Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture

Direct determination of diploid genome sequences

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

Application of next generation sequencing in clinical microbiology and infection prevention

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

Use of the GeneReader NGS System in a clinical pathology laboratory: a comparative study

(2017) Ulrike Koitzsch et al.   JOURNAL OF CLINICAL PATHOLOGY

Production of transgenic pig as an Alzheimer’s disease model using a multi-cistronic vector system

(2017) Seung-Eun Lee et al.   PLoS One

Ancient genomic changes associated with domestication of the horse

(2017) Pablo Librado et al.   SCIENCE

The Mitochondrial Basis of Aging and Age-Related Disorders

(2017) Sarika Srivastava   Genes

Prevalence of colistin resistance gene (mcr-1) containing Enterobacteriaceae in feces of patients attending a tertiary care hospital and detection of a mcr-1 containing, colistin susceptible E. coli

(2017) Elisabeth M. Terveer et al.   PLoS One

Comparative Transcriptomic Analyses by RNA-seq to Elucidate Differentially Expressed Genes in the Muscle of Korean Thoroughbred Horses

(2016) Mrinmoy Ghosh et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs

(2016) Mrinmoy Ghosh et al.   BMC GENETICS

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

(2016) Marjolein F. Q. Kluytmans-van den Bergh et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases

(2016) Mikolaj M. Raszek et al.   Frontiers in Genetics

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

High-throughput sequencing in veterinary infection biology and diagnostics

(2016) S. BELAK et al.   REVUE SCIENTIFIQUE ET TECHNIQUE-OFFICE INTERNATIONAL DES EPIZOOTIES

Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae

(2016) Kai Zhou et al.   Scientific Reports

Evaluation of body growth and immunity-related differentially expressed genes through deep RNA sequencing in the piglets of Jeju native pig and Berkshire

(2015) M. Ghosh et al.   ANIMAL GENETICS

An Integrated In Silico Approach for the Structural and Functional Exploration of Lipocalin 2 and its Functional Insights with Metalloproteinase 9 and Lipoprotein Receptor-Related Protein 2

(2015) Mrinmoy Ghosh et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Third Report on Chicken Genes and Chromosomes 2015

(2015) Michael Schmid et al.   CYTOGENETIC AND GENOME RESEARCH

An outbreak of colistin-resistant Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae in the Netherlands (July to December 2013), with inter-institutional spread

(2015) V. Weterings et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Isolation of an NDM-5-producing ST16Klebsiella pneumoniaefrom a Dutch patient without travel history abroad, August 2015

(2015) Erik Bathoorn et al.   Eurosurveillance

Detection of selective sweeps in structured populations: a comparison of recent methods

(2015) Alexandra I. Vatsiou et al.   MOLECULAR ECOLOGY

Bovine Genome Database: new tools for gleaning function from theBos taurusgenome

(2015) Christine G. Elsik et al.   NUCLEIC ACIDS RESEARCH

Third generation sequencing: technology and its potential impact on evolutionary biodiversity research

(2015) Christoph Bleidorn   SYSTEMATICS AND BIODIVERSITY

Comprehensive Characterization of Escherichia coli O104:H4 Isolated from Patients in the Netherlands

(2015) Mithila Ferdous et al.   Frontiers in Microbiology

Nanopore-based Fourth-generation DNA Sequencing Technology

(2015) Yanxiao Feng et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Next generation sequencing technology: Advances and applications

(2014) H.P.J. Buermans et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Whole genome sequence and analysis of the Marwari horse breed and its genetic origin

(2014) JeHoon Jun et al.   BMC GENOMICS

Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq

(2014) Simrinder Singh Sodhi et al.   MOLECULAR BIOLOGY REPORTS

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

(2014) Mikkel Schubert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of novel bovine group A rotavirus G15P[14] strain from epizootic diarrhea of adult cows by de novo sequencing using a next-generation sequencer

(2014) Tsuneyuki Masuda et al.   VETERINARY MICROBIOLOGY

RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis

(2014) Kirsten E. McLoughlin et al.   Frontiers in Immunology

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

Using state machines to model the Ion Torrent sequencing process and to improve read error rates

(2013) D. Golan et al.   BIOINFORMATICS

Detection of selective sweeps in cattle using genome-wide SNP data

(2013) Holly R Ramey et al.   BMC GENOMICS

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Microarray resources for genetic and genomic studies in chicken: A review

(2013) Almas A. Gheyas et al.   GENESIS

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

(2013) Ludovic Orlando et al.   NATURE

Approaches to define the viral genetic basis of classical swine fever virus virulence

(2013) Immanuel Leifer et al.   VIROLOGY

Private Selective Sweeps Identified from Next-Generation Pool-Sequencing Reveal Convergent Pathways under Selection in Two Inbred Schistosoma mansoni Strains

(2013) Julie A. J. Clément et al.   PLoS Neglected Tropical Diseases

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

(2013) Laurent AF Frantz et al.   GENOME BIOLOGY

Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip

(2012) Yuliaxis Ramayo-Caldas et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Key Principles and Clinical Applications of "Next-Generation" DNA Sequencing

(2012) J. M. Rizzo et al.   Cancer Prevention Research

Next-generation sequencing approaches for genetic mapping of complex diseases

(2012) Ferran Casals et al.   JOURNAL OF NEUROIMMUNOLOGY

Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples

(2012) S. Boitard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analyses of pig genomes provide insight into porcine demography and evolution

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

Signatures of Selection in the Genomes of Commercial and Non-Commercial Chicken Breeds

(2012) Martin G. Elferink et al.   PLoS One

Strong signatures of selection in the domestic pig genome

(2012) C.-J. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape

(2012) Mirte Bosse et al.   PLoS Genetics

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

(2012) Roman Biek et al.   PLoS Pathogens

Current Status and Future Perspectives for Sequencing Livestock Genomes

(2012) Yongsheng Bai et al.   Journal of Animal Science and Biotechnology

From genotype to phenotype in bovine functional genomics

(2011) C. S. Pareek et al.   Briefings in Functional Genomics

Chicken domestication: From archeology to genomics

(2011) Michèle Tixier-Boichard et al.   COMPTES RENDUS BIOLOGIES

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

Pig genome sequence - analysis and publication strategy

(2010) Alan L Archibald et al.   BMC GENOMICS

Beyond the Consensus: Dissecting Within-Host Viral Population Diversity of Foot-and-Mouth Disease Virus by Using Next-Generation Genome Sequencing

(2010) C. F. Wright et al.   JOURNAL OF VIROLOGY

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Third-generation sequencing fireworks at Marco Island

(2010) David J Munroe et al.   NATURE BIOTECHNOLOGY

High throughput DNA sequencing: The new sequencing revolution

(2010) Michel Delseny et al.   PLANT SCIENCE

The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius

(2010) Hiromi Sawai et al.   PLoS One

Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing

(2010) Shuqi Xiao et al.   PLoS One

Studies of porcine circovirus type 2, porcine boca-like virus and torque teno virus indicate the presence of multiple viral infections in postweaning multisystemic wasting syndrome pigs

(2010) Anne-Lie Blomström et al.   VIRUS RESEARCH

Next Generation DNA Sequencing and the Future of Genomic Medicine

(2010) Matthew W. Anderson et al.   Genes

Unlocking the bovine genome

(2009) Ross L Tellam et al.   BMC GENOMICS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Next-generation DNA sequencing techniques

(2009) Wilhelm J. Ansorge   New Biotechnology

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

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

Next-Generation Sequencing: The Race Is On

(2008) Andreas von Bubnoff   CELL

The Horse Genome Derby: racing from map to whole genome sequence

(2008) Bhanu P. Chowdhary et al.   CHROMOSOME RESEARCH

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

The Pig Genome Database (PiGenome): an integrated database for pig genome research

(2008) Dajeong Lim et al.   MAMMALIAN GENOME

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Single-molecule DNA sequencing technologies for future genomics research

(2008) Pushpendra K. Gupta   TRENDS IN BIOTECHNOLOGY