Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution

A chromosome-level assembly of blunt snout bream (Megalobrama amblycephala) reveals an expansion of olfactory receptor genes in freshwater fish

(2021) Han Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mesenchymal Niche-Derived Neuregulin-1 Drives Intestinal Stem Cell Proliferation and Regeneration of Damaged Epithelium

(2020) Thierry Jardé et al.   Cell Stem Cell

Whole genome sequencing of silver carp ( Hypophthalmichthys molitrix ) and bighead carp ( Hypophthalmichthys nobilis ) provide novel insights into their evolution and speciation

(2020) Jianbo Jian et al.   Molecular Ecology Resources

H1 histones control the epigenetic landscape by local chromatin compaction

(2020) Michael A. Willcockson et al.   NATURE

Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture

(2020) Nevin Yusufova et al.   NATURE

Midline morphogenesis of zebrafish foregut endoderm is dependent on Hoxb5b

(2020) Gökhan Dalgin et al.   DEVELOPMENTAL BIOLOGY

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

(2019) Lei Chen et al.   SCIENCE

Immunomodulatory Effects and Induction of Apoptosis by Different Molecular Weight Chitosan Oligosaccharides in Head Kidney Macrophages From Blunt Snout Bream (Megalobrama amblycephala)

(2019) Changsong Wu et al.   Frontiers in Immunology

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

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Hybrid genome assembly and annotation of Danionella translucida

(2019) Mykola Kadobianskyi et al.   Scientific Data

The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus

(2019) Li Ren et al.   GENOME RESEARCH

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

(2019) Peng Xu et al.   Nature Communications

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast

(2018) Jingchuan Luo et al.   NATURE

Creating a functional single-chromosome yeast

(2018) Yangyang Shao et al.   NATURE

The Sinocyclocheilus cavefish genome provides insights into cave adaptation

(2016) Junxing Yang et al.   BMC BIOLOGY

The Realization of the Brain-Gut Interactions with Corticotropin-Releasing Factor and Glucocorticoids

(2016) Ludmila Filaretova et al.   Current Neuropharmacology

The seahorse genome and the evolution of its specialized morphology

(2016) Qiang Lin et al.   NATURE

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

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

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A novel field technique to assess ploidy in introduced Grass Carp (Ctenopharyngodon idella, Cyprinidae)

(2015) Katherine L. Krynak et al.   BIOLOGICAL INVASIONS

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

(2015) Yaping Wang et al.   NATURE GENETICS

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

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics

(2013) Faysal Bibi   BMC EVOLUTIONARY BIOLOGY

Zebrafish Foxi1 provides a neuronal ground state during inner ear induction preceding the Dlx3b/4b-regulated sensory lineage

(2013) S. Hans et al.   DEVELOPMENT

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

(2013) Kerstin Howe et al.   NATURE

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

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research

(2012) C. Kilkenny et al.   OSTEOARTHRITIS AND CARTILAGE

Immunohistochemical Analysis of Histone H3 Modifications in Germ Cells during Mouse Spermatogenesis

(2011) Ning Song et al.   ACTA HISTOCHEMICA ET CYTOCHEMICA

Adaptive seeds tame genomic sequence comparison

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

Human-specific loss of regulatory DNA and the evolution of human-specific traits

(2011) Cory Y. McLean et al.   NATURE

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Cephalic phase responses and appetite

(2010) Paul AM Smeets et al.   NUTRITION REVIEWS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultraconserved coding regions outside the homeobox of mammalian Hox genes

(2008) Zhenguo Lin et al.   BMC EVOLUTIONARY BIOLOGY

Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes

(2008) Pavla Navratilova et al.   DEVELOPMENTAL BIOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY