Reducing INDEL calling errors in whole genome and exome sequencing data

The Pivotal Regulatory Landscape of RNA Modifications

(2014) Sheng Li et al.   Annual Review of Genomics and Human Genetics

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Variant detection sensitivity and biases in whole genome and exome sequencing

(2014) Alison M Meynert et al.   BMC BIOINFORMATICS

Analytical validation of whole exome and whole genome sequencing for clinical applications

(2014) Michael D Linderman et al.   BMC Medical Genomics

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

The landscape of human STR variation

(2014) Thomas Willems et al.   GENOME RESEARCH

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Guidelines for investigating causality of sequence variants in human disease

(2014) D. G. MacArthur 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

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

Diagnostic Clinical Genome and Exome Sequencing

(2014) Leslie G. Biesecker et al.   NEW ENGLAND JOURNAL OF MEDICINE

A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record

(2013) Peter Tarczy-Hornoch et al.   GENETICS IN MEDICINE

Will Formal Genetics Become Dispensable?

(2013) Françoise Clerget-Darpoux et al.   HUMAN HEREDITY

Increasing the Yield in Targeted Next-Generation Sequencing by Implicating CNV Analysis, Non-Coding Exons and the Overall Variant Load: The Example of Retinal Dystrophies

(2013) Tobias Eisenberger et al.   PLoS One

Whole genome sequencing in support of wellness and health maintenance

(2013) Chirag J Patel et al.   Genome Medicine

The human genome project: big science transforms biology and medicine

(2013) Leroy Hood et al.   Genome Medicine

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

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

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Integrating precision medicine in the study and clinical treatment of a severely mentally ill person

(2013) Jason A. O’Rawe et al.   PeerJ

Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes

(2012) Mingfu Zhu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Centers for Mendelian Genomics: A new large-scale initiative to identify the genes underlying rare Mendelian conditions

(2012) Michael J. Bamshad et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

lobSTR: A short tandem repeat profiler for personal genomes

(2012) Melissa Gymrek et al.   GENOME RESEARCH

Bring clinical standards to human-genetics research

(2012) Gholson J. Lyon   NATURE

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

A study based on whole-genome sequencing yields a rare variant at 8q24 associated with prostate cancer

(2012) Julius Gudmundsson et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

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

(2012) Gareth Highnam et al.   NUCLEIC ACIDS RESEARCH

Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

(2012) Gholson J Lyon et al.   Genome Medicine

Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency

(2011) Alan F. Rope et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Clan Genomics and the Complex Architecture of Human Disease

(2011) James R. Lupski et al.   CELL

Natural genetic variation caused by small insertions and deletions in the human genome

(2011) R. E. Mills et al.   GENOME RESEARCH

Accurate and comprehensive sequencing of personal genomes

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

Performance comparison of whole-genome sequencing platforms

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

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark 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

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Gene–environment interactions in human disease: nuisance or opportunity?

(2011) Carole Ober et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genetic Heterogeneity in Human Disease

(2010) Jon McClellan et al.   CELL

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

Characterization of missing human genome sequences and copy-number polymorphic insertions

(2010) Jeffrey M Kidd et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(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

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE