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Results: 15

1.

The regulatory landscape of osteogenic differentiation.

Håkelien AM, Bryne JC, Harstad KG, Lorenz S, Paulsen J, Sun J, Mikkelsen TS, Myklebost O, Meza-Zepeda LA.

Stem Cells. 2014 Oct;32(10):2780-93. doi: 10.1002/stem.1759.

PMID:
24898411
[PubMed - in process]
2.

Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos.

Armant O, März M, Schmidt R, Ferg M, Diotel N, Ertzer R, Bryne JC, Yang L, Baader I, Reischl M, Legradi J, Mikut R, Stemple D, Ijcken Wv, van der Sloot A, Lenhard B, Strähle U, Rastegar S.

Dev Biol. 2013 Aug 15;380(2):351-62. doi: 10.1016/j.ydbio.2013.05.006. Epub 2013 May 14.

PMID:
23684812
[PubMed - indexed for MEDLINE]
Free Article
3.

Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells.

Herlofsen SR, Bryne JC, Høiby T, Wang L, Issner R, Zhang X, Coyne MJ, Boyle P, Gu H, Meza-Zepeda LA, Collas P, Mikkelsen TS, Brinchmann JE.

BMC Genomics. 2013 Feb 15;14:105. doi: 10.1186/1471-2164-14-105.

PMID:
23414147
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A novel complex, RUNX1-MYEF2, represses hematopoietic genes in erythroid cells.

van Riel B, Pakozdi T, Brouwer R, Monteiro R, Tuladhar K, Franke V, Bryne JC, Jorna R, Rijkers EJ, van Ijcken W, Andrieu-Soler C, Demmers J, Patient R, Soler E, Lenhard B, Grosveld F.

Mol Cell Biol. 2012 Oct;32(19):3814-22. doi: 10.1128/MCB.05938-11. Epub 2012 Jul 16.

PMID:
22801375
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner.

Sleutels F, Soochit W, Bartkuhn M, Heath H, Dienstbach S, Bergmaier P, Franke V, Rosa-Garrido M, van de Nobelen S, Caesar L, van der Reijden M, Bryne JC, van Ijcken W, Grootegoed JA, Delgado MD, Lenhard B, Renkawitz R, Grosveld F, Galjart N.

Epigenetics Chromatin. 2012 Jun 18;5(1):8. doi: 10.1186/1756-8935-5-8.

PMID:
22709888
[PubMed]
Free PMC Article
6.

Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development.

Stadhouders R, Thongjuea S, Andrieu-Soler C, Palstra RJ, Bryne JC, van den Heuvel A, Stevens M, de Boer E, Kockx C, van der Sloot A, van den Hout M, van Ijcken W, Eick D, Lenhard B, Grosveld F, Soler E.

EMBO J. 2012 Feb 15;31(4):986-99. doi: 10.1038/emboj.2011.450. Epub 2011 Dec 13.

PMID:
22157820
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes.

Engelen E, Akinci U, Bryne JC, Hou J, Gontan C, Moen M, Szumska D, Kockx C, van Ijcken W, Dekkers DH, Demmers J, Rijkers EJ, Bhattacharya S, Philipsen S, Pevny LH, Grosveld FG, Rottier RJ, Lenhard B, Poot RA.

Nat Genet. 2011 Jun;43(6):607-11. doi: 10.1038/ng.825. Epub 2011 May 1.

PMID:
21532573
[PubMed - indexed for MEDLINE]
8.

BioXSD: the common data-exchange format for everyday bioinformatics web services.

Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I.

Bioinformatics. 2010 Sep 15;26(18):i540-6. doi: 10.1093/bioinformatics/btq391.

PMID:
20823319
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T.

J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8.

PMID:
20727200
[PubMed]
Free PMC Article
10.

A systems approach to analyze transcription factors in mammalian cells.

Soler E, Andrieu-Soler C, Boer Ed, Bryne JC, Thongjuea S, Rijkers E, Demmers J, Ijcken Wv, Grosveld F.

Methods. 2011 Feb;53(2):151-62. doi: 10.1016/j.ymeth.2010.08.002. Epub 2010 Aug 10. Review.

PMID:
20705139
[PubMed - indexed for MEDLINE]
11.

The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation.

Soler E, Andrieu-Soler C, de Boer E, Bryne JC, Thongjuea S, Stadhouders R, Palstra RJ, Stevens M, Kockx C, van Ijcken W, Hou J, Steinhoff C, Rijkers E, Lenhard B, Grosveld F.

Genes Dev. 2010 Feb 1;24(3):277-89. doi: 10.1101/gad.551810. Erratum in: Genes Dev. 2010 Mar 15;24(6):623.

PMID:
20123907
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

ELM: the status of the 2010 eukaryotic linear motif resource.

Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ.

Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016. Epub 2009 Nov 17.

PMID:
19920119
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

An active registry for bioinformatics web services.

Pettifer S, Thorne D, McDermott P, Attwood T, Baran J, Bryne JC, Hupponen T, Mowbray D, Vriend G.

Bioinformatics. 2009 Aug 15;25(16):2090-1. doi: 10.1093/bioinformatics/btp329. Epub 2009 May 21.

PMID:
19460889
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Transcriptional features of genomic regulatory blocks.

Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B.

Genome Biol. 2009;10(4):R38. doi: 10.1186/gb-2009-10-4-r38. Epub 2009 Apr 19.

PMID:
19374772
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6. Epub 2007 Nov 15.

PMID:
18006571
[PubMed - indexed for MEDLINE]
Free PMC Article

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