Incipient diploidization of the medicinal plant Perilla within 10,000 years

Genomics of Evolutionary Novelty in Hybrids and Polyploids

(2020) Gonzalo Nieto Feliner et al.   Frontiers in Genetics

Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

(2019) Weijian Zhuang et al.   NATURE GENETICS

Reducing MSH4 copy number prevents meiotic crossovers between non-homologous chromosomes in Brassica napus

(2019) Adrián Gonzalo et al.   Nature Communications

Impact of whole-genome duplication events on diversification rates in angiosperms

(2018) Jacob B. Landis et al.   AMERICAN JOURNAL OF BOTANY

Meiotic Recombination: Mixing It Up in Plants

(2018) Yingxiang Wang et al.   Annual Review of Plant Biology

The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation

(2018) Jonathan F Wendel et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A 2.833-kb Insertion in BnFLC.A2 and Its Homeologous Exchange with BnFLC.C2 during Breeding Selection Generated Early-Flowering Rapeseed

(2018) Lei Chen et al.   Molecular Plant

Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

(2018) Ren Ren et al.   Molecular Plant

The causes and consequences of subgenome dominance in hybrids and recent polyploids

(2018) Kevin A. Bird et al.   NEW PHYTOLOGIST

Pseudogenization and Resurrection of a Speciation Gene

(2018) Korinna Esfeld et al.   CURRENT BIOLOGY

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

(2018) Jisen Zhang et al.   NATURE GENETICS

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement

(2017) Kelly J. Vining et al.   Molecular Plant

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus

(2017) Anna Stein et al.   PLANT BIOTECHNOLOGY JOURNAL

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

(2017) Patrick P. Edger et al.   PLANT CELL

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC BIOLOGY

Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens

(2016) Hyun Uk Kim et al.   BMC GENOMICS

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

In Vivoandin VitroEvidence for Biochemical Coupling of Reactions Catalyzed by Lysophosphatidylcholine Acyltransferase and Diacylglycerol Acyltransferase

(2015) Xue Pan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome

(2015) Atsushi Fukushima et al.   PLoS One

GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana

(2015) Johanna A. Bac-Molenaar et al.   PLoS One

Extensive and Biased Intergenomic Nonreciprocal DNA Exchanges Shaped a Nascent Polyploid Genome, Gossypium (Cotton)

(2014) Hui Guo et al.   GENETICS

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

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

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

(2014) B. Chalhoub et al.   SCIENCE

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

(2013) MARC LOHSE et al.   PLANT CELL AND ENVIRONMENT

The Promoter Structure Differentiation of a MYB Transcription Factor RLC1 Causes Red Leaf Coloration in Empire Red Leaf Cotton under Light

(2013) Zhenrui Gao et al.   PLoS One

Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat

(2013) Huakun Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

(2012) S. Kumar et al.   BIOINFORMATICS

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

(2012) Elizabeth P. Murchison et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metabolic Interactions between the Lands Cycle and the Kennedy Pathway of Glycerolipid Synthesis in Arabidopsis Developing Seeds

(2012) L. Wang et al.   PLANT CELL

Acyl Editing and Headgroup Exchange Are the Major Mechanisms That Direct Polyunsaturated Fatty Acid Flux into Triacylglycerols

(2012) P. D. Bates et al.   PLANT PHYSIOLOGY

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

(2012) M. Chester et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lignin content in Brassica napus seeds

(2012) Liezhao Liu et al.   THEORETICAL AND APPLIED GENETICS

Comparison of seed characteristics between the cultivated and the weedy types of Perilla species

(2012) Kyu Jin Sa et al.   Horticulture Environment and Biotechnology

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

(2011) Z. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Chromosomal evolution in the plant family Solanaceae

(2010) Feinan Wu et al.   BMC GENOMICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Homoeologous recombination in allopolyploids: the polyploid ratchet

(2009) Robert T. Gaeta et al.   NEW PHYTOLOGIST

Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings

(2008) Antonio Gonzalez et al.   PLANT JOURNAL

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY