Publications
Identification of constrained sequence elements across 239 primate genomes. Nature. 2024 ;625(7996):735-742.
. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol. 2020 ;12(7):1099-1188.
. Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. BMC Evol Biol. 2020 ;20(1):33.
. Framework for microRNA variant annotation and prioritization using human population and disease datasets. Hum Mutat. 2019 ;40(1):73-89.
. A comprehensive transcriptional map of primate brain development. Nature. 2016 ;535(7612):367-75.
. . Hemichordate genomes and deuterostome origins. Nature. 2015 ;527(7579):459-65.
. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet. 2014 ;46(1):17-23.
. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 ;491(7422):56-65.
. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature. 2012 ;483(7387):82-6.
. 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.
. 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.
. 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.
. 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.
. Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments. Proc Natl Acad Sci U S A. 2006 ;103(35):13121-5.
. 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.
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