Pandit: a database of protein and associated nucleotide domains with inferred trees.

Detecting amino acid sites under positive selection and purifying selection. Genetics (2005) 3.35

The Molecular Biology Database Collection: 2005 update. Nucleic Acids Res (2005) 3.25

International Union of Basic and Clinical Pharmacology. LXXXV: calcium-activated chloride channels. Pharmacol Rev (2011) 1.67

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res (2006) 1.58

Genomic scale sub-family assignment of protein domains. Nucleic Acids Res (2006) 1.42

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol (2008) 1.30

XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics (2006) 1.29

Estimating the frequency of events that cause multiple-nucleotide changes. Genetics (2004) 1.18

Bayesian analysis of amino acid substitution models. Philos Trans R Soc Lond B Biol Sci (2008) 1.07

Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models. PLoS One (2012) 0.97

Nexplorer: phylogeny-based exploration of sequence family data. Bioinformatics (2005) 0.96

Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. PLoS One (2011) 0.94

Phylogenetic properties of RNA viruses. PLoS One (2012) 0.83

A generalized mechanistic codon model. Mol Biol Evol (2014) 0.76

Efficient methods for estimating amino acid replacement rates. J Mol Evol (2006) 0.76

Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty. Genome Biol Evol (2015) 0.76

xREI: a phylo-grammar visualization webserver. Nucleic Acids Res (2008) 0.75

Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins. BMC Bioinformatics (2006) 0.75

PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet (2007) 209.92

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science (2007) 51.70

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet (2008) 35.06

Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins (2003) 32.38

Integrating common and rare genetic variation in diverse human populations. Nature (2010) 32.30

Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet (2008) 20.66

Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet (2008) 19.55

Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27

Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics (2008) 15.77

Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat Genet (2006) 14.76

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature (2011) 13.23

Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet (2010) 13.18

Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study. Lancet (2012) 12.10

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res (2003) 11.12

Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet (2010) 9.90

STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med (2007) 9.80

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (2010) 9.61

Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet (2007) 8.74

A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67

TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. N Engl J Med (2006) 7.75

Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One (2008) 7.16

Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nat Genet (2009) 7.16

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science (2008) 6.35

An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A (2005) 6.26

Common variants at ten loci influence QT interval duration in the QTGEN Study. Nat Genet (2009) 5.20

Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat Genet (2012) 5.11

Interleukin-6 receptor pathways in coronary heart disease: a collaborative meta-analysis of 82 studies. Lancet (2012) 4.63

High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat Genet (2012) 4.46

Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet (2012) 4.41

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22

Common missense variant in the glucokinase regulatory protein gene is associated with increased plasma triglyceride and C-reactive protein but lower fasting glucose concentrations. Diabetes (2008) 4.20

Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12

Exome sequencing and the genetic basis of complex traits. Nat Genet (2012) 4.11

Common variants in KCNN3 are associated with lone atrial fibrillation. Nat Genet (2010) 3.97

Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE collaboration): a meta-analysis of genome-wide association studies. Lancet Neurol (2012) 3.93

HLA-A*3101 and carbamazepine-induced hypersensitivity reactions in Europeans. N Engl J Med (2011) 3.93

Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. PLoS Genet (2011) 3.68

Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet (2010) 3.55

Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci. Ann Neurol (2011) 3.52

Detecting amino acid sites under positive selection and purifying selection. Genetics (2005) 3.35

Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure (2004) 3.32

Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One (2013) 3.07

Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods (2013) 2.92

Common NOS1AP variants are associated with a prolonged QTc interval in the Rotterdam Study. Circulation (2007) 2.82

Seventy-five genetic loci influencing the human red blood cell. Nature (2012) 2.77

Myosin IXB variant increases the risk of celiac disease and points toward a primary intestinal barrier defect. Nat Genet (2005) 2.71

Comprehensive association testing of common mitochondrial DNA variation in metabolic disease. Am J Hum Genet (2006) 2.60

Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci. Am J Hum Genet (2012) 2.53

Knowledge-based real-space explorations for low-resolution structure determination. Structure (2006) 2.52

Haplotype structure and genotype-phenotype correlations of the sulfonylurea receptor and the islet ATP-sensitive potassium channel gene region. Diabetes (2004) 2.52

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet (2012) 2.50

Crystallographic refinement by knowledge-based exploration of complex energy landscapes. Structure (2005) 2.42

The role of the CD58 locus in multiple sclerosis. Proc Natl Acad Sci U S A (2009) 2.38

Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases. Proc Natl Acad Sci U S A (2009) 2.31

Biases and reconciliation in estimates of linkage disequilibrium in the human genome. Am J Hum Genet (2006) 2.26

Different versions of the Dayhoff rate matrix. Mol Biol Evol (2004) 2.23

An empirical codon model for protein sequence evolution. Mol Biol Evol (2007) 2.20

Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis. Arthritis Rheum (2013) 2.17

Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol (2003) 2.16

Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet (2010) 2.15

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics (2012) 2.07

Common variants in 40 genes assessed for diabetes incidence and response to metformin and lifestyle intervention in the diabetes prevention program. Diabetes (2010) 2.02

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics (2010) 1.99

Next-generation sequencing for HLA typing of class I loci. BMC Genomics (2011) 1.99

Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis. PLoS Genet (2012) 1.97

Searching for signals of evolutionary selection in 168 genes related to immune function. Hum Genet (2005) 1.97

Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci. Am J Hum Genet (2012) 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

Genomic DNA k-mer spectra: models and modalities. Genome Biol (2009) 1.92

GWAS identifies novel susceptibility loci on 6p21.32 and 21q21.3 for hepatocellular carcinoma in chronic hepatitis B virus carriers. PLoS Genet (2012) 1.86

Meta-analysis in more than 17,900 cases of ischemic stroke reveals a novel association at 12q24.12. Neurology (2014) 1.85

Stroke Genetics Network (SiGN) study: design and rationale for a genome-wide association study of ischemic stroke subtypes. Stroke (2013) 1.80

Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat Genet (2013) 1.72

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proc Natl Acad Sci U S A (2012) 1.72

Genome-wide association study of coronary and aortic calcification implicates risk loci for coronary artery disease and myocardial infarction. Atherosclerosis (2013) 1.69

Genome-wide association analysis identifies multiple loci related to resting heart rate. Hum Mol Genet (2010) 1.67

Effective detection of human leukocyte antigen risk alleles in celiac disease using tag single nucleotide polymorphisms. PLoS One (2008) 1.64

Evidence for an oligogenic basis of amyotrophic lateral sclerosis. Hum Mol Genet (2012) 1.62

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res (2006) 1.58

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins (2003) 1.56

The effects of alignment error and alignment filtering on the sitewise detection of positive selection. Mol Biol Evol (2011) 1.55

Fine-mapping the genetic association of the major histocompatibility complex in multiple sclerosis: HLA and non-HLA effects. PLoS Genet (2013) 1.55

Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control. Am J Hum Genet (2009) 1.51

Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis. Ann Neurol (2011) 1.45

Evolutionary footprints of nucleosome positions in yeast. Trends Genet (2008) 1.43

Resource-aware taxon selection for maximizing phylogenetic diversity. Syst Biol (2007) 1.42

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA (2011) 1.42

All Your Base: a fast and accurate probabilistic approach to base calling. Genome Biol (2012) 1.38

Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS Pathog (2013) 1.33

XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics (2006) 1.29

Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies. PLoS One (2009) 1.28

Loci influencing blood pressure identified using a cardiovascular gene-centric array. Hum Mol Genet (2013) 1.27

Variation in evolutionary processes at different codon positions. Mol Biol Evol (2006) 1.26