Genomic consequences of domestication of the Siamese fighting fish

Significantly improving the quality of genome assemblies through curation

(2021) Kerstin Howe et al.   GigaScience

Genomic basis of striking fin shapes and colours in the fighting fish

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

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

fastsimcoal2: demographic inference under complex evolutionary scenarios

(2021) Laurent Excofffier et al.   BIOINFORMATICS

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Animal domestication in the era of ancient genomics

(2020) Laurent A. F. Frantz et al.   NATURE REVIEWS GENETICS

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into human genetic variation and population history from 929 diverse genomes

(2020) Anders Bergström et al.   SCIENCE

Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master's Course

(2020) Stefan Prost et al.   G3-Genes Genomes Genetics

Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase

(2020) Anahita Daruwalla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genetic mechanism for sexual dichromatism in birds

(2020) Małgorzata A. Gazda et al.   SCIENCE

The human mitochondrial enzyme BCO2 exhibits catalytic activity towards carotenoids and apocarotenoids

(2020) Linda D Thomas et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files

(2020) Milan Malinsky et al.   Molecular Ecology Resources

A comparison of humans and baboons suggests germline mutation rates do not track cell divisions

(2020) Felix L. Wu et al.   PLOS BIOLOGY

Genetic Adaptation in New York City Rats

(2020) Arbel Harpak et al.   Genome Biology and Evolution

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

(2020) Young Mi Kwon et al.   PLOS BIOLOGY

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication

(2019) Zelin Chen et al.   Science Advances

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Accurate, scalable and integrative haplotype estimation

(2019) Olivier Delaneau et al.   Nature Communications

Structural and mechanistic aspects of carotenoid cleavage dioxygenases (CCDs)

(2019) Anahita Daruwalla et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color

(2019) Hanna Helgeland et al.   Scientific Reports

Male-specific Dmrt1 is a candidate sex determination gene in spotted scat ( Scatophagus argus )

(2018) Umar Farouk Mustapha et al.   AQUACULTURE

Genetic Diversity on the Sex Chromosomes

(2018) Melissa A Wilson Sayres   Genome Biology and Evolution

ALKALs are in vivo ligands for ALK family receptor tyrosine kinases in the neural crest and derived cells

(2018) Andrey Fadeev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Association mapping from sequencing reads using k-mers

(2018) Atif Rahman et al.   eLife

Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity

(2018) Alexandre M. Harris et al.   GENETICS

Unusual Diversity of Sex Chromosomes in African Cichlid Fishes

(2018) William J. Gammerdinger et al.   Genes

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

(2018) Milan Malinsky et al.   Nature Ecology & Evolution

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman et al.   GENOME RESEARCH

Hidden genetic variation shapes the structure of functional elements in Drosophila

(2017) Mahul Chakraborty et al.   NATURE GENETICS

Alk and Ltk ligands are essential for iridophore development in zebrafish mediated by the receptor tyrosine kinase Ltk

(2017) Elizabeth S. Mo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Centromere evolution and CpG methylation during vertebrate speciation

(2017) Kazuki Ichikawa et al.   Nature Communications

A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy

(2017) Russell Corbett-Detig et al.   PLoS Genetics

Genome editing reveals dmrt1 as an essential male sex-determining gene in Chinese tongue sole (Cynoglossus semilaevis)

(2017) Zhongkai Cui et al.   Scientific Reports

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

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

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks

(2015) L. Bunnefeld et al.   GENETICS

Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

(2015) Florencia Schlamp et al.   MOLECULAR ECOLOGY

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

(2015) M. Malinsky et al.   SCIENCE

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

Note on the karyotype and NOR location of Siamese fighting fish Betta splendens (Perciformes, Osphronemidae)

(2014) Furgala-Selezniow Grazyna et al.   CARYOLOGIA

TALEN-mediated mutagenesis in zebrafish reveals a role forr-spondin 2in fin ray and vertebral development

(2014) Yoshiaki Tatsumi et al.   FEBS LETTERS

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

(2014) C. A. Wilson et al.   GENETICS

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

Leucophores are similar to xanthophores in their specification and differentiation processes in medaka

(2014) T. Kimura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

(2013) Gro Nilsen et al.   BMC GENOMICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Tracing the Emergence of a Novel Sex-Determining Gene in Medaka, Oryzias luzonensis

(2012) T. Myosho et al.   GENETICS

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou 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

A Y-linked anti-Mullerian hormone duplication takes over a critical role in sex determination

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

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

(2011) H. Li   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Opposite roles of DMRT1 and its W-linked paralogue, DM-W, in sexual dimorphism of Xenopus laevis: implications of a ZZ/ZW-type sex-determining system

(2010) S. Yoshimoto et al.   DEVELOPMENT

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

(2010) A. McKenna et al.   GENOME RESEARCH

Molecular and morphological evidence supports the species status of the Mahachai fighter Betta sp. Mahachai and reveals new species of Betta from Thailand

(2010) N. Sriwattanarothai et al.   JOURNAL OF FISH BIOLOGY

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Modularity in the Hippo signaling pathway

(2010) Marius Sudol et al.   TRENDS IN BIOCHEMICAL SCIENCES

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Zebrafish mutations in gart and paics identify crucial roles for de novo purine synthesis in vertebrate pigmentation and ocular development

(2009) A. Ng et al.   DEVELOPMENT

Fast model-based estimation of ancestry in unrelated individuals

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

The avian Z-linked gene DMRT1 is required for male sex determination in the chicken

(2009) Craig A. Smith et al.   NATURE

Unknown

(2009) Adisorn Monvises et al.   SCIENCEASIA

Defects in ErbB-Dependent Establishment of Adult Melanocyte Stem Cells Reveal Independent Origins for Embryonic and Regeneration Melanocytes

(2009) Keith A. Hultman et al.   PLoS Genetics