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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. Expand
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. Expand
End-to-end scene text recognition
- K. Wang, Boris Babenko, Serge J. Belongie
- Computer Science
- International Conference on Computer Vision
- 6 November 2011
While scene text recognition has generally been treated with highly domain-specific methods, the results demonstrate the suitability of applying generic computer vision methods. Expand
Circular RNAs are abundant, conserved, and associated with ALU repeats.
High-throughput sequencing of libraries prepared from ribosome-depleted RNA with or without digestion with the RNA exonuclease showed that ecircRNAs are abundant, stable, conserved and nonrandom products of RNA splicing that could be involved in control of gene expression. Expand
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
A second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency is introduced, which indicates that Map Splice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Expand
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. Expand
Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies.
- Chengliang Dong, P. Wei, +4 authors Xiaoming Liu
- Biology, Medicine
- Human molecular genetics
- 15 April 2015
The authors' scores achieved the highest discriminative power compared with all the deleteriousness prediction scores tested and showed low false-positive prediction rate for benign yet rare nonsynonymous variants, which demonstrated the value of combining information from multiple orthologous approaches. Expand
Autism genome-wide copy number variation reveals ubiquitin and neuronal genes
Several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls, and duplications 55 kilobases upstream of complementary DNA AK123120 indicate that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD. Expand
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis
Moderate powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Expand
Circulating microRNAs, potential biomarkers for drug-induced liver injury
- K. Wang, Shile Zhang, +5 authors D. Galas
- Biology, Medicine
- Proceedings of the National Academy of Sciences
- 17 March 2009
It is demonstrated that specific microRNA species, such as mir-122 and mir-192, both are enriched in the liver tissue and exhibit dose- and exposure duration-dependent changes in the plasma that parallel serum aminotransferase levels and the histopathology of liver degeneration, but their changes can be detected significantly earlier. Expand