Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change

QUICK SEARCH:

[advanced]

	Author:		Keyword(s):

Home Help Feedback Subscriptions Archive Search Table of Contents

This Article

	Summary
	Full Text (PDF)
	Alert me when this article is cited
	Alert me if a correction is posted

Services

	Email this article to a friend
	Similar articles in this journal
	Similar articles in PubMed
	Alert me to new issues of the journal
	Download to citation manager


Citing Articles

	Citing Articles via HighWire
	Citing Articles via Google Scholar

Google Scholar

	Articles by Ludwig, M. Z.
	Articles by Kreitman, M.
	Search for Related Content

PubMed

	PubMed Citation
	Articles by Ludwig, M. Z.
	Articles by Kreitman, M.

Ahringer, J (1996). Posterior patterning by the Caenorhabditis elegans even-skipped homolog vab-7. Genes Dev 10, 1120-1130.[Abstract/Free Full Text]

Akashi, H (1995). Inferring weak selection from patterns of polymorphism and divergence at \324silent' sites in Drosophila DNA. Genetics 139, 1067-1076.[Abstract]

Arnone, M. I. and Davidson, E. H (1997). The hardwiring of development: organization and function of genomic regulatory systems. Development 124, 1851-1864.[Abstract]

Arnosti, D., Barolo, S., Levine, M. and Small, S (1996). The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development 122, 205-214.[Abstract]

Bastian, H. and Gruss, P (1990). A murine even-skipped homologue, Evx1 , is expressed during early embryogenesis and neurogenesis in a biphasic manner. EMBO J 9, 1839-1852.[Medline]

Fujioka, M., Jaynes, J. B. and Goto, T (1995). Early even-skipped stripes act as morphogentic gradients at the single cell level to establish engrailed expression. Development 121, 4371-4382.[Abstract]

Goto, T., Macdonald, P. and Maniatis, T (1989). Early and late periodic patterns of even-skipped expression are controlled by distinct regulatory elements that respond to different spatial cues. Cell 57, 413-422.[Medline]

Gray, S., Szymanski, P. and Levine, M (1994). Short-range repressionpermits multiple enhancers to function autonomously within a complex promoter. Genes Dev 8, 1829-1838.[Abstract/Free Full Text]

Hanes, S. D., Riddihough, G., Ish-Horowicz, D. and Brent, R (1994). Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen. Mol. Cell Biol 14, 3364-3375.[Abstract/Free Full Text]

Harding, K., Hoey, T., Warrior, R. and Levine, M (1989). Autoregulatory and gap response elements of the even-skipped promoter of Drosophila. EMBO J 8, 1205-1212.[Medline]

Jeffs, P. S., Holmes, E. C. and Ashburner, M (1994). The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup. Mol. Biol. Evol 11, 287-304.[Abstract]

Jiang, J., Kosman, D., Ip, Y. T. and Levine, M (1991). The dorsal morphogen gradient regulates the mesoderm determinant twist in early Drosophila embryos. Genes Dev 5, 1881-1891.[Abstract/Free Full Text]

Jiang, J., Hoey, T. and Levine, M (1991). Autoregulation of a segmentation gene in Drosophila: Combinatorial interaction of the even-skipped homeo box protein with a distal enhancer element. Genes Dev 5, 265-277.[Abstract/Free Full Text]

Kenyon, C (1994). If birds can fly, why can't we? Homeotic genes and evolution. Cell 78, 175-180.[Medline]

Kimura, M (1981). Possibility of extensive neutral evolution under stabilizing selection with special reference to non-random usage of synonymous codons. Proc. Natl. Acad. Sci. USA 78, 5773-5777.[Abstract/Free Full Text]

Langland, J. A. and Carroll, S. B (1993). Conservation of regulatory elements controlling hairy pair-rule stripe formation. Development 117, 585-596.[Abstract]

Lawrence, P. A., Johnston, P., Macdonald, P. and Struhl, G (1987). Borders of parasegments in Drosophila embryos are delimited by the fushi tarazu and even-skipped genes. Nature 328, 440-442.[Medline]

Ludwig, M, Z. and Kreitman, M (1995). Evolutionary dynamics of the enhancer region of even-skipped in Drosophila. Mol. Biol. Evol 12, 1002-1011.[Abstract]

Ludwig, M. Z., Tamarina, N. A. and Richmond, R. C (1993). Localization of sequences controlling the spatial, temporal, and sex-specific expression of the esterase 6 locus in Drosophila melanogaster adults. Proc. Natl. Acad. Sci. USA 90, 6233-6237.[Abstract/Free Full Text]

Ma, X., Yuan, D., Diepold, K., Scarborough, T. and Ma, J (1996). The Drosophila morphogenic protein Bicoid binds DNA cooperatively. Development 122, 1195-1206.[Abstract]

Nusslein-Volhard, C., Kluding, H. and Jurgens, G (1985). Genes affecting the segmental subdivision of the Drosophila embryo. Cold Spring Harbor Symp. Quant. Biol 50, 145-154.[Medline]

Patel, N. H., Ball, E. E. and Goodman, C. S (1992). Changing role of even-skipped during the evolution of insect pattern formation. Nature 357, 339-342.[Medline]

Patel, N. H., Condron, B. G. and Zinn, K (1994). Pair-rule expression patterns of even-skipped are found in both short-and long-germ beetles. Nature 367, 429-434.[Medline]

Robertson, H. M., Preston, C. R., Phillis, R. W., Johnson-Schlitz, D. M., Benz, W. K. and Engels, W. R (1988). A stable genomic source of P element transposase in Drosophila melanogaster. Genetics 118, 461-470.[Abstract/Free Full Text]

Ruiz i Altaba, A. and Melton, D. A (1989). Involvement of the Xenopus homeobox gene Xho3 in pattern formation along the anterior-posterior axis. Cell 57, 317-326.[Medline]

Small, S., Blair, A. and Levine, M (1992). Regulation of even-skipped stripe 2 in the Drosophila embryo. EMBO J 11, 4047-4057.[Medline]

Small, S., Arnosti, D. N. and Levine, M (1993). Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter. Development 119, 767-772.[Abstract]

Small, S., Blair, A. and Levine, M (1996). Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo. Dev. Biol 175, 314-324.[Medline]

Sommer, R. and Tautz, D (1991). Segmentation gene expression in the housefly Musca domestica. Development 113, 419-430.[Abstract]

Stanojevic, D., Small, S. and Levine, M (1991). Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science 254, 1385-1387.[Abstract/Free Full Text]

Thummel, C. S., Boulet, A. M. and Lipshitz, H. D (1988). Vectors for Drosophila P element-mediated transformation and tissue culture transfection. Gene 74, 445-456.[Medline]

Williams, J. A., Paddock, S. W., Vorwerk, K. and Carroll, S. B (1994). Organization of wing formation and induction of a wing-patterning gene at the dorsal/ventral compartment boundary. Nature 368, 299-305.[Medline]

Warrior, R. and Levine, M (1990). Dose-dependent regulation of pair-rule stripes by gap proteins and the initiation segment polarity. Development 110, 759-767.[Abstract/Free Full Text]

This article has been cited by other articles:

S. Hannenhalli
Eukaryotic transcription factor binding sites--modeling and integrative search methods
Bioinformatics, June 1, 2008; 24(11): 1325 - 1331.
[Abstract] [Full Text] [PDF]

R. Satija, L. Pachter, and J. Hein
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements
Bioinformatics, May 15, 2008; 24(10): 1236 - 1242.
[Abstract] [Full Text] [PDF]

M. B. Noyes, X. Meng, A. Wakabayashi, S. Sinha, M. H. Brodsky, and S. A. Wolfe
A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
Nucleic Acids Res., May 1, 2008; 36(8): 2547 - 2560.
[Abstract] [Full Text] [PDF]

A. M. Moses, M. E. Liku, J. J. Li, and R. Durbin
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites
PNAS, November 6, 2007; 104(45): 17713 - 17718.
[Abstract] [Full Text] [PDF]

R. R. Copley, M. Totrov, J. Linnell, S. Field, J. Ragoussis, and I. A. Udalova
Functional conservation of Rel binding sites in drosophilid genomes
Genome Res., September 1, 2007; 17(9): 1327 - 1335.
[Abstract] [Full Text] [PDF]

A. Chabot, R. A. Shrit, R. Blekhman, and Y. Gilad
Using Reporter Gene Assays to Identify cis Regulatory Differences Between Humans and Chimpanzees
Genetics, August 1, 2007; 176(4): 2069 - 2076.
[Abstract] [Full Text] [PDF]

M. Nei
The new mutation theory of phenotypic evolution
PNAS, July 24, 2007; 104(30): 12235 - 12242.
[Abstract] [Full Text] [PDF]

M. Brandstrom and H. Ellegren
The Genomic Landscape of Short Insertion and Deletion Polymorphisms in the Chicken (Gallus gallus) Genome: A High Frequency of Deletions in Tandem Duplicates
Genetics, July 1, 2007; 176(3): 1691 - 1701.
[Abstract] [Full Text] [PDF]

S. E. Lott, M. Kreitman, A. Palsson, E. Alekseeva, and M. Z. Ludwig
Canalization of segmentation and its evolution in Drosophila
PNAS, June 26, 2007; 104(26): 10926 - 10931.
[Abstract] [Full Text] [PDF]

D. C. King, J. Taylor, Y. Zhang, Y. Cheng, H. A. Lawson, J. Martin, ENCODE groups for Transcriptional Regulation and M, F. Chiaromonte, W. Miller, and R. C. Hardison
Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
Genome Res., June 1, 2007; 17(6): 775 - 786.
[Abstract] [Full Text] [PDF]

C. Tian, T. Kasuga, M. S. Sachs, and N. L. Glass
Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons
Eukaryot. Cell, June 1, 2007; 6(6): 1018 - 1029.
[Abstract] [Full Text] [PDF]

M. Freeling, L. Rapaka, E. Lyons, B. Pedersen, and B. C. Thomas
G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences in Arabidopsis
PLANT CELL, May 1, 2007; 19(5): 1441 - 1457.
[Abstract] [Full Text] [PDF]

A. S. Bais, S. Grossmann, and M. Vingron
Simultaneous alignment and annotation of cis-regulatory regions
Bioinformatics, January 15, 2007; 23(2): e44 - e49.
[Abstract] [Full Text] [PDF]

J. Taylor, S. Tyekucheva, D. C. King, R. C. Hardison, W. Miller, and F. Chiaromonte
ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
Genome Res., December 1, 2006; 16(12): 1596 - 1604.
[Abstract] [Full Text] [PDF]

J. R. t. Bosch, J. A. Benavides, and T. W. Cline
The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription
Development, May 15, 2006; 133(10): 1967 - 1977.
[Abstract] [Full Text] [PDF]

M. Ronshaugen, F. Biemar, J. Piel, M. Levine, and E. C. Lai
The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings
Genes & Dev., December 15, 2005; 19(24): 2947 - 2952.
[Abstract] [Full Text] [PDF]

R. A. Cameron, S. H. Chow, K. Berney, T.-Y. Chiu, Q.-A. Yuan, A. Kramer, A. Helguero, A. Ransick, M. Yun, and E. H. Davidson
An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules
PNAS, August 16, 2005; 102(33): 11769 - 11774.
[Abstract] [Full Text] [PDF]

J. Gertz, L. Riles, P. Turnbaugh, S.-W. Ho, and B. A. Cohen
Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics
Genome Res., August 1, 2005; 15(8): 1145 - 1152.
[Abstract] [Full Text] [PDF]

J. C. Fay and J. A. Benavides
Hypervariable Noncoding Sequences in Saccharomyces cerevisiae
Genetics, August 1, 2005; 170(4): 1575 - 1587.
[Abstract] [Full Text] [PDF]

J. P. Balhoff and G. A. Wray
Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites
PNAS, June 14, 2005; 102(24): 8591 - 8596.
[Abstract] [Full Text] [PDF]

A. Tanay, A. Regev, and R. Shamir
Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
PNAS, May 17, 2005; 102(20): 7203 - 7208.
[Abstract] [Full Text] [PDF]

M. M. Kulkarni and D. N. Arnosti
cis-Regulatory Logic of Short-Range Transcriptional Repression in Drosophila melanogaster
Mol. Cell. Biol., May 1, 2005; 25(9): 3411 - 3420.
[Abstract] [Full Text] [PDF]

S. W. Doniger, J. Huh, and J. C. Fay
Identification of functional transcription factor binding sites using closely related Saccharomyces species
Genome Res., May 1, 2005; 15(5): 701 - 709.
[Abstract] [Full Text] [PDF]

A. Force, W. A. Cresko, F. B. Pickett, S. R. Proulx, C. Amemiya, and M. Lynch
The Origin of Subfunctions and Modular Gene Regulation
Genetics, May 1, 2005; 170(1): 433 - 446.
[Abstract] [Full Text] [PDF]

D. Papatsenko and M. Levine
Gene Regulatory Networks Special Feature: Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo
PNAS, April 5, 2005; 102(14): 4966 - 4971.
[Abstract] [Full Text] [PDF]

B. M. Hersh and S. B. Carroll
Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila
Development, April 1, 2005; 132(7): 1567 - 1577.
[Abstract] [Full Text] [PDF]

I. Oda-Ishii, V. Bertrand, I. Matsuo, P. Lemaire, and H. Saiga
Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis
Development, April 1, 2005; 132(7): 1663 - 1674.
[Abstract] [Full Text] [PDF]

S. Sinha and E. D. Siggia
Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila
Mol. Biol. Evol., April 1, 2005; 22(4): 874 - 885.
[Abstract] [Full Text] [PDF]

L. Ometto, W. Stephan, and D. De Lorenzo
Insertion/Deletion and Nucleotide Polymorphism Data Reveal Constraints in Drosophila melanogaster Introns and Intergenic Regions
Genetics, March 1, 2005; 169(3): 1521 - 1527.
[Abstract] [Full Text] [PDF]

S. Richards, Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky, R. Nielsen, K. Thornton, M. J. Hubisz, R. Chen, R. P. Meisel, et al.
Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
Genome Res., January 1, 2005; 15(1): 1 - 18.
[Abstract] [Full Text] [PDF]

R. Sharan, A. Ben-Hur, G. G. Loots, and I. Ovcharenko
CREME: Cis-Regulatory Module Explorer for the human genome
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W253 - W256.
[Abstract] [Full Text] [PDF]

S. MacArthur and J. F. Y. Brookfield
Expected Rates and Modes of Evolution of Enhancer Sequences
Mol. Biol. Evol., June 1, 2004; 21(6): 1064 - 1073.
[Abstract] [Full Text] [PDF]

P. Struffi, M. Corado, M. Kulkarni, and D. N. Arnosti
Quantitative contributions of CtBP-dependent and -independent repression activities of Knirps
Development, May 15, 2004; 131(10): 2419 - 2429.
[Abstract] [Full Text] [PDF]

J. Phinchongsakuldit, S. MacArthur, and J. F. Y. Brookfield
Evolution of Developmental Genes: Molecular Microevolution of Enhancer Sequences at the Ubx Locus in Drosophila and Its Impact on Developmental Phenotypes
Mol. Biol. Evol., February 1, 2004; 21(2): 348 - 363.
[Abstract] [Full Text] [PDF]

M. M. Kulkarni and D. N. Arnosti
Information display by transcriptional enhancers
Development, December 29, 2003; 130(26): 6569 - 6575.
[Abstract] [Full Text] [PDF]

I. Ruvinsky and G. Ruvkun
Functional tests of enhancer conservation between distantly related species
Development, November 1, 2003; 130(21): 5133 - 5142.
[Abstract] [Full Text] [PDF]

V. J. Makeev, A. P. Lifanov, A. G. Nazina, and D. A. Papatsenko
Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information
Nucleic Acids Res., October 15, 2003; 31(20): 6016 - 6026.
[Abstract] [Full Text] [PDF]

L. A. Romano and G. A. Wray
Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation
Development, September 1, 2003; 130(17): 4187 - 4199.
[Abstract] [Full Text] [PDF]

G. A. Wray, M. W. Hahn, E. Abouheif, J. P. Balhoff, M. Pizer, M. V. Rockman, and L. A. Romano
The Evolution of Transcriptional Regulation in Eukaryotes
Mol. Biol. Evol., September 1, 2003; 20(9): 1377 - 1419.
[Abstract] [Full Text] [PDF]

R. L. Hong, L. Hamaguchi, M. A. Busch, and D. Weigel
Regulatory Elements of the Floral Homeotic Gene AGAMOUS Identified by Phylogenetic Footprinting and Shadowing
PLANT CELL, June 1, 2003; 15(6): 1296 - 1309.
[Abstract] [Full Text]

E. T. Dermitzakis, C. M. Bergman, and A. G. Clark
Tracing the Evolutionary History of Drosophila Regulatory Regions with Models that Identify Transcription Factor Binding Sites
Mol. Biol. Evol., May 1, 2003; 20(5): 703 - 714.
[Abstract] [Full Text] [PDF]

A. P. Lifanov, V. J. Makeev, A. G. Nazina, and D. A. Papatsenko
Homotypic Regulatory Clusters in Drosophila
Genome Res., April 1, 2003; 13(4): 579 - 588.
[Abstract] [Full Text] [PDF]

J. M. Comeron and M. Kreitman
Population, Evolutionary and Genomic Consequences of Interference Selection
Genetics, May 1, 2002; 161(1): 389 - 410.
[Abstract] [Full Text] [PDF]

B. P. Berman, Y. Nibu, B. D. Pfeiffer, P. Tomancak, S. E. Celniker, M. Levine, G. M. Rubin, and M. B. Eisen
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
PNAS, January 22, 2002; 99(2): 757 - 762.
[Abstract] [Full Text] [PDF]

L. P. M. Andrioli, V. Vasisht, E. Theodosopoulou, A. Oberstein, and S. Small
Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms
Development, January 11, 2002; 129(21): 4931 - 4940.
[Abstract] [Full Text] [PDF]

J. R. Stone and G. A. Wray
Rapid Evolution of cis-Regulatory Sequences via Local Point Mutations
Mol. Biol. Evol., September 1, 2001; 18(9): 1764 - 1770.
[Abstract] [Full Text] [PDF]

C. M. Bergman and M. Kreitman
Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences
Genome Res., August 1, 2001; 11(8): 1335 - 1345.
[Abstract] [Full Text] [PDF]

G. K. Christophides, I. Livadaras, C. Savakis, and K. Komitopoulou
Two Medfly Promoters That Have Originated by Recent Gene Duplication Drive Distinct Sex, Tissue and Temporal Expression Patterns
Genetics, September 1, 2000; 156(1): 173 - 182.
[Abstract] [Full Text]

F. Piano, M. J. Parisi, R. Karess, and M. P. Kambysellis
Evidence for Redundancy But Not trans Factor�cis Element Coevolution in the Regulation of Drosophila Yp Genes
Genetics, June 1, 1999; 152(2): 605 - 616.
[Abstract] [Full Text]

M Fujioka, Y Emi-Sarker, G. Yusibova, T Goto, and J. Jaynes
Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients
Development, January 6, 1999; 126(11): 2527 - 2538.
[Abstract] [PDF]

G. Hewitt, B. Strunk, C Margulies, T Priputin, X. Wang, R Amey, B. Pabst, D Kosman, J Reinitz, and D. Arnosti
Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient
Development, January 3, 1999; 126(6): 1201 - 1210.
[Abstract] [PDF]

K. Sumiyama, S. Q. Irvine, D. W. Stock, K. M. Weiss, K. Kawasaki, N. Shimizu, C. S. Shashikant, W. Miller, and F. H. Ruddle
Genomic structure and functional control of the Dlx3-7 bigene cluster
PNAS, January 22, 2002; 99(2): 780 - 785.
[Abstract] [Full Text] [PDF]

D. A. Papatsenko, V. J. Makeev, A. P. Lifanov, M. Regnier, A. G. Nazina, and C. Desplan
Extraction of Functional Binding Sites from Unique Regulatory Regions: The Drosophila Early Developmental Enhancers
Genome Res., March 1, 2002; 12(3): 470 - 481.
[Abstract] [Full Text] [PDF]

This Article

Summary

Full Text (PDF)

Alert me when this article is cited

Alert me if a correction is posted

Services

Email this article to a friend

Similar articles in this journal

Similar articles in PubMed

Alert me to new issues of the journal

Download to citation manager

Citing Articles

Citing Articles via HighWire

Citing Articles via Google Scholar

Google Scholar

				R. Satija, L. Pachter, and J. Hein Combining statistical alignment and phylogenetic footprinting to detect regulatory elements Bioinformatics, May 15, 2008; 24(10): 1236 - 1242. [Abstract] [Full Text] [PDF]

				M. B. Noyes, X. Meng, A. Wakabayashi, S. Sinha, M. H. Brodsky, and S. A. Wolfe A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system Nucleic Acids Res., May 1, 2008; 36(8): 2547 - 2560. [Abstract] [Full Text] [PDF]

				A. M. Moses, M. E. Liku, J. J. Li, and R. Durbin Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites PNAS, November 6, 2007; 104(45): 17713 - 17718. [Abstract] [Full Text] [PDF]

				R. R. Copley, M. Totrov, J. Linnell, S. Field, J. Ragoussis, and I. A. Udalova Functional conservation of Rel binding sites in drosophilid genomes Genome Res., September 1, 2007; 17(9): 1327 - 1335. [Abstract] [Full Text] [PDF]

				A. Chabot, R. A. Shrit, R. Blekhman, and Y. Gilad Using Reporter Gene Assays to Identify cis Regulatory Differences Between Humans and Chimpanzees Genetics, August 1, 2007; 176(4): 2069 - 2076. [Abstract] [Full Text] [PDF]

				M. Nei The new mutation theory of phenotypic evolution PNAS, July 24, 2007; 104(30): 12235 - 12242. [Abstract] [Full Text] [PDF]

				M. Brandstrom and H. Ellegren The Genomic Landscape of Short Insertion and Deletion Polymorphisms in the Chicken (Gallus gallus) Genome: A High Frequency of Deletions in Tandem Duplicates Genetics, July 1, 2007; 176(3): 1691 - 1701. [Abstract] [Full Text] [PDF]

				S. E. Lott, M. Kreitman, A. Palsson, E. Alekseeva, and M. Z. Ludwig Canalization of segmentation and its evolution in Drosophila PNAS, June 26, 2007; 104(26): 10926 - 10931. [Abstract] [Full Text] [PDF]

				D. C. King, J. Taylor, Y. Zhang, Y. Cheng, H. A. Lawson, J. Martin, ENCODE groups for Transcriptional Regulation and M, F. Chiaromonte, W. Miller, and R. C. Hardison Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data Genome Res., June 1, 2007; 17(6): 775 - 786. [Abstract] [Full Text] [PDF]

				C. Tian, T. Kasuga, M. S. Sachs, and N. L. Glass Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons Eukaryot. Cell, June 1, 2007; 6(6): 1018 - 1029. [Abstract] [Full Text] [PDF]

				M. Freeling, L. Rapaka, E. Lyons, B. Pedersen, and B. C. Thomas G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences in Arabidopsis PLANT CELL, May 1, 2007; 19(5): 1441 - 1457. [Abstract] [Full Text] [PDF]

				A. S. Bais, S. Grossmann, and M. Vingron Simultaneous alignment and annotation of cis-regulatory regions Bioinformatics, January 15, 2007; 23(2): e44 - e49. [Abstract] [Full Text] [PDF]

				J. Taylor, S. Tyekucheva, D. C. King, R. C. Hardison, W. Miller, and F. Chiaromonte ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements Genome Res., December 1, 2006; 16(12): 1596 - 1604. [Abstract] [Full Text] [PDF]

				J. R. t. Bosch, J. A. Benavides, and T. W. Cline The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription Development, May 15, 2006; 133(10): 1967 - 1977. [Abstract] [Full Text] [PDF]

				M. Ronshaugen, F. Biemar, J. Piel, M. Levine, and E. C. Lai The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings Genes & Dev., December 15, 2005; 19(24): 2947 - 2952. [Abstract] [Full Text] [PDF]

				R. A. Cameron, S. H. Chow, K. Berney, T.-Y. Chiu, Q.-A. Yuan, A. Kramer, A. Helguero, A. Ransick, M. Yun, and E. H. Davidson An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules PNAS, August 16, 2005; 102(33): 11769 - 11774. [Abstract] [Full Text] [PDF]

				J. Gertz, L. Riles, P. Turnbaugh, S.-W. Ho, and B. A. Cohen Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics Genome Res., August 1, 2005; 15(8): 1145 - 1152. [Abstract] [Full Text] [PDF]

				J. C. Fay and J. A. Benavides Hypervariable Noncoding Sequences in Saccharomyces cerevisiae Genetics, August 1, 2005; 170(4): 1575 - 1587. [Abstract] [Full Text] [PDF]

				J. P. Balhoff and G. A. Wray Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites PNAS, June 14, 2005; 102(24): 8591 - 8596. [Abstract] [Full Text] [PDF]

				A. Tanay, A. Regev, and R. Shamir Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast PNAS, May 17, 2005; 102(20): 7203 - 7208. [Abstract] [Full Text] [PDF]

				M. M. Kulkarni and D. N. Arnosti cis-Regulatory Logic of Short-Range Transcriptional Repression in Drosophila melanogaster Mol. Cell. Biol., May 1, 2005; 25(9): 3411 - 3420. [Abstract] [Full Text] [PDF]

				S. W. Doniger, J. Huh, and J. C. Fay Identification of functional transcription factor binding sites using closely related Saccharomyces species Genome Res., May 1, 2005; 15(5): 701 - 709. [Abstract] [Full Text] [PDF]

				A. Force, W. A. Cresko, F. B. Pickett, S. R. Proulx, C. Amemiya, and M. Lynch The Origin of Subfunctions and Modular Gene Regulation Genetics, May 1, 2005; 170(1): 433 - 446. [Abstract] [Full Text] [PDF]

				D. Papatsenko and M. Levine Gene Regulatory Networks Special Feature: Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo PNAS, April 5, 2005; 102(14): 4966 - 4971. [Abstract] [Full Text] [PDF]

				B. M. Hersh and S. B. Carroll Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila Development, April 1, 2005; 132(7): 1567 - 1577. [Abstract] [Full Text] [PDF]

				I. Oda-Ishii, V. Bertrand, I. Matsuo, P. Lemaire, and H. Saiga Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis Development, April 1, 2005; 132(7): 1663 - 1674. [Abstract] [Full Text] [PDF]

				S. Sinha and E. D. Siggia Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila Mol. Biol. Evol., April 1, 2005; 22(4): 874 - 885. [Abstract] [Full Text] [PDF]

				L. Ometto, W. Stephan, and D. De Lorenzo Insertion/Deletion and Nucleotide Polymorphism Data Reveal Constraints in Drosophila melanogaster Introns and Intergenic Regions Genetics, March 1, 2005; 169(3): 1521 - 1527. [Abstract] [Full Text] [PDF]

				S. Richards, Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky, R. Nielsen, K. Thornton, M. J. Hubisz, R. Chen, R. P. Meisel, et al. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution Genome Res., January 1, 2005; 15(1): 1 - 18. [Abstract] [Full Text] [PDF]

				R. Sharan, A. Ben-Hur, G. G. Loots, and I. Ovcharenko CREME: Cis-Regulatory Module Explorer for the human genome Nucleic Acids Res., July 1, 2004; 32(suppl_2): W253 - W256. [Abstract] [Full Text] [PDF]