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Tag key--crm [44 articles]

Recent papers classified by the tag key--crm.
  • Transcriptional regulation and the evolution of development.
    Int J Dev Biol, Vol. 47, No. 7-8. (2003), pp. 675-684.
    by GA Wray
    posted to key--crm key--molecular_evolution type--review by adepace to the group EisenLab on 2006-12-03 16:40:08 as ***** along with 2 people nsamways balicea
  • Conservation of regulatory elements controlling hairy pair-rule stripe formation.
    Development, Vol. 117, No. 2. (February 1993), pp. 585-596.
    by JA Langeland, SB Carroll
    posted to tech--phylogenetic_comparison system--drosophilidae key--expression_pattern key--evolution key--crm gene--h by adepace to the group EisenLab on 2007-01-17 02:00:55 as ****
  • Large-scale turnover of functional transcription factor binding sites in Drosophila.
    PLoS Comput Biol, Vol. 2, No. 10. (October 2006)
    by AM Moses, DA Pollard, DA Nix, VN Iyer, XY Li, MD Biggin, MB Eisen
    posted to key--crm key--molecular_evolution system--drosophilidae by adepace to the group EisenLab on 2006-12-22 21:14:43 as read along with 6 people and 1 group caseybrown eukfn lusk maximilianh cisevol emptyhb cis-regulatory-evolution
  • cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster.
    Mol Cell Biol, Vol. 25, No. 9. (May 2005), pp. 3411-3420.
    by MM Kulkarni, DN Arnosti
    posted to key--crm key--transcription system--dmel by adepace to the group EisenLab on 2006-12-23 11:59:48 as ***** along with 2 people olympos lusk
  • Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster
    Evolution & Development, Vol. 8, No. 1. (January 2006), pp. 6-15.
    by Naomi S Wratten, Alistair P Mcgregor, Philip J Shaw, Gabriel A Dover
    posted to system--diptera key--evolution key--crm gene--tll by adepace to the group EisenLab on 2007-01-17 02:17:20 as ***
  • Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila.
    Development, Vol. 132, No. 7. (April 2005), pp. 1567-1577.
    by BM Hersh, SB Carroll
    posted to gene--hox key--crm key--molecular_evolution system--dmel system--dpse by adepace to the group EisenLab on 2006-12-23 17:24:53 as ***
  • Regulatory and coding regions of the segmentation gene hunchback are functionally conserved between Drosophila virilis and Drosophila melanogaster.
    Mech Dev, Vol. 45, No. 2. (February 1994), pp. 105-115.
    by W Lukowitz, C Schröder, G Glaser, M Hülskamp, D Tautz
    posted to system--drosophilidae key--expression_pattern key--evolution key--crm gene--hb by adepace to the group EisenLab on 2007-01-17 02:05:54 as read
  • Rapid evolution of cis-regulatory sequences via local point mutations.
    Mol Biol Evol, Vol. 18, No. 9. (September 2001), pp. 1764-1770.
    by JR Stone, GA Wray
    posted to key--molecular_evolution key--crm key--binding_sites by adepace to the group EisenLab on 2007-01-17 01:01:47 as ***** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Conservation of RET Regulatory Function from Human to Zebrafish Without Sequence Similarity.
    Science (23 March 2006)
    by Shannon Fisher, Elizabeth A A Grice, Ryan M M Vinton, Seneca L L Bessling, Andrew S S McCallion
    posted to key--evolution key--crm system--primates system--fish by adepace to the group EisenLab on 2007-01-26 20:37:51 as read along with 5 people and 2 groups aprasad nickluscombe maximilianh cisevol emptyhb EBI-regulation cis-regulatory-evolution
  • Evolution: Spot on (and off)
    Nature, Vol. 440, No. 7087. (20 April 2006), pp. 1001-1002.
    by Gregory A Wray
    posted to key--crm key--molecular_evolution key--phenotypic_evolution system--dmel type--comment by adepace to the group EisenLab on 2006-12-03 16:41:41 as *****
  • Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites.
    Proc Natl Acad Sci U S A, Vol. 102, No. 24. (14 June 2005), pp. 8591-8596.
    by JP Balhoff, GA Wray
    posted to key--crm key--molecular_evolution system--sea_urchin tech--population_genetics by adepace to the group EisenLab on 2006-12-23 17:20:08 as ***** along with 2 people and 1 group cisevol emptyhb cis-regulatory-evolution
  • 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, Vol. 126, No. 11. (1 June 1999), pp. 2527-2538.
    by M Fujioka, Y Emi-Sarker, Gl Yusibova, T Goto, Jb Jaynes
    posted to key--expression_pattern key--crm gene--eve by adepace to the group EisenLab on 2007-02-05 06:21:29 as read
  • Autoregulatory and gap gene response elements of the even-skipped promoter of Drosophila.
    EMBO J, Vol. 8, No. 4. (April 1989), pp. 1205-1212.
    by K Harding, T Hoey, R Warrior, M Levine
    posted to system--dpse_embryo key--crm gene--eve by adepace to the group EisenLab on 2007-02-05 06:36:36 as *
  • Activation of posterior pair-rule stripe expression in response to maternal caudal and zygotic knirps activities.
    Mech Dev, Vol. 71, No. 1-2. (February 1998), pp. 177-186.
    by T Häder, A La Rosée, U Ziebold, M Busch, H Taubert, H Jäckle, R Rivera-Pomar
    posted to gene--caudal gene--h gene--kni key--crm by adepace to the group EisenLab on 2007-02-18 20:09:59 as *****
  • The Evolution of Transcriptional Regulation in Eukaryotes
    Mol Biol Evol, Vol. 20, No. 9. (1 September 2003), pp. 1377-1419.
    by Gregory A Wray, Matthew W Hahn, Ehab Abouheif, James P Balhoff, Margaret Pizer, Matthew V Rockman, Laura A Romano
    posted to key--crm key--molecular_evolution key--phenotypic_evolution type--review by adepace to the group EisenLab on 2006-12-03 16:35:23 as read along with 8 people and 4 groups ana dpollard nickluscombe anatiferous mimulus_99 cisevol emptyhb emmahe structural_bioinformatics Bioinformatics EBI-regulation cis-regulatory-evolution
  • Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.
    Development, Vol. 125, No. 5. (March 1998), pp. 949-958.
    by MZ Ludwig, NH Patel, M Kreitman
    posted to gene--eve key--crm key--molecular_evolution system--dmel_embryo system--dpse_embryo by adepace to the group EisenLab on 2006-12-03 23:30:08 as read along with 3 people and 1 group cisevol emptyhb brant cis-regulatory-evolution
  • Analysis and function of transcriptional regulatory elements: insights from Drosophila.
    Annu Rev Entomol, Vol. 48 (2003), pp. 579-602.
    by DN Arnosti
    posted to key--crm key--gene_expression key--transcription system--dmel type--review by adepace to the group EisenLab on 2006-12-23 12:01:42 as ***** along with 1 person emmahe
  • cis-DECODER discovers constellations of conserved DNA sequences shared among tissue-specific enhancers
    Genome Biology, Vol. 8 (09 May 2007), R75.
    by Thomas Brody, Wayne Rasband, Kevin Baler, Alexander Kuzin, Mukta Kundu, Ward F Odenwald
    posted to tech--phylogenetic_comparison key--crm by adepace to the group EisenLab on 2007-05-14 22:38:17 as **
  • Predicting gene expression from sequence.
    Cell, Vol. 117, No. 2. (16 April 2004), pp. 185-198.
    by MA Beer, S Tavazoie
    posted to key--crm key--expression_pattern key--transcription tech--motif_analysis tech--network_modeling by adepace to the group EisenLab on 2007-01-02 01:27:37 as ***** along with 9 people and 4 groups tharris ana xwbcn nickluscombe noano koller jrest phoenixzxl klo C. elegans / WormBase structural_bioinformatics Bioinformatics EBI-regulation
  • Expected rates and modes of evolution of enhancer sequences.
    Mol Biol Evol, Vol. 21, No. 6. (June 2004), pp. 1064-1073.
    by S MacArthur, JF Brookfield
    posted to key--crm key--molecular_evolution system--dmel by adepace to the group EisenLab on 2006-12-23 17:30:20 as ***** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues.
    Cell, Vol. 57, No. 3. (5 May 1989), pp. 413-422.
    by T Goto, P Macdonald, T Maniatis
    posted to system--dmel_embryo key--crm gene--eve by adepace to the group EisenLab on 2007-02-05 06:35:33 as *
  • Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation.
    Development, Vol. 130, No. 17. (September 2003), pp. 4187-4199.
    by LA Romano, GA Wray
    posted to system--sea_urchin key--regulatory_network key--expression_pattern key--crm by adepace to the group EisenLab on 2007-01-17 02:28:28 as ***** along with 1 person pradiptaray
  • Comparative genomics using Fugu reveals insights into regulatory subfunctionalization
    Genome Biology, Vol. 8 (11 April 2007), R53.
    by Adam Woolfe, Greg Elgar
    posted to system--fish key--evolution key--crm by adepace to the group EisenLab on 2007-04-13 20:46:01 as ** along with 2 people ajgentles ajpowell
  • REDfly: a Regulatory Element Database for Drosophila.
    Bioinformatics, Vol. 22, No. 3. (1 February 2006), pp. 381-383.
    by SM Gallo, L Li, Z Hu, MS Halfon
    posted to type--method key--crm by adepace to the group EisenLab on 2007-01-21 22:18:18 as * along with 2 people roys postrational
  • Comparison of diverged Hoxc8 early enhancer activities reveals modification of regulatory interactions at conserved cis-acting elements.
    J Exp Zoolog B Mol Dev Evol (14 December 2006)
    by Cooduvalli S S Shashikant, Stacey A A Bolanowsky, Sanjay Anand, Shawn M M Anderson
    posted to key--crm key--expression_pattern key--molecular_evolution system--mouse by adepace to the group EisenLab on 2006-12-22 20:46:19 as **
  • A role of Ultrabithorax in morphological differences between Drosophila species
    Nature, Vol. 396, No. 6710. (3 December 1998), pp. 463-466.
    by David L Stern
    posted to system--drosophilidae key--phenotypic_evolution key--evolution key--crm gene--ubx by adepace to the group EisenLab on 2007-01-18 02:21:04 as ***
  • Comparative analyses of multi-species sequences from targeted genomic regions.
    Nature, Vol. 424, No. 6950. (14 August 2003), pp. 788-793.
    by JW Thomas, JW Touchman, RW Blakesley, GG Bouffard, SM Beckstrom-Sternberg, EH Margulies, M Blanchette, AC Siepel, PJ Thomas, JC McDowell, B Maskeri, NF Hansen, MS Schwartz, RJ Weber, WJ Kent, D Karolchik, TC Bruen, R Bevan, DJ Cutler, S Schwartz, L Elnitski, JR Idol, AB Prasad, SQ Lee-Lin, VV Maduro, TJ Summers, ME Portnoy, NL Dietrich, N Akhter, K Ayele, B Benjamin, K Cariaga, CP Brinkley, SY Brooks, S Granite, X Guan, J Gupta, P Haghighi, SL Ho, MC Huang, E Karlins, PL Laric, R Legaspi, MJ Lim, QL Maduro, CA Masiello, SD Mastrian, JC McCloskey, R Pearson, S Stantripop, EE Tiongson, JT Tran, C Tsurgeon, JL Vogt, MA Walker, KD Wetherby, LS Wiggins, AC Young, LH Zhang, K Osoegawa, B Zhu, B Zhao, CL Shu, PJ De Jong, CE Lawrence, AF Smit, A Chakravarti, D Haussler, P Green, W Miller, ED Green
    posted to key--genome key--evolution key--crm by adepace to the group EisenLab on 2007-01-26 22:19:09 as *** along with 3 people aprasad radek AaronDarling
  • Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms.
    Development, Vol. 129, No. 21. (November 2002), pp. 4931-4940.
    by LP Andrioli, V Vasisht, E Theodosopoulou, A Oberstein, S Small
    posted to key--crm key--expression_pattern system--dmel_embryo by adepace to the group EisenLab on 2006-12-03 23:28:06 as ****
  • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
    BMC Bioinformatics, Vol. 3 (24 October 2002)
    by N Rajewsky, M Vergassola, U Gaul, ED Siggia
    posted to tech--motif_analysis key--gene_expression key--crm by adepace to the group EisenLab on 2007-01-17 02:11:05 as **** along with 6 people isimpson ansobol indigoviolet koller Stew csdhwang
  • The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila.
    Proc Natl Acad Sci U S A, Vol. 102, No. 14. (5 April 2005), pp. 4960-4965.
    by A Ochoa-Espinosa, G Yucel, L Kaplan, A Pare, N Pura, A Oberstein, D Papatsenko, S Small
    posted to gene--bcd key--crm key--expression_pattern key--morphogen by adepace to the group EisenLab on 2007-01-01 19:49:48 as ***** along with 1 person emptyhb
  • Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis
    Mechanisms of Development, Vol. 80, No. 1. (January 1999), pp. 87-99.
    by Christian Wolff, Melissa Pepling, Peter Gergen, Martin Klingler
    posted to tech--phylogenetic_comparison system--drosophilidae key--evolution key--crm gene--runt by adepace to the group EisenLab on 2007-01-17 01:09:26 as *****
  • Evolution of developmental genes: molecular microevolution of enhancer sequences at the Ubx locus in Drosophila and its impact on developmental phenotypes.
    Mol Biol Evol, Vol. 21, No. 2. (February 2004), pp. 348-363.
    by J Phinchongsakuldit, S MacArthur, JF Brookfield
    posted to gene--hox key--crm key--molecular_evolution key--phenotypic_evolution tech--population_genetics by adepace to the group EisenLab on 2006-12-23 17:32:12 as **** along with 2 people and 1 group cisevol emptyhb cis-regulatory-evolution
  • Enhancer Responses to Similarly Distributed Antagonistic Gradients in Development
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e84.
    by Robert P Zinzen, Dmitri Papatsenko
    posted to key--crm key--morphogen key--segmentation system--dmel tech--simulation by adepace on 2007-05-14 22:21:13 as ***** along with 1 person and 1 group dpollard EisenLab
  • Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
    Genome Biol, Vol. 5, No. 9. (2004)
    by BP Berman, BD Pfeiffer, TR Laverty, SL Salzberg, GM Rubin, MB Eisen, SE Celniker
    posted to key--crm key--expression_pattern system--dmel_embryo tech--phylogenetic_comparison by adepace on 2007-01-01 19:47:18 as read along with 7 people and 3 groups mbeisen indigoviolet Stew nklee cisevol maximilianh Auger EisenLab cis-regulatory-evolution Dead 60's
  • Transcriptional Control in the Segmentation Gene Network of Drosophila
    PLoS Biology, Vol. 2, No. 9. (1 September 2004), e271.
    by Mark D Schroeder, Michael Pearce, John Fak, Hongqing Fan, Ulrich Unnerstall, Eldon Emberly, Nikolaus Rajewsky, Eric D Siggia, Ulrike Gaul
    posted to key--crm key--expression_pattern key--transcription system--dmel_embryo tech--phylogenetic_comparison by adepace on 2007-01-01 19:52:24 as read along with 7 people and 3 groups indigoviolet dpollard wrowell emptyhb dlmace pradiptaray balicea EisenLab Cline_lab UH - Computational Biology
  • Parallel evolution of conserved noncoding elements that target a common set of developmental regulatory genes from worms to humans.
    Genome Biology, Vol. 8 (02 February 2007), R15.
    by Tanya Vavouri, Klaudia Walter, Walter R Gilks, Ben Lehner, Greg Elgar
    posted to key--crm key--evolution tech--motif_analysis tech--phylogenetic_comparison by adepace on 2007-04-27 19:52:54 as ***** along with 7 people and 2 groups indigoviolet dpollard djkt sujaikumar Stew cisevol smbe2008 EisenLab cis-regulatory-evolution
  • Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila.
    Nature, Vol. 433, No. 7025. (3 February 2005), pp. 481-487.
    by N Gompel, B Prud'homme, PJ Wittkopp, VA Kassner, SB Carroll
    posted to system--drosophilidae key--phenotypic_evolution key--expression_pattern key--crm by adepace on 2007-01-18 02:39:14 as read along with 5 people and 2 groups dpollard emilyhare cisevol emptyhb pradiptaray EisenLab cis-regulatory-evolution
  • Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.
    Nat Genet (17 September 2006)
    by Hilde Janssens, Shuling Hou, Johannes Jaeger, Ah-Ram R Kim, Ekaterina Myasnikova, David Sharp, John Reinitz
    posted to key--crm key--expression_pattern system--dmel_embryo tech--network_modeling tech--quantitative_imaging by adepace on 2006-09-26 21:34:03 as read along with 6 people and 2 groups okarsligil brant dpollard allPowerde Stew emptyhb Bioinformatics EisenLab
  • Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene
    Nature, Vol. 440, No. 7087., pp. 1050-1053.
    by Benjamin Prud'homme, Nicolas Gompel, Antonis Rokas, Victoria A Kassner, Thomas M Williams, Shu-Dan Yeh, John R True, Sean B Carroll
    posted to key--crm key--molecular_evolution key--phenotypic_evolution system--dmel by adepace on 2006-12-03 16:43:17 as ***** along with 9 people and 1 group carlfulp RMGraze dpollard balicea tny ranb Garamonfok blobbybirdman emptyhb EisenLab
  • notes Two medfly promoters that have originated by recent gene duplication drive distinct sex, tissue and temporal expression patterns.
    Genetics, Vol. 156, No. 1. (September 2000), pp. 173-182.
    by GK Christophides, I Livadaras, C Savakis, K Komitopoulou
    posted to system--diptera key--expression_pattern key--evolution key--crm by adepace on 2007-01-17 02:42:59 as ** along with 2 people and 1 group brant dpollard EisenLab
  • Evolution of cis-regulatory sequence and function in Diptera
    Heredity, Vol. aop, No. current.
    by PJ Wittkopp,
    posted to key--crm key--evolution key--molecular_evolution key--phenotypic_evolution system--drosophilidae type--review by adepace on 2006-12-22 21:46:16 as ***** along with 5 people and 2 groups indigoviolet dpollard emmahe cisevol emptyhb EisenLab cis-regulatory-evolution
  • Two or Four Bristles: Functional Evolution of an Enhancer of scute in Drosophilidae
    PLoS Biology, Vol. 4, No. 12. (1 November 2006), e386.
    by Sylvain Marcellini, Pat Simpson
    posted to gene--scute key--crm key--molecular_evolution key--phenotypic_evolution system--drosophilidae by adepace on 2006-12-22 20:53:52 as ***** along with 3 people and 1 group dpollard emmahe emptyhb EisenLab
  • Cis-regulatory variations: A study of SNPs around genes showing cis-linkage in segregating mouse populations
    BMC Genomics, Vol. 7 (15 September 2006), 235.
    by Debraj Guhathakurta, Tao Xie, Manish Anand, Stephen W Edwards, Guoya Li, Susana Wang, Eric E Schadt
    posted to tech--population_genetics system--mouse key--crm by adepace on 2007-01-25 23:57:00 as ** along with 2 people and 1 group dpollard natstreet EisenLab
  • Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both.
    Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402.
    by T Vavouri, G Elgar
    posted to type--review key--crm key--binding_sites by adepace on 2007-02-05 21:02:06 as ***** along with 6 people and 2 groups troels_marstrand kaspermunch dpollard lusk Stew brant Bioinformatics EisenLab
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