Research summary
ANNOVAR was developed to annotate single-nucleotide variants and insertions/deletions from high-throughput sequencing data, supporting functional consequence assignment, cytogenetic band inference, functional importance scoring, conserved region tagging and cross-referencing against 1000 Genomes and dbSNP, using databases from UCSC or any GFF-compliant source [1]. RNA-seq of ribosome-depleted RNA with and without RNase R digestion in human fibroblasts identified >25,000 distinct RNA species containing non-colinear exon junctions (backsplices) that were enriched by exonuclease degradation of linear RNA, validating widespread endogenous circular RNAs that were more stable than associated linear RNAs and enriched in ALU repeats [2]. A quantitative-PCR survey of microRNA spectra across 12 human body fluids and urine from women in different pregnancy stages or with urothelial cancers profiled the global distribution of miRNAs as candidate biomarkers [3]. STM2 was identified as a candidate gene for the chromosome 1 familial Alzheimer's disease locus, homologous to the chromosome 14 S182 (presenilin 1) gene; an N141I missense mutation cosegregated with disease in Volga German AD kindreds at a residue conserved with mouse and human S182 [4]. PennCNV used a hidden Markov model on Illumina high-density SNP data to detect copy-number variants at kilobase resolution, integrating signal intensity, allelic intensity ratio, inter-SNP distance, allele frequency and pedigree information [5]. A whole-genome CNV study on 859 autism spectrum disorder cases and 1,409 European-ancestry healthy children genotyped at ~550,000 SNPs (replicated in 1,336 cases and 1,110 controls) identified CNVs enriched in ubiquitin and neuronal genes [6]. Hierarchical PANI nanowire/graphene oxide nanocomposites were prepared by aligning PANI nanowire arrays vertically on GO; the composite showed higher electrochemical capacitance and stability than either component as a supercapacitor electrode through a synergistic effect [7]. MapSplice was introduced as a second-generation splice-detection algorithm focused on sensitivity, specificity and CPU/memory efficiency, applicable to short (<75 bp) and long (>=75 bp) reads, detecting both canonical and non-canonical splice junctions independent of splice-site features or intron length [8].
Recent publications
- ANNOVAR: functional annotation of genetic variants from high-throughput sequencing dataDOI
- Circular RNAs are abundant, conserved, and associated with ALU repeatsDOI
- The MicroRNA Spectrum in 12 Body FluidsDOI
- Candidate Gene for the Chromosome 1 Familial Alzheimer's Disease LocusDOI
- Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility lociDOI
- Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencingDOI
- PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping dataDOI
- Autism genome-wide copy number variation reveals ubiquitin and neuronal genesDOI
- Hierarchical Nanocomposites of Polyaniline Nanowire Arrays on Graphene Oxide Sheets with Synergistic Effect for Energy StorageDOI
- MapSplice: Accurate mapping of RNA-seq reads for splice junction discoveryDOI
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External profiles
- ORCID: https://orcid.org/0000-0002-6170-4744
- OpenAlex: openalex.org
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