Blar i Bergen Open Research Archive på forfatter "Fredman, David"
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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 ... -
Axis patterning by BMPs: cnidarian network reveals evolutionary constraints
Genikhovich, Grigory; Fried, Patrick; Prünster, M. Mandela; Schinko, Johannes B.; Gilles, Anna F.; Fredman, David; Meier, Karin; Iber, Dagmar; Technau, Ulrich (Peer reviewed; Journal article, 2015-03)BMP signaling plays a crucial role in the establishment of the dorso-ventral body axis in bilaterally symmetric animals. However, the topologies of the bone morphogenetic protein (BMP) signaling networks vary drastically ... -
Evolutionary turnover of mammalian transcription start sites
Frith, Martin C.; Ponjavic, Jasmina; Fredman, David; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Sandelin, Albin (Peer reviewed; Journal article, 2006-05-06)Alignments of homologous genomic sequences are widely used to identify functional genetic elements and study their evolution. Most studies tacitly equate homology of functional elements with sequence homology. This assumption ... -
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) ... -
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 ... -
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 ...