxLR-Like Effectors into Plant and Animal Cells Is Specific and Reproducible	Tyler	Molecular Plant-Microbe Interactions	https://doi.org/10.1094/MPMI-02-13-0051-IA
2013	Identification, Characterization of an AP2/ERF Transcription Factor That Promotes Adventitious, Lateral Root Formation in Populus	Trupiano	Planta	https://doi.org/10.1007/s00425-013-1890-4
2013	Genome of an Arbuscular Mycorrhizal Fungus Provides Insight into the Oldest Plant Symbiosis	Tisserant	Proceedings of the National Academy of Sciences, USA	https://doi.org/10.1073/pnas.1313452110
2013	Involvement of Auxin Pathways in Modulating Root Architecture during Beneficial Plant-Microorganism Interactions	Sukumar	Plant, Cell & Environment	https://doi.org/10.1111/pce.12036
2013	Comparative Metagenomic and rRNA Microbial Diversity Characterization Using Archaeal and Bacterial Synthetic Communities	Shakya	Environmental Microbiology	https://doi.org/10.1111/1462-2920.12086
2013	A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees	Shakya	PLoS One	https://doi.org/10.1371/journal.pone.0076382
2013	Mycorrhizas and New Phytologist: Une Vraie Histoire D'Amour	Selosse	New Phytologist	https://doi.org/10.1111/nph.12545
2013	LuxR- and LuxI-Type Quorum-Sensing Circuits Are Prevalent in Members of the Populus deltoides Microbiome	Schaefer	Applied and Environmental Microbiology	https://doi.org/10.1128/AEM.01417-13
2013	Inside Arbuscular Mycorrhizal Roots-Molecular Probes to Understand the Symbiosis	Ruzicka	Plant Genome	https://doi.org/10.3835/plantgenome2012.06.0007
2013	Carbohydrate Utilization and Metabolism Is Highly Differentiated in Agaricus bisporus	Patyshakuliyeva	BMC Genomics	https://doi.org/10.1186/1471-2164-14-663
2013	Temperature-Dependent Shade Avoidance Involves the Receptor-Like Kinase ERECTA	Patel	The Plant Journal	https://doi.org/10.1111/tpj.12088
2013	Genome Anchored QTLs for Biomass Productivity in Hybrid Populus Grown under Contrasting Environments	Muchero	PLoS One	https://doi.org/10.1371/journal.pone.0054468
2013	Lectin-Functionalized Poly(Glycidyl Methacrylate)-Block-Poly(Vinyldimethyl Azlactone) Surface Scaffolds for High Avidity Microbial Capture	Hansen	Biomacromolecules	https://doi.org/10.1021/bm4011358
2013	Laser Microdissection and Microarray Analysis of Tuber melanosporum Ectomycorrhizas Reveal Functional Heterogeneity between Mantle and Hartig Net Compartments	Hacquard	Environmental Microbiology	https://doi.org/10.1111/1462-2920.12080
2013	New North American Truffles (Tuber spp.) and Their Ectomycorrhizal Associations	Guevara	Mycologia	https://doi.org/10.3852/12-087
2013	A Dual Role of Strigolactones in Phosphate Acquisition and Utilization in Plants	Czarnecki	International Journal of Molecular Medicine	https://doi.org/10.3390/ijms14047681
2013	Leaf Endophytes and Populus Genotype Affect Severity of Damage from the Necrotrophic Leaf Pathogen, Drepanopeziza populi	Busby	Ecosphere	https://doi.org/10.1890/Es13-00127.1
2012	Pseudomonas fluorescens Induces Strain-Dependent and Strain-Independent Host Plant Responses in Defense Networks, Primary Metabolism, Photosynthesis, and Fitness	Weston	Molecular Plant-Microbe Interactions	https://doi.org/10.1094/MPMI-09-11-0253
2012	Secretome of the Free-Living Mycelium from the Ectomycorrhizal Basidiomycete Laccaria bicolor	Vincent	Journal of Proteome Research	https://doi.org/10.1021/pr200895f
2012	The Transcriptome of the Arbuscular Mycorrhizal Fungus Glomus intraradices (Daom 197198) Reveals Functional Tradeoffs in an Obligate Symbiont	Tisserant	New Phytologist	https://doi.org/10.1111/j.1469-8137.2011.03948.x
2012	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	Schnabel	Plant Signaling & Behavior	https://doi.org/10.4161/psb.7.1.18491
2012	The AINTEGUMENTA LIKE1 Homeotic Transcription Factor PtAIL1 Controls the Formation of Adventitious Root Primordia in Poplar	Rigal	Plant Physiology	https://doi.org/10.1104/pp.112.204453
2012	Poplar Root Exudates Contain Compounds That Induce the Expression of MiSSP7 in Laccaria bicolor	Plett	Plant Signaling & Behavior	https://doi.org/10.4161/psb.7.1.18357
2012	Phylogenetic, Genomic Organization and Expression Analysis of Hydrophobin Genes in the Ectomycorrhizal Basidiomycete Laccaria bicolor	Plett	Fungal Genetics and Biology	https://doi.org/10.1016/j.fgb.2012.01.002
2012	Enhancing a Pathway-Genome Database (PGDB) to Capture Subcellular Localization of Metabolites and Enzymes: The Nucleotide-Sugar Biosynthetic Pathways of Populus trichocarpa	Nag	Database	https://doi.org/10.1093/database/bas013
2012	Genome Sequence of the Button Mushroom Agaricus bisporus Reveals Mechanisms Governing Adaptation to a Humic-Rich Ecological Niche	Morin	Proceedings of the National Academy of Sciences, USA	https://doi.org/10.1073/pnas.1206847109
2012	Monodisperse Alginate Microgel Formation in a Three-Dimensional Microfluidic Droplet Generator	Lian	Biomicrofluidics	https://doi.org/10.1063/1.4765337
2012	Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos	Li	Journal of Proteome Research	https://doi.org/10.1021/pr200748h
2012	Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators Crp and Arca	Leuze	Gene Regulation and Systems Biology	https://doi.org/10.4137/GRSB.S9357
2012	Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor	Labbe	PLoS One	https://doi.org/10.1371/journal.pone.0040197
2012	Initial Characterization of Shade Avoidance Response Suggests Functional Diversity between Populus Phytochrome B Genes	Karve	New Phytologist.	https://doi.org/10.1111/j.1469-8137.2012.04288.x
2012	Analyzing Large Biological Datasets with Association Networks	Karpinets	Nucleic Acids Research	https://doi.org/10.1093/nar/gks403
2012	The Importance of Individuals: Intraspecific Diversity of Mycorrhizal Plants and Fungi in Ecosystems	Johnson	New Phytologist	https://doi.org/10.1111/j.1469-8137.2012.04087.x
2012	Gene and Translation Initiation Site Prediction in Metagenomic Sequences	Hyatt	Bioinformatics	https://doi.org/10.1093/bioinformatics/bts429
2012	Photoautotrophic Symbiont and Geography Are Major Factors Affecting Highly Structured and Diverse Bacterial Communities in the Lichen Microbiome	Hodkinson	Environmental Microbiology	https://doi.org/10.1111/j.1462-2920.2011.02560.x
2012	Highly Efficient Isolation of Populus Mesophyll Protoplasts and Its Application in Transient Expression Assays	Guo	PLoS One	https://doi.org/10.1371/journal.pone.0044908
2012	System-Wide Studies of N-Lysine Acetylation in Rhodopseudomonas palustris Reveal Substrate Specificity of Protein Acetyltransferases	Crosby	The Journal of Biological Chemistry	https://doi.org/10.1074/jbc.M112.352104
2012	Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides.	Brown	Journal of Bacteriology	https://doi.org/10.1128/JB.01243-12
2012	Draft Genome Sequence of Rhizobium sp. Strain Pdo1-076, a Bacterium Isolated from Populus deltoides.	Brown	Journal of Bacteriology	https://doi.org/10.1128/JB.00198-12
2011	Genomic Aspects of Research Involving Polyploid Plants	Yang	Plant Cell Tissue and Organ Culture	https://doi.org/10.1007/s11240-010-9826-1
2011	Discovery and Annotation of Small Proteins Using Genomics, Proteomics, and Computational Approaches	Yang	Genome Research	https://doi.org/10.1101/gr.109280.110
2011	Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments	Wisniewski-Dye	PLoS Genetics	https://doi.org/10.1371/journal.pgen.1002430
2011	Comparative Physiology and Transcriptional Networks Underlying the Heat Shock Response in Populus trichocarpa, Arabidopsis thaliana and Glycine max	Weston	Plant, Cell and Environment	https://doi.org/10.1111/j.1365-3040.2011.02347.x
2011	Mutualistic Interactions on a Knife-Edge between Saprotrophy and Pathogenesis	Veneault-Fourrey	Current Opinion in Plant Biology	https://doi.org/10.1016/j.pbi.2011.03.022
2011	Lifestyle Lessons from Ectomycorrhizal Fungal Genomes	Plett	Trends in Genetics	https://doi.org/10.1016/j.tig.2010.10.005
2011	A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development	Plett	Current Biology	https://doi.org/10.1016/j.cub.2011.05.033
2011	Measuring Dissociation Rate Constants of Protein Complexes through Subunit Exchange: Experimental Design and Theoretical Modeling	Pan	PLoS One	https://doi.org/10.1371/journal.pone.0028827
2011	Sequencing the Fungal Tree of Life	Martin	New Phytologist	https://doi.org/10.1111/j.1469-8137.2011.03688.x
2011	Structure and Expression Profile of the Phosphate Pht1 Transporter Gene Family in Mycorrhizal Populus trichocarpa	Loth-Pereda	Plant Physiology	https://doi.org/10.1104/pp.111.180646
2011	Survey and Analysis of Simple Sequence Repeats in the Laccaria bicolor Genome, with Development of Microsatellite Markers	Labbe	Current Genetics	https://doi.org/10.1007/s00294-010-0328-9
2011	Identification 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 trichocarpa	Labbe	Tree Genetics & Genomes	https://doi.org/10.1007/s11295-010-0361-3
2011	Abscisic Acid Receptors: Past, Present and Future	Guo	Journal of Integrative Plant Biology	https://doi.org/10.1111/j.1744-7909.2011.01044.x
2011	Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types	Gottel	Applied and Environmental Microbiology	https://doi.org/10.1128/AEM.05255-11
2011	Characterization of Cell Surface and Extracellular Matrix Remodeling of Azospirillum brasilense Chemotaxis-Like 1 Signal Transduction Pathway Mutants by Atomic Force Microscopy	Edwards	FEMS Microbiology Letters	https://doi.org/10.1111/j.1574-6968.2010.02156.x
2011	Bacterial immobilization for imaging by Atomic Force Microscopy	Allison	Journal of Visualized Experiments	https://doi.org/10.3791/2880
2010	Apoplast Proteome Reveals That Extracellular Matrix Contributes to Multistress Response in Poplar	Pechanova	BMC Genomics	https://doi.org/10.1186/1471-2164-11-674
2010	CAZymes Analysis Toolkit (CAT): Web Service for Searching and Analyzing Carbohydrate-Active Enzymes in a Newly Sequenced Organism Using CAZy Database	Park	Glycobiology	https://doi.org/10.1093/glycob/cwq106
2010	Biosynthesis and Emission of Insect-Induced Methyl Salicylate and Methyl Benzoate from Rice	Zhao	Plant Physiology and Biochemistry	https://doi.org/10.1016/j.plaphy.2010.01.023
2010	Shewanella Knowledgebase: Integration of the Experimental Data and Computational Predictions Suggests a Biological Role for Transcription of Intergenic Regions	Karpinets	Database	https://doi.org/10.1093/database/baq012