Published in Nature on May 22, 2013
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res (2014) 4.29
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res (2013) 2.71
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol (2014) 1.90
MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol (2013) 1.48
The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun (2014) 1.47
Sequencing and assembly of the 22-gb loblolly pine genome. Genetics (2014) 1.46
Assembly information services in the European Nucleotide Archive. Nucleic Acids Res (2013) 1.40
Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness. PLoS One (2016) 1.39
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol (2015) 1.38
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics (2014) 1.32
Cassava genome from a wild ancestor to cultivated varieties. Nat Commun (2014) 1.25
Investigation of terpene diversification across multiple sequenced plant genomes. Proc Natl Acad Sci U S A (2014) 1.16
A field guide to whole-genome sequencing, assembly and annotation. Evol Appl (2014) 1.12
New evidence for grain specific C4 photosynthesis in wheat. Sci Rep (2016) 1.09
Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data. Gigascience (2013) 1.04
Targeted capture in evolutionary and ecological genomics. Mol Ecol (2015) 1.01
Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum. Plant Cell (2015) 1.00
Autophagy and metacaspase determine the mode of cell death in plants. J Cell Biol (2013) 0.99
Regulation of specialized metabolism by WRKY transcription factors. Plant Physiol (2014) 0.98
Early genome duplications in conifers and other seed plants. Sci Adv (2015) 0.97
Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol (2013) 0.96
Genetic anchoring of whole-genome shotgun assemblies. Front Genet (2014) 0.96
Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites. Sci Rep (2015) 0.95
Insights into conifer giga-genomes. Plant Physiol (2014) 0.93
Genomics reveals new landscapes for crop improvement. Genome Biol (2013) 0.93
Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes. PLoS One (2014) 0.93
Evolution of the bHLH genes involved in stomatal development: implications for the expansion of developmental complexity of stomata in land plants. PLoS One (2013) 0.93
MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants. Ann Bot (2014) 0.93
Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytol (2015) 0.93
Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes. Plant Cell (2016) 0.92
Large-scale screening of transcription factor-promoter interactions in spruce reveals a transcriptional network involved in vascular development. J Exp Bot (2014) 0.92
Next-generation sequencing: The genome jigsaw. Nature (2013) 0.92
NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants. Front Plant Sci (2015) 0.91
What's in a genome? The C-value enigma and the evolution of eukaryotic genome content. Philos Trans R Soc Lond B Biol Sci (2015) 0.91
BESST--efficient scaffolding of large fragmented assemblies. BMC Bioinformatics (2014) 0.91
Transposable elements and genome size variations in plants. Genomics Inform (2014) 0.90
Between two fern genomes. Gigascience (2014) 0.90
Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing. BMC Genomics (2015) 0.90
Unique responsiveness of angiosperm stomata to elevated CO2 explained by calcium signalling. PLoS One (2013) 0.88
An Exploration into Fern Genome Space. Genome Biol Evol (2015) 0.88
A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene. PLoS One (2014) 0.87
Diversification of the C-TERMINALLY ENCODED PEPTIDE (CEP) gene family in angiosperms, and evolution of plant-family specific CEP genes. BMC Genomics (2014) 0.86
Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biol Evol (2015) 0.86
Flavan-3-ols in Norway spruce: biosynthesis, accumulation, and function in response to attack by the bark beetle-associated fungus Ceratocystis polonica. Plant Physiol (2014) 0.86
Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana. Nucleic Acids Res (2015) 0.86
The evolution of the actin binding NET superfamily. Front Plant Sci (2014) 0.85
Ancient Origin and Recent Innovations of RNA Polymerase IV and V. Mol Biol Evol (2015) 0.85
Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants. Plant Cell (2015) 0.85
Bioinformatic and phylogenetic analysis of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) and the CLE-LIKE signal peptide genes in the Pinophyta. BMC Plant Biol (2014) 0.85
Oriented cell division shapes carnivorous pitcher leaves of Sarracenia purpurea. Nat Commun (2015) 0.85
Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. BMC Plant Biol (2014) 0.84
Phylogenomics of MADS-Box Genes in Plants - Two Opposing Life Styles in One Gene Family. Biology (Basel) (2013) 0.84
Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform. Mol Ecol Resour (2014) 0.84
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation. Genome Biol Evol (2015) 0.84
PlantCAZyme: a database for plant carbohydrate-active enzymes. Database (Oxford) (2014) 0.84
Conserved Gene Expression Programs in Developing Roots from Diverse Plants. Plant Cell (2015) 0.84
Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events. BMC Plant Biol (2015) 0.84
Draft genome of the living fossil Ginkgo biloba. Gigascience (2016) 0.83
Opposite action of R2R3-MYBs from different subgroups on key genes of the shikimate and monolignol pathways in spruce. J Exp Bot (2013) 0.83
A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. BMC Genomics (2014) 0.83
Polyploidy-associated genome modifications during land plant evolution. Philos Trans R Soc Lond B Biol Sci (2014) 0.83
Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC Plant Biol (2014) 0.83
Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots. New Phytol (2015) 0.82
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics (2017) 0.82
Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine. BMC Genomics (2014) 0.82
Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway. Genome Biol Evol (2015) 0.82
The landscape of nucleotide polymorphism among 13,500 genes of the conifer picea glauca, relationships with functions, and comparison with medicago truncatula. Genome Biol Evol (2013) 0.82
Novel dehydrins lacking complete K-segments in Pinaceae. The exception rather than the rule. Front Plant Sci (2014) 0.82
Wuschel-related homeobox 8/9 is important for proper embryo patterning in the gymnosperm Norway spruce. J Exp Bot (2014) 0.82
Transcriptome analysis of callus from Picea balfouriana. BMC Genomics (2014) 0.82
It's more than stamp collecting: how genome sequencing can unify biological research. Trends Genet (2015) 0.82
Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants. Mol Biol Evol (2015) 0.82
Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures. New Phytol (2015) 0.81
Transcriptional profiling of epigenetic regulators in somatic embryos during temperature induced formation of an epigenetic memory in Norway spruce. Planta (2016) 0.81
Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower. Front Plant Sci (2016) 0.81
The redox-sensitive chloroplast trehalose-6-phosphate phosphatase AtTPPD regulates salt stress tolerance. Antioxid Redox Signal (2014) 0.81
Ceratopteris richardii (C-fern): a model for investigating adaptive modification of vascular plant cell walls. Front Plant Sci (2013) 0.81
Identification of Salt Stress Biomarkers in Romanian Carpathian Populations of Picea abies (L.) Karst. PLoS One (2015) 0.81
Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation. BMC Plant Biol (2015) 0.81
Comprehensive Phylogenetic Analysis Sheds Light on the Diversity and Origin of the MLO Family of Integral Membrane Proteins. Genome Biol Evol (2016) 0.81
Selective acquisition and retention of genomic sequences by Pack-Mutator-like elements based on guanine-cytosine content and the breadth of expression. Plant Physiol (2013) 0.81
Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae). Genetics (2014) 0.81
Transcriptome Characterization of Gnetum parvifolium Reveals Candidate Genes Involved in Important Secondary Metabolic Pathways of Flavonoids and Stilbenoids. Front Plant Sci (2016) 0.81
Comprehensive Genomic Analysis and Expression Profiling of the NOX Gene Families under Abiotic Stresses and Hormones in Plants. Genome Biol Evol (2016) 0.81
A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue. Nat Protoc (2014) 0.80
Transcriptional Responses Associated with Virulence and Defence in the Interaction between Heterobasidion annosum s.s. and Norway Spruce. PLoS One (2015) 0.80
A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection. PLoS One (2014) 0.80
A conifer genome spruces up plant phylogenomics. Genome Biol (2013) 0.80
Evolution and targeting of Omp85 homologs in the chloroplast outer envelope membrane. Front Plant Sci (2014) 0.80
High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species. BMC Genomics (2014) 0.80
Epigenetic variability in the genetically uniform forest tree species Pinus pinea L. PLoS One (2014) 0.80
From plant genomes to protein families: computational tools. Comput Struct Biotechnol J (2013) 0.80
The 2-C-methylerythritol 4-phosphate pathway in melon is regulated by specialized isoforms for the first and last steps. J Exp Bot (2014) 0.80
Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom. PLoS One (2016) 0.80
Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain. Front Plant Sci (2015) 0.80
Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). PLoS One (2015) 0.80
Dynamics of genome size evolution in birds and mammals. Proc Natl Acad Sci U S A (2017) 0.80
Phylogenetic analysis reveals dynamic evolution of the poly(A)-binding protein gene family in plants. BMC Evol Biol (2014) 0.79
LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome. DNA Res (2014) 0.79
Dramatic improvement in genome assembly achieved using doubled-haploid genomes. Sci Rep (2014) 0.79
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature (2007) 18.04
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
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Epigenetic inheritance in plants. Nature (2007) 7.40
Ancestral polyploidy in seed plants and angiosperms. Nature (2011) 7.00
Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A (2004) 5.35
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res (2002) 5.15
Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev (2005) 4.47
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Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res (2006) 3.02
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res (2008) 2.70
Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res (2006) 2.69
Long noncoding RNAs are rarely translated in two human cell lines. Genome Res (2012) 2.64
The flowering world: a tale of duplications. Trends Plant Sci (2009) 2.38
Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol (2004) 2.24
Presidential address. Transposable elements, epigenetics, and genome evolution. Science (2012) 1.99
Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol Biol Evol (2003) 1.88
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Feature-by-feature--evaluating de novo sequence assembly. PLoS One (2012) 1.83
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A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics (2008) 1.55
Evolution of genome size and complexity in Pinus. PLoS One (2009) 1.52
Hemisphere-scale differences in conifer evolutionary dynamics. Proc Natl Acad Sci U S A (2012) 1.43
A hitchhiker's guide to the MADS world of plants. Genome Biol (2010) 1.42
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics (2010) 1.40
Conifers have a unique small RNA silencing signature. RNA (2008) 1.26
A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biol (2012) 1.26
Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol (2012) 1.18
Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiol (2011) 1.17
Inference of genome duplications from age distributions revisited. Mol Biol Evol (2012) 1.16
Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS One (2011) 1.10
Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing. BMC Plant Biol (2012) 1.09
A mystery unveiled. Genome Biol (2011) 1.08
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Analysis of conifer FLOWERING LOCUS T/TERMINAL FLOWER1-like genes provides evidence for dramatic biochemical evolution in the angiosperm FT lineage. New Phytol (2012) 1.02
Improved gap size estimation for scaffolding algorithms. Bioinformatics (2012) 0.97
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50 million years of genomic stasis in endosymbiotic bacteria. Science (2002) 6.65
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A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc Natl Acad Sci U S A (2004) 3.67
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Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal. Nat Cell Biol (2005) 3.61
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The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A (2007) 3.58
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Genome duplication and the origin of angiosperms. Trends Ecol Evol (2005) 3.46
p53 suppresses the self-renewal of adult neural stem cells. Development (2006) 3.35
Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nat Methods (2009) 3.35
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Poplar carbohydrate-active enzymes. Gene identification and expression analyses. Plant Physiol (2006) 3.30
The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature (2011) 3.29
mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves. Mol Biol Evol (2009) 3.23
SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet (2002) 3.23
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Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell (2005) 3.17
Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell (2007) 3.14
Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci U S A (2009) 3.13
Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci U S A (2004) 3.13
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res (2007) 3.13
The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science (2011) 3.10
Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromosome 2p16.3, 2p21 and 9q33.3. Nat Genet (2010) 3.02
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02
Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol (2010) 3.00
Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy. J Genet Genomics (2012) 2.98
AUX1 promotes lateral root formation by facilitating indole-3-acetic acid distribution between sink and source tissues in the Arabidopsis seedling. Plant Cell (2002) 2.95
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Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol Ecol (2008) 2.91
Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol (2003) 2.90
Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila. Genetics (2013) 2.87
Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci U S A (2011) 2.84
Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol (2007) 2.84
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Rapid regulation of light harvesting and plant fitness in the field. Science (2002) 2.74
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Heat Loss Prevention (HeLP) in the delivery room: A randomized controlled trial of polyethylene occlusive skin wrapping in very preterm infants. J Pediatr (2004) 2.73
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