Assembly and diploid architecture of an individual human genome via single-molecule technologies

Resolving complex tandem repeats with long reads

(2014) Ajay Ummat et al.   BIOINFORMATICS

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

(2014) Adam C English et al.   BMC BIOINFORMATICS

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

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

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

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability

(2014) Francesca Antonacci et al.   NATURE GENETICS

Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations

(2013) A. Patel et al.   GENOME RESEARCH

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

(2013) Alex R. Hastie et al.   PLoS One

Performance of High-Throughput Sequencing for the Discovery of Genetic Variation Across the Complete Size Spectrum

(2013) Andy Wing Chun Pang et al.   G3-Genes Genomes Genetics

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

AGORA: Assembly Guided by Optical Restriction Alignment

(2012) Henry C Lin et al.   BMC BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

(2012) Mauricio O Carneiro et al.   BMC GENOMICS

Finished bacterial genomes from shotgun sequence data

(2012) F. J. Ribeiro et al.   GENOME RESEARCH

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

Detecting false-positive signals in exome sequencing

(2012) Karin V. Fuentes Fajardo et al.   HUMAN MUTATION

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles

(2012) Gareth Highnam et al.   NUCLEIC ACIDS RESEARCH

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Performance comparison of whole-genome sequencing platforms

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

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

Lipoprotein(a) and ischemic heart disease—A causal association? A review

(2010) Pia R. Kamstrup   ATHEROSCLEROSIS

Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons

(2010) Rebecca C. Iskow et al.   CELL

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

(2010) A. McKenna et al.   GENOME RESEARCH

A window into third-generation sequencing

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

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

(2010) Christopher E. Mason 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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Multiple whole-genome alignments without a reference organism

(2009) I. Dubchak et al.   GENOME RESEARCH

5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome

(2009) A. Damert et al.   GENOME RESEARCH

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY

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

(2008) V. Bansal et al.   BIOINFORMATICS

An MCMC algorithm for haplotype assembly from whole-genome sequence data

(2008) V. Bansal et al.   GENOME RESEARCH

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer

(2008) Ali Bashir et al.   PLoS Computational Biology