Blar i Bergen Open Research Archive på forfatter "Akalin, Altuna"
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Complex Loci in Human and Mouse Genomes
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 (Peer reviewed; Journal article, 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 ... -
Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions
Royo, José Luis; Hidalgo, Carmen; Roncero, Yolanda; Seda, María Angeles; Akalin, Altuna; Lenhard, Boris; Casares, Fernando; Gómez-Skarmeta, José Luis (Peer reviewed; Journal article, 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 ... -
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
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 (Peer reviewed; Journal article, 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 ... -
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 ... -
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 ...