Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

(2019) Bruno Louro et al.   GigaScience

Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

(2019) Nina O. Therkildsen et al.   SCIENCE

Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation

(2019) Qiaowei Pan et al.   PLoS Genetics

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Identification of the sex-determining locus in grass puffer (Takifugu niphobles) provides evidence for sex-chromosome turnover in a subset of Takifugu species

(2018) Risa Ieda et al.   PLoS One

Draft genome of the Peruvian scallop Argopecten purpuratus

(2018) Chao Li et al.   GigaScience

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser 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

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

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

(2017) Olga Dudchenko et al.   SCIENCE

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA

(2017) S. Austin Hammond et al.   Nature Communications

Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron

(2016) William J. Gammerdinger et al.   BMC GENOMICS

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database

(2016) Jeremy Pasquier et al.   BMC GENOMICS

Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

(2016) Nina Overgaard Therkildsen et al.   Molecular Ecology Resources

Signaling Receptors for TGF-β Family Members

(2016) Carl-Henrik Heldin et al.   Cold Spring Harbor Perspectives in Biology

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

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

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish

(2015) Kathrin Reichwald et al.   CELL

A Tandem Duplicate of Anti-Müllerian Hormone with a Missense SNP on the Y Chromosome Is Essential for Male Sex Determination in Nile Tilapia, Oreochromis niloticus

(2015) Minghui Li et al.   PLoS Genetics

Physical–biological coupling and the challenge of understanding fish recruitment in freshwater lakes

(2014) Stuart A. Ludsin et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Mechanisms driving recruitment variability in fish: comparisons between the Laurentian Great Lakes and marine systems

(2014) J. J. Pritt et al.   ICES JOURNAL OF MARINE SCIENCE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

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

Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene

(2013) Eric B Rondeau et al.   BMC GENOMICS

Meta-analysis reveals lower genetic diversity in overfished populations

(2013) Malin L. Pinsky et al.   MOLECULAR ECOLOGY

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

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 Trans-Species Missense SNP in Amhr2 Is Associated with Sex Determination in the Tiger Pufferfish, Takifugu rubripes (Fugu)

(2012) Takashi Kamiya et al.   PLoS Genetics

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Are homologies in vertebrate sex determination due to shared ancestry or to limited options?

(2010) Jennifer A Marshall Graves et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic and morphological divergence reveals local subdivision of perch (Perca fluviatilis L.)

(2009) SARA BERGEK et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Quantitative measures for the management and comparison of annotated genomes

(2009) Karen Eilbeck et al.   BMC BIOINFORMATICS

Yellow perch (Perca flavescens) stock structure in Lake Michigan: an analysis using mark–recapture data

(2008) David C. Glover et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES