Published in Nat Protoc on June 25, 2009
Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet (2011) 18.88
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med (2015) 16.87
Ensembl 2012. Nucleic Acids Res (2011) 14.55
Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet (2011) 14.29
De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature (2012) 13.61
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Somatic coding mutations in human induced pluripotent stem cells. Nature (2011) 9.50
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature (2012) 8.91
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet (2011) 8.53
A high-coverage genome sequence from an archaic Denisovan individual. Science (2012) 7.89
dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat (2011) 6.97
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat (2013) 5.11
MuSiC: identifying mutational significance in cancer genomes. Genome Res (2012) 4.73
SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res (2012) 4.45
A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing. Genome Res (2011) 4.15
Identification of seven loci affecting mean telomere length and their association with disease. Nat Genet (2013) 3.87
Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes. Nat Genet (2010) 3.82
Taxonomizing, sizing, and overcoming the incidentalome. Genet Med (2012) 3.82
Mutations in GNAL cause primary torsion dystonia. Nat Genet (2012) 3.66
Pleiotropy in complex traits: challenges and strategies. Nat Rev Genet (2013) 3.65
A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform (2013) 3.60
Abundant pleiotropy in human complex diseases and traits. Am J Hum Genet (2011) 3.60
Hypomyelination with atrophy of the basal ganglia and cerebellum: further delineation of the phenotype and genotype-phenotype correlation. Brain (2014) 3.51
Recurrent SETBP1 mutations in atypical chronic myeloid leukemia. Nat Genet (2012) 3.43
Rare-variant association analysis: study designs and statistical tests. Am J Hum Genet (2014) 3.42
Dysfunction of lipid sensor GPR120 leads to obesity in both mouse and human. Nature (2012) 3.41
Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. Lancet (2014) 3.39
Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell (2013) 3.26
A probabilistic disease-gene finder for personal genomes. Genome Res (2011) 3.23
Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease. Nat Genet (2010) 3.22
Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature (2013) 3.06
The genetic landscape of mutations in Burkitt lymphoma. Nat Genet (2012) 3.03
Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides. Blood (2012) 2.98
Functional impact bias reveals cancer drivers. Nucleic Acids Res (2012) 2.96
Validating therapeutic targets through human genetics. Nat Rev Drug Discov (2013) 2.94
Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci. Nat Genet (2013) 2.87
Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. PLoS Genet (2013) 2.83
Somatic FAS mutations are common in patients with genetically undefined autoimmune lymphoproliferative syndrome. Blood (2010) 2.77
Recoded organisms engineered to depend on synthetic amino acids. Nature (2015) 2.71
CUBN is a gene locus for albuminuria. J Am Soc Nephrol (2011) 2.70
Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors. Cancer Discov (2014) 2.64
Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in Middle Eastern families. Genome Biol (2011) 2.62
Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature (2015) 2.50
Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet (2013) 2.47
Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nat Genet (2013) 2.44
wANNOVAR: annotating genetic variants for personal genomes via the web. J Med Genet (2012) 2.43
A de novo mutation in the β-tubulin gene TUBB4A results in the leukoencephalopathy hypomyelination with atrophy of the basal ganglia and cerebellum. Am J Hum Genet (2013) 2.42
Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors. Genome Res (2010) 2.41
The 1000 Genomes Project: data management and community access. Nat Methods (2012) 2.41
Functional annotation of noncoding sequence variants. Nat Methods (2014) 2.41
An activating NLRC4 inflammasome mutation causes autoinflammation with recurrent macrophage activation syndrome. Nat Genet (2014) 2.40
Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia. Nat Genet (2013) 2.38
Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer. J Clin Endocrinol Metab (2013) 2.34
Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance. Nat Genet (2016) 2.28
Whole-exome re-sequencing in a family quartet identifies POP1 mutations as the cause of a novel skeletal dysplasia. PLoS Genet (2011) 2.23
Mutations in IL36RN/IL1F5 are associated with the severe episodic inflammatory skin disease known as generalized pustular psoriasis. Am J Hum Genet (2011) 2.21
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics (2015) 2.19
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet (2013) 2.14
The deleterious mutation load is insensitive to recent population history. Nat Genet (2014) 2.14
A decision support framework for genomically informed investigational cancer therapy. J Natl Cancer Inst (2015) 2.13
Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. Nat Genet (2012) 2.12
Whole-genome haplotyping using long reads and statistical methods. Nat Biotechnol (2014) 2.11
A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol (2014) 2.10
PSORS2 is due to mutations in CARD14. Am J Hum Genet (2012) 2.10
Oligogenic basis of isolated gonadotropin-releasing hormone deficiency. Proc Natl Acad Sci U S A (2010) 2.10
Germline mutations of regulator of telomere elongation helicase 1, RTEL1, in Dyskeratosis congenita. Hum Genet (2013) 2.10
IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods (2013) 2.10
A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. Nucleic Acids Res (2012) 2.08
Brown-Vialetto-Van Laere syndrome, a ponto-bulbar palsy with deafness, is caused by mutations in c20orf54. Am J Hum Genet (2010) 2.08
SNP set association analysis for familial data. Genet Epidemiol (2012) 2.08
Mutations in the profilin 1 gene cause familial amyotrophic lateral sclerosis. Nature (2012) 2.08
Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly. Nat Genet (2013) 2.06
Molecular genetic testing and the future of clinical genomics. Nat Rev Genet (2013) 2.03
Epigenetic and genetic features of 24 colon cancer cell lines. Oncogenesis (2013) 2.02
ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn (2012) 1.99
Molecular genetic studies of complex phenotypes. Transl Res (2011) 1.95
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol (2014) 1.95
Cancer evolution is associated with pervasive positive selection on globally expressed genes. PLoS Genet (2014) 1.94
DGKE variants cause a glomerular microangiopathy that mimics membranoproliferative GN. J Am Soc Nephrol (2012) 1.93
Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet (2014) 1.92
Phylogenetic and physicochemical analyses enhance the classification of rare nonsynonymous single nucleotide variants in type 1 and 2 long-QT syndrome. Circ Cardiovasc Genet (2012) 1.91
Exome sequencing reveals mutations in TRPV3 as a cause of Olmsted syndrome. Am J Hum Genet (2012) 1.91
Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes. Nat Genet (2013) 1.91
Mutations in the autoregulatory domain of β-tubulin 4a cause hereditary dystonia. Ann Neurol (2013) 1.90
Whole genome sequencing of matched primary and metastatic acral melanomas. Genome Res (2011) 1.90
The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun (2014) 1.90
The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study. PLoS Genet (2015) 1.87
Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet (2014) 1.86
The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan. Cell (2015) 1.86
General framework for meta-analysis of rare variants in sequencing association studies. Am J Hum Genet (2013) 1.86
Whole-exome sequencing efficiently detects rare mutations in autosomal recessive nonsyndromic hearing loss. PLoS One (2012) 1.83
DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res (2013) 1.83
A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet (2011) 1.83
Development and characterization of an oat TILLING-population and identification of mutations in lignin and beta-glucan biosynthesis genes. BMC Plant Biol (2010) 1.82
Haploinsufficiency of CSF-1R and clinicopathologic characterization in patients with HDLS. Neurology (2013) 1.81
Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy. Am J Hum Genet (2011) 1.80
Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med (2014) 1.80
The Ensembl Variant Effect Predictor. Genome Biol (2016) 1.80
Excess of rare variants in non-genome-wide association study candidate genes in patients with hypertriglyceridemia. Circ Cardiovasc Genet (2011) 1.78
Mutations in axonemal dynein assembly factor DNAAF3 cause primary ciliary dyskinesia. Nat Genet (2012) 1.78
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res (2003) 52.26
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
Predicting deleterious amino acid substitutions. Genome Res (2001) 28.95
Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet (1999) 24.24
PANTHER: a library of protein families and subfamilies indexed by function. Genome Res (2003) 21.64
SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics (2006) 21.54
Accounting for human polymorphisms predicted to affect protein function. Genome Res (2002) 14.10
PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics (2005) 9.88
Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet (2006) 9.80
Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J Mol Biol (2002) 7.79
Human gene mutation database-a biomedical information and research resource. Hum Mutat (2000) 6.87
Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res (2005) 5.62
Melanocortin-1 receptor polymorphisms and risk of melanoma: is the association explained solely by pigmentation phenotype? Am J Hum Genet (2000) 4.74
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods. Nucleic Acids Res (2006) 4.00
In silico prediction of the deleterious effect of a mutation: proceed with caution in clinical genetics. Clin Chem (2004) 3.43
Denaturing HPLC-identified novel FBN1 mutations, polymorphisms, and sequence variants in Marfan syndrome and related connective tissue disorders. Genet Test (1999) 3.42
Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol (2003) 3.39
Skin type, melanoma, and melanocortin 1 receptor variants. J Invest Dermatol (1999) 3.09
SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res (2003) 52.26
The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80
Accounting for human polymorphisms predicted to affect protein function. Genome Res (2002) 14.10
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet (2006) 11.88
Unlocking the secrets of the genome. Nature (2009) 11.80
Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet (2006) 9.80
The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell (2002) 9.80
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
The epigenetic progenitor origin of human cancer. Nat Rev Genet (2006) 9.65
Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol (2009) 9.59
Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet (2005) 7.22
Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc Natl Acad Sci U S A (2004) 4.88
Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science (2010) 4.72
Centromeric nucleosomes induce positive DNA supercoils. Cell (2009) 4.57
DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci U S A (2007) 4.55
SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res (2012) 4.45
Histone variants--ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol (2010) 4.45
Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res (2003) 4.39
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature (2008) 4.20
Histone replacement marks the boundaries of cis-regulatory domains. Science (2007) 4.06
Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics (2003) 3.70
Sequencing of a rice centromere uncovers active genes. Nat Genet (2004) 3.66
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res (2003) 3.55
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol (2005) 3.54
Phylogenomics of the nucleosome. Nat Struct Biol (2003) 3.52
DNA demethylation by DNA repair. Trends Genet (2009) 3.49
Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr Biol (2002) 3.37
Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science (2009) 3.33
Power to detect risk alleles using genome-wide tag SNP panels. PLoS Genet (2007) 3.29
A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet (2010) 3.25
Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol (2007) 3.25
Histone H3 variants specify modes of chromatin assembly. Proc Natl Acad Sci U S A (2002) 3.06
Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell (2002) 2.72
Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol (2013) 2.71
Spreading of silent chromatin: inaction at a distance. Nat Rev Genet (2006) 2.64
Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol (2004) 2.57
Major evolutionary transitions in centromere complexity. Cell (2009) 2.49
Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol (2007) 2.46
Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J (2004) 2.45
A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell (2010) 2.24
Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A (2011) 2.22
A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. J Immunol (2011) 2.20
Conflict begets complexity: the evolution of centromeres. Curr Opin Genet Dev (2002) 2.14
Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res (2004) 2.14
TILLING to detect induced mutations in soybean. BMC Plant Biol (2008) 2.13
Genome-wide analysis of DNA methylation patterns. Development (2007) 2.13
A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc (2006) 2.09
Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics (2003) 2.05
Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell (2004) 2.01
Chaperone-mediated assembly of centromeric chromatin in vitro. Proc Natl Acad Sci U S A (2006) 1.98
Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev (2003) 1.96
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol (2014) 1.95
TILLING: practical single-nucleotide mutation discovery. Plant J (2006) 1.94
Adaptive evolution of centromere proteins in plants and animals. J Biol (2004) 1.90
The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat Protoc (2010) 1.87
A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin (2012) 1.82
Structure, dynamics, and evolution of centromeric nucleosomes. Proc Natl Acad Sci U S A (2007) 1.81
Maintenance of chromatin states: an open-and-shut case. Curr Opin Cell Biol (2003) 1.72
High-throughput TILLING for functional genomics. Methods Mol Biol (2003) 1.70
Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis. Genome Res (2010) 1.69
Centromere targeting element within the histone fold domain of Cid. Mol Cell Biol (2002) 1.64
Epigenetic consequences of nucleosome dynamics. Cell (2002) 1.60
Doxorubicin enhances nucleosome turnover around promoters. Curr Biol (2013) 1.58
Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila. PLoS Genet (2005) 1.57
Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol (2005) 1.55
Automated band mapping in electrophoretic gel images using background information. Nucleic Acids Res (2005) 1.49
Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone. Proc Natl Acad Sci U S A (2002) 1.48
Tripartite organization of centromeric chromatin in budding yeast. Proc Natl Acad Sci U S A (2011) 1.47
Genomic analysis of parent-of-origin allelic expression in Arabidopsis thaliana seeds. PLoS One (2011) 1.45
Germline histone dynamics and epigenetics. Curr Opin Cell Biol (2007) 1.42
Histone H3.3 variant dynamics in the germline of Caenorhabditis elegans. PLoS Genet (2006) 1.42
H2A.Z nucleosomes enriched over active genes are homotypic. Nat Struct Mol Biol (2010) 1.41
DNA methylation dynamics in plant genomes. Biochim Biophys Acta (2007) 1.41
Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell (2005) 1.37
Adaptive evolution of the histone fold domain in centromeric histones. Mol Biol Evol (2004) 1.35
Predicting the effects of frameshifting indels. Genome Biol (2012) 1.33
Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res (2012) 1.32
A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans. Nucleic Acids Res (2009) 1.30
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling. Nucleic Acids Res (2006) 1.28
Centromeres put epigenetics in the driver's seat. Trends Biochem Sci (2006) 1.28
Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev (2011) 1.26
ISWI and CHD chromatin remodelers bind promoters but act in gene bodies. PLoS Genet (2013) 1.25
Histone variants: dynamic punctuation in transcription. Genes Dev (2014) 1.22
Centromeres convert but don't cross. PLoS Biol (2010) 1.22
Histone variants in pluripotency and disease. Development (2013) 1.21
Epigenomic profiling using microarrays. Biotechniques (2003) 1.21
Silencing of transposons in plant genomes: kick them when they're down. Genome Biol (2004) 1.15
Retention of induced mutations in a Drosophila reverse-genetic resource. Genetics (2008) 1.14
The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. Elife (2014) 1.13
Intergenic locations of rice centromeric chromatin. PLoS Biol (2008) 1.13
Phylogeny as the basis for naming histones. Trends Genet (2013) 1.12
The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres. Proc Natl Acad Sci U S A (2013) 1.11
Tech.Sight. Phage display. Affinity selection from biological libraries. Science (2002) 1.11
Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster. PLoS Genet (2005) 1.09
Transcribing through the nucleosome. Trends Biochem Sci (2014) 1.07
Quantitative epigenetics. Nat Genet (2003) 1.07
SIFT Indel: predictions for the functional effects of amino acid insertions/deletions in proteins. PLoS One (2013) 1.06
Fly-TILL: reverse genetics using a living point mutation resource. Fly (Austin) (2008) 1.05