High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

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The influence of population structure on gene expression and flowering time variation in the ubiquitous weedCapsella bursa-pastoris(Brassicaceae)

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A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants

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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

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A high resolution map of theArabidopsis thalianadevelopmental transcriptome based on RNA-seq profiling

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Expression partitioning of homeologs and tandem duplications contribute to salt tolerance in wheat (Triticum aestivum L.)

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Transcriptome shock invokes disruption of parental expression-conserved genes in tetraploid wheat

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ArabidopsisTOE proteins convey a photoperiodic signal to antagonize CONSTANS and regulate flowering time

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Frequent Introgressions from Diploid Species Contribute to the Adaptation of the Tetraploid Shepherd’s Purse (Capsella bursa-pastoris)

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HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

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JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

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Boosting AthaMap Database Content with Data from Protein Binding Microarrays

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Regulation of the Arabidopsis CBF regulon by a complex low-temperature regulatory network

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Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploidCapsella bursa-pastoris

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Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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Comparing reference-based RNA-Seq mapping methods for non-human primate data

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Mating system shifts and transposable element evolution in the plant genus Capsella

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An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae

(2014) Xiaoyong Du et al.   BMC GENOMICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

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A promoter-level mammalian expression atlas

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The legacy of diploid progenitors in allopolyploid gene expression patterns

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Jaccard index based similarity measure to compare transcription factor binding site models

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ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

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Architecture and evolution of a minute plant genome

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The Capsella rubella genome and the genomic consequences of rapid mating system evolution

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Antagonistic Basic Helix-Loop-Helix/bZIP Transcription Factors Form Transcriptional Modules That Integrate Light and Reactive Oxygen Species Signaling inArabidopsis

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STAR: ultrafast universal RNA-seq aligner

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Coalescent-Based Analysis Distinguishes between Allo- and Autopolyploid Origin in Shepherd's Purse (Capsella bursa-pastoris)

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The tomato genome sequence provides insights into fleshy fruit evolution

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RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome

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FLASH: fast length adjustment of short reads to improve genome assemblies

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Phytozome: a comparative platform for green plant genomics

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Deep and wide digging for binding motifs in ChIP-Seq data

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TobEA: an atlas of tobacco gene expression from seed to senescence

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Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics

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RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

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AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

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Differential expression analysis for sequence count data

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Biopython: freely available Python tools for computational molecular biology and bioinformatics

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BLAST+: architecture and applications

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Splicing Variation at a FLOWERING LOCUS C Homeolog Is Associated With Flowering Time Variation in the Tetraploid Capsella bursa-pastoris

(2009) T. Slotte et al.   GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

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TheArabidopsisbZIP transcription factor HY5 regulates expression of thePFG1/MYB12gene in response to light and ultraviolet-B radiation

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

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