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

A comprehensive analysis of teleost MHC class I sequences

(2015) Unni Grimholt et al.   BMC EVOLUTIONARY BIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Long-Read Single Molecule Sequencing to Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome

(2015) F. J. Krsticevic et al.   G3-Genes Genomes Genetics

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Early Depletion of Primordial Germ Cells in Zebrafish Promotes Testis Formation

(2015) Keh-Weei Tzung et al.   Stem Cell Reports

Ragout--a reference-assisted assembly tool for bacterial genomes

(2014) M. Kolmogorov et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses

(2014) Guilherme T. Valente et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle

(2014) Songlin Chen et al.   NATURE GENETICS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Small-scale transcriptomics reveals differences among gonadal stages in Asian seabass (Lates calcarifer)

(2014) Preethi Ravi et al.   Reproductive Biology and Endocrinology

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

(2014) Mbaye Tine et al.   Nature Communications

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

Genes on B chromosomes of vertebrates

(2014) Alexey I Makunin et al.   Molecular Cytogenetics

Annotated features of domestic cat – Felis catus genome

(2014) Gaik Tamazian et al.   GigaScience

Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome

(2014) Inna S. Kuznetsova et al.   Frontiers in Genetics

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Gonad Differentiation in Zebrafish Is Regulated by the Canonical Wnt Signaling Pathway1

(2013) Rajini Sreenivasan et al.   BIOLOGY OF REPRODUCTION

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Zebrafish sex: a complicated affair

(2013) W. C. Liew et al.   Briefings in Functional Genomics

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

(2013) Manfred Schartl et al.   NATURE GENETICS

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

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

WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes

(2013) K. J. Hoff et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

Roundup 2.0: enabling comparative genomics for over 1800 genomes

(2012) T. F. DeLuca et al.   BIOINFORMATICS

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

(2012) M. B. Stocks et al.   BIOINFORMATICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Activation of NF-κB Protein Prevents the Transition from Juvenile Ovary to Testis and Promotes Ovarian Development in Zebrafish

(2012) Ajay Pradhan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evidence for Female-Biased Dispersal in the Protandrous Hermaphroditic Asian Seabass, Lates calcarifer

(2012) Gen Hua Yue et al.   PLoS One

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

(2011) Chun Ming Wang et al.   BMC GENOMICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Genetic variation and population structure of Asian seabass (Lates calcarifer) in the Asia-Pacific region

(2009) Gen Hua Yue et al.   AQUACULTURE

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication

(2009) Yukuto Sato et al.   BMC EVOLUTIONARY BIOLOGY

Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway

(2009) Yukuto Sato et al.   BMC Systems Biology

Genetic variation exists for telomeric array organization within and among the genomes of normal, immortalized, and transformed chicken systems

(2009) Thomas H. O’Hare et al.   CHROMOSOME RESEARCH

Pigmentation Pathway Evolution after Whole-Genome Duplication in Fish

(2009) Ingo Braasch et al.   Genome Biology and Evolution

Fast model-based estimation of ancestry in unrelated individuals

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

PatMaN: rapid alignment of short sequences to large databases

(2008) Kay Prüfer et al.   BIOINFORMATICS

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

(2008) Véronique Douard et al.   BMC EVOLUTIONARY BIOLOGY

Analysis of the largest tandemly repeated DNA families in the human genome

(2008) Peter E Warburton et al.   BMC GENOMICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Rapidly evolving fish genomes and teleost diversity

(2008) Vydianathan Ravi et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

genBlastA: Enabling BLAST to identify homologous gene sequences

(2008) R. She et al.   GENOME RESEARCH

DNA barcoding reveals a likely second species of Asian sea bass (barramundi) (Lates calcarifer)

(2008) R. D. Ward et al.   JOURNAL OF FISH BIOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE