Publications
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One. 2011 ;6(1):e16327.
. Whole-exome sequencing identifies compound heterozygous mutations in WDR62 in siblings with recurrent polymicrogyria. Am J Med Genet A. 2011 ;155A(9):2071-7.
. Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error. Genome Res. 2010 ;20(1):101-9.
. A full-length cDNA resource for the pea aphid, Acyrthosiphon pisum. Insect Mol Biol. 2010 ;19 Suppl 2(0 2):23-31.
. Identification and removal of colanic acid from plasmid DNA preparations: implications for gene therapy. Gene Ther. 2010 ;17(12):1484-99.
. Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res. 2010 ;20(7):981-8.
. A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol. 2010 ;337(2):484-95.
. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A. 2009 ;106(6):1954-9.
. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics. 2009 ;10:512.
. Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences. Mol Biol Evol. 2009 ;26(7):1479-90.
. Acquisition of uncharacterized sequences from Candidatus liberibacter, an unculturable bacterium, using an improved genomic walking method. Mol Cell Probes. 2008 ;22(1):30-7.
. cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation. Bioinformatics. 2008 ;24(20):2418-9.
. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genome Res. 2008 ;18(10):1571-81.
. PDX-1 acts as a potential molecular target for treatment of human pancreatic cancer. Pancreas. 2008 ;37(2):210-20.
. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007 ;17(12):1797-808.
. Conservation of virally encoded microRNAs in Kaposi sarcoma--associated herpesvirus in primary effusion lymphoma cell lines and in patients with Kaposi sarcoma or multicentric Castleman disease. J Infect Dis. 2007 ;195(5):645-59.
. Corticotropin releasing hormone (CRH) gene variation: comprehensive resequencing for variant and molecular haplotype discovery in monosomic hybrid cell lines. DNA Seq. 2007 ;18(6):434-44.
. Elevated expression of DNA polymerase II increases spontaneous mutagenesis in Escherichia coli. Mutat Res. 2007 ;625(1-2):29-39.
. Family-based association study of matrix metalloproteinase-3 and -9 haplotypes with susceptibility to ischemic white matter injury. Hum Genet. 2007 ;120(5):671-80.
. First complete genome sequence of two Staphylococcus epidermidis bacteriophages. J Bacteriol. 2007 ;189(5):2086-100.
. Forerunner genes contiguous to RB1 contribute to the development of in situ neoplasia. Proc Natl Acad Sci U S A. 2007 ;104(34):13732-7.
. The genome of Apis mellifera: dialog between linkage mapping and sequence assembly. Genome Biol. 2007 ;8(3):403.
. Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium. PLoS One. 2007 ;2(7):e659.
. Identification of a novel tumor suppressor gene p34 on human chromosome 6q25.1. Cancer Res. 2007 ;67(1):93-9.
. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol. 2007 ;7:99.
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