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Results: 1 to 20 of 43

1.

An atlas of combinatorial transcriptional regulation in mouse and man.

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y.

Cell. 2010 Mar 5;140(5):744-52. doi: 10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr 16;141(2):369. Kamburov, Atanas [added]; Kaur, Mandeep [added]; MacPherson, Cameron Ross [added]; Radovanovic, Aleksandar [added]; Schwartz, Ariel [added].

PMID:
20211142
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs.

Giorgetti L, Siggers T, Tiana G, Caprara G, Notarbartolo S, Corona T, Pasparakis M, Milani P, Bulyk ML, Natoli G.

Mol Cell. 2010 Feb 12;37(3):418-28. doi: 10.1016/j.molcel.2010.01.016.

PMID:
20159560
[PubMed - indexed for MEDLINE]
Free Article
3.

Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis.

Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB.

Mol Cell. 2009 Nov 25;36(4):682-95. doi: 10.1016/j.molcel.2009.11.002.

PMID:
19941827
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.

Yokoyama KD, Ohler U, Wray GA.

Nucleic Acids Res. 2009 Jul;37(13):e92. doi: 10.1093/nar/gkp423. Epub 2009 May 29.

PMID:
19483094
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MEME SUITE: tools for motif discovery and searching.

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8. doi: 10.1093/nar/gkp335. Epub 2009 May 20.

PMID:
19458158
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors.

Berger MF, Bulyk ML.

Nat Protoc. 2009;4(3):393-411. doi: 10.1038/nprot.2008.195.

PMID:
19265799
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A.

Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246.

PMID:
19160518
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.

Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4.

PMID:
19122651
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

PASTAA: identifying transcription factors associated with sets of co-regulated genes.

Roider HG, Manke T, O'Keeffe S, Vingron M, Haas SA.

Bioinformatics. 2009 Feb 15;25(4):435-42. doi: 10.1093/bioinformatics/btn627. Epub 2008 Dec 9.

PMID:
19073590
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.

Newburger DE, Bulyk ML.

Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82. doi: 10.1093/nar/gkn660. Epub 2008 Oct 8.

PMID:
18842628
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Discovering sequence motifs with arbitrary insertions and deletions.

Frith MC, Saunders NF, Kobe B, Bailey TL.

PLoS Comput Biol. 2008 May 9;4(4):e1000071. doi: 10.1371/journal.pcbi.1000071.

PMID:
18437229
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

C/EBP alpha:AP-1 leucine zipper heterodimers bind novel DNA elements, activate the PU.1 promoter and direct monocyte lineage commitment more potently than C/EBP alpha homodimers or AP-1.

Cai DH, Wang D, Keefer J, Yeamans C, Hensley K, Friedman AD.

Oncogene. 2008 Apr 24;27(19):2772-9. Epub 2007 Nov 19.

PMID:
18026136
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Krüppel-like transcription factors: a functional family.

Pearson R, Fleetwood J, Eaton S, Crossley M, Bao S.

Int J Biochem Cell Biol. 2008;40(10):1996-2001. Epub 2007 Aug 7. Review.

PMID:
17904406
[PubMed - indexed for MEDLINE]
14.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

PMID:
17571346
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Second derivatives in generalized Born theory.

Brown RA, Case DA.

J Comput Chem. 2006 Nov 15;27(14):1662-75.

PMID:
16900491
[PubMed - indexed for MEDLINE]
16.

Expression of adipose differentiation-related protein (ADRP) is conjointly regulated by PU.1 and AP-1 in macrophages.

Wei P, Taniguchi S, Sakai Y, Imamura M, Inoguchi T, Nawata H, Oda S, Nakabeppu Y, Nishimura J, Ikuyama S.

J Biochem. 2005 Oct;138(4):399-412.

PMID:
16272134
[PubMed - indexed for MEDLINE]
17.

Interaction of phosphorylated c-Jun with TCF4 regulates intestinal cancer development.

Nateri AS, Spencer-Dene B, Behrens A.

Nature. 2005 Sep 8;437(7056):281-5. Epub 2005 Jul 10.

PMID:
16007074
[PubMed - indexed for MEDLINE]
Free Article
18.

A novel E2 box-GATA element modulates Cdc6 transcription during human cells polyploidization.

Vilaboa N, Bermejo R, Martinez P, Bornstein R, Calés C.

Nucleic Acids Res. 2004 Dec 8;32(21):6454-67. Print 2004.

PMID:
15590906
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Dimerization is required for transactivation by estrogen-receptor-related (ERR) orphan receptors: evidence from amphioxus ERR.

Horard B, Castet A, Bardet PL, Laudet V, Cavailles V, Vanacker JM.

J Mol Endocrinol. 2004 Oct;33(2):493-509.

PMID:
15525604
[PubMed - indexed for MEDLINE]
Free Article
20.

Detection of functional DNA motifs via statistical over-representation.

Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z.

Nucleic Acids Res. 2004 Feb 26;32(4):1372-81. Print 2004.

PMID:
14988425
[PubMed - indexed for MEDLINE]
Free PMC Article
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