• Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes 

      Engström, Pär G.; Fredman, David; Lenhard, Boris (Journal article; Peer reviewed, 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 ...
    • CNEr: A toolkit for exploring extreme noncoding conservation 

      Tan, Ge; Polychronopoulos, Dimitris; Lenhard, Boris (Journal article; Peer reviewed, 2019-08-26)
      Conserved Noncoding Elements (CNEs) are elements exhibiting extreme noncoding conservation in Metazoan genomes. They cluster around developmental genes and act as long-range enhancers, yet nothing that we know about their ...
    • Conservative route to genome compaction in a miniature annelid 

      Martin-Duran, José M.; Vellutini, Bruno Cossermelli; Marletaz, Ferdinand; Cetrangolo, Viviana; Cvetesic, Nevena; Thiel, Daniel; Henriet, Simon; Grau-Bové, Xavier; Carrillo-Baltodano, Allan M.; Gu, Wenjia; Kerbl, Alexandra; Marquez, Yamile; Bekkouche, Nicolas; Chourrout, Daniel; Gómez-Skarmeta, José Luis; Irimia, Manuel; Lenhard, Boris; Worsaae, Katrine; Hejnol, Andreas (Journal article; Peer reviewed, 2021)
      The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact ...
    • Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons 

      Dong, Xianjun; Navratilova, Pavla; Fredman, David; Drivenes, Øyvind; Becker, Thomas S.; Lenhard, Boris (Journal article; Peer reviewed, 2009-12-06)
      Using a comparative genomics approach to reconstruct the fate of genomic regulatory blocks (GRBs) and identify exonic remnants that have survived the disappearance of their host genes after whole-genome duplication (WGD) ...
    • Functional annotation of human long noncoding RNAs via molecular phenotyping 

      Ramilowski, Jordan; Yip, Chiu Wai Mickey; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan; Mendez, Mickaël; Ching Ooi, Jasmine Li; Ouyang, John F; Parkinson, Nick; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; De Hoon, Michiel J L; Shin, Jay W; Piero, Carninci (Journal article; Peer reviewed, 2020)
      Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression ...
    • Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates 

      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, 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 ...
    • Genomic regulatory blocks underlie extensive microsynteny conservation in insects 

      Engström, Pär G.; Sui, Shannan J. Ho; Drivenes, Øyvind; Becker, Thomas S.; Lenhard, Boris (Journal article, 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 large ...
    • In Silico Detection of Sequence Variations Modifying Transcriptional Regulation 

      Andersen, Malin C.; Engström, Pär G.; Lithwick, Stuart; Lithwick, David; Eriksson, Per; Lenhard, Boris; Wasserman, Wyeth W.; Odeberg, Jacob (Journal article; Peer reviewed, 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 ...
    • 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 ...
    • 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 ...
    • 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 ...