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Publications by Jan-Christian Bryne

17 publications found

Original articles

Lorenz S, Barøy T, Sun J, Nome T, Vodák D, Bryne JC, Håkelien AM, Fernandez-Cuesta L, Möhlendick B, Rieder H, Szuhai K, Zaikova O, Ahlquist TC, Thomassen GO, Skotheim RI, Lothe RA, Tarpey PS, Campbell P, Flanagan A, Myklebost O, Meza-Zepeda LA (2016)
Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations
Oncotarget, 7 (5), 5273-88
DOI 10.18632/oncotarget.6567, PubMed 26672768

Håkelien AM, Bryne JC, Harstad KG, Lorenz S, Paulsen J, Sun J, Mikkelsen TS, Myklebost O, Meza-Zepeda LA (2014)
The regulatory landscape of osteogenic differentiation
Stem Cells, 32 (10), 2780-93
DOI 10.1002/stem.1759, PubMed 24898411

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, van IJcken W, van der Sloot A, Lenhard B, Strähle U, Rastegar S (2013)
Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos
Dev Biol, 380 (2), 351-62
DOI 10.1016/j.ydbio.2013.05.006, PubMed 23684812

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 (2013)
Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells
BMC Genomics, 14, 105
DOI 10.1186/1471-2164-14-105, PubMed 23414147

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 (2012)
A novel complex, RUNX1-MYEF2, represses hematopoietic genes in erythroid cells
Mol Cell Biol, 32 (19), 3814-22
DOI 10.1128/MCB.05938-11, PubMed 22801375

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 (2012)
The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner
Epigenetics Chromatin, 5 (1), 8
DOI 10.1186/1756-8935-5-8, PubMed 22709888

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 (2011)
Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development
EMBO J, 31 (4), 986-99
DOI 10.1038/emboj.2011.450, PubMed 22157820

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 (2011)
Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes
Nat Genet, 43 (6), 607-11
DOI 10.1038/ng.825, PubMed 21532573

Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I (2010)
BioXSD: the common data-exchange format for everyday bioinformatics web services
Bioinformatics, 26 (18), i540-6
DOI 10.1093/bioinformatics/btq391, PubMed 20823319

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 et al. (2010)
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*
J Biomed Semantics, 1 (1), 8
DOI 10.1186/2041-1480-1-8, PubMed 20727200

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 (2010)
The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation
Genes Dev, 24 (3), 277-89
DOI 10.1101/gad.551810, PubMed 20123907

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 (2009)
ELM: the status of the 2010 eukaryotic linear motif resource
Nucleic Acids Res, 38 (Database issue), D167-80
DOI 10.1093/nar/gkp1016, PubMed 19920119

Pettifer S, Thorne D, McDermott P, Attwood T, Baran J, Bryne JC, Hupponen T, Mowbray D, Vriend G (2009)
An active registry for bioinformatics web services
Bioinformatics, 25 (16), 2090-1
DOI 10.1093/bioinformatics/btp329, PubMed 19460889

Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B (2009)
Transcriptional features of genomic regulatory blocks
Genome Biol, 10 (4), R38
DOI 10.1186/gb-2009-10-4-r38, PubMed 19374772

Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A (2007)
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Nucleic Acids Res, 36 (Database issue), D102-6
DOI 10.1093/nar/gkm955, PubMed 18006571

Review articles

Soler E, Andrieu-Soler C, Boer Ed, Bryne JC, Thongjuea S, Rijkers E, Demmers J, van IJcken W, Grosveld F (2010)
A systems approach to analyze transcription factors in mammalian cells
Methods, 53 (2), 151-62
DOI 10.1016/j.ymeth.2010.08.002, PubMed 20705139

Other articles

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 (2010)
The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation (vol 24, pg 277, 2010)
Genes Dev., 24 (6), 623