Below is a list of selected research publications using Fly Enhancer.
- Parnell TJ, Kuhn EJ, Gilmore BL, Helou C, Wold MS, Geyer PK. (2006)
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Identification of genomic sites that bind the Drosophila suppressor of
Hairy-wing insulator protein.
Molecular and Cell Biology 26(16):5983-93.
[abstract] - Ramos E, Ghosh D, Baxter E, Corces VG. (2006)
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Genomic organization of gypsy chromatin insulators in Drosophila melanogaster. Genetics 172(4):2337-49.
[abstract] - Markstein M, Zinzen R, Markstein P, Yee KP, Erives A, Stathopolous A, Levine M (2004)
- A regulatory code for neurogenic gene expression in the
Drosophila embryo. Development 131(10):2387-94.
First MERmaid paper.
[full-text(PDF)] [supplement(PDF)] [abstract] - Senger K, Armstrong GW, Rowell WJ, Kwan JM, Markstein M, Levine M (2004)
- Immunity regulatory DNAs share common organizational features in Drosophila. Molecular
Cell 13(1):19-32.
[abstract] - Calhoun VC, Levine M (2003)
- Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex. PNAS 100: 9878-83.
[abstract] - Kelley RL, Kuroda MI (2003)
- The Drosophila roX1 RNA gene can overcome silent chromatin by recruiting the male-specific lethal dosage compensation complex.
Genetics 164(2):565-74.
[abstract] - Markstein M and Levine M [review] (2002)
- Decoding cis-regulatory DNAs in the Drosophila genome. Curr
Opin Genet Dev 12(5):601-6.
[full-text (PDF)] [abstract] - Markstein M, Markstein P, Markstein V, Levine MS (2002)
- Genome-wide analysis of clustered Dorsal binding sites
identifies putative target genes in the Drosophila embryo. PNAS 99(2):763-8.
First Fly Enhancer paper.
[full-text (PDF)] [abstract]The web version of Fly Enhancer is continually updated and now reports clusters using a slightly different definition than found in this paper. Fly Enhancer now allows sites that overlap a window boundary to be included in that window's cluster. As a result of this more permissive definition, Fly Enhancer now reports that there are 16 clusters of Dl binding sites (defined as at least 3 sites in a window of 400 bp) rather than the 15 reported in the PNAS paper.
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