The Rosa genome provides new insights into the domestication of modern roses

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

Partial preferential chromosome pairing is genotype dependent in tetraploid rose

(2017) Peter M. Bourke et al.   PLANT JOURNAL

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

(2017) Pascal Schläpfer et al.   PLANT PHYSIOLOGY

Ancestors of modern plant crops

(2016) Jérôme Salse   CURRENT OPINION IN PLANT BIOLOGY

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

DELAY OF GERMINATION1(DOG1) regulates both seed dormancy and flowering time through microRNA pathways

(2016) Heqiang Huo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stem-Loop RT-qPCR as an Efficient Tool for the Detection and Quantification of Small RNAs in Giardia lamblia

(2016) Jaime Marcial-Quino et al.   Genes

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome

(2016) Alaguraj Veluchamy et al.   PLoS One

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Progressive Regulation of Sesquiterpene Biosynthesis in Arabidopsis and Patchouli (Pogostemon cablin) by the miR156-Targeted SPL Transcription Factors

(2015) Zong-Xia Yu et al.   Molecular Plant

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

Biosynthesis of monoterpene scent compounds in roses

(2015) J.-L. Magnard et al.   SCIENCE

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Phylogeny and biogeography of wild roses with specific attention to polyploids

(2014) Marie Fougère-Danezan et al.   ANNALS OF BOTANY

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Genome-wide analysis of local chromatin packing inArabidopsis thaliana

(2014) Congmao Wang et al.   GENOME RESEARCH

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Genetics and genomics of flower initiation and development in roses

(2013) Mohammed Bendahmane et al.   JOURNAL OF EXPERIMENTAL BOTANY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA

(2013) F. E. Vaistij et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

PAP1 transcription factor enhances production of phenylpropanoid and terpenoid scent compounds in rose flowers

(2012) Michal Moyal Ben Zvi et al.   NEW PHYTOLOGIST

Negative Regulation of Anthocyanin Biosynthesis inArabidopsisby a miR156-Targeted SPL Transcription Factor

(2011) Jin-Ying Gou et al.   PLANT CELL

The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry

(2011) Hikaru Iwata et al.   PLANT JOURNAL

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Genomic Approach to Study Floral Development Genes in Rosa sp.

(2011) Annick Dubois et al.   PLoS One

An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods

(2010) G. Carrier et al.   AMERICAN JOURNAL OF BOTANY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae

(2010) Kui Lin-Wang et al.   BMC PLANT BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

(2010) L. Cottret et al.   NUCLEIC ACIDS RESEARCH

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Tinkering with the C-Function: A Molecular Frame for the Selection of Double Flowers in Cultivated Roses

(2010) Annick Dubois et al.   PLoS One

Translationally controlled tumor protein is a conserved mitotic growth integrator in animals and plants

(2010) F. Brioudes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Somatic embryogenesis and transformation of the diploid Rosa chinensis cv Old Blush

(2009) Philippe Vergne et al.   PLANT CELL TISSUE AND ORGAN CULTURE

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

(2008) Sylvain Foissac et al.   Current Bioinformatics

Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: Problems and solutions

(2008) Andrey Zharkikh et al.   JOURNAL OF BIOTECHNOLOGY