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

First draft genome of an iconic clownfish species (Amphiprion frenatus )

(2018) Anna Marcionetti et al.   Molecular Ecology Resources

Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly

(2018) Mun Hua Tan et al.   GigaScience

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

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

STRIDE: Species Tree Root Inference from Gene Duplication Events

(2017) David M Emms et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Clownfish in hypoxic anemones replenish host O2 at only localised scales

(2017) N. A. Herbert et al.   Scientific Reports

Larval fish dispersal in a coral-reef seascape

(2017) Glenn R. Almany et al.   Nature Ecology & Evolution

Diel CO2 cycles reduce severity of behavioural abnormalities in coral reef fish under ocean acidification

(2017) Michael D. Jarrold et al.   Scientific Reports

The four elements of within-group conflict in animal societies: an experimental test using the clown anemonefish, Amphiprion percula

(2016) MYL Wong et al.   BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY

Anemonefish personalities influence the strength of mutualistic interactions with host sea anemones

(2016) Philip F. P. Schmiege et al.   MARINE BIOLOGY

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

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

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

First genealogy for a wild marine fish population reveals multigenerational philopatry

(2016) Océane C. Salles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reef fishes can recognize bleached habitat during settlement: sea anemone bleaching alters anemonefish host selection

(2016) Anna Scott et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Genomics Are Transforming Our Understanding of Responses to Climate Change

(2015) Jonathon H. Stillman et al.   BIOSCIENCE

The First Chromosomal Characteristics of Nucleolar Organizer Regions and Karyological Analysis of Pink Anemonefish, Amphiprion perideraion (Perciformes, Amphiprioninae)

(2015) Weerayuth Supiwong et al.   CYTOLOGIA

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

Exposure of clownfish larvae to suspended sediment levels found on the Great Barrier Reef: Impacts on gill structure and microbiome

(2015) Sybille Hess et al.   Scientific Reports

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Mitochondrial DNA Genomes Organization and Phylogenetic Relationships Analysis of Eight Anemonefishes (Pomacentridae: Amphiprioninae)

(2015) Jianlong Li et al.   PLoS One

Why Some Animals Forgo Reproduction in Complex Societies

(2014) Peter Buston et al.   AMERICAN SCIENTIST

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Hybridisation and diversification in the adaptive radiation of clownfishes

(2014) Glenn Litsios et al.   BMC EVOLUTIONARY BIOLOGY

The radiation of the clownfishes has two geographical replicates

(2014) Glenn Litsios et al.   JOURNAL OF BIOGEOGRAPHY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Coral reef fish incorporate multiple sources of visual and chemical information to mediate predation risk

(2013) R.P. Manassa et al.   ANIMAL BEHAVIOUR

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

First Report of Chromosome Analysis of Saddleback Anemonefish, Amphiprion polymnus (Perciformes, Amphiprioninae), in Thailand

(2013) Alongklod Tanomtong et al.   CYTOLOGIA

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Suspended sediment prolongs larval development in a coral reef fish

(2013) A. S. Wenger et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Anemonefish oxygenate their anemone hosts at night

(2013) J. T. Szczebak et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

(2013) W. Iwasaki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Experimental evaluation of imprinting and the role innate preference plays in habitat selection in a coral reef fish

(2013) Danielle L. Dixson et al.   OECOLOGIA

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Climate change and the performance of larval coral reef fishes: the interaction between temperature and food availability

(2013) I. M. McLeod et al.   Conservation Physiology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Near-future carbon dioxide levels alter fish behaviour by interfering with neurotransmitter function

(2012) Göran E. Nilsson et al.   Nature Climate Change

Persistence of self-recruitment and patterns of larval connectivity in a marine protected area network

(2012) Michael L. Berumen et al.   Ecology and Evolution

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Ocean acidification erodes crucial auditory behaviour in a marine fish

(2011) S. D. Simpson et al.   Biology Letters

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Detrimental effects of host anemone bleaching on anemonefish populations

(2011) P. Saenz-Agudelo et al.   CORAL REEFS

Predation risk assessment by larval reef fishes during settlement-site selection

(2011) D. L. Dixson   CORAL REEFS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ocean acidification disrupts the innate ability of fish to detect predator olfactory cues

(2009) Danielle L. Dixson et al.   ECOLOGY LETTERS

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Larval dispersal connects fish populations in a network of marine protected areas

(2009) S. Planes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ocean acidification impairs olfactory discrimination and homing ability of a marine fish

(2009) Philip L. Munday et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemical biology of the mutualistic relationships of sea anemones with fish and crustaceans

(2009) Dietrich Mebs   TOXICON

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

High-throughput functional annotation and data mining with the Blast2GO suite

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

Coral reef fish smell leaves to find island homes

(2008) D. L Dixson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES