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.
10.1111/1462-2920.14273
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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.
10.1186/s12862-018-1193-2
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(2018) A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein.
G3 (Bethesda) .
10.1534/g3.118.200188
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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) .
10.1038/s41437-018-0058-1
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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.
10.1073/pnas.1717900115
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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.
10.1371/journal.pgen.1007267
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(2018) Extensive Genetic Diversity is Present within North American Switchgrass Germplasm.
Plant Genome 11(1).
10.3835/plantgenome2017.06.0055
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(2018) Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.
J Vis Exp (134).
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(2018) A mosaic monoploid reference sequence for the highly complex genome of sugarcane.
Nat Commun 9(1), 2638.
10.1038/s41467-018-05051-5
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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 .
10.1111/tpj.14047
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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.
10.1111/tpj.13801
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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.
10.1186/s13068-018-1033-z
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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.
10.1186/s13068-018-1033-z
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(2018) Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.
Gene 663, 165-177.
10.1016/j.gene.2018.04.024
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(2018) The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data.
Plant J 95(1), 168-182.
10.1111/tpj.13940
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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) Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought.
BMC Genomics 19(1), 679.
10.1186/s12864-018-5055-5
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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.
10.12688/gatesopenres.12777.1
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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.
10.12688/gatesopenres.12777.1
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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.
10.1038/s41588-018-0040-0
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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.
10.1093/gbe/evx276
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(2018) Broad spectrum developmental role of Brachypodium AUX1.
New Phytol .
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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.
New Phytol 217(1), 16-25.
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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.
The Plant Cell .
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(2018) Amplification and adaptation of centromeric repeats in polyploid switchgrass species.
New Phytol .
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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 .
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(2018) Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).
Mol Genet Genomics .
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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.
Biotechnol Biofuels 11, 170.
10.1186/s13068-018-1167-z
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2017
(2017) Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.
Cell 171(2), 287-304 e15.
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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.
10.1073/pnas.1703088114
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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).
10.1128/genomeA.00215-17
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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).
10.1128/genomeA.00215-17
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(2017) Genome-wide identification of bacterial plant colonization genes.
PLoS Biol 15(9), e2002860.
10.1371/journal.pbio.2002860
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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.
Front Plant Sci 8, 184.
10.3389/fpls.2017.00184
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(2017) Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.
Nat Commun 8(1), 2184.
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(2017) Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.
Nat Commun 8(1), 2184.
10.1038/s41467-017-02292-8
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(2017) Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.
New Phytol 214(2), 808-819.
10.1111/nph.14421
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(2017) Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection.
Plant J .
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(2017) Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection.
Plant J .
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(2017) Sparse panicle1 is required for inflorescence development in Setaria viridis and maize.
Nat Plants 3, 17054.
10.1038/nplants.2017.54
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(2017) Sparse panicle1 is required for inflorescence development in Setaria viridis and maize.
Nat Plants 3, 17054.
10.1038/nplants.2017.54
https://www.nature.com/articles/nplants201754#supplementary-information
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(2017) The P. patens chromosome-scale assembly reveals moss genome structure and evolution.
Plant J .
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(2017) Young inversion with multiple linked QTLs under selection in a hybrid zone.
Nature Ecology & Evolution 1, 0119.
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(2017) The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.
Plant Cell 29(6), 1218-1231.
10.1105/tpc.17.00154
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(2017) The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.
Plant Cell 29(6), 1218-1231.
10.1105/tpc.17.00154
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(2017) Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes.
Stand Genomic Sci 12, 78.
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(2017) Rice SNP-seek database update: new SNPs, indels, and queries.
Nucleic Acids Res 45(D1), D1075-D1081.
10.1093/nar/gkw1135
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(2017) QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert.
Theor Appl Genet .
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(2017) The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization.
Plant J .
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(2017) The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization.
Plant J .
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(2017) QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii.
Front Plant Sci 8, 1168.
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(2017) Cross-species functional diversity within the PIN auxin efflux protein family.
Elife 6.
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(2017) Draft Nuclear Genome Sequence of the Halophilic and Beta-Carotene-Accumulating Green Alga Dunaliella salina Strain CCAP19/18.
Genome Announc 5(43).
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(2017) Transcriptome analysis of Brachypodium during fungal pathogen infection reveals both shared and distinct defense responses with wheat.
Sci Rep 7(1), 17212.
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(2017) Mobile MUTE specifies subsidiary cells to build physiologically improved grass stomata.
Science 355(6330), 1215-1218.
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(2017) Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes.
New Phytol .
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(2017) Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes.
New Phytol .
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(2017) Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.
Sci Rep 7(1), 15274.
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(2017) 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 .
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(2017) DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor.
New Phytol .
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(2017) The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.
BMC Genomics 18(1), 225.
10.1186/s12864-017-3606-9
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(2017) Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon.
Plant Physiol 173(1), 269-279.
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(2017) The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.
Nat Commun 8(1), 1899.
10.1038/s41467-017-01491-7
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(2017) Insights of biomass recalcitrance in natural Populus trichocarpa variants for biomass conversion.
Green Chemistry 19(22), 5467-5478.
10.1039/c7gc02219k
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2016
(2016) On the origin and evolutionary consequences of gene body DNA methylation.
Proc Natl Acad Sci U S A 113(32), 9111-6.
10.1073/pnas.1604666113
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(2016) Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.
Nat Biotechnol 34(5), 562-70.
10.1038/nbt.3535
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(2016) Use of Agrobacterium rhizogenes Strain 18r12v and Paromomycin Selection for Transformation of Brachypodium distachyon and Brachypodium sylvaticum.
Front Plant Sci 7, 716.
10.3389/fpls.2016.00716
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(2016) Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei.
PLoS One 11(12), e0167171.
10.1371/journal.pone.0167171
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(2016) Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass.
BMC Genomics 17(1), 892.
10.1186/s12864-016-3201-5
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(2016) Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data.
New Phytol .
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(2016) Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis.
PLoS One 11(3), e0151883.
10.1371/journal.pone.0151883
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(2016) Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation.
Mol Plant .
10.1016/j.molp.2016.03.009
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(2016) Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass.
Genome Res 26(4), 510-8.
10.1101/gr.198135.115
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(2016) Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean.
Plant Genome 9(2).
10.3835/plantgenome2015.09.0092
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(2016) Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean.
Plant Genome 9(3).
10.3835/plantgenome2016.02.0012
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(2016) Widespread natural variation of DNA methylation within angiosperms.
Genome Biol 17(1), 194.
10.1186/s13059-016-1059-0
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(2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.
Nature 530(7590), 331-5.
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(2016) BdCESA7, BdCESA8, and BdPMT Utility Promoter Constructs for Targeted Expression to Secondary Cell-Wall-Forming Cells of Grasses.
Front Plant Sci 7, 55.
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(2016) A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem.
Elife 5.
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(2016) Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity.
Proc Natl Acad Sci U S A .
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(2016) Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani AG8.
Functional Plant Biology 43(2), 189-198.
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(2016) The Sphagnum Genome Project: A New Model for Ecological and Evolutionary Genomics.
Genomes and Evolution of Charophytes, Bryophytes, Lycophytes and Ferns 78, 167-187.
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(2016) Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01.
BMC Genomics 17(1), 33.
10.1186/s12864-015-2344-0
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(2016) Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE (ANR), a regulator of ABA responses unique to basal land plants and required for desiccation tolerance.
Plant Cell .
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(2016) Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.
BMC Genomics 17(1), 267.
10.1186/s12864-016-2585-6
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(2016) Genome-wide analysis of lectin receptor-like kinases in Populus.
BMC Genomics 17, 699.
10.1186/s12864-016-3026-2
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2015
(2015) High-Resolution Linkage Map and Chromosome-Scale Genome Assembly for Cassava (Manihot esculenta Crantz) from 10 Populations.
G3-Genes Genomes Genetics 5(1), 133-144.
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(2015) Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses.
Annu Rev Plant Biol 66, 465-85.
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(2015) A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.
Genome Biol 16, 26.
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(2015) Variation in Adult Plant Phenotypes and Partitioning among Seed and Stem-Borne Roots across Brachypodium distachyon Accessions to Exploit in Breeding Cereals for Well-Watered and Drought Environments.
Plant Physiol 168(3), 953-67.
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(2015) Diversity and Population Structure of Northern Switchgrass as Revealed Through Exome Capture Sequencing.
Plant J .
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(2015) Diversity and Population Structure of Northern Switchgrass as Revealed Through Exome Capture Sequencing.
Plant J .
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(2015) High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing.
The Plant Genome 8(2).
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Ann Bot 115(5), 717-31.
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(2015) Examining the cause of high inbreeding depression: analysis of whole-genome sequence data in 28 selfed progeny of Eucalyptus grandis.
New Phytol .
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(2015) Proteome profile of the endomembrane of developing coleoptiles from switchgrass (Panicum virgatum).
Proteomics .
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Mol Plant .
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(2015) Identification and distribution of the NBS-LRR gene family in the Cassava genome.
BMC Genomics 16, 360.
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(2015) High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.
BMC Genomics 16, 24.
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(2015) Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome.
Plant J .
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(2015) GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems.
Elife 4.
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(2015) Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses.
PLoS Pathog 11(3), e1004809.
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(2015) Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte?.
Sci Rep 5, 10134.
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(2015) Targeted Switchgrass BAC Library Screening and Sequence Analysis Identifies Predicted Biomass and Stress Response-Related Genes.
Bioenerg Res , 1-14.
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(2015) The BioMart community portal: an innovative alternative to large, centralized data repositories.
Nucleic Acids Res 43(W1), W589-98.
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(2015) SNP Assay Development for Linkage Map Construction, Anchoring Whole Genome Sequence and Other Genetic and Genomic Applications in Common Bean.
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(2015) A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world.
New Phytol 207(3), 491-504.
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2014
(2014) High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.
New Phytol .
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(2014) A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number.
Genetics 196(3), 829-40.
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(2014) The Chlamydomonas genome project: a decade on.
Trends Plant Sci .
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(2014) Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass.
Plant Genome 7(2).
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(2014) Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations.
Nat Genet 46(10), 1089-96.
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(2014) Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris).
Front Plant Sci 5, 339.
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(2014) Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines.
Plant J .
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(2014) Insights into the maize pan-genome and pan-transcriptome.
Plant Cell 26(1), 121-35.
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(2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.
Science 345(6194), 1251788.
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(2014) Fuzzy GIS-based multi-criteria evaluation for US Agave production as a bioenergy feedstock.
GCB Bioenergy .
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(2014) The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii.
New Phytol .
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(2014) Ancient hybridizations among the ancestral genomes of bread wheat.
Science 345(6194), 1250092.
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(2014) A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.
Sci Rep 4, 4519.
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(2014) The genome of Eucalyptus grandis.
Nature 509(7505), 356-62.
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(2014) Genome interplay in the grain transcriptome of hexaploid bread wheat.
Science 345(6194), 1250091.
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(2014) A reference genome for common bean and genome-wide analysis of dual domestications..
Nature 46(7), 707-713.
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(2014) The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.
Nat Commun 5, 3311.
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(2014) Sphagnum physiology in the context of changing climate: Emergent influences of genomics, modeling and host-microbiome interactions on understanding ecosystem function.
Plant Cell Environ .
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(2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.
Nat Biotechnol 32(7), 656-62.
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2013
(2013) A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes.
BMC Genomics 14, 864.
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(2013) A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.
Mol Ecol Resour 13(2), 306-23.
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(2013) De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana.
BMC Genomics 14, 563.
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(2013) Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing.
Proc Natl Acad Sci U S A 110(48), 19478-82.
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(2013) Identification and characterization of functional centromeres of the common bean.
Plant J 76(1), 47-60.
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(2013) Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).
Plant J 76(4), 718-27.
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(2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions.
Proc Natl Acad Sci U S A 110(16), 6548-53.
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(2013) Pan genome of the phytoplankton Emiliania underpins its global distribution.
Nature 499(7457), 209-13.
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(2013) Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella.
Science 342(6165), 1468-73.
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(2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution.
Nat Genet 45(7), 831-5.
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(2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.
Nat Genet 45(5), 487-94.
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(2013) Revisiting the sequencing of the first tree genome: Populus trichocarpa.
Tree Physiol 33(4), 357-64.
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(2013) The Reference Genome of the Halophytic Plant Eutrema salsugineum.
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(2013) Cyanobacterial-based approaches to improving photosynthesis in plants.
J Exp Bot 64(3), 787-98.
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(2013) Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.).
Plant J 74(1), 160-73.
10.1111/tpj.12104
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2012
(2012) Defining the Boundaries and Characterizing the Landscape of Functional Genome Expression in Vascular Tissues of Populus using Shotgun Proteomics.
Journal of Proteome Research 11(1), 449-460.
Doi 10.1021/Pr200851y
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(2012) Reference genome sequence of the model plant Setaria.
Nat Biotechnol 30(6), 555-61.
10.1038/nbt.2196
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(2012) Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism.
Journal of Phycology 48(6), 1328-1342.
DOI 10.1111/j.1529-8817.2012.01229.x
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(2012) Analysis of Porphyra Membrane Transporters Demonstrates Gene Transfer among Photosynthetic Eukaryotes and Numerous Sodium-Coupled Transport Systems.
Plant Physiology 158(4), 2001-2012.
DOI 10.1104/pp.112.193896
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(2012) Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon.
PLoS One 7(6), e38333.
10.1371/journal.pone.0038333
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(2012) Phytozome: a comparative platform for green plant genomics.
Nucleic Acids Research 40(D1), D1178-D1186.
Doi 10.1093/Nar/Gkr944
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(2012) A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks.
Curr Biol 22(1), 83-90.
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(2012) Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species.
Tree Genetics & Genomes 8(6), 1477-1485.
Doi 10.1007/S11295-012-0547-Y
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(2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
Nature 492(7429), 423-7.
10.1038/nature11798
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(2012) The Cassava Genome: Current Progress, Future Directions.
Trop Plant Biol 5(1), 88-94.
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(2012) A genome-wide survey of switchgrass genome structure and organization.
PLoS One 7(4), e33892.
10.1371/journal.pone.0033892
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(2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa.
New Phytol 196(3), 713-25.
10.1111/j.1469-8137.2012.04258.x
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(2012) A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy.
Bmc Genomics 13.
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2011
(2011) Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar.
New Phytologist 192(1), 151-163.
DOI 10.1111/j.1469-8137.2011.03786.x
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(2011) The Switchgrass Genome: Tools and Strategies.
Plant Genome 4(3), 273-282.
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(2011) Meraculous: de novo genome assembly with short paired-end reads.
PLoS One 6(8), e23501.
10.1371/journal.pone.0023501
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(2011) Chemical, ultrastructural and supramolecular analysis of tension wood in Populus tremula x alba as a model substrate for reduced recalcitrance.
Energy & Environmental Science 4(12), 4962-4971.
Doi 10.1039/C1ee02073k
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(2011) FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar.
Proc Natl Acad Sci U S A 108(26), 10756-61.
10.1073/pnas.1104713108
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(2011) The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage.
J Biol Chem 286(24), 21427-39.
10.1074/jbc.M111.233734
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(2011) Lignin content in natural Populus variants affects sugar release.
Proc Natl Acad Sci U S A 108(15), 6300-5.
10.1073/pnas.1009252108
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(2011) Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants.
Plant Cell Physiol 52(2), 317-32.
10.1093/pcp/pcq188
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(2011) Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics.
Plant Science 181(6), 675-687.
DOI 10.1016/j.plantsci.2011.01.020
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(2011) Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis.
Plant Science 181(6), 688-695.
DOI 10.1016/j.plantsci.2011.01.021
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2010
(2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.
Science 327(5963), 302-5.
10.1126/science.1182213
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(2010) The dynamic genome of Hydra.
Nature 464(7288), 592-596.
Doi 10.1038/Nature08830
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(2010) Evolution of an expanded sex-determining locus in Volvox.
Science 328(5976), 351-4.
10.1126/science.1186222
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(2010) The genome of Naegleria gruberi illuminates early eukaryotic versatility.
Cell 140(5), 631-42.
10.1016/j.cell.2010.01.032
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(2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence.
Bmc Genomics 11.
Artn 38Doi 10.1186/1471-2164-11-38
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(2010) Genome sequencing and analysis of the model grass Brachypodium distachyon.
Nature 463(7282), 763-8.
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(2010) Parallel evolution of nacre building gene sets in molluscs.
Mol Biol Evol 27(3), 591-608.
10.1093/molbev/msp278
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(2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.
Proceedings of the National Academy of Sciences of the United States of America 107(51), 22032-22037.
DOI 10.1073/pnas.1009526107
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(2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.
Science 329(5988), 223-6.
10.1126/science.1188800
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(2010) Genome sequence of the palaeopolyploid soybean.
Nature 463(7278), 178-83.
10.1038/nature08670
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(2010) Genome sequence of the palaeopolyploid soybean.
Nature 463(7278), 178-83.
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(2010) Early evolution of the LIM homeobox gene family.
BMC Biol 8, 4.
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(2010) Antisense down-regulation of 4CL expression alters lignification, tree growth, and saccharification potential of field-grown poplar.
Plant Physiol 154(2), 874-86.
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(2010) SoyDB: a knowledge database of soybean transcription factors.
BMC Plant Biol 10, 14.
10.1186/1471-2229-10-14
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2009
(2009) A recommendation for naming transcription factor proteins in the grasses.
Plant Physiol 149(1), 4-6.
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(2009) Old can be new again: HAPPY whole genome sequencing, mapping and assembly.
International Journal of Biological Sciences 5(4), 298-303.
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(2009) Domain shuffling and the evolution of vertebrates.
Genome Res 19(8), 1393-403.
10.1101/gr.087072.108
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(2009) Anatomy and development of the nervous system of Nematostella vectensis, an anthozoan cnidarian.
Dev Neurobiol 69(4), 235-54.
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(2009) The Sorghum bicolor genome and the diversification of grasses.
Nature 457(7229), 551-6.
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(2009) Brachypodium distachyon: a New Model for Biomass Crops.
In Vitro Cellular & Developmental Biology-Animal 45, S6-S6.
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2008
(2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes.
Nature 456(7219), 239-44.
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(2008) Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis.
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.
Dev Genes Evol 218(11-12), 613-28.
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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.
New Phytol 180(2), 408-20.
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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.
Doi 10.1111/J.1365-313x.2007.03112.X
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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.
Doi 10.1126/Science.1128691
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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.
Nature 431(7006), 268-74.
10.1038/nature02919
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