Next-generation sequencing technologies: An overview

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

(2021) Søren M. Karst et al.   NATURE METHODS

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

(2020) Rute Pereira et al.   Journal of Clinical Medicine

Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements

(2020) Yung-Chien Chou et al.   ACS Nano

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus

(2020) Bas Berbers et al.   Scientific Reports

Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method

(2020) Fumiko Yamamoto et al.   Frontiers in Immunology

Rapid high‐resolution HLA genotyping by MinION Oxford nanopore sequencing for deceased donor organ allocation

(2020) Dianne De Santis et al.   HLA

Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing

(2020) Timothy L. Mosbruger et al.   HUMAN IMMUNOLOGY

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

Recipients Receiving Better HLA-Matched Hematopoietic Cell Transplantation Grafts, Uncovered by a Novel HLA Typing Method, Have Superior Survival: A Retrospective Study

(2019) Neema P. Mayor et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Single-Stranded DNA Translocation Recordings through Solid-State Nanopores on Glass Chips at 10 MHz Measurement Bandwidth

(2019) Chen-Chi Chien et al.   ACS Nano

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping

(2019) Steffen Klasberg et al.   TRANSFUSION MEDICINE AND HEMOTHERAPY

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Next-Generation Sequencing Technologies

(2018) W. Richard McCombie et al.   Cold Spring Harbor Perspectives in Medicine

The role of HLA genes in pharmacogenomics: unravelling HLA associated adverse drug reactions

(2017) Patricia T. Illing et al.   IMMUNOGENETICS

DNA sequencing at 40: past, present and future

(2017) Jay Shendure et al.   NATURE

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data

(2017) Sarah Sandmann et al.   Scientific Reports

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity

(2016) Johannes Dapprich et al.   BMC GENOMICS

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies

(2016) Kevin E. Fisher et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

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

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Determining performance characteristics of an NGS-based HLA typing method for clinical applications

(2016) J. L. Duke et al.   HLA

Library construction for next-generation sequencing: Overviews and challenges

(2016) Steven R. Head et al.   BIOTECHNIQUES

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

(2016) Spyros Oikonomopoulos et al.   Scientific Reports

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

(2015) Malachi Griffith et al.   PLoS Computational Biology

PacBio Sequencing and Its Applications

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

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Next-generation sequencing technologies: breaking the sound barrier of human genetics

(2014) E. M. Bahassi et al.   MUTAGENESIS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Next-Generation Sequencing Platforms

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

Dominant Form of Congenital Hyperinsulinism Maps to HK1 Region on 10q

(2013) Sara E. Pinney et al.   Hormone Research in Paediatrics

Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing

(2013) Marisa P. Dolled-Filhart et al.   TheScientificWorldJOURNAL

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

(2012) Lukas Habegger et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

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

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

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Progress in Ion Torrent semiconductor chip based sequencing

(2012) Barry Merriman et al.   ELECTROPHORESIS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

HLA typing from RNA-Seq sequence reads

(2012) Sebastian Boegel et al.   Genome Medicine

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next generation sequencing in epigenetics: Insights and challenges

(2011) Emma Meaburn et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing

(2011) Nikhil Wagle et al.   Cancer Discovery

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) C. Lind et al.   HUMAN IMMUNOLOGY

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Microtubule Actin Crosslinking Factor 1 Regulates the Balbiani Body and Animal-Vegetal Polarity of the Zebrafish Oocyte

(2010) Tripti Gupta et al.   PLoS Genetics

Massively Parallel Sequencing: The Next Big Thing in Genetic Medicine

(2009) Tracy Tucker et al.   AMERICAN JOURNAL OF HUMAN GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

High-resolution, high-throughput HLA genotyping by next-generation sequencing

(2009) G. Bentley et al.   TISSUE ANTIGENS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS