Publications
Identification of new members of a carbohydrate kinase-encoding gene family. J Comput Biol. 1995 ;2(3):451-8.
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Comparing vertebrate whole-genome shotgun reads to the human genome. Genome Res. 2001 ;11(11):1807-16.
. Initial sequencing and analysis of the human genome. Nature. 2001 ;409(6822):860-921.
. Evolutionary traces of functional surfaces along G protein signaling pathway. Methods Enzymol. 2002 ;344:536-56.
. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 ;420(6915):520-62.
. Human genetics. Primate shadow play. Science. 2003 ;299(5611):1331-3.
. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 ;432(7018):695-716.
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005 ;15(1):1-18.
. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 ;15(8):1034-50.
. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 2005 ;434(7034):724-31.
. The genome of the social amoeba Dictyostelium discoideum. Nature. 2005 ;435(7038):43-57.
. . Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments. Proc Natl Acad Sci U S A. 2006 ;103(35):13121-5.
. 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.
. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 ;447(7146):799-816.
. cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation. Bioinformatics. 2008 ;24(20):2418-9.
. Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells. PLoS One. 2008 ;3(7):e2548.
. The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Mol Biol Evol. 2010 ;27(10):2322-32.
. Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins. J Gen Virol. 2010 ;91(Pt 9):2203-15.
. A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol. 2010 ;337(2):484-95.
. Diversity of the fsr-gelE region of the Enterococcus faecalis genome but conservation in strains with partial deletions of the fsr operon. Appl Environ Microbiol. 2011 ;77(2):442-51.
. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 ;491(7422):56-65.
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