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

Genetic basis of ruminant headgear and rapid antler regeneration

(2019) Yu Wang et al.   SCIENCE

CRISPR/Cas9-mediated MSTN disruption and heritable mutagenesis in goats causes increased body mass

(2018) X. Wang et al.   ANIMAL GENETICS

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

DiscoVista: Interpretable visualizations of gene tree discordance

(2018) Erfan Sayyari et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring Phylogenetic Networks Using PhyloNet

(2018) Dingqiao Wen et al.   SYSTEMATIC BIOLOGY

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

PAX9 regulates squamous cell differentiation and carcinogenesis in the oro-oesophageal epithelium

(2017) Zhaohui Xiong et al.   JOURNAL OF PATHOLOGY

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus 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

On the origin of modern humans: Asian perspectives

(2017) Christopher J. Bae et al.   SCIENCE

Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands

(2017) Olja Toljagić et al.   SYSTEMATIC BIOLOGY

Draft genome of the milu (Elaphurus davidianus)

(2017) Chenzhou Zhang et al.   GigaScience

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

(2017) Panayotis Vlastaridis et al.   GigaScience

Establishment and phenotypic analysis of an Mstn knockout rat

(2016) Hao Gu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Epithelial sodium channel (ENaC) family: Phylogeny, structure–function, tissue distribution, and associated inherited diseases

(2016) Israel Hanukoglu et al.   GENE

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection

(2016) Adriana García-Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Giraffe genome sequence reveals clues to its unique morphology and physiology

(2016) Morris Agaba et al.   Nature Communications

Isozygous and selectable marker-free MSTN knockout cloned pigs generated by the combined use of CRISPR/Cas9 and Cre/LoxP

(2016) Yanzhen Bi et al.   Scientific Reports

Systematic relationships of five newly sequenced cervid species

(2016) Nicola S. Heckeberg et al.   PeerJ

Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues

(2016) Ruidong Xiang et al.   PeerJ

Generation of biallelic knock-out sheep via gene-editing and somatic cell nuclear transfer

(2016) Honghui Li et al.   Scientific Reports

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)

(2015) S. Gallus et al.   GENE

Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations?

(2015) Zhengting Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ballgown bridges the gap between transcriptome assembly and expression analysis

(2015) Alyssa C Frazee et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Systematics and Evolution of the Miocene Three-Horned Palaeomerycid Ruminants (Mammalia, Cetartiodactyla)

(2015) Israel M. Sánchez et al.   PLoS One

Old World Ruminant Morphophysiology, Life History, and Fossil Record: Exploring Key Innovations of a Diversification Sequence

(2014) Marcus Clauss et al.   ANNALES ZOOLOGICI FENNICI

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger 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

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

(2014) Min Tang et al.   NUCLEIC ACIDS RESEARCH

Efficient Generation of Myostatin (MSTN) Biallelic Mutations in Cattle Using Zinc Finger Nucleases

(2014) Junjie Luo et al.   PLoS One

The sheep genome illuminates biology of the rumen and lipid metabolism

(2014) Y. Jiang et al.   SCIENCE

Statistical binning enables an accurate coalescent-based estimation of the avian tree

(2014) S. Mirarab et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Camelid genomes reveal evolution and adaptation to desert environments

(2014) Huiguang Wu et al.   Nature Communications

Phylogenetic analyses and improved resolution of the family Bovidae based on complete mitochondrial genomes

(2013) Chengzhong Yang et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

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

Serpins, Immunity and Autoimmunity: Old Molecules, New Functions

(2013) Mariele Gatto et al.   CLINICAL REVIEWS IN ALLERGY & IMMUNOLOGY

BMP signaling controls muscle mass

(2013) Roberta Sartori et al.   NATURE GENETICS

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Fibroblast growth factor signaling in mammalian tooth development

(2013) Chun-Ying Li et al.   Odontology

SOX9 Duplication Linked to Intersex in Deer

(2013) Regina Kropatsch et al.   PLoS One

Are There Really Twice as Many Bovid Species as We Thought?

(2013) Rasmus Heller et al.   SYSTEMATIC BIOLOGY

The tiger genome and comparative analysis with lion and snow leopard genomes

(2013) Yun Sung Cho et al.   Nature Communications

Draft genome sequence of the Tibetan antelope

(2013) Ri-Li Ge et al.   Nature Communications

Generation length for mammals

(2013) Moreno Di Marco et al.   Nature Conservation-Bulgaria

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

The bonobo genome compared with the chimpanzee and human genomes

(2012) Kay Prüfer et al.   NATURE

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

The yak genome and adaptation to life at high altitude

(2012) Qiang Qiu et al.   NATURE GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Mechanisms of Leukocyte Transendothelial Migration

(2011) William A. Muller   Annual Review of Pathology-Mechanisms of Disease

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Aldo-keto reductases AKR1C1, AKR1C2 and AKR1C3 may enhance progesterone metabolism in ovarian endometriosis

(2011) N. Hevir et al.   CHEMICO-BIOLOGICAL INTERACTIONS

Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes

(2011) Alexandre Hassanin et al.   COMPTES RENDUS BIOLOGIES

Adaptive seeds tame genomic sequence comparison

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

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

(2011) A. Hobolth et al.   GENOME RESEARCH

A new, early Puercan (earliest Paleocene) species of Purgatorius (Plesiadapiformes, Primates) from Saskatchewan, Canada

(2011) Richard C. Fox et al.   JOURNAL OF PALEONTOLOGY

Overexpression of SERPIN B3 promotes epithelial proliferation and lung fibrosis in mice

(2011) Francesca Lunardi et al.   LABORATORY INVESTIGATION

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Species-specific responses of Late Quaternary megafauna to climate and humans

(2011) Eline D. Lorenzen et al.   NATURE

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

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics

(2011) Christopher M. Seabury et al.   PLoS One

Evolution of ruminant headgear: a review

(2011) E. B. Davis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

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

Age-dependent chromosomal distribution of male-biased genes in Drosophila

(2010) Y. E. Zhang et al.   GENOME RESEARCH

RUMINANT NUTRITION SYMPOSIUM: Molecular adaptation of ruminal epithelia to highly fermentable diets1

(2010) G. B. Penner et al.   JOURNAL OF ANIMAL SCIENCE

Invited review: Ruminant ecology and evolution: Perspectives useful to ruminant livestock research and production

(2010) T.J. Hackmann et al.   JOURNAL OF DAIRY SCIENCE

The genus Hispanomeryx (Mammalia, Ruminantia, Moschidae) and its bearing on musk deer phylogeny and systematics

(2010) ISRAEL M. SÁNCHEZ et al.   PALAEONTOLOGY

Transcriptional regulation of bone formation by the osteoblast-specific transcription factor Osx

(2010) Chi Zhang   Journal of Orthopaedic Surgery and Research

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

(2010) Yong E. Zhang et al.   PLOS BIOLOGY

Genetics of Athletic Performance

(2009) Elaine A. Ostrander et al.   Annual Review of Genomics and Human Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes

(2009) Bhanu Telugu et al.   BMC GENOMICS

Pathogen Recognition and Inflammatory Signaling in Innate Immune Defenses

(2009) T. H. Mogensen   CLINICAL MICROBIOLOGY REVIEWS

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

(2009) R. Li et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Bovidae (Mammalia) from the Lower Pliocene of Chad

(2009) Denis Geraads et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

(2009) J. E. Decker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

(2009) C. M. Wade et al.   SCIENCE

A whole-genome assembly of the domestic cow, Bos taurus

(2009) Aleksey V Zimin et al.   GENOME BIOLOGY

Enamel Defects and Ameloblast-specific Expression inEnamKnock-out/lacZKnock-in Mice

(2008) Jan C.-C. Hu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

New hippotragini (Bovidae, Mammalia) from the Late Miocene of Toros-Menalla (Chad)

(2008) Denis Geraads et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

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

(2008) Brian J Haas et al.   GENOME BIOLOGY

Regulation of bone development and maintenance by Runx2

(2007) Toshihisa Komori   Frontiers in Bioscience-Landmark