Publications
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res. 2012 ;22(10):2079-87.
. Association studies for next-generation sequencing. Genome Res. 2011 ;21(7):1099-108.
. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat. 2011 ;32(8):894-9.
. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One. 2011 ;6(1):e16327.
. Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol. 2011 ;12(7):R68.
. A catalog of reference genomes from the human microbiome. Science. 2010 ;328(5981):994-9.
. Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error. Genome Res. 2010 ;20(1):101-9.
. A map of human genome variation from population-scale sequencing. Nature. 2010 ;467(7319):1061-73.
. A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol. 2010 ;337(2):484-95.
. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 ;19(12):2324-33.
. Developing a tissue resource to characterize the genome of pancreatic cancer. World J Surg. 2009 ;33(4):723-31.
. Genomics. Genome project standards in a new era of sequencing. Science. 2009 ;326(5950):236-7.
. Metagenomic pyrosequencing and microbial identification. Clin Chem. 2009 ;55(5):856-66.
. cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation. Bioinformatics. 2008 ;24(20):2418-9.
. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008 ;452(7189):872-6.
. Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells. PLoS One. 2008 ;3(7):e2548.
. Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pac Symp Biocomput. 2008 ;:102-13.
. PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences. BMC Microbiol. 2008 ;8:185.
. VitisExpDB: a database resource for grape functional genomics. BMC Plant Biol. 2008 ;8:23.
. What everybody should know about the rat genome and its online resources. Nat Genet. 2008 ;40(5):523-7.
. High mobility group (HMG-box) genes in the honeybee fungal pathogen Ascosphaera apis. Mycologia. 2007 ;99(4):553-61.
. nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms. In Silico Biol. 2007 ;7(2):195-200.
. Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa. BMC Genomics. 2006 ;7:225.
. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006 ;314(5801):941-52.
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