Chromosome‐level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water

A de novo chromosome‐level genome assembly of Coregonus sp. “ Balchen ”: One representative of the Swiss Alpine whitefish radiation

(2020) Rishi De‐Kayne et al.   Molecular Ecology Resources

Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae

(2019) Yongshuang Xiao et al.   GigaScience

Chromosome‐level genome assembly of Triplophysa tibetana , a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

(2019) Xuefen Yang et al.   Molecular Ecology Resources

Divergence, evolution and adaptation in ray-finned fish genomes

(2019) Chao Bian et al.   Science China-Life Sciences

Chromosome-Level Assembly of the Chinese Seabass (Lateolabrax maculatus) Genome

(2019) Baohua Chen et al.   Frontiers in Genetics

A chromosome‐level genome assembly of the giant grouper ( Epinephelus lanceolatus ) provides insights into its innate immunity and rapid growth

(2019) Qian Zhou et al.   Molecular Ecology Resources

A key metabolic gene for recurrent freshwater colonization and radiation in fishes

(2019) Asano Ishikawa et al.   SCIENCE

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

(2019) Mats E. Pettersson et al.   GENOME RESEARCH

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

(2018) Lily C. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Divergent Genomes of Teleosts

(2018) Vydianathan Ravi et al.   Annual Review of Animal Biosciences

Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii

(2018) Zhiyong Zhang et al.   GigaScience

Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

(2018) Robert Lehmann et al.   Molecular Ecology Resources

Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon

(2018) Kyle Wellband et al.   MOLECULAR ECOLOGY

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

(2017) Sergey Koren et al.   GENOME RESEARCH

claudin-10 isoform expression and cation selectivity change with salinity in salt-secreting epithelia of Fundulus heteroclitus

(2017) William S. Marshall et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

A perspective on Na and K channel inactivation

(2017) Clay M. Armstrong et al.   JOURNAL OF GENERAL PHYSIOLOGY

Genome architecture enables local adaptation of Atlantic cod despite high connectivity

(2017) Julia M. I. Barth 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

Regulation of gill claudin paralogs by salinity, cortisol and prolactin in Mozambique tilapia ( Oreochromis mossambicus )

(2016) Christian K. Tipsmark et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Chromosome-Specific Centromere Sequences Provide an Estimate of the Ancestral Chromosome 2 Fusion Event in Hominin Genomes

(2016) Karen H. Miga   JOURNAL OF HEREDITY

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

(2016) Shubha Vij et al.   PLoS Genetics

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

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

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Water Transport and Functional Dynamics of Aquaporins in Osmoregulatory Organs of Fishes

(2015) Steffen S. Madsen et al.   BIOLOGICAL BULLETIN

Chromosomal polymorphism in mammals: an evolutionary perspective

(2015) Gauthier Dobigny et al.   BIOLOGICAL REVIEWS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

LOCAL ADAPTATION AND THE EVOLUTION OF CHROMOSOME FUSIONS

(2014) Rafael F. Guerrero et al.   EVOLUTION

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

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

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

Phylogenetic revision of the claudin gene family

(2013) David A. Baltzegar et al.   Marine Genomics

Adaptation of teleosts to very high salinity

(2012) Gary Laverty et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Genome evolution: extinction, continuation or explosion?

(2012) JS (Pat) Heslop-Harrison   CURRENT OPINION IN PLANT BIOLOGY

Effects of temperature, salinity and body size on routine metabolism of coastal largemouth bassMicropterus salmoides

(2012) D. C. Glover et al.   JOURNAL OF FISH BIOLOGY

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Why are there so few fish in the sea?

(2012) G. Carrete Vega et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mechanisms and models of the active transport of ions and the transformation of energy in intracellular compartments

(2012) Alexey V. Melkikh et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Intestinal fluid absorption in anadromous salmonids: importance of tight junctions and aquaporins

(2012) Kristina S. Sundell et al.   Frontiers in Physiology

Predicted expansion of the claudin multigene family

(2011) Katsuhiko Mineta et al.   FEBS LETTERS

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Genetic Relationships among Populations of Florida Bass

(2011) Brandon L. Barthel et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A ‘higher order’ of telomere regulation: telomere heterochromatin and telomeric RNAs

(2009) Stefan Schoeftner et al.   EMBO JOURNAL

Regulation and roles for claudin-family tight junction proteins

(2009) Mary K. Findley et al.   IUBMB LIFE

Physiology and Function of the Tight Junction

(2009) J. M. Anderson et al.   Cold Spring Harbor Perspectives in Biology

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH