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Items: 17


Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.

Hiller M, Agarwal S, Notwell JH, Parikh R, Guturu H, Wenger AM, Bejerano G.

Nucleic Acids Res. 2013 Aug;41(15):e151. doi: 10.1093/nar/gkt557. Epub 2013 Jun 27.


Enhancers: five essential questions.

Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G.

Nat Rev Genet. 2013 Apr;14(4):288-95. doi: 10.1038/nrg3458. Review.


Evolutionary biology for the 21st century.

Losos JB, Arnold SJ, Bejerano G, Brodie ED 3rd, Hibbett D, Hoekstra HE, Mindell DP, Monteiro A, Moritz C, Orr HA, Petrov DA, Renner SS, Ricklefs RE, Soltis PS, Turner TL.

PLoS Biol. 2013;11(1):e1001466. doi: 10.1371/journal.pbio.1001466. Epub 2013 Jan 8. No abstract available.


Hundreds of conserved non-coding genomic regions are independently lost in mammals.

Hiller M, Schaar BT, Bejerano G.

Nucleic Acids Res. 2012 Dec;40(22):11463-76. doi: 10.1093/nar/gks905. Epub 2012 Oct 5.


A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species.

Hiller M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G.

Cell Rep. 2012 Oct 25;2(4):817-23. doi: 10.1016/j.celrep.2012.08.032. Epub 2012 Sep 27.


Human developmental enhancers conserved between deuterostomes and protostomes.

Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G.

PLoS Genet. 2012;8(8):e1002852. doi: 10.1371/journal.pgen.1002852. Epub 2012 Aug 2.


Human-specific loss of regulatory DNA and the evolution of human-specific traits.

McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM.

Nature. 2011 Mar 10;471(7337):216-9. doi: 10.1038/nature09774.


Endangered species hold clues to human evolution.

Lowe CB, Bejerano G, Salama SR, Haussler D.

J Hered. 2010 Jul-Aug;101(4):437-47. doi: 10.1093/jhered/esq016. Epub 2010 Mar 23.


Dispensability of mammalian DNA.

McLean C, Bejerano G.

Genome Res. 2008 Nov;18(11):1743-51. doi: 10.1101/gr.080184.108. Epub 2008 Oct 2.


Human genome ultraconserved elements are ultraselected.

Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D.

Science. 2007 Aug 17;317(5840):915.


Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.

Lowe CB, Bejerano G, Haussler D.

Proc Natl Acad Sci U S A. 2007 May 8;104(19):8005-10. Epub 2007 Apr 26.


Identification and classification of conserved RNA secondary structures in the human genome.

Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D.

PLoS Comput Biol. 2006 Apr;2(4):e33. Epub 2006 Apr 21.


A distal enhancer and an ultraconserved exon are derived from a novel retroposon.

Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D.

Nature. 2006 May 4;441(7089):87-90. Epub 2006 Apr 16.


Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D.

Genome Res. 2005 Aug;15(8):1034-50. Epub 2005 Jul 15.


Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

International Chicken Genome Sequencing Consortium.

Nature. 2004 Dec 9;432(7018):695-716. Erratum in: Nature. 2005 Feb 17;433(7027):777.


Into the heart of darkness: large-scale clustering of human non-coding DNA.

Bejerano G, Haussler D, Blanchette M.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i40-8.


Ultraconserved elements in the human genome.

Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D.

Science. 2004 May 28;304(5675):1321-5. Epub 2004 May 6.

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