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ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed.
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.
PennCNV, a hidden Markov model (HMM) based approach, is presented for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data, demonstrating the feasibility of whole-genome fine-mapping ofCNVs via high- density SNP genotypesing.
Biological, Clinical, and Population Relevance of 95 Loci for Blood Lipids
The results identify several novel loci associated with plasma lipids that are also associated with CAD and provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.
Pathway-based approaches for analysis of genomewide association studies.
It is demonstrated that pathway-based approaches, which jointly consider multiple contributing factors in the same pathway, might complement the most-significant SNPs/genes approach and provide additional insights into interpretation of GWA data on complex diseases.
Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study
Analysing biological pathways in genome-wide association studies
The development of pathway-based approaches for GWA studies are reviewed, their practical use and caveats are discussed, and it is suggested that pathway- based approaches may also be useful for future GWA study data sets with sequencing data.
SAVER: Gene expression recovery for single-cell RNA sequencing
SAVER (single-cell analysis via expression recovery), an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.
A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants
The results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.
Bulk tissue cell type deconvolution with multi-subject single-cell expression reference
A new method for estimating cell type proportions from bulk tissue RNA-seq data guided by multi-subject single-cell expression reference, which enables the characterization of cellular heterogeneity of complex tissues for understanding of disease mechanisms.
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants
SNPs at nine loci were reproducibly associated with myocardial infarction, but tests of common and rare CNVs failed to identify additional associations with my Cardiovascular Infarction risk.