Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium

3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis

(2021) Xin Luo et al.   CELL

Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton

(2021) Maojun Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic basis of geographic differentiation and fiber improvement in cultivated cotton

(2021) Shoupu He et al.   NATURE GENETICS

Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton

(2021) Daojun Yuan et al.   Advanced Science

Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence

(2021) Zhaoen Yang et al.   BMC BIOLOGY

Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

(2021) Yuyun Zhang et al.   GENOME RESEARCH

Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes

(2021) Xiaohui Zhang et al.   Molecular Plant

Multi‐omics assisted identification of the key and species‐specific regulatory components of drought‐tolerant mechanisms in Gossypium stocksii

(2021) Dongliang Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility

(2021) Corrinne E Grover et al.   G3-Genes Genomes Genetics

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

(2020) Arya Kaul et al.   Nature Protocols

The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution

(2020) Corrinne E. Grover et al.   G3-Genes Genomes Genetics

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

(2020) Gai Huang et al.   NATURE GENETICS

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

(2020) Z. Jeffrey Chen et al.   NATURE GENETICS

Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication

(2020) Sijia Lu et al.   NATURE GENETICS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

(2019) Joshua A. Udall et al.   G3-Genes Genomes Genetics

The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants

(2019) Joshua A. Udall et al.   Frontiers in Plant Science

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

(2018) Karl A. G. Kremling et al.   NATURE

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

(2018) Sarah M. Urbut et al.   NATURE GENETICS

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

(2018) Maojun Wang et al.   NATURE GENETICS

Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing

(2017) Corrinne E Grover et al.   Genome Biology and Evolution

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

(2017) Xiao-Tao Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton

(2016) Jinlei Han et al.   PLANT JOURNAL

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

(2015) Olgert Denas et al.   BMC GENOMICS

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

Re-evaluating the phylogeny of allopolyploid Gossypium L.

(2015) Corrinne E. Grover et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Identification of chromosomal translocation hotspots via scan statistics

(2014) Israel T. Silva 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

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

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

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

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

(2012) Hui Li et al.   NATURE GENETICS

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

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

Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants

(2009) J. S. Hawkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Last Glacial Maximum

(2009) P. U. Clark et al.   SCIENCE

Heterochromatin: A Rapidly Evolving Species Barrier

(2009) Stacie E. Hughes et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY