DNA sequencing at 40: past, present and future

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

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

Using high-throughput barcode sequencing to efficiently map connectomes

(2017) Ian D. Peikon et al.   NUCLEIC ACIDS RESEARCH

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Graphene Nanopores for Protein Sequencing

(2016) James Wilson et al.   ADVANCED FUNCTIONAL MATERIALS

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

Decoding DNA, RNA and peptides with quantum tunnelling

(2016) Massimiliano Di Ventra et al.   Nature Nanotechnology

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Molecular recordings by directed CRISPR spacer acquisition

(2016) Seth L. Shipman et al.   SCIENCE

Pim Kinase Inhibitors Evaluated with a Single-Molecule Engineered Nanopore Sensor

(2015) Leon Harrington et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Genetic studies in intellectual disability and related disorders

(2015) Lisenka E. L. M. Vissers et al.   NATURE REVIEWS GENETICS

Haplotype-resolved genome sequencing: experimental methods and applications

(2015) Matthew W. Snyder et al.   NATURE REVIEWS GENETICS

Nanopore Sequencing: From Imagination to Reality

(2014) H. Bayley   CLINICAL CHEMISTRY

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Decoding long nanopore sequencing reads of natural DNA

(2014) Andrew H Laszlo et al.   NATURE BIOTECHNOLOGY

Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

(2014) Yanan Zhao et al.   Nature Nanotechnology

Continuous observation of the stochastic motion of an individual small-molecule walker

(2014) Gökçe Su Pulcu et al.   Nature Nanotechnology

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Protein co-translocational unfolding depends on the direction of pulling

(2014) David Rodriguez-Larrea et al.   Nature Communications

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

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

(2013) Kerstin Howe et al.   NATURE

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Unfoldase-mediated protein translocation through an α-hemolysin nanopore

(2013) Jeff Nivala et al.   NATURE BIOTECHNOLOGY

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

The microbiome explored: recent insights and future challenges

(2013) Martin Blaser et al.   NATURE REVIEWS MICROBIOLOGY

Identifying Personal Genomes by Surname Inference

(2013) M. Gymrek et al.   SCIENCE

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

The expanding scope of DNA sequencing

(2012) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase

(2012) Elizabeth A Manrao et al.   NATURE BIOTECHNOLOGY

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

(2012) Gerald M Cherf et al.   NATURE BIOTECHNOLOGY

Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing

(2012) Bradley Michael Zamft et al.   PLoS One

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin 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

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Identifying single bases in a DNA oligomer with electron tunnelling

(2010) Shuo Huang et al.   Nature Nanotechnology

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

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

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

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

(2009) N. T. Ingolia et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

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

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

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

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

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