The expanding scope of DNA sequencing

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

Nanopores as protein sensors

(2012) Stefan Howorka et al.   NATURE BIOTECHNOLOGY

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

What's a Genome Worth?

(2012) I. S. Kohane et al.   Science Translational Medicine

Noninvasive Whole-Genome Sequencing of a Human Fetus

(2012) J. O. Kitzman et al.   Science Translational Medicine

The Predictive Capacity of Personal Genome Sequencing

(2012) N. J. Roberts et al.   Science Translational Medicine

Traces of post-transcriptional RNA modifications in deep sequencing data

(2011) Sven Findeiß et al.   BIOLOGICAL CHEMISTRY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene

(2011) John S. Welch   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Activators of the Glutamate-Dependent Acid Resistance System Alleviate Deleterious Effects of YidC Depletion in Escherichia coli

(2011) Z. Yu et al.   JOURNAL OF BACTERIOLOGY

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Somatic coding mutations in human induced pluripotent stem cells

(2011) Athurva Gore et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

Global gene disruption in human cells to assign genes to phenotypes by deep sequencing

(2011) Jan E Carette et al.   NATURE BIOTECHNOLOGY

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Increased exonic de novo mutation rate in individuals with schizophrenia

(2011) Simon L Girard et al.   NATURE GENETICS

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations

(2011) Brian J O'Roak et al.   NATURE GENETICS

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Decoding cell lineage from acquired mutations using arbitrary deep sequencing

(2011) Cheryl A Carlson et al.   NATURE METHODS

Next-generation sequencing to generate interactome datasets

(2011) Haiyuan Yu et al.   NATURE METHODS

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Added Value of Deep Sequencing Relative to Population Sequencing in Heavily Pre-Treated HIV-1-Infected Subjects

(2011) Francisco M. Codoñer et al.   PLoS One

High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment

(2011) A. C. Logan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

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

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

Whole-Genome Sequencing for Optimized Patient Management

(2011) M. N. Bainbridge et al.   Science Translational Medicine

Genome-Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq

(2011) L. A. Gallagher et al.   mBio

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

(2010) Elizabeth A Worthey et al.   GENETICS IN MEDICINE

Nucleosome landscape and control of transcription in the human malaria parasite

(2010) N. Ponts et al.   GENOME RESEARCH

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis

(2010) Sergio E. Baranzini et al.   NATURE

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Whole-genome molecular haplotyping of single cells

(2010) H Christina Fan et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

A de novo paradigm for mental retardation

(2010) Lisenka E L M Vissers et al.   NATURE GENETICS

Direct determination of molecular haplotypes by chromosome microdissection

(2010) Li Ma et al.   NATURE METHODS

Parallel, tag-directed assembly of locally derived short sequence reads

(2010) Joseph B Hiatt et al.   NATURE METHODS

FRT-seq: amplification-free, strand-specific transcriptome sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale

(2010) Anastasia Baryshnikova et al.   NATURE METHODS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Rapid interactome profiling by massive sequencing

(2010) Roberto Di Niro et al.   NUCLEIC ACIDS RESEARCH

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets

(2010) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Construction of Empirical RNA Fitness Landscapes

(2010) J. N. Pitt et al.   SCIENCE

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing

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

A combinatorial genetic library approach to target heterologous glycosylation enzymes to the endoplasmic reticulum or the Golgi apparatus of Pichia pastoris

(2010) Juergen H. Nett et al.   YEAST

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors

(2010) Steven JM Jones et al.   GENOME BIOLOGY

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Protein Quantification in Complex Mixtures by Solid Phase Single-Molecule Counting

(2009) Lee A. Tessler et al.   ANALYTICAL CHEMISTRY

Genotype Imputation

(2009) Yun Li et al.   Annual Review of Genomics and Human Genetics

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

(2009) J. D. Freeman et al.   GENOME RESEARCH

Public clonotype usage identifies protective Gag-specific CD8+T cell responses in SIV infection

(2009) David A. Price et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

(2009) Joseph Schacherer et al.   NATURE

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Virus-free induction of pluripotency and subsequent excision of reprogramming factors

(2009) Keisuke Kaji et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Sensitive digital quantification of DNA methylation in clinical samples

(2009) Meng Li et al.   NATURE BIOTECHNOLOGY

Massively parallel exon capture and library-free resequencing across 16 genomes

(2009) Emily H Turner et al.   NATURE METHODS

Integrated analysis of receptor activation and downstream signaling with EXTassays

(2009) Anna Botvinnik et al.   NATURE METHODS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

Rapid creation and quantitative monitoring of high coverage shRNA libraries

(2009) Michael C Bassik et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

(2009) R. S. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Human Induced Pluripotent Stem Cells Free of Vector and Transgene Sequences

(2009) J. Yu et al.   SCIENCE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing

(2009) S. D. Boyd et al.   Science Translational Medicine

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

(2008) J. R. Sanford et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

(2008) Katy C Kao et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma

(2008) R. W. K. Chiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood

(2008) H. C. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induced Pluripotent Stem Cells Generated Without Viral Integration

(2008) M. Stadtfeld et al.   SCIENCE

Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast

(2008) A. Roguev et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

(2008) David Gresham et al.   PLoS Genetics