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LETTER: Structured RNAs in the ENCODE selected regions of the human genome
- Stefan Washietl,
- Jakob S. Pedersen,
- Jan O. Korbel,
- Claudia Stocsits,
- Andreas R. Gruber,
- Jörg Hackermüller,
- Jana Hertel,
- Manja Lindemeyer,
- Kristin Reiche,
- Andrea Tanzer,
- Catherine Ucla,
- Carine Wyss,
- Stylianos E. Antonarakis,
- France Denoeud,
- Julien Lagarde,
- Jorg Drenkow,
- Philipp Kapranov,
- Thomas R. Gingeras,
- Roderic Guigó,
- Michael Snyder,
- Mark B. Gerstein,
- Alexandre Reymond,
- Ivo L. Hofacker,
- and Peter F. Stadler
Genome Res. June 2007 17: 852-864; doi:10.1101/gr.5650707
...techniques seems necessary to address this question. On the experimental side, we can draw upon the evidence from large-scale oligonucleotide tiling array studies performed on the ENCODE regions as well as a small set of verification experiments (The ENCODE Project Consortium 2007). Unfortunately...
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Research: The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important
- Erika M. Kvikstad and
- Kateryna D. Makova
Genome Res. May 2010 20: 600-613; Published in Advance March 10, 2010, doi:10.1101/gr.099044.109
...chromosomes. Here, using a multiple regression framework, we investigate primate Alu and L1 densities shaped by regional genome features and location on a particular chromosome type. As a result of our analysis, first, we build statistical models explaining up to 79% and 44% of variation in Alu and L1...
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Letter: Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
- Erika M. Kvikstad,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. July 2009 19: 1153-1164; Published in Advance June 5, 2009, doi:10.1101/gr.088922.108
...in their mutagenesis. Third, substantial similarity in frequency profiles exists between pairs of individual motifs flanking insertions (and separately deletions), suggesting “cooperation” among motifs, and thus molecular mechanisms, during indel formation. Fourth, the wavelet analyses demonstrate that all...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
.... , Makova, K. , et al. ( 2007 ) A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly . Genome Res. (in press) . ↵ Bode, J. , Henco, K. , Wingender, E. ( 1980 ) Modulation of the nucleosome structure by histone acetylation . Eur. J. Biochem. 10 : 143 – 152...
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Resource: Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
- Ozren Bogdanović,
- Ana Fernandez-Miñán,
- Juan J. Tena,
- Elisa de la Calle-Mustienes,
- Carmen Hidalgo,
- Ila van Kruysbergen,
- Simon J. van Heeringen,
- Gert Jan C. Veenstra,
- and José Luis Gómez-Skarmeta
Genome Res. October 2012 22: 2043-2053; Published in Advance May 16, 2012, doi:10.1101/gr.134833.111
.... Development 131: 5627– 5637. Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, et al. 2007. A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Res 17: 960–964. Blow MJ, McCulley DJ, Li Z, Zhang...
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RESOURCE: 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
- Webb Miller,
- Kate Rosenbloom,
- Ross C. Hardison,
- Minmei Hou,
- James Taylor,
- Brian Raney,
- Richard Burhans,
- David C. King,
- Robert Baertsch,
- Daniel Blankenberg,
- Sergei L. Kosakovsky Pond,
- Anton Nekrutenko,
- Belinda Giardine,
- Robert S. Harris,
- Svitlana Tyekucheva,
- Mark Diekhans,
- Thomas H. Pringle,
- William J. Murphy,
- Arthur Lesk,
- George M. Weinstock,
- Kerstin Lindblad-Toh,
- Richard A. Gibbs,
- Eric S. Lander,
- Adam Siepel,
- David Haussler,
- and W. James Kent
Genome Res. December 2007 17: 1797-1808; Published in Advance November 5, 2007, doi:10.1101/gr.6761107
...1 identifies the producers of the individual sequences.) The sequences are being immediately and freely released to the public to allow scientists to use the genomic information in their own research. (The scientific community is expected to postpone publications of large-scale analyses of the data...
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Research: Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes
- Nagesha A.S. Rao,
- Melysia T. McCalman,
- Panagiotis Moulos,
- Kees-Jan Francoijs,
- Aristotelis Chatziioannou,
- Fragiskos N. Kolisis,
- Michael N. Alexis,
- Dimitra J. Mitsiou,
- and Hendrik G. Stunnenberg
Genome Res. September 2011 21: 1404-1416; Published in Advance July 12, 2011, doi:10.1101/gr.118042.110
...binds to kB response elements (NFKB RE) and regulates expression of genes encoding various proteins such as proinflammatory cytokines, chemokines, receptors, and adhesion molecules (Barnes 1997; Barnes and Karin 1997; Baeuerle 1998; Hayden and Ghosh 2008). Given that NFKB is a key mediator of immune...
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Research: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
- Ozren Bogdanović,
- Steven W. Long,
- Simon J. van Heeringen,
- Arie B. Brinkman,
- Jose Luis Gómez-Skarmeta,
- Hendrik G. Stunnenberg,
- Peter L. Jones,
- and Gert Jan C. Veenstra
Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110

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