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Methods: Footer: A quantitative comparative genomics method for efficient recognition of cis-regulatory elements
- David L. Corcoran,
- Eleanor Feingold,
- Jessica Dominick,
- Marietta Wright,
- Jo Harnaha,
- Massimo Trucco,
- Nick Giannoukakis,
- and Panayiotis V. Benos
Genome Res. June 2005 15: 840-847; doi:10.1101/gr.2952005
...: 815 -824. ↵ Jegga, A.G., Sherwood, S.P., Carman, J.W., Pinski, A.T., Phillips, J.L., Pestian, J.P., and Aronow, B.J. 2002 . Detection and visualization of compositionally similar cis -regulatory element clusters in orthologous and coordinately controlled genes. Genome Res. 12 : 1408 -1417. ↵ Le Naour...
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RESOURCE: CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting
- Eugene Berezikov,
- Victor Guryev,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. January 2004 14: 170-178; Published in Advance December 12, 2003, doi:10.1101/gr.1642804
....W., Pinski, A.T., Phillips, J.L., Pestian, J.P., and Aronow, B.J. 2002 . Detection and visualization of compositionally similar cis -regulatory element clusters in orthologous and coordinately controlled genes. Genome Res. 12 : 1408 -1417. ↵ Kadonaga, J.T. and Tjian, R. 1986 . Affinity purification...
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Methods: Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
- Diana Kolbe,
- James Taylor,
- Laura Elnitski,
- Pallavi Eswara,
- Jia Li,
- Webb Miller,
- Ross Hardison,
- and Francesca Chiaromonte
Genome Res. April 2004 14: 700-707; doi:10.1101/gr.1976004
.... Detection and visualization of compositionally similar cis -regulatory element clusters in orthologous and coordinately controlled genes. Genome Res. 12 : 1408 -1417. ↵ Levy, S. and Hannenhalli, S. 2002 . Identification of transcription factor binding sites in the human . Mamm. Genome 13 : 510 -514. ↵ Loots...
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ARTICLE: Pattern of Sequence Variation Across 213 Environmental Response Genes
- Robert J. Livingston,
- Andrew von Niederhausern,
- Anil G. Jegga,
- Dana C. Crawford,
- Christopher S. Carlson,
- Mark J. Rieder,
- Sivakumar Gowrisankar,
- Bruce J. Aronow,
- Robert B. Weiss,
- and Deborah A. Nickerson
Genome Res. October 2004 14: 1821-1831; Published in Advance September 13, 2004, doi:10.1101/gr.2730004
...cis -elements between human and mouse sequences in the context of their sequence similarity. By identifying conserved mouse-human regions with consensus cis -regulatory elements and mapping noncoding SNPs, Trafac can be used to predict the potential adverse affects of polymorphisms on the regulation...
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LETTER: Distinguishing Regulatory DNA From Neutral Sites
- Laura Elnitski,
- Ross C. Hardison,
- Jia Li,
- Shan Yang,
- Diana Kolbe,
- Pallavi Eswara,
- Michael J. O'Connor,
- Scott Schwartz,
- Webb Miller,
- and Francesca Chiaromonte
Genome Res. January 1, 2003 13: 64-72; doi:10.1101/gr.817703
....W. , Pinski A.T. , Phillips J.L. , Pestian J.P. , Aronow B.J. ( 2002 ) Detection and visualization of compositionally similar cis -regulatory element clusters in orthologous and coordinately controlled genes. Genome Res. 12 : 1408 – 1417 . ↵ Kent W.J. , Sugnet C.W. , Furey T.S. , Roskin K.M. , Pringle T...

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