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Items: 1 to 20 of 21

1.

Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data.

Tuteja G, Moreira KB, Chung T, Chen J, Wenger AM, Bejerano G.

PLoS Comput Biol. 2014 Jan 30;10(1):e1003449. doi: 10.1371/journal.pcbi.1003449. eCollection 2014 Jan.

2.

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements.

Guturu H, Doxey AC, Wenger AM, Bejerano G.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130029. doi: 10.1098/rstb.2013.0029. Print 2013 Dec 19.

3.

The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option.

Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G.

PLoS Genet. 2013 Aug;9(8):e1003728. doi: 10.1371/journal.pgen.1003728. Epub 2013 Aug 29.

4.

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.

5.

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.

6.

PRISM offers a comprehensive genomic approach to transcription factor function prediction.

Wenger AM, Clarke SL, Guturu H, Chen J, Schaar BT, McLean CY, Bejerano G.

Genome Res. 2013 May;23(5):889-904. doi: 10.1101/gr.139071.112. Epub 2013 Feb 4.

7.

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.

8.

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.

9.

A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb.

Laurell T, Vandermeer JE, Wenger AM, Grigelioniene G, Nordenskjöld A, Arner M, Ekblom AG, Bejerano G, Ahituv N, Nordgren A.

Hum Mutat. 2012 Jul;33(7):1063-6. doi: 10.1002/humu.22097. Epub 2012 May 11.

10.

Coding exons function as tissue-specific enhancers of nearby genes.

Birnbaum RY, Clowney EJ, Agamy O, Kim MJ, Zhao J, Yamanaka T, Pappalardo Z, Clarke SL, Wenger AM, Nguyen L, Gurrieri F, Everman DB, Schwartz CE, Birk OS, Bejerano G, Lomvardas S, Ahituv N.

Genome Res. 2012 Jun;22(6):1059-68. doi: 10.1101/gr.133546.111. Epub 2012 Mar 22.

11.

Control of pelvic girdle development by genes of the Pbx family and Emx2.

Capellini TD, Handschuh K, Quintana L, Ferretti E, Di Giacomo G, Fantini S, Vaccari G, Clarke SL, Wenger AM, Bejerano G, Sharpe J, Zappavigna V, Selleri L.

Dev Dyn. 2011 May;240(5):1173-89. doi: 10.1002/dvdy.22617. Epub 2011 Mar 31.

12.

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.

13.

GREAT improves functional interpretation of cis-regulatory regions.

McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G.

Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.

14.

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.

15.

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.

16.

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.

PMID:
16625209
17.

Computational screening of conserved genomic DNA in search of functional noncoding elements.

Bejerano G, Siepel AC, Kent WJ, Haussler D.

Nat Methods. 2005 Jul;2(7):535-45. No abstract available.

PMID:
16170870
18.

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.

19.

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.

PMID:
15592404
20.

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.

PMID:
15262779

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