Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

(2019) Yan Hu et al.   NATURE GENETICS

Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield

(2018) Zhiying Ma et al.   NATURE GENETICS

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

(2018) Xiongming Du et al.   NATURE GENETICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

(2018) Hong-Qing Ling et al.   NATURE

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

(2018) Maojun Wang et al.   NATURE GENETICS

Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

(2017) Simon H. Martin et al.   GENETICS

Cotton functional genomics reveals global insight into genome evolution and fiber development

(2017) Zhiguo Wu et al.   Journal of Genetics and Genomics

The draft genome of tropical fruit durian (Durio zibethinus)

(2017) Bin Tean Teh et al.   NATURE GENETICS

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

(2017) Lei Fang et al.   NATURE GENETICS

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

(2017) Simon H. Martin et al.   GENETICS

Complex modular architecture around a simple toolkit of wing pattern genes

(2017) Steven M. Van Belleghem et al.   Nature Ecology & Evolution

Independent Domestication of Two Old World Cotton Species

(2016) Simon Renny-Byfield et al.   Genome Biology and Evolution

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient hybridization and genomic stabilization in a swordtail fish

(2016) Molly Schumer et al.   MOLECULAR ECOLOGY

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

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

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

Genome-scale analysis of the cottonKCSgene family revealed a binary mode of action for gibberellin A regulated fiber growth

(2015) Guang-Hui Xiao et al.   Journal of Integrative Plant Biology

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of the cultivated cotton Gossypium arboreum

(2014) Fuguang Li et al.   NATURE GENETICS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

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

MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING

(2013) James B. Pease et al.   EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Archaeogenomic Evidence of Punctuated Genome Evolution in Gossypium

(2012) S. A. Palmer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

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

(2010) A. McKenna et al.   GENOME RESEARCH

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS