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Items: 1 to 20 of 59

1.

A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.

Yang J, Ramsey SA.

Bioinformatics. 2015 Nov 1;31(21):3445-50. doi: 10.1093/bioinformatics/btv391.

2.

Defining functional DNA elements in the human genome.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Review.

3.
4.

Regulatory genomics: Insights from the zebrafish.

Chatterjee S, Lufkin T.

Curr Top Genet. 2012;5:1-10.

5.

Discriminative prediction of mammalian enhancers from DNA sequence.

Lee D, Karchin R, Beer MA.

Genome Res. 2011 Dec;21(12):2167-80. doi: 10.1101/gr.121905.111.

6.

Identification of distal cis-regulatory elements at mouse mitoferrin loci using zebrafish transgenesis.

Amigo JD, Yu M, Troadec MB, Gwynn B, Cooney JD, Lambert AJ, Chi NC, Weiss MJ, Peters LL, Kaplan J, Cantor AB, Paw BH.

Mol Cell Biol. 2011 Apr;31(7):1344-56. doi: 10.1128/MCB.01010-10.

7.

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials.

Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S.

PLoS Biol. 2010 Aug 17;8(8). pii: e1000456. doi: 10.1371/journal.pbio.1000456. Erratum in: PLoS Biol. 2013 Oct;11(10). doi: 10.1371/annotation/e38f4ae8-0776-42e6-b912-50800f54436e.

8.

LRF is an essential downstream target of GATA1 in erythroid development and regulates BIM-dependent apoptosis.

Maeda T, Ito K, Merghoub T, Poliseno L, Hobbs RM, Wang G, Dong L, Maeda M, Dore LC, Zelent A, Luzzatto L, Teruya-Feldstein J, Weiss MJ, Pandolfi PP.

Dev Cell. 2009 Oct;17(4):527-40. doi: 10.1016/j.devcel.2009.09.005.

9.

Chromatin architecture and transcription factor binding regulate expression of erythrocyte membrane protein genes.

Steiner LA, Maksimova Y, Schulz V, Wong C, Raha D, Mahajan MC, Weissman SM, Gallagher PG.

Mol Cell Biol. 2009 Oct;29(20):5399-412. doi: 10.1128/MCB.00777-09.

10.

GATA-2 reinforces megakaryocyte development in the absence of GATA-1.

Huang Z, Dore LC, Li Z, Orkin SH, Feng G, Lin S, Crispino JD.

Mol Cell Biol. 2009 Sep;29(18):5168-80. doi: 10.1128/MCB.00482-09.

11.

Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons.

Liu R, Hannenhalli S, Bucan M.

Genome Biol. 2009;10(7):R72. doi: 10.1186/gb-2009-10-7-r72.

12.

SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies.

Xu Z, Taylor JA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W600-5. doi: 10.1093/nar/gkp290.

13.

Local DNA topography correlates with functional noncoding regions of the human genome.

Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH.

Science. 2009 Apr 17;324(5925):389-92. doi: 10.1126/science.1169050.

14.

Integrating sequence, evolution and functional genomics in regulatory genomics.

Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E.

Genome Biol. 2009;10(1):202. doi: 10.1186/gb-2009-10-1-202. Review.

15.

Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity.

Jia L, Berman BP, Jariwala U, Yan X, Cogan JP, Walters A, Chen T, Buchanan G, Frenkel B, Coetzee GA.

PLoS One. 2008;3(11):e3645. doi: 10.1371/journal.pone.0003645.

16.

DiRE: identifying distant regulatory elements of co-expressed genes.

Gotea V, Ovcharenko I.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W133-9. doi: 10.1093/nar/gkn300.

17.

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

Van Loo P, Aerts S, Thienpont B, De Moor B, Moreau Y, Marynen P.

Genome Biol. 2008 Apr 7;9(4):R66. doi: 10.1186/gb-2008-9-4-r66.

18.

A GATA-1-regulated microRNA locus essential for erythropoiesis.

Dore LC, Amigo JD, Dos Santos CO, Zhang Z, Gai X, Tobias JW, Yu D, Klein AM, Dorman C, Wu W, Hardison RC, Paw BH, Weiss MJ.

Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3333-8. doi: 10.1073/pnas.0712312105.

19.

Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus.

Jing H, Vakoc CR, Ying L, Mandat S, Wang H, Zheng X, Blobel GA.

Mol Cell. 2008 Feb 1;29(2):232-42. doi: 10.1016/j.molcel.2007.11.020.

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