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

EGPS 1.0: Comprehensive software for multi-omic and evolutionary analyses

(2019) Dalang Yu et al.   National Science Review

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

The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation

(2018) Jonathan F Wendel et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross

(2016) Shaojun Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family

(2016) You-Yi Kuang et al.   Scientific Reports

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

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

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

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

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

New insights into the maternal to zygotic transition

(2014) A. R. Langley et al.   DEVELOPMENT

Tempo and mode of recurrent polyploidization in the Carassius auratus species complex (Cypriniformes, Cyprinidae)

(2014) J Luo et al.   HEREDITY

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

(2014) Shengyi Liu et al.   Nature Communications

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

Polyploids and hybrids in changing environments: winners or losers in the struggle for adaptation?

(2013) B K Mable   HEREDITY

Two Evolutionarily Distinct Classes of Paleopolyploidy

(2013) Olivier Garsmeur et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Kerstin Howe et al.   NATURE

Origin of Chinese Goldfish and Sequential Loss of Genetic Diversity Accompanies New Breeds

(2013) Shu-Yan Wang et al.   PLoS One

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

(2013) Alex R. Hastie et al.   PLoS One

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Altered Patterns of Fractionation and Exon Deletions in Brassica rapa Support a Two-Step Model of Paleohexaploidy

(2012) H. Tang et al.   GENETICS

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

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

Genomic and transcriptomic alterations following hybridisation and genome doubling in trigenomic allohexaploid Brassica carinata × Brassica rapa

(2012) Y. Xu et al.   PLANT BIOLOGY

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

(2012) J. A. Birchler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Genomic Clues to the Evolutionary Success of Polyploid Plants

(2008) Matthew J. Hegarty et al.   CURRENT BIOLOGY