A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection

Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin

(2019) Jason Hill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

(2017) P R Berg et al.   HEREDITY

Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly

(2017) Catherine L Peichel et al.   JOURNAL OF HEREDITY

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

(2017) Sangeet Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Centromere evolution and CpG methylation during vertebrate speciation

(2017) Kazuki Ichikawa et al.   Nature Communications

Tracing the origin and evolution of supergene mimicry in butterflies

(2017) Wei Zhang et al.   Nature Communications

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

(2017) Chungang Feng et al.   eLife

The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population

(2017) Axel Künstner et al.   PLoS One

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

(2016) Elaina M. Tuttle et al.   CURRENT BIOLOGY

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

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

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

(2016) Alvaro Martinez Barrio et al.   eLife

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

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

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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

Female ovarian abnormalities and reproductive failure of autumn-spawning herring (Clupea harengus membras) in the Baltic Sea

(2015) Henn Ojaveer et al.   ICES JOURNAL OF MARINE SCIENCE

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

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

(2014) Suhas S.P. Rao et al.   CELL

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

A RAD-Tag Genetic Map for the Platyfish ( Xiphophorus maculatus ) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish

(2014) Angel Amores et al.   GENETICS

The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei

(2014) Eric B. Rondeau 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

Lep-MAP: fast and accurate linkage map construction for large SNP datasets

(2013) Pasi Rastas et al.   BIOINFORMATICS

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

Thermal windows supporting survival of the earliest life stages of Baltic herring (Clupea harengus)

(2012) M. A. Peck et al.   ICES JOURNAL OF MARINE SCIENCE

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

(2012) MORTEN T. LIMBORG et al.   MOLECULAR ECOLOGY

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility

(2012) Freyja Imsland et al.   PLoS Genetics

An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci

(2011) Kevin M. Bradley et al.   G3-Genes Genomes Genetics

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

Genetic variability in Atlantic herring (Clupea harengus harengus): description of protein loci and population data

(2009) LEIF ANDERSSON et al.   HEREDITAS

Temporally stable genetic structure of heavily exploited Atlantic herring (Clupea harengus) in Swedish waters

(2009) L C Larsson et al.   HEREDITY

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE