Sequencing technologies and genome sequencing

Water Buffalo Genome Science Comes of Age

(2012) Vanessa N. Michelizzi et al.   International Journal of Biological Sciences

A Global View of 54,001 Single Nucleotide Polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and Their Transferability to Water Buffalo

(2012) Vanessa N. Michelizzi et al.   International Journal of Biological Sciences

New developments in the molecular pathogenesis of head and neck tumors: a review of tumor-specific fusion oncogenes in mucoepidermoid carcinoma, adenoid cystic carcinoma, and NUT midline carcinoma

(2011) Feriyl Bhaijee et al.   Annals of Diagnostic Pathology

New methods for next generation sequencing based microRNA expression profiling

(2011) Henk PJ Buermans et al.   BMC GENOMICS

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis

(2011) Xuefeng Fang et al.   BMC GENOMICS

Detecting structural variations in the human genome using next generation sequencing

(2011) R. Xi et al.   Briefings in Functional Genomics

Profiling of regulatory microRNA transcriptomes in various biological processes: a review

(2011) A. A. Shah et al.   JOURNAL OF APPLIED GENETICS

Complete sequences of maternally inherited mitochondrial genomes in musselsUnio pictorum (Bivalvia, Unionidae)

(2011) M. Soroka et al.   JOURNAL OF APPLIED GENETICS

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Judging the Archon Genomics X PRIZE for whole human genome sequencing

(2011) Larry Kedes et al.   NATURE GENETICS

Carrier Testing for Severe Childhood Recessive Diseases by Next-Generation Sequencing

(2011) C. J. Bell et al.   Science Translational Medicine

Targeted Next-Generation Sequencing of a 12.5 Mb Homozygous Region Reveals ANO10 Mutations in Patients with Autosomal-Recessive Cerebellar Ataxia

(2010) Sascha Vermeer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Massive parallel sequencing in animal genetics: wherefroms and wheretos

(2010) M. Pérez-Enciso et al.   ANIMAL GENETICS

The sheep genome reference sequence: a work in progress

(2010) et al.   ANIMAL GENETICS

Structural annotation of equine protein-coding genes determined by mRNA sequencing

(2010) S. J. Coleman et al.   ANIMAL GENETICS

Analysis of ancient human genomes

(2010) Beth Shapiro et al.   BIOESSAYS

Classification of ncRNAs using position and size information in deep sequencing data

(2010) F. Erhard et al.   BIOINFORMATICS

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha et al.   BIOINFORMATICS

A statistical method for the detection of variants from next-generation resequencing of DNA pools

(2010) V. Bansal   BIOINFORMATICS

Complete characterization of the microRNAome in a patient with acute myeloid leukemia

(2010) G. Ramsingh et al.   BLOOD

SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools

(2010) Stefan Marklund et al.   BMC GENOMICS

Next generation sequencing in functional genomics

(2010) T. Werner   BRIEFINGS IN BIOINFORMATICS

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Sequence Capture and Next-Generation Resequencing of Multiple Tagged Nucleic Acid Samples for Mutation Screening of Urea Cycle Disorders

(2010) U. Amstutz et al.   CLINICAL CHEMISTRY

Next-generation sequencing: emerging lessons on the origins of human cancer

(2010) Gerd P Pfeifer et al.   CURRENT OPINION IN ONCOLOGY

Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors

(2010) David J. McBride et al.   GENES CHROMOSOMES & CANCER

Index-Free De Novo Assembly and Deconvolution of Mixed Mitochondrial Genomes

(2010) B. J. McComish et al.   Genome Biology and Evolution

Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing

(2010) C. Lind et al.   HUMAN IMMUNOLOGY

Analysis of next-generation genomic data in cancer: accomplishments and challenges

(2010) L. Ding et al.   HUMAN MOLECULAR GENETICS

Fine-scale population structure and the era of next-generation sequencing

(2010) B. M. Henn et al.   HUMAN MOLECULAR GENETICS

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Novel genomic techniques open new avenues in the analysis of monogenic disorders

(2010) Gregor Kuhlenbäumer et al.   HUMAN MUTATION

Uncovering the Complexity of Transcriptomes with RNA-Seq

(2010) Valerio Costa et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Semi-Automated Library Preparation for High-Throughput DNA Sequencing Platforms

(2010) Eveline Farias-Hesson et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Molecular epidemiology of current classical swine fever virus isolates of wild boar in Germany

(2010) I. Leifer et al.   JOURNAL OF GENERAL VIROLOGY

Next Generation Sequencing for Clinical Diagnostics-Principles and Application to Targeted Resequencing for Hypertrophic Cardiomyopathy

(2010) Karl V. Voelkerding et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using ultra-deep sequencing technologies

(2010) S. Clay Isom et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency

(2010) Christian Popp et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Next-generation sequencing of the next generation

(2010) Darren J. Burgess   NATURE REVIEWS GENETICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Neurogenetics: Advancing the “Next-Generation” of Brain Research

(2010) Huda Y. Zoghbi et al.   NEURON

Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy

(2010) James R. Lupski et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies

(2010) Matthew S. Hestand et al.   NUCLEIC ACIDS RESEARCH

TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology

(2010) Dongwan Hong et al.   NUCLEIC ACIDS RESEARCH

NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data

(2010) M. Hackenberg et al.   NUCLEIC ACIDS RESEARCH

A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius)

(2010) Ceiridwen J. Edwards et al.   PLoS One

Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding

(2010) Christina A. Bormann Chung et al.   PLoS One

Targeted Genome-Wide Enrichment of Functional Regions

(2010) Periannan Senapathy et al.   PLoS One

Molecular prenatal diagnosis: the impact of modern technologies

(2010) F. Lucy Raymond et al.   PRENATAL DIAGNOSIS

Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing

(2010) Tom Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complexity of the microRNA repertoire revealed by next-generation sequencing

(2010) L. W. Lee et al.   RNA

Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing

(2010) R. J. Leary et al.   Science Translational Medicine

New Technologies for the Identification of Novel Genetic Markers of Disorders of Sex Development (DSD)

(2010) A. Bashamboo et al.   Sexual Development

Towards a complete resolution of the genetic architecture of disease

(2010) Andrew B. Singleton et al.   TRENDS IN GENETICS

PPARG: Gene Expression Regulation and Next-Generation Sequencing for Unsolved Issues

(2010) Valerio Costa et al.   PPAR Research

Genome-scale DNA methylation analysis

(2010) Shaun D Fouse et al.   Epigenomics

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

Identification of the Bovine Arachnomelia Mutation by Massively Parallel Sequencing Implicates Sulfite Oxidase (SUOX) in Bone Development

(2010) Cord Drögemüller et al.   PLoS Genetics

Swift: primary data analysis for the Illumina Solexa sequencing platform

(2009) Nava Whiteford et al.   BIOINFORMATICS

Structural and functional-annotation of an equine whole genome oligoarray

(2009) Lauren A Bright et al.   BMC BIOINFORMATICS

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

(2009) Wei-Chi Wang et al.   BMC BIOINFORMATICS

Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome

(2009) Andreia J Amaral et al.   BMC GENOMICS

Bos taurus genome assembly

(2009) Yue Liu et al.   BMC GENOMICS

RNA-seq: from technology to biology

(2009) Samuel Marguerat et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

(2009) S.-M. Ahn et al.   GENOME RESEARCH

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

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

(2009) R. Li et al.   GENOME RESEARCH

Chromatin maps, histone modifications and leukemia

(2009) T Neff et al.   LEUKEMIA

Next-generation sequencing of vertebrate experimental organisms

(2009) Daniel J. Turner et al.   MAMMALIAN GENOME

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Cheap third-generation sequencing

(2009) Nicole Rusk   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes

(2009) A. R. Jex et al.   NUCLEIC ACIDS RESEARCH

deepBase: a database for deeply annotating and mining deep sequencing data

(2009) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

(2009) Antonio M. Ramos et al.   PLoS One

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

Gene Expression Profiling of the Host Response toMycobacterium bovisInfection in Cattle

(2009) D. E. MacHugh et al.   Transboundary and Emerging Diseases

New strategies and emerging technologies for massively parallel sequencing: applications in medical research

(2009) Elaine R Mardis   Genome Medicine

Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery

(2009) Sebastian H Eck et al.   GENOME BIOLOGY

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

(2009) Aleksey V Zimin et al.   GENOME BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

SNP discovery in swine by reduced representation and high throughput pyrosequencing

(2008) Ralph T Wiedmann et al.   BMC GENETICS

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

Single-Molecule DNA Sequencing of a Viral Genome

(2008) T. D. Harris et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS