The role of replicates for error mitigation in next-generation sequencing

Quantifying single nucleotide variant detection sensitivity in exome sequencing

(2013) Alison M Meynert et al.   BMC BIOINFORMATICS

The emerging CHO systems biology era: harnessing the ‘omics revolution for biotechnology

(2013) Helene Faustrup Kildegaard et al.   CURRENT OPINION IN BIOTECHNOLOGY

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Systematic investigation of cancer-associated somatic point mutations in SNP databases

(2013) HyunChul Jung et al.   NATURE BIOTECHNOLOGY

Chinese hamster genome sequenced from sorted chromosomes

(2013) Karina Brinkrolf et al.   NATURE BIOTECHNOLOGY

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

(2013) Nathan E Lewis et al.   NATURE BIOTECHNOLOGY

Using population admixture to help complete maps of the human genome

(2013) Giulio Genovese et al.   NATURE GENETICS

Computational approaches to identify functional genetic variants in cancer genomes

(2013)   NATURE METHODS

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample

(2013) Aakrosh Ratan et al.   PLoS One

Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene

(2013) William P. Robins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

Next-generation sequencing in the clinic: Promises and challenges

(2012) Jiekun Xuan et al.   CANCER LETTERS

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

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

(2012) Brock A. Peters et al.   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Detectable clonal mosaicism from birth to old age and its relationship to cancer

(2012) Cathy C Laurie et al.   NATURE GENETICS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Computational tools for prioritizing candidate genes: boosting disease gene discovery

(2012) Yves Moreau et al.   NATURE REVIEWS GENETICS

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens

(2012) Shawn E. Yost et al.   NUCLEIC ACIDS RESEARCH

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Generalized DNA Barcode Design Based on Hamming Codes

(2012) Leonid V. Bystrykh   PLoS One

Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing

(2012) Bradley Michael Zamft et al.   PLoS One

A public resource facilitating clinical use of genomes

(2012) Madeleine P. Ball et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and Analytical Validation of Clinical DNA Sequencing Assays

(2011) Genevieve Pont-Kingdon et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity

(2011) Martin Kerick et al.   BMC Medical Genomics

Accurate and comprehensive sequencing of personal genomes

(2011) S. S. Ajay et al.   GENOME RESEARCH

Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing

(2011) Jennifer Becker et al.   JOURNAL OF BIOTECHNOLOGY

Microbial laboratory evolution in the era of genome-scale science

(2011) T. M. Conrad et al.   Molecular Systems Biology

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

(2011) Joke Reumers et al.   NATURE BIOTECHNOLOGY

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

One genome, two haplotypes

(2011) Nicole Rusk   NATURE METHODS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Family-based designs for genome-wide association studies

(2011) Jurg Ott et al.   NATURE REVIEWS GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Error and Error Mitigation in Low-Coverage Genome Assemblies

(2011) Melissa J. Hubisz et al.   PLoS One

Next generation sequencing in epigenetics: Insights and challenges

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

Genome-wide association studies and systems biology: together at last

(2011) Mika Ala-Korpela et al.   TRENDS IN GENETICS

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

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

Quantifying the relative amount of mouse and human DNA in cancer xenografts using species-specific variation in gene length

(2010) Ming-Tseh Lin et al.   BIOTECHNIQUES

Challenges of sequencing human genomes

(2010) D. C. Koboldt et al.   BRIEFINGS IN BIOINFORMATICS

Quality control and quality assurance in genotypic data for genome-wide association studies

(2010) Cathy C. Laurie et al.   GENETIC EPIDEMIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia

(2010) J. Rios et al.   HUMAN MOLECULAR GENETICS

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

(2010) Sergio E. Baranzini et al.   NATURE

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee 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

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

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

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

Rate, molecular spectrum, and consequences of human mutation

(2010) M. Lynch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

The Characterization of Twenty Sequenced Human Genomes

(2010) Kimberly Pelak et al.   PLoS Genetics

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner 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

Swift: primary data analysis for the Illumina Solexa sequencing platform

(2009) Nava Whiteford et al.   BIOINFORMATICS

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

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

(2009) R. Drmanac et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

(2008) V. Bansal et al.   BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE