Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish

The Genetic Basis of Morphological Diversity in Domesticated Goldfish

(2020) Tetsuo Kon et al.   CURRENT BIOLOGY

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

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish

(2020) Jing Luo et al.   Science Advances

Deeply conserved synteny resolves early events in vertebrate evolution

(2020) Oleg Simakov et al.   Nature Ecology & Evolution

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

(2019) Xiaojun Zhang et al.   Nature Communications

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

(2019) Weijian Zhuang et al.   NATURE GENETICS

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

The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio

(2019) Peng Xu et al.   Nature Communications

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

A re-evaluation of the domestication bottleneck from archaeogenomic evidence

(2018) Robin G Allaby et al.   Evolutionary Applications

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

GSA: Genome Sequence Archive *

(2017) Yanqing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A full-body transcriptome and proteome resource for the European common carp

(2016) I. C. R. M. Kolder et al.   BMC GENOMICS

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

(2016) Xuzhen Wang et al.   Science China-Life Sciences

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

(2016) Wenzhu Peng et al.   Scientific Reports

Rapid divergence and diversification of mammalian duplicate gene functions

(2015) Raquel Assis et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny and polyploidy: Resolving the classification of cyprinine fishes (Teleostei: Cypriniformes)

(2015) Lei Yang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation

(2015) Yaping Wang et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The evolutionary landscape of intergenic trans-splicing events in insects

(2015) Yimeng Kong et al.   Nature Communications

The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio)

(2015) Jiong-Tang Li et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Allopolyploidization is Not So Simple: Evidence from the Origin of the Tribe Cyprinini (Teleostei: Cypriniformes)

(2014) W. Ma et al.   CURRENT MOLECULAR MEDICINE

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Peng Xu et al.   NATURE GENETICS

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

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Measuring gene expression divergence: the distance to keep

(2010) Galina Glazko et al.   Biology Direct

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox 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

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population

(2010) S. M. Bray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

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

Neofunctionalization of Duplicated Genes Under the Pressure of Gene Conversion

(2008) K. M. Teshima et al.   GENETICS