Published in Nat Methods on February 02, 2014
Rare-variant association analysis: study designs and statistical tests. Am J Hum Genet (2014) 3.42
The Ensembl Variant Effect Predictor. Genome Biol (2016) 1.80
A spectral approach integrating functional genomic annotations for coding and noncoding variants. Nat Genet (2016) 1.75
Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods (2015) 1.72
A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. Am J Hum Genet (2016) 1.52
A method to predict the impact of regulatory variants from DNA sequence. Nat Genet (2015) 1.51
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet (2017) 1.42
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. Genome Biol (2014) 1.36
An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics (2015) 1.28
A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat Genet (2015) 1.27
Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res (2014) 1.13
Role of non-coding sequence variants in cancer. Nat Rev Genet (2016) 1.10
A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events. PLoS Comput Biol (2015) 1.07
Retracted Mutation pattern is an influential factor on functional mutation rates in cancer. Cancer Cell Int (2016) 1.06
Non-coding genetic variants in human disease. Hum Mol Genet (2015) 1.04
Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease. Nat Genet (2016) 1.03
Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation. Nat Commun (2015) 1.01
Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants. Am J Hum Genet (2014) 0.99
Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser. Nat Biotechnol (2015) 0.97
GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res (2015) 0.96
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Res (2016) 0.95
Common variation near ROBO2 is associated with expressive vocabulary in infancy. Nat Commun (2014) 0.94
Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process. Biomed Res Int (2015) 0.93
The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity. PLoS Genet (2015) 0.90
OncoCis: annotation of cis-regulatory mutations in cancer. Genome Biol (2014) 0.89
Genome-wide association study of maternal and inherited effects on left-sided cardiac malformations. Hum Mol Genet (2014) 0.88
Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. Nat Rev Genet (2016) 0.88
A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing. Front Genet (2015) 0.88
A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data. Sci Rep (2015) 0.87
Analysis of stop-gain and frameshift variants in human innate immunity genes. PLoS Comput Biol (2014) 0.87
Identification of context-dependent expression quantitative trait loci in whole blood. Nat Genet (2016) 0.85
Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans. Am J Hum Genet (2016) 0.85
Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. BMC Bioinformatics (2016) 0.84
rVarBase: an updated database for regulatory features of human variants. Nucleic Acids Res (2015) 0.84
Determining causality and consequence of expression quantitative trait loci. Hum Genet (2014) 0.84
Disease-associated variants in different categories of disease located in distinct regulatory elements. BMC Genomics (2015) 0.83
Computational approaches to interpreting genomic sequence variation. Genome Med (2014) 0.82
Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken. PLoS One (2014) 0.82
dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions. Database (Oxford) (2016) 0.82
Genome-wide association study with 1000 genomes imputation identifies signals for nine sex hormone-related phenotypes. Eur J Hum Genet (2015) 0.82
3D genome organization in health and disease: emerging opportunities in cancer translational medicine. Nucleus (2015) 0.81
Genome-wide time-to-event analysis on smoking progression stages in a family-based study. Brain Behav (2016) 0.81
Progress towards the integration of pharmacogenomics in practice. Hum Genet (2014) 0.81
The road from next-generation sequencing to personalized medicine. Per Med (2015) 0.81
Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants. Sci Rep (2015) 0.81
In-silico analysis of inflammatory bowel disease (IBD) GWAS loci to novel connections. PLoS One (2015) 0.80
DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles. Genome Biol (2016) 0.80
Predicting gene expression in massively parallel reporter assays: A comparative study. Hum Mutat (2017) 0.80
Accurate eQTL prioritization with an ensemble-based framework. Hum Mutat (2017) 0.79
Chromatin interactions and candidate genes at ten prostate cancer risk loci. Sci Rep (2016) 0.79
Genomic approaches for understanding the genetics of complex disease. Genome Res (2015) 0.79
BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations. Nucleic Acids Res (2015) 0.79
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PLoS Comput Biol (2016) 0.78
The search for cis-regulatory driver mutations in cancer genomes. Oncotarget (2015) 0.78
PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned. Hum Mutat (2017) 0.78
A genome-wide association study of congenital cardiovascular left-sided lesions shows association with a locus on chromosome 20. Hum Mol Genet (2016) 0.78
VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants. BMC Genomics (2014) 0.77
Transcriptome outlier analysis implicates schizophrenia susceptibility genes and enriches putatively functional rare genetic variants. Hum Mol Genet (2015) 0.77
Global inference of disease-causing single nucleotide variants from exome sequencing data. BMC Bioinformatics (2016) 0.77
Prioritization of non-coding disease-causing variants and long non-coding RNAs in liver cancer. Oncol Lett (2016) 0.77
Predicting enhancer activity and variant impact using gkm-SVM. Hum Mutat (2017) 0.77
Path from schizophrenia genomics to biology: gene regulation and perturbation in neurons derived from induced pluripotent stem cells and genome editing. Neurosci Bull (2015) 0.76
Purifying selection in deeply conserved human enhancers is more consistent than in coding sequences. PLoS One (2014) 0.76
Discovery of rare variants for complex phenotypes. Hum Genet (2016) 0.76
Functional annotation of noncoding variants and prioritization of cancer-associated lncRNAs in lung cancer. Oncol Lett (2016) 0.76
SuRFing the genomics wave: an R package for prioritising SNPs by functionality. Genome Med (2014) 0.76
Integrative analysis of functional genomic annotations and sequencing data to identify rare causal variants via hierarchical modeling. Front Genet (2015) 0.76
Human Knockout Carriers: Dead, Diseased, Healthy, or Improved? Trends Mol Med (2016) 0.76
A systematic variant annotation approach for ranking genes associated with autism spectrum disorders. Mol Autism (2016) 0.76
cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes. Genome Biol (2017) 0.75
Genome-wide association study using family-based cohorts identifies the WLS and CCDC170/ESR1 loci as associated with bone mineral density. BMC Genomics (2016) 0.75
Running spell-check to identify regulatory variants. Nat Genet (2015) 0.75
Semantic prioritization of novel causative genomic variants. PLoS Comput Biol (2017) 0.75
A sequence-based method to predict the impact of regulatory variants using random forest. BMC Syst Biol (2017) 0.75
Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. PLoS Genet (2017) 0.75
A comprehensive analysis of cancer-driving mutations and genes in kidney cancer. Oncol Lett (2017) 0.75
Diving deeper to predict noncoding sequence function. Nat Methods (2015) 0.75
Allele-specific quantitative proteomics unravels molecular mechanisms modulated by cis-regulatory PPARG locus variation. Nucleic Acids Res (2017) 0.75
Quantitative Trait Loci Identify Functional Noncoding Variation in Cancer. PLoS Genet (2016) 0.75
Identifying a novel locus for psoriatic arthritis. Rheumatology (Oxford) (2015) 0.75
Assessing models for genetic prediction of complex traits: a comparison of visualization and quantitative methods. BMC Genomics (2015) 0.75
Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. Mol Psychiatry (2017) 0.75
GAVIN: Gene-Aware Variant INterpretation for medical sequencing. Genome Biol (2017) 0.75
Genome-Wide Prioritization and Transcriptomics Reveal Novel Signatures Associated With Thiazide Diuretics Blood Pressure Response. Circ Cardiovasc Genet (2017) 0.75
Sexual Dimorphisms in Genetic Loci Linked to Body Fat Distribution. Biosci Rep (2017) 0.75
Separating the wheat from the chaff: systematic identification of functionally relevant noncoding variants in ADHD. Mol Psychiatry (2016) 0.75
Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer. BMC Genomics (2017) 0.75
Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer's disease. PLoS Genet (2017) 0.75
HIPred: an integrative approach to predicting haploinsufficient genes. Bioinformatics (2017) 0.75
Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PLoS One (2017) 0.75
Genome-Wide Association Studies and Meta-Analyses for Congenital Heart Defects. Circ Cardiovasc Genet (2017) 0.75
Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms. Trends Genet (2016) 0.75
Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits. Am J Hum Genet (2017) 0.75
Regulatory element-based prediction identifies new susceptibility regulatory variants for osteoporosis. Hum Genet (2017) 0.75
Annotating pathogenic non-coding variants in genic regions. Nat Commun (2017) 0.75
Challenges and progress in interpretation of non-coding genetic variants associated with human disease. Exp Biol Med (Maywood) (2017) 0.75
Association analyses based on false discovery rate implicate new loci for coronary artery disease. Nat Genet (2017) 0.75
Association of a functional TNF variant with Plasmodium falciparum parasitaemia in a congolese population. Genes Immun (2017) 0.75
Adaptive evolution of interleukin-3 (IL3), a gene associated with brain volume variation in general human populations. Hum Genet (2016) 0.75
A method and server for predicting damaging missense mutations. Nat Methods (2010) 78.53
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
An integrated map of genetic variation from 1,092 human genomes. Nature (2012) 59.82
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A (2009) 54.68
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc (2009) 38.62
COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res (2010) 25.55
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods (2010) 16.61
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics (2010) 15.90
Systematic localization of common disease-associated variation in regulatory DNA. Science (2012) 14.47
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature (2010) 12.07
The Human Gene Mutation Database: 2008 update. Genome Med (2009) 11.72
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol (2010) 8.69
ChromHMM: automating chromatin-state discovery and characterization. Nat Methods (2012) 7.66
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (2010) 7.41
A map of open chromatin in human pancreatic islets. Nat Genet (2010) 6.75
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89
Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus. Nat Genet (2011) 2.54
Whole-exome sequencing in an isolated population from the Dalmatian island of Vis. Eur J Hum Genet (2016) 0.77