2022
(2022) Bioenergy sorghum’s deep roots: A key to sustainable biomass production on annual cropland.
GCB Bioenergy 14(2), 132-156.
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2021
(2021) Genomic variation within the maize stiff-stalk heterotic germplasm pool.
Plant Genome .
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(2021) Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar.
Phytobiomes Journal .
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(2021) Gene-rich UV sex chromosomes harbor conserved regulators of sexual development.
Science Advances 7(27).
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(2021) Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism.
The ISME Journal: Multidisciplinary Journal of Microbial Ecology , 1-12.
10.1038/s41396-021-01136-0
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(2021) Plant single-cell solutions for energy and the environment.
Communications Biology 4(1).
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(2021) Gamete expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha.
eLife 10, e57088.
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(2021) The contributions from the progenitor genomes of the mesopolyploid brassiceae are evolutionarily distinct but functionally compatible.
Genome Research 31(5), 799-810.
10.1101/GR.270033.120
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(2021) Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae.
Journal of Integrative Plant Biology n/a(n/a).
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(2021) Pests, diseases, and aridity have shaped the genome of Corymbia citriodora.
Communications Biology 4(1).
10.1038/s42003-021-02009-0
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(2021) Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat.
Frontiers in Plant Science 12.
10.3389/fpls.2021.657796
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(2021) Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae).
Frontiers in Plant Science 11, 16.
10.3389/fpls.2020.573767
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(2021) Integrative genomics reveals paths to sex dimorphism in Salix purpurea L.
Horticulture Research 8(1).
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(2021) Vision, challenges and opportunities for a plant cell atlas.
eLife 10.
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(2021) Plant Pan-Genomics Comes of Age.
Annual Review of Plant Biology 72, 411-435.
10.1146/annurev-arplant-080720-105454
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(2021) Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping.
Plant Genome .
10.1002/tpg2.20110
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(2021) Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding.
Nature Communications 12(1).
10.1038/s41467-021-24328-w
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(2021) Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.
Nature , 23.
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(2021) Current status and impending progress for cassava structural genomics.
Plant Molecular Biology , 15.
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(2021) Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass) [version 1; peer review: 1 approved].
F1000Research 10(289).
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(2021) Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus.
Molecular Biology and Evolution .
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(2021) KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular‐mycorrhizal symbiosis in Brachypodium distachyon.
The Plant Journal .
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(2021) Cytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.).
Plant Journal .
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(2021) Three founding ancestral genomes involved in the origin of sugarcane.
Annals of Botany 127(6), 827-840.
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(2021) Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting.
Proceedings of the National Academy of Sciences of the United States of America 118(29).
10.1073/pnas.2104445118
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(2021) BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon.
BMC Plant Biology 21(1).
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(2021) Tracking the Ancestry of Known and ‘Ghost’ Homeologous Subgenomes in Model Grass Brachypodium Polyploids.
The Plant Journal .
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(2021) Cell Wall Compositions of Sorghum bicolor Leaves and Roots Remain Relatively Constant Under Drought Conditions.
Frontiers in Plant Science 12, 747225.
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(2021) Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome.
Phytobiomes Journal 5(2).
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(2021) Diversification of mandarin citrus by hybrid speciation and apomixis.
Nature Communications 12.
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(2021) The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa.
Genome Biology and Evolution 13(9).
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(2021) Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers.
Journal of visualized experiments : JoVE (169).
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2020
(2020) Natural Variation in Lignin and Pectin Biosynthesis-Related Genes in Switchgrass (Panicum virgatum L.) and Association of SNP Variants with Dry Matter Traits.
Bioenergy Research 13(1), 79-99.
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(2020) The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum.
Plant J .
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(2020) Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor.
G3 (Bethesda) 10(5), 1511-1520.
10.1534/g3.119.400921
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(2020) Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus.
Front Microbiol 11, 341.
10.3389/fmicb.2020.00341
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(2020) Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.
Nat Genet 52(5), 525-533.
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(2020) Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9.
Nat Commun 11(1), 1178.
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(2020) Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics.
Nat Commun 11(1), 34.
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(2020) Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors.
Nat Commun 11(1), 3670.
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(2020) A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa.
Genome Biol 21(1), 259.
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(2020) Single-parent expression drives dynamic gene expression complementation in maize hybrids.
Plant J .
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(2020) Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation.
New Phytologist .
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(2020) Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean.
Genetics 215(1), 267-284.
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(2020) A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci.
Nat Biotechnol 38(10), 1203-1210.
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(2020) Genome biology of the paleotetraploid perennial biomass crop Miscanthus.
Nature Communications 11(1).
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(2020) A chromosome-scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus.
Plant J 104(5), 1215-1232.
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(2020) Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway.
Mol Phylogenet Evol 151, 106904.
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(2020) Impacts of directed evolution and soil management legacy on the maize rhizobiome.
Soil Biology & Biochemistry 145.
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(2020) Rationale for reconsidering current regulations restricting use of hybrids in orange juice.
Horticulture Research 7(1).
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(2020) Correlation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing tolerance.
Sci Rep 10(1), 4489.
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(2020) Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyon.
New Phytol .
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(2020) Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect.
Plant Direct 4(1), e00178.
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(2020) Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoe fedtschenkoi, a plant with crassulacean acid metabolism.
Gigascience 9(3).
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(2020) A willow sex chromosome reveals convergent evolution of complex palindromic repeats.
Genome Biol 21(1), 38.
10.1186/s13059-020-1952-4
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2019
(2019) High-density linkage map reveals QTL underlying growth traits in AP13xVS16 biparental population of switchgrass.
Global Change Biology Bioenergy 11(5), 672-690.
10.1111/gcbb.12592
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(2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea.
Nat Genet 51(5), 877-884.
10.1038/s41588-019-0405-z
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(2019) A New Method to Correct for Habitat Filtering in Microbial Correlation Networks.
Frontiers in Microbiology 10.
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(2019) Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil.
Sci Rep 9(1), 15611.
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(2019) Agrobacterium-Mediated Transformation of Brachypodium distachyon.
Curr Protoc Plant Biol , e20088.
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(2019) Agrobacterium-Mediated Transformation of Brachypodium distachyon.
Curr Protoc Plant Biol , e20088.
10.1002/cppb.20088
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(2019) Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits.
New Phytol 223(1), 293-309.
10.1111/nph.15777
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(2019) PMR5, an acetylation protein at the intersection of pectin biosynthesis and defense against fungal pathogens.
Plant J 100(5), 1022-1035.
10.1111/tpj.14497
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(2019) A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism.
BMC Genomics 20(1), 420.
10.1186/s12864-019-5734-x
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(2019) PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens.
Plant J .
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(2019) Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence.
Front Plant Sci 10, 1249.
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(2019) Metabotyping as a Stopover in Genome-to-Phenome Mapping.
Sci Rep 9(1), 1858.
10.1038/s41598-019-38483-0
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(2019) Genome sequence of the model rice variety KitaakeX.
BMC Genomics 20(1), 905.
10.1186/s12864-019-6262-4
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(2019) Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9-1.
Rice 12.
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(2019) The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass.
Front Plant Sci 10, 366.
10.3389/fpls.2019.00366
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(2019) Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase.
Nat Plants 5(7), 676-680.
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(2019) Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium).
Theor Appl Genet .
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(2019) QTL x environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient.
Proc Natl Acad Sci U S A 116(26), 12933-12941.
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(2019) The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes.
BMC Genomics 20(1), 119.
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(2019) Genome-wide association analysis of stalk biomass and anatomical traits in maize.
BMC Plant Biol 19(1), 45.
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(2019) Enhancing microRNA167A expression in seed decreases the alpha-linolenic acid content and increases seed size in Camelina sativa.
Plant J .
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(2019) Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication.
BMC Evol Biol 19(1), 77.
10.1186/s12862-019-1398-z
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(2019) Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample.
G3 (Bethesda) 9(3), 789-805.
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(2019) Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum).
Plant Biotechnol J 17(3), 580-593.
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(2019) Salicylic acid activates poplar defense against the biotrophic rust fungus Melampsora larici-populina via increased biosynthesis of catechin and proanthocyanidins.
New Phytol 221(2), 960-975.
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(2019) Construction and comparison of three reference-quality genome assemblies for soybean.
Plant J 100(5), 1066-1082.
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(2019) Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses.
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(2019) Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.
Genome Biol 20(1), 126.
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(2019) Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.
Front Genet 10, 487.
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(2019) Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate.
Genetics 211(1), 317-331.
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(2019) Overexpression of a Prefoldin beta subunit gene reduces biomass recalcitrance in the bioenergy crop Populus.
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2018
(2018) Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions.
Environ Microbiol 20(8), 2898-2912.
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(2018) Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.).
BMC Evol Biol 18(1), 91.
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(2018) Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon.
Plant Journal 96(2), 438-451.
10.1111/tpj.14042
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(2018) A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein.
G3 (Bethesda) .
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(2018) Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus.
Heredity (Edinb) .
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(2018) Phytophthora palmivora establishes tissue-specific intracellular infection structures in the earliest divergent land plant lineage.
Proc Natl Acad Sci U S A 115(16), E3846-E3855.
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(2018) Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.
PLoS Genet 14(3), e1007267.
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(2018) Extensive Genetic Diversity is Present within North American Switchgrass Germplasm.
Plant Genome 11(1).
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(2018) The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history.
Elife 7.
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(2018) Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.
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(2018) A mosaic monoploid reference sequence for the highly complex genome of sugarcane.
Nat Commun 9(1), 2638.
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(2018) Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae).
BMC Genomics 19(1), 792.
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(2018) SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae.
Plant J 96(3), 532-545.
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(2018) Climate-smart crops with enhanced photosynthesis.
J Exp Bot 69(16), 3801-3809.
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(2018) The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.
Plant J 93(3), 515-533.
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(2018) The genomic landscape of molecular responses to natural drought stress in Panicum hallii.
Nature Communications 9(1), 5213.
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(2018) Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii.
Biotechnol Biofuels 11, 25.
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(2018) Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii.
Biotechnol Biofuels 11, 25.
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(2018) Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree.
Proc Natl Acad Sci U S A 115(45), 11573-11578.
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(2018) Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.
Gene 663, 165-177.
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(2018) The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data.
Plant J 95(1), 168-182.
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(2018) Salt tolerance of two perennial grass Brachypodium sylvaticum accessions.
Plant Mol Biol 96(3), 305-314.
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(2018) Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass.
New Phytologist 0.
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(2018) Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought.
BMC Genomics 19(1), 679.
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(2018) Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).
Gates Open Res 2, 7.
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(2018) Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).
Gates Open Res 2, 7.
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(2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.
Nat Genet 50(2), 285-296.
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(2018) Evolution and expression of core SWI/SNF genes in red algae.
J Phycol 54(6), 879-887.
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(2018) Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon.
Genome Biol Evol 10(1), 304-318.
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(2018) Hardwood Tree Genomics: Unlocking Woody Plant Biology.
Frontiers in Plant Science 9, 9.
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(2018) Broad spectrum developmental role of Brachypodium AUX1.
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(2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice.
Nature 557(7703), 43-49.
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(2018) The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project.
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(2018) Genomics of the origin and evolution of Citrus.
Nature 554(7692), 311-316.
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(2018) A 5-enolpyruvylshikimate 3-phosphate synthase functions as a transcriptional repressor in Populus.
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(2018) Amplification and adaptation of centromeric repeats in polyploid switchgrass species.
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(2018) Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus.
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(2018) Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus.
New Phytol 220(2), 502-516.
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(2018) Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).
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(2018) Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).
Mol Genet Genomics 293(6), 1437-1452.
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(2018) Analysis of Brachypodium genomes with genome-wide optical maps.
Genome .
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(2018) Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing.
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2017
(2017) Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.
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(2017) Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).
Proc Natl Acad Sci U S A 114(31), E6361-E6370.
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(2017) Draft Nuclear Genome Sequence of the Liquid Hydrocarbon-Accumulating Green Microalga Botryococcus braunii Race B (Showa).
Genome Announc 5(16).
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(2017) Draft Nuclear Genome Sequence of the Liquid Hydrocarbon-Accumulating Green Microalga Botryococcus braunii Race B (Showa).
Genome Announc 5(16).
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(2017) Genome-wide identification of bacterial plant colonization genes.
PLoS Biol 15(9), e2002860.
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(2017) Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species.
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(2017) Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.
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(2017) Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection.
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(2017) Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection.
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(2017) Sparse panicle1 is required for inflorescence development in Setaria viridis and maize.
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(2017) Sparse panicle1 is required for inflorescence development in Setaria viridis and maize.
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Biotechnol Biofuels 1(1), 15.
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(2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals.
Nature 455(7217), 1193-7.
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(2008) Promoter elements associated with RNA Pol 11 stalling in the Drosophila embryo.
Proceedings of the National Academy of Sciences of the United States of America 105(22), 7762-7767.
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(2008) The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
Genome Research 18(7), 1100-1111.
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(2008) Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs.
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(2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
Nature 451(7180), 783-788.
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(2008) Genesis and expansion of metazoan transcription factor gene classes.
Mol Biol Evol 25(5), 980-96.
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(2008) Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism.
Proc Natl Acad Sci U S A 105(39), 14802-7.
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(2008) The amphioxus genome and the evolution of the chordate karyotype.
Nature 453(7198), 1064-71.
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(2008) Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms.
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(2008) Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding.
Bmc Genomics 9.
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(2008) The genome sequence of Bifidobacterium longum subsp infantis reveals adaptations for milk utilization within the infant microbiome.
Proceedings of the National Academy of Sciences of the United States of America 105(48), 18964-18969.
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(2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies.
Genome Research 18(10), 1638-1642.
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(2008) The Trichoplax genome and the nature of placozoans.
Nature 454(7207), 955-60.
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(2008) Genome structure and emerging evidence of an incipient sex chromosome in Populus.
Genome Res 18(3), 422-30.
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2007
(2007) Novel metabolism in Chlamydomonas through the lens of genomics.
Current Opinion in Plant Biology 10(2), 190-198.
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(2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa.
Bmc Plant Biology 7.
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(2007) A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation.
Plant Journal 50(6), 1063-1078.
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(2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Science 318(5848), 245-251.
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(2007) Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana.
Journal of Phycology 43(3), 585-604.
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2006
(2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Science 313(5793), 1596-1604.
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2004
(2004) The sequence and analysis of duplication-rich human chromosome 16.
Nature 432(7020), 988-94.
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(2004) The DNA sequence and comparative analysis of human chromosome 5.
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