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

Less effective selection leads to larger genomes

(2017) Tristan Lefébure et al.   GENOME RESEARCH

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

(2017) Amanda R. De La Torre et al.   MOLECULAR BIOLOGY AND EVOLUTION

The true tempo of evolutionary radiation and decline revealed on the Hawaiian archipelago

(2017) Jun Y. Lim et al.   NATURE

Dynamics of genome size evolution in birds and mammals

(2017) Aurélie Kapusta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response

(2017) Vivien Horváth et al.   TRENDS IN GENETICS

The mode and tempo of genome size evolution in the subgenus Sophophora

(2017) Carl E. Hjelmen et al.   PLoS One

Recent and dynamic transposable elements contribute to genomic divergence under asexuality

(2016) Julie Ferreira de Carvalho et al.   BMC GENOMICS

Genetic drift and mutational hazard in the evolution of salamander genomic gigantism

(2016) Erik Roger Mohlhenrich et al.   EVOLUTION

Independent Domestication of Two Old World Cotton Species

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

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Genome Stability and Evolution: Attempting a Holistic View

(2016) Ingo Schubert et al.   TRENDS IN PLANT SCIENCE

Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data

(2016) Hannah M. Tetreault et al.   G3-Genes Genomes Genetics

Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life

(2016) Way Sung et al.   G3-Genes Genomes Genetics

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Sealer: a scalable gap-closing application for finishing draft genomes

(2015) Daniel Paulino et al.   BMC BIOINFORMATICS

Analysis of the giant genomes ofFritillaria(Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size

(2015) Laura J. Kelly et al.   NEW PHYTOLOGIST

Genome size correlates with reproductive fitness in seed beetles

(2015) Göran Arnqvist et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus

(2015) Giang T. H. Vu et al.   Plant Genome

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

(2015) Jiří Macas et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The hidden side of plant invasions: the role of genome size

(2014) Jan Suda et al.   NEW PHYTOLOGIST

Genetic Diversity of the Endangered Endemic Hawaiian Genus Kokia (Malvaceae)

(2014) Alison R. Sherwood et al.   PACIFIC SCIENCE

Insights into the Maize Pan-Genome and Pan-Transcriptome

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

Genome-Wide Analysis of Repeat Diversity across the Family Musaceae

(2014) Petr Novák 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

Role of adaptive and non-adaptive mechanisms forming complex patterns of genome size variation in six cytotypes of polyploid Allium oleraceum (Amaryllidaceae) on a continental scale

(2013) M. Duchoslav et al.   ANNALS OF BOTANY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Genome size variation in wild and cultivated maize along altitudinal gradients

(2013) Concepción M. Díez et al.   NEW PHYTOLOGIST

BLAST: a more efficient report with usability improvements

(2013) Grzegorz M. Boratyn et al.   NUCLEIC ACIDS RESEARCH

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton

(2012) Lex E Flagel et al.   BMC GENOMICS

Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation

(2012) Tim Kahlke et al.   BMC GENOMICS

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

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

Paleocene Malvaceae from northern South America and their biogeographical implications

(2011) Mónica R. Carvalho et al.   AMERICAN JOURNAL OF BOTANY

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Drift and Genome Complexity Revisited

(2011) Kenneth D. Whitney et al.   PLoS Genetics

Statistical Inference on the Mechanisms of Genome Evolution

(2011) Michael Lynch   PLoS Genetics

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

Gravity anomalies of the Northern Hawaiian Islands: Implications on the shield evolutions of Kauai and Niihau

(2010) Ashton F. Flinders et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Did Genetic Drift Drive Increases in Genome Complexity?

(2010) Kenneth D. Whitney et al.   PLoS Genetics

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

(2009) Z. Tian et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Impact of transposable elements on the organization and function of allopolyploid genomes

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

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

Intrapopulation Genome Size Dynamics in Festuca pallens

(2008) Petr Šmarda et al.   ANNALS OF BOTANY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Population size and genome size in fishes: a closer look

(2008) T. Ryan Gregory et al.   GENOME

Genome size evolution: Within-species variation in genome size

(2008) C Biémont   HEREDITY

A Phylogenetic Analysis of Indel Dynamics in the Cotton Genus

(2008) C. E. Grover et al.   MOLECULAR BIOLOGY AND EVOLUTION