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Method: Genome-wide identification of conserved regulatory function in diverged sequences
- Leila Taher,
- David M. McGaughey,
- Samantha Maragh,
- Ivy Aneas,
- Seneca L. Bessling,
- Webb Miller,
- Marcelo A. Nobrega,
- Andrew S. McCallion,
- and Ivan Ovcharenko
Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
...diverged regulatory elements that we term ‘‘covert.’’ [Supplemental material is available for this article. Generated data sets of covert elements are available at http:// www.dcode.org/covert/.] In recent years, sequence constraint has been widely used as a powerful filter to identify regulatory sequences...
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Method: Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control
- Grzegorz M. Burzynski,
- Xylena Reed,
- Leila Taher,
- Zachary E. Stine,
- Takeshi Matsui,
- Ivan Ovcharenko,
- and Andrew S. McCallion
Genome Res. November 2012 22: 2278-2289; Published in Advance July 3, 2012, doi:10.1101/gr.139717.112
...↵ 4 These authors contributed equally to this work. Abstract Illuminating the primary sequence encryption of enhancers is central to understanding the regulatory architecture of genomes. We have developed a machine learning approach to decipher motif patterns of hindbrain enhancers...
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Method: Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
- David U. Gorkin,
- Dongwon Lee,
- Xylena Reed,
- Christopher Fletez-Brant,
- Seneca L. Bessling,
- Stacie K. Loftus,
- Michael A. Beer,
- William J. Pavan,
- and Andrew S. McCallion
Genome Res. November 2012 22: 2290-2301; Published in Advance September 27, 2012, doi:10.1101/gr.139360.112
...Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes David U. Gorkin 1 , 2 , Dongwon Lee 3 , Xylena Reed 1 , 2 , Christopher Fletez-Brant 1 , Seneca L. Bessling 1...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
.... Nevertheless, correctly identifying even two-thirds of all C. elegans regulatory elements with a low false-positive rate, as we did prior to refinement, could significantly advance our knowledge of the worm regulatory . Recent uses of sequence constraint in vertebrates have been less sensitive in finding...
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PERSPECTIVE: Qualifying the relationship between sequence conservation and molecular function
- Gregory M. Cooper and
- Christopher D. Brown
Genome Res. February 2008 18: 201-205; doi:10.1101/gr.7205808
....M. , Vinton, R.M. , Huynh, J. , Al-Saif, A. , Beer, M.A. , McCallion, A.S. ( 2008 ) Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b . Genome Res. 18 , doi: 10.1101/gr.6929408 , (this issue) . ↵ Mirny, L.A. , Gelfand, M.S. ( 2002 ) Structural analysis...
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Method: Discriminative prediction of mammalian enhancers from DNA sequence
- Dongwon Lee,
- Rachel Karchin,
- and Michael A. Beer
Genome Res. December 2011 21: 2167-2180; Published in Advance August 29, 2011, doi:10.1101/gr.121905.111
...; 2Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21218, USA; 3McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA Abstract Accurately predicting regulatory sequences and enhancers...
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Method: Integrating multiple evidence sources to predict transcription factor binding in the human genome
- Jason Ernst,
- Heather L. Plasterer,
- Itamar Simon,
- and Ziv Bar-Joseph
Genome Res. April 2010 20: 526-536; Published in Advance March 10, 2010, doi:10.1101/gr.096305.109
...of sequence binding specificities for hundreds of additional transcription factors. Despite the availability of binding specificity for transcription factors, the large size of mammalian s including human makes detecting regulatory sites a particular challenge as there can be many sequences in the , which...
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LETTER: Evolution of the mammalian transcription factor binding repertoire via transposable elements
- Guillaume Bourque,
- Bernard Leong,
- Vinsensius B. Vega,
- Xi Chen,
- Yen Ling Lee,
- Kandhadayar G. Srinivasan,
- Joon-Lin Chew,
- Yijun Ruan,
- Chia-Lin Wei,
- Huck Hui Ng,
- and Edison T. Liu
Genome Res. November 2008 18: 1752-1762; Published in Advance August 5, 2008, doi:10.1101/gr.080663.108
...-species conservation has been successfully used to identify functional regulatory sequences in s ( Thomas et al. 2003 ; Boffelli et al. 2004 ; Wang et al. 2006 ), there is growing evidence that changes in cis -regulatory elements are important in determining key phenotypic differences, as shown in yeast ( Ihmels et al...
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Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
...not unreasonable to expect that 40% and perhaps more of the sequence encodes regulatory information—a number that would have been considered heretical at the outset of the ENCODE project. It is important to recognize, however, that this figure encompasses regulatory regions wherein only a subset of the individual...
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