Blar i Bergen Open Research Archive på forfatter "Lenhard, Boris"

Viser treff 21-36 av 36

    • JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles 

      Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T.; Arenillas, David; Zhao, Xiaobei; Valen, Eivind; Yusuf, Dimas; Lenhard, Boris; Wasserman, Wyeth W.; Sandelin, Albin (Peer reviewed; Journal article, 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 ...

    • JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles 

      Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J.; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W. (Peer reviewed; Journal article, 2014-01)
      JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly ...

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

      Bryne, Jan Christian; Valen, Eivind; Tang, Man-Hung Eric; Marstrand, Troels; Winther, Ole; da Piedade, Isabelle; Krogh, Anders; Lenhard, Boris; Sandelin, Albin (Journal article; Peer reviewed, 2007-11-15)
      JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with ...

    • Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome 

      Naville, Magali; Ishibashi, Minaka; Ferg, Marco; Bengani, Hemant; Rinkwitz, Silke; Krecsmarik, Monika; Hawkins, Thomas A.; Wilson, Stephen W.; Manning, Elizabeth; Chilamakuri, Chandra Sekhar Reddy; Wilson, David I.; Louis, Alexandra; Raymond, F. Lucy; Rastegar, Sepand; Strähle, Uwe; Lenhard, Boris; Bally-Cuif, Laure; van Heyningen, Veronica; Fitzpatrick, David R.; Becker, Thomas S.; Crollius, Hugues Roest (Peer reviewed; Journal article, 2015-04-24)
      Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test ...

    • 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, 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 (Peer reviewed; Journal article, 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 epigenetic ...

    • Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin 

      Weiss, Felix D.; Calderon, Lesly; Wang, Yi-Fang; Georgieva, Radina; Guo, Ya; Cvetesic, Nevena; Kaur, Maninder; Dharmalingam, Gopuraja; Krantz, Ian D.; Lenhard, Boris; Fisher, Amanda G.; Merkenschlager, Matthias (Journal article; Peer reviewed, 2021)
      Cornelia de Lange Syndrome (CdLS) is a human developmental disorder caused by mutations that compromise the function of cohesin, a major regulator of 3D genome organization. Cognitive impairment is a universal and as yet ...

    • A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates 

      Nash, Alexander J.; Lenhard, Boris (Journal article; Peer reviewed, 2018-12-07)
      Motivation Clusters of extremely conserved non-coding elements (CNEs) mark genomic regions devoted to cis-regulation of key developmental genes in Metazoa. We have recently shown that their span coincides with that of ...

    • OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica 

      Danks, Gemma Barbara; Campsteijn, Coen; Parida, Mruyunjaya; Butcher, Stephen; Doddapaneni, Harsha; Fu, Bolei; Petrin, Raul; Metpally, Raghu; Lenhard, Boris; Wincker, Patrick; Chourrout, Daniel; Thompson, Eric; Manak, J Robert (Peer reviewed; Journal article, 2013-11-26)
      We report the development of OikoBase (http://oikoarrays.biology.uiowa.edu/Oiko/), a tiling array-based genome browser resource for Oikopleura dioica, a metazoan belonging to the urochordates, the closest extant group to ...

    • r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data 

      Thongjuea, Supat; Stadhouders, Ralph; Grosveld, Frank; Soler, Eric; Lenhard, Boris (Peer reviewed; Journal article, 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 DNA ...

    • RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions 

      Bonetti, Alessandro; Agostini, Federico; Suzuki, Ana Maria; Hashimoto, Kosuke; Pascarella, Giovanni; Gimenez, Juliette; Roos, Leonie; Nash, Alex J.; Ghilotti, Marco; Cameron, Christopher J.  F.; Valentine, Matthew; Medvedeva, Yulia A.; Noguchi, Shuhei; Agirre, Eneritz; Kashi, Kaori; Samudyata, Samudyata; Luginbühl, Joachim; Cazzoli, Riccardo; Agrawal, Saumya; Luscombe, Nicholas M.; Blanchette, Mathieu; Kasukawa, Takeya; de Hoon, Michiel; Arner, Erik; Lenhard, Boris; Plessy, Charles; Castelo-Branco, Gonçalo; Orlando, Valerio; Carninci, Piero (Journal article; Peer reviewed, 2020)
      Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. ...

    • Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes 

      Kikuta, Hiroshi; Fredman, David; Rinkwitz, Silke; Lenhard, Boris; Becker, Thomas S. (Journal article; Peer reviewed, 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 ...

    • Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes 

      Dong, Xianjun; Fredman, David; Lenhard, Boris (Journal article; Peer reviewed, 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 ...

    • Transcription start site mapping using super-low input carrier-CAGE 

      Cvetesic, Nevena; Pahita, Elena; Lenhard, Boris (Journal article; Peer reviewed, 2019-06-26)
      Cap analysis of gene expression (CAGE) is a method used for single-nucleotide resolution detection of RNA polymerase II transcription start sites (TSSs). Accurate detection of TSSs enhances identification and discovery of ...

    • Translog, a web browser for studying the expression divergence of homologous genes 

      Dong, Xianjun; Akalin, Altuna; Sharma, Yogita; Lenhard, Boris (Journal article; Peer reviewed, 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 ...

    • Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks 

      Barešić, Anja; Nash, Alexander Jolyon; Dahoun, Tarik; Howes, Oliver; Lenhard, Boris (Journal article; Peer reviewed, 2019)
      Recent genome-wide association studies have identified numerous loci associated with neuropsychiatric disorders. The majority of these are in non-coding regions, and are commonly assigned to the nearest gene along the ...

    • Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods 

      Lewis, Samuel H.; Ross, Laura; Bain, Stevie A.; Pahita, Eleni; Smith, Stephen A.; Cordaux, Richard; Miska, Eric A.; Lenhard, Boris; Jiggins, Francis M.; Sarkies, Peter (Journal article; Peer reviewed, 2020)
      Cytosine methylation is an ancient epigenetic modification yet its function and extent within genomes is highly variable across eukaryotes. In mammals, methylation controls transposable elements and regulates the promoters ...