The pangenome of an agronomically important crop plant Brassica oleracea

Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed inBrassica rapa

(2015) Jifang Zhang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Structural Variation: Mechanisms of Chromosome Rearrangements

(2015) Brooke Weckselblatt et al.   TRENDS IN GENETICS

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence

(2014) T. Arias et al.   AMERICAN JOURNAL OF BOTANY

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

(2014) V. Obenchain et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage

(2014) Ke Lin et al.   BMC GENOMICS

The role of BoFLC2 in cauliflower (Brassica oleracea var. botrytis L.) reproductive development

(2014) Stephen Ridge et al.   JOURNAL OF EXPERIMENTAL BOTANY

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Identification of Metabolic QTLs and Candidate Genes for Glucosinolate Synthesis in Brassica oleracea Leaves, Seeds and Flower Buds

(2014) Tamara Sotelo et al.   PLoS One

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Whole Genome and Tandem Duplicate Retention Facilitated Glucosinolate Pathway Diversification in the Mustard Family

(2013) Johannes A. Hofberger et al.   Genome Biology and Evolution

The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks

(2013) Dong Xiao et al.   JOURNAL OF EXPERIMENTAL BOTANY

Presence–Absence Variation in A. thaliana Is Primarily Associated with Genomic Signatures Consistent with Relaxed Selective Constraints

(2013) Stephen J. Bush et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements

(2013) Jianbo Zhang et al.   PLoS Genetics

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

(2011) K. Schneeberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

BrFLC2 (FLOWERING LOCUS C) as a candidate gene for a vernalization response QTL in Brassica rapa

(2010) Jianjun Zhao et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY