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Bergen Open Research Archive

Browsing by Author "Lenhard, Boris"

Bergen Open Research Archive

Browsing by Author "Lenhard, Boris"

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  • Engström, Pär G.; Fredman, David; Lenhard, Boris (Journal article, BioMed Central, 2008-02-12)
    Metazoan genomes contain arrays of highly conserved noncoding elements (HCNEs) that span developmental regulatory genes and define regulatory domains. We describe Ancora http:// ancora.genereg.net, a web resource that ...
  • Zuin, Jessica; Franke, Vedran; van Ijcken, Wilfred F.J.; van der Sloot, Antoine A.J.; Krantz, Ian D.; van der Reijden, Michael I.J.A.; Nakato, Ryuichiro; Lenhard, Boris; Wendt, Kerstin S. (Journal article, Public Library of Science, 2014-02-13)
    The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture. The NIPBL protein is required for the loading of ...
  • Engström, Pär G.; Suzuki, Harukazu; Ninomiya, Norika; Akalin, Altuna; Sessa, Luca; Lavorgna, Giovanni; Brozzi, Alessandro; Luzi, Lucilla; Lam Tan, Sin; Yang, Liang; Kunarso, Galih; Lian-Chong, Edwin Ng; Batalov, Serge; Wahlestedt, Claes; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Wells, Christine; Bajic, Vladimir B.; Orlando, Valerio; Reid, James F.; Lenhard, Boris; Lipovich, Leonard (Journal article; Peer reviewed, PLoS, 2006-04-28)
    Mammalian genomes harbor a larger than expected number of complex loci, in which multiple genes are coupled by shared transcribed regions in antisense orientation and/or by bidirectional core promoters. To determine the ...
  • Sharma, Yogita; Chilamakuri, Chandra Sekhar Reddy; Bakke, Marit; Lenhard, Boris (Journal article, PLOS, 2014-02-13)
    Background: Nuclear receptors are a large structural class of transcription factors that act with their co-regulators and repressors to maintain a variety of biological and physiological processes such as metabolism, ...
  • Royo, José Luis; Hidalgo, Carmen; Roncero, Yolanda; Seda, María Angeles; Akalin, Altuna; Lenhard, Boris; Casares, Fernando; Gómez-Skarmeta, José Luis (Peer reviewed; Journal article, Public Library of Science, 2011-09-13)
    Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions ...
  • Nepal, Chirag; Hadzhiev, Yavor; Previti, A. Christopher; Haberle, Vanja; Li, Nan; Takahashi, Hazuki; Suzuki, Ana Maria; Sheng, Ying; Abdelhamid, Rehab; Anand, Santosh; Gehrig, Jochen; Akalin, Altuna; Kockx, Christel E.M.; van der Sloot, Antoine A.J.; van Ijcken, Wilfred F.J.; Armant, Olivier; Rastegar, Sepand; Watson, Craig; Strähle, Uwe; Stupka, Elia; Carninci, Piero; Lenhard, Boris; Müller, Ferenc (Journal article, Cold Spring Harbor Laboratory Press, 2013)
    Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in ...
  • Carvalho, Rejane Hughes; Haberle, Vanja; Hou, Jun; van Gent, Teus; Thongjuea, Supat; van Ijcken, Wilfred F.J.; Kockx, Christel; Brouwer, Rutger; Rijkers, Erikjan; Sieuwerts, Anieta; Foekens, John; van Vroonhoven, Mirjam; Aerts, Joachim; Grosveld, Frank; Lenhard, Boris; Philipsen, Sjaak (Journal article, BioMed Central, 2012-06-22)
    Background: Non-small cell lung carcinoma (NSCLC) is a complex malignancy that owing to its heterogeneity and poor prognosis poses many challenges to diagnosis, prognosis and patient treatment. DNA methylation is an ...
  • Soler, Eric; Andrieu-Soler, Charlotte; Boer, Ernie de; Bryne, Jan Christian; Thongjuea, Supat; Stadhouders, Ralph; Palstra, Robert-Jan; Stevens, Mary; Kockx, Christel; IJcken, Wilfred van; Hou, Jun; Steinhoff, Christine; Rijkers, Erikjan; Lenhard, Boris; Grosveld, Frank (Journal article, Cold Spring Harbor Laboratory Press, 2009)
    One of the complexes formed by the hematopoietic transcription factor Gata1 is a complex with the Ldb1 (LIM domain-binding protein 1) and Tal1 proteins. It is known to be important for the development and differentiation ...
  • Kikuta, Hiroshi; Laplante, Mary; Navrátilová, Pavla; Komisarczuk, Anna Zofia; Engström, Pär G.; Fredman, David; Akalin, Altuna; Caccamo, Mario; Sealy, Ian; Howe, Kerstin; Ghislain, Julien; Pezeron, Guillaume; Mourrain, Philippe; Ellingsen, Staale; Oates, Andrew C.; Thisse, Christine; Thisse, Bernard; Foucher, Isabelle; Adolf, Birgit; Geling, Andrea; Lenhard, Boris; Becker, Thomas S. (Peer reviewed; Journal article, Cold Spring Harbor Laboratory Press, 2007-03-06)
    We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding ...
  • Engström, Pär G.; Sui, Shannan J. Ho; Drivenes, Øyvind; Becker, Thomas S.; Lenhard, Boris (Journal article, Cold Spring Harbor Laboratory Press, 2007-11-07)
    Insect genomes contain larger blocks of conserved gene order (microsynteny) than would be expected under a random breakage model of chromosome evolution. We present evidence that microsynteny has been retained to keep ...
  • Andersen, Malin C.; Engström, Pär G.; Lithwick, Stuart; Lithwick, David; Eriksson, Per; Lenhard, Boris; Wasserman, Wyeth W.; Odeberg, Jacob (Journal article, PLoS, 2008-01-18)
    Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked ...
  • Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T.; Arenillas, David; Zhao, Xiaobei; Valen, Eivind; Yusuf, Dimas; Lenhard, Boris; Wasserman, Wyeth W.; Sandelin, Albin (Journal article, Oxford University Press, 2010)
    JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific ...
  • Sleutels, Frank; Soochit, Widia; Bartkuhn, Marek; Heath, Helen; Dienstbach, Sven; Bergmaier, Philipp; Franke, Vedran; Rosa-Garrido, Manuel; van de Nobelen, Suzanne; Caesar, Lisa; van der Reijden, Michael I.J.A.; Bryne, Jan Christian; van Ijcken, Wilfred F.J.; Grootegoed, J. Anton; Delgado, M. Dolores; Lenhard, Boris; Renkawitz, Rainer; Grosveld, Frank; Galjart, Niels (Journal article, BioMed Central, 2012-06-18)
    Background: CTCF is a highly conserved and essential zinc finger protein expressed in virtually all cell types. In conjunction with cohesin, it organizes chromatin into loops, thereby regulating gene expression and ...
  • Thongjuea, Supat; Stadhouders, Ralph; Grosveld, Frank; Soler, Eric; Lenhard, Boris (Journal article, Oxford University Press, 2013)
    The coupling of chromosome conformation capture (3C) with next-generation sequencing technologies enables the high-throughput detection of longrange genomic interactions, via the generation of ligation products between ...
  • Kikuta, Hiroshi; Fredman, David; Rinkwitz, Silke; Lenhard, Boris; Becker, Thomas S. (Journal article, BioMed Central, 2007-10-31)
    A large-scale enhancer detection screen was performed in the zebrafish using a retroviral vector carrying a basal promoter and a fluorescent protein reporter cassette. Analysis of insertional hotspots uncovered areas around ...
  • Dong, Xianjun; Fredman, David; Lenhard, Boris (Journal article; Peer reviewed, BioMed Central, 2009-08-21)
    Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into ...
  • Dong, Xianjun; Akalin, Altuna; Sharma, Yogita; Lenhard, Boris (Journal article, BioMed Central, 2010-01-18)
    Background: Increasing amount of data from comparative genomics, and newly developed technologies producing accurate gene expression data facilitate the study of the expression divergence of homologous genes. Previous ...

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