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Tag cis_regulatory_elements [93 articles]

Recent papers classified by the tag cis_regulatory_elements.
  • Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression
    Science, Vol. 317, No. 5844. (14 September 2007), pp. 1557-1560.
    by Christopher D Brown, David S Johnson, Arend Sidow
    posted to cis_regulatory_elements colin_presented conservation eisen_journal_club grammar in_depth regulatory_evolution round_robin stew_presented by dpollard to the group EisenLab on 2007-10-29 18:57:23 as *** along with 9 people and 1 group djkt joepickrell zwang Garamonfok Stew mimulus_99 maximilianh cisevol emptyhb cis-regulatory-evolution
  • Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction
    Genome Biology, Vol. 8 (08 June 2007), R106.
    by Yavor Hadzhiev, Michael Lang, Raymond Ertzer, Axel Meyer, Uwe Straehle, Ferenc Mueller
    posted to round_robin rich_presented regulatory_sequence_evolution regulatory_evolution in_depth_suggestion grammar eisen_journal_club crm cis_regulatory_elements by dpollard to the group EisenLab on 2007-08-01 22:37:08 as ** along with 2 people and 1 group cjeans cisevol cis-regulatory-evolution
  • SPACER: identification of cis-regulatory elements with non-contiguous critical residues.
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1029-1031.
    by A Chakravarty, JM Carlson, RS Khetani, CE DeZiel, RH Gross
    posted to prediction method clustering cis_regulatory_elements binding_site by dpollard to the group EisenLab on 2007-05-23 01:10:50 as **
  • Smad Affinity Can Direct Distinct Readouts of the Embryonic Extracellular Dpp Gradient in Drosophila
    Current Biology, Vol. 14, No. 17. (7 September 2004), pp. 1550-1558.
    by Stephen J Wharton, Sanjay P Basu, Hilary L Ashe
    posted to cis_regulatory_elements expression_pattern modeling by dpollard to the group EisenLab on 2007-11-05 21:13:34 as **
  • Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
    Genome Biology, Vol. 8 (05 June 2007), R101.
    by Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon
    posted to round_robin regulatory_sequence_evolution enhancer eisen_journal_club drosophila crm cis_regulatory_elements angela_presented by dpollard to the group EisenLab on 2007-07-02 21:12:58 as *** along with 4 people lusk cjeans maximilianh isimpson
  • CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.
    Proc Natl Acad Sci U S A, Vol. 101, No. 33. (17 August 2004), pp. 12114-12119.
    by Q Zhou, WH Wong
    posted to ab_initio cis_regulatory_elements clustering method prediction by dpollard to the group EisenLab on 2007-12-05 22:46:33 as read along with 2 people indigoviolet ep161302
  • Gradients and thresholds: BMP response gradients unveiled in Drosophila embryos
    Trends in Genetics, Vol. 19, No. 12. (December 2003), pp. 701-708.
    by Laurel A Raftery, David J Sutherland
    posted to cis_regulatory_elements drosophila embryonic_patterning expression_pattern modeling by dpollard to the group EisenLab on 2007-11-05 21:19:39 as **
  • Transcriptional regulation by the numbers: applications.
    Curr Opin Genet Dev, Vol. 15, No. 2. (April 2005), pp. 125-135.
    by L Bintu, NE Buchler, HG Garcia, U Gerland, T Hwa, J Kondev, T Kuhlman, R Phillips
    posted to cis_regulatory_elements expression_pattern modeling by dpollard to the group EisenLab on 2007-11-05 21:14:35 as ** along with 4 people imouthesmp madhadron dquest discreteonyxorb
  • Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter.
    Proc Natl Acad Sci U S A, Vol. 72, No. 3. (March 1975), pp. 784-788.
    by D Pribnow
    posted to binding_site cis_regulatory_elements conservation seminal_paper by dpollard to the group EisenLab on 2007-11-26 00:28:07 as read
  • 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 binding_site cis_regulatory_elements method motif pattern prediction pwm regulatory_sequence by dpollard to the group EisenLab on 2007-03-15 00:24:34 as *** along with 6 people and 1 group troels_marstrand kaspermunch adepace lusk Stew brant Bioinformatics
  • Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.
    Nucleic Acids Res, Vol. 31, No. 20. (15 October 2003), pp. 6016-6026.
    by VJ Makeev, AP Lifanov, AG Nazina, DA Papatsenko
    posted to binding_site cis_regulatory_elements drosophila grammar helical_phasing by dpollard to the group EisenLab on 2007-10-31 22:40:43 as read along with 2 people and 1 group oannes lusk Regulomics_UCHSC
  • Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome
    Genome Biology, Vol. 8 (16 May 2007), R84.
    by Shaun Mahony, David L Corcoran, Eleanor Feingold, Panayiotis V Benos
    posted to mammal in_depth_suggestion eisen_journal_club conservation comparative_genomics cis_regulatory_elements binding_site by dpollard to the group EisenLab on 2007-06-14 23:45:44 as ** along with 3 people and 1 group andersbj dorotagospodarczyk maralena microRNA
  • PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation
    Genome Biology, Vol. 8 (04 October 2007), R207.
    by Elodie Portales-Casamar, Stefan Kirov, Jonathan Lim, Stuart Lithwick, Magdalena I Swanson, Amy Ticoll, Jay Snoddy, Wyeth W Wasserman
    posted to cis_regulatory_elements database by dpollard to the group EisenLab on 2007-10-25 01:54:33 as * along with 2 people and 2 groups cisevol pradiptaray cis-regulatory-evolution BergmanLab
  • From gradients to stripes in Drosophila embryogenesis: filling in the gaps
    Trends in Genetics, Vol. 12, No. 11. (November 1996), pp. 478-483.
    by Rolando Rivera-Pomar, Herbert Jackle
    posted to cis_regulatory_elements drosophila embryonic_patterning expression_pattern modeling by dpollard to the group EisenLab on 2007-11-05 21:21:07 as **
  • Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e90.
    by Timothy E Reddy, Charles Delisi, Boris E Shakhnovich
    posted to prediction method cis_regulatory_elements by dpollard to the group EisenLab on 2007-05-31 23:16:30 as ** along with 2 people adepace ajgentles
  • Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals.
    Nat Genet, Vol. 10, No. 2. (June 1995), pp. 224-228.
    by C Tournamille, Y Colin, JP Cartron, C Le Van Kim
    posted to binding_site cis_regulatory_elements regulatory_evolution regulatory_polymorphism regulatory_sequence_evolution turnover by dpollard to the group EisenLab on 2007-12-05 22:51:02 as *** along with 1 group cis-regulatory-evolution
  • A phylogenetic Gibbs sampler that yields centroid solutions for cis regulatory site prediction.
    Bioinformatics (8 May 2007)
    by Lee A A Newberg, William A A Thompson, Sean Conlan, Thomas M M Smith, Lee Ann A McCue, Charles E E Lawrence
    posted to prediction motif method discovery clustering cis_regulatory_elements by dpollard to the group EisenLab on 2007-05-23 00:29:25 as ** along with 3 people cjeans sconlan siebert
  • Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus.
    Evol Dev, Vol. 6, No. 5. (t 2004), pp. 325-335.
    by J Costas, PS Pereira, CP Vieira, S Pinho, J Vieira, F Casares
    posted to cis_regulatory_elements drosophila expression_divergence expression_pattern turnover by dpollard to the group EisenLab on 2007-11-21 01:23:45 as read along with 1 group cis-regulatory-evolution
  • Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus.
    Am J Hum Genet, Vol. 66, No. 5. (May 2000), pp. 1669-1679.
    by MT Hamblin, A Di Rienzo
    posted to binding_site cis_regulatory_elements regulatory_evolution regulatory_polymorphism regulatory_sequence_evolution turnover by dpollard to the group EisenLab on 2007-12-05 22:53:19 as *** along with 1 group cis-regulatory-evolution
  • Computational methods for transcriptional regulation.
    Curr Opin Genet Dev, Vol. 15, No. 2. (April 2005), pp. 214-221.
    by ED Siggia
    posted to cis_regulatory_elements gene_expression method prediction by dpollard to the group EisenLab on 2007-03-15 00:30:41 as *** along with 7 people and 1 group barry koller bertelsen Borelli nklee balicea jjray Bioinformatics
  • Dominant gain-of-function mutations that lead to misregulation of the C. elegans heterochronic gene lin-14, and the evolutionary implications of dominant mutations in pattern-formation genes.
    Dev Suppl, Vol. 1 (1991), pp. 47-54.
    by G Ruvkun, B Wightman, T Bürglin, P Arasu
    posted to cis_regulatory_elements co_dominance dominance nematode semi_dominance seminal_paper by dpollard to the group EisenLab on 2007-11-26 00:38:21 as *** along with 1 person and 1 group tharris C. elegans / WormBase
  • Characterization of the Duffy gene promoter: evidence for tissue-specific abolishment of expression in Fy(a-b-) of black individuals.
    Biochem Biophys Res Commun, Vol. 222, No. 3. (24 May 1996), pp. 852-859.
    by S Iwamoto, J Li, N Sugimoto, H Okuda, E Kajii
    posted to cis_regulatory_elements expression_divergence expression_pattern expression_polymorphism human modularity regulatory_evolution regulatory_sequence_evolution by dpollard to the group EisenLab on 2007-12-05 23:03:10 as *** along with 1 group cis-regulatory-evolution
  • The stars and stripes of animal bodies: evolution of regulatory elements mediating pigment and bristle patterns in Drosophila.
    Trends Genet (10 May 2007)
    by Pat Simpson
    posted to review morphological_evolution drosophila cis_regulatory_elements by dpollard to the group EisenLab on 2007-06-13 22:25:39 as **
  • Quantitative models of developmental pattern formation.
    Dev Cell, Vol. 11, No. 3. (September 2006), pp. 289-300.
    by GT Reeves, CB Muratov, T Schüpbach, SY Shvartsman
    posted to cis_regulatory_elements development expression_pattern modeling review by brant to the group EisenLab on 2006-09-14 07:47:08 as *** along with 1 person dpollard
  • Cis-Regulatory Elements in the Accord Retrotransposon Result in Tissue-Specific Expression of the Drosophila melanogaster Insecticide Resistance Gene Cyp6g1
    Genetics, Vol. 175, No. 3. (1 March 2007), pp. 1071-1077.
    by Henry Chung, Michael R Bogwitz, Caroline Mccart, Alex Andrianopoulos, Richard H Ffrench-Constant, Philip Batterham, Phillip J Daborn
    posted to transposable_elements tissue_specific expression drosophila cis_regulatory_elements by dpollard to the group EisenLab on 2007-03-26 07:55:30 as ** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Programming gene expression with combinatorial promoters
    Mol Syst Biol, Vol. 3 (13 November 2007)
    by Robert S Cox, Michael G Surette, Michael B Elowitz
    posted to cis_regulatory_elements eisen_journal_club grammar rich_presented round_robin by dpollard to the group EisenLab on 2007-11-16 23:56:56 as ** along with 14 people and 1 group Retchless tmmurali austin balicea kengg dbikard margaritis lusk cjeans zwang discreteonyxorb cabbagezs Ema tresch SynBioSys
  • Reverse Engineering the Gap Gene Network of Drosophila melanogaster
    PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e51.
    by Theodore J Perkins, Johannes Jaeger, John Reinitz, Leon Glass
    posted to cis_regulatory_elements drosophila embryonic_patterning expression_pattern modeling network by brant to the group EisenLab on 2006-09-27 20:03:50 as *** along with 2 people emilyhare adepace
  • Modeling DNA-binding of Escherichia coli sigma70 exhibits a characteristic energy landscape around strong promoters
    Nucl. Acids Res. (16 October 2007), gkm720.
    by Johanna Weindl, Pavol Hanus, Zaher Dawy, Juergen Zech, Joachim Hagenauer, Jakob C Mueller
    posted to bacteria cis_regulatory_elements energy_landscape promoter by dpollard to the group EisenLab on 2007-10-25 01:24:56 as ** along with 2 people operon maximilianh
  • Histone replacement marks the boundaries of cis-regulatory domains.
    Science, Vol. 315, No. 5817. (9 March 2007), pp. 1408-1411.
    by Y Mito, JG Henikoff, S Henikoff
    posted to round_robin rich_presented nucleosome in_depth_suggestion eisen_journal_club dynamics cis_regulatory_elements by dpollard to the group EisenLab on 2007-03-16 20:42:42 as *** along with 3 people olympos epigenetics bpcusack
  • Making connections: boundaries and insulators in Drosophila.
    Curr Opin Genet Dev (26 September 2007)
    by Robert K K Maeda, François Karch
    posted to chromatin chromatin_modification cis_regulatory_elements drosophila insulators by dpollard to the group EisenLab on 2007-10-25 02:15:41 as ** along with 1 person dchughes
  • An equilibrium partitioning model connecting gene expression and cis-motif content
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e368-374.
    by Joe Mellor, Charles Delisi
    posted to cis_regulatory_elements expression_pattern modeling by dpollard to the group EisenLab on 2007-11-05 22:10:49 as ** along with 1 person yevishere
  • A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms
    PLoS Computational Biology, Vol. 3, No. 6. (1 June 2007), e106.
    by Stephen B Montgomery, Obi L Griffith, Johanna M Schuetz, Angela Brooks-Wilson, Steven J Jones
    posted to venky_presented snp sequence_properties round_robin regulatory_polymorphism prediction eisen_journal_club cis_regulatory_elements by dpollard to the group EisenLab on 2007-06-15 22:54:33 as *** along with 1 person and 2 groups cisevol Bioinformatics cis-regulatory-evolution
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
    posted to chip_chip cis_regulatory_elements yeast by dpollard to the group EisenLab on 2007-12-04 00:29:15 as read along with 24 people and 7 groups alokm tuck chad_davis lyongu kaspermunch balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee cisevol njcitulike xili03 brant mariakmejia kristallreiner snow_dragon aalibes Bioinformatics FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216.
    by Saurabh Sinha, Xin He
    posted to alignment alignment_accuracy binding_site_alignment brant_presented cis_regulatory_elements eisen_journal_club method round_robin by dpollard to the group EisenLab on 2007-11-16 23:53:34 as **** along with 7 people and 1 group ana cjeans zwang maximilianh hpaces Ema uwe cis-regulatory-evolution
  • Reliable prediction of regulator targets using 12 Drosophila genomes.
    Genome Res (7 November 2007)
    by Alexander Stark, Pouya Kheradpour, Sushmita Roy, Manolis Kellis
    posted to cis_regulatory_elements drosophila eisen_journal_club matt_presented prediction round_robin by dpollard to the group EisenLab on 2007-11-17 00:01:35 as *** along with 7 people and 1 group lp2 nklee maximilianh roys caseybrown emptyhb barwil cis-regulatory-evolution
  • Interaction of Gal repressor with inducer and operator: induction of gal transcription from repressor-bound DNA.
    Proc Natl Acad Sci U S A, Vol. 94, No. 7. (1 April 1997), pp. 2957-2962.
    by S Chatterjee, YN Zhou, S Roy, S Adhya
    posted to binding_site cis_regulatory_elements grammar steric_repression yeast by dpollard to the group EisenLab on 2007-10-31 21:26:00 as **
  • Colloquium Papers: Emerging principles of regulatory evolution.
    Proc Natl Acad Sci U S A, Vol. 104 Suppl 1 (15 May 2007), pp. 8605-8612.
    by B Prud'homme, N Gompel, SB Carroll
    posted to review regulatory_evolution evolution cis_regulatory_elements by dpollard to the group EisenLab on 2007-06-14 23:47:29 as *** along with 3 people and 1 group blobbybirdman cisevol emptyhb cis-regulatory-evolution
  • Turnover of binding sites for transcription factors involved in early Drosophila development.
    Gene, Vol. 310 (22 May 2003), pp. 215-220.
    by J Costas, F Casares, J Vieira
    posted to binding_site cis_regulatory_elements drosophila turnover by dpollard to the group EisenLab on 2007-11-21 01:22:24 as read along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Computational annotation of transcription factor binding sites in D. Melanogaster developmental genes.
    Genome Inform, Vol. 17, No. 2. (2006), pp. 14-24.
    by V Narang, WK Sung, A Mittal
    posted to prediction drosophila crm cis_regulatory_elements binding_site by dpollard to the group EisenLab on 2007-06-13 22:20:42 as ***
  • The identification and functional characterisation of conserved regulatory elements in developmental genes.
    Brief Funct Genomic Proteomic, Vol. 3, No. 4. (February 2005), pp. 332-350.
    by T Dickmeis, F Müller
    posted to cis_regulatory_elements conserved development prediction regulatory_sequence transcription_factor by dpollard to the group EisenLab on 2007-03-15 00:27:26 as *** along with 1 person brant
  • Ultraconservation identifies a small subset of extremely constrained developmental enhancers.
    Nat Genet (6 January 2008)
    by Axel Visel, Shyam Prabhakar, Jennifer A A Akiyama, Malak Shoukry, Keith D D Lewis, Amy Holt, Ingrid Plajzer-Frick, Veena Afzal, Edward M M Rubin, Len A A Pennacchio
    posted to cis_regulatory_elements by emptyhb on 2008-02-26 03:36:27 as ** along with 5 people Stew maximilianh gjuggler bpcusack isimpson
  • Mechanism and Bicoid-dependent control of hairy stripe 7 expression in the posterior region of the Drosophila embryo.
    EMBO J, Vol. 16, No. 14. (16 July 1997), pp. 4403-4411.
    by A La Rosée, T Häder, H Taubert, R Rivera-Pomar, H Jäckle
    posted to cis_regulatory_elements drosophila function_study by emptyhb on 2007-12-20 21:33:19 as **
  • notes Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover
    Mol Biol Evol, Vol. 19, No. 7. (1 July 2002), pp. 1114-1121.
    by Emmanouil T Dermitzakis, Andrew G Clark
    posted to binding_sites_turnover cis_regulatory_elements by emptyhb on 2007-12-09 16:53:51 as ***** along with 3 people and 2 groups adepace cisevol xili03 EisenLab cis-regulatory-evolution
  • BioSAVE: Display of scored annotation within a sequence context
    BMC Bioinformatics, Vol. 9 (20 March 2008), 157.
    by Richard F Pollock, Boris Adryan
    posted to software motif_searching cis_regulatory_elements by emptyhb on 2008-09-01 17:56:15 as ** along with 2 people jyuh dquest
  • Complex Regulation of cyp26a1 Creates a Robust Retinoic Acid Gradient in the Zebrafish Embryo
    PLoS Biology, Vol. 5, No. 11. (1 November 2007), e304.
    by Richard J White, Qing Nie, Arthur D Lander, Thomas F Schilling
    posted to cis_regulatory_elements function_study by emptyhb on 2007-12-08 06:24:06 as **
  • Levers and fulcrums: progress in cis-regulatory motif models
    Nature Methods, Vol. 5, No. 4., pp. 297-298.
    by Ewan Birney
    posted to cis_regulatory_elements modeling_gene_network by emptyhb on 2008-05-16 00:34:33 as ** along with 3 people and 3 groups stajich pradiptaray isimpson EisenLab Berkeley Mycology Jarman Lab
  • Extensive low-affinity transcriptional interactions in the yeast genome.
    Genome Res (29 June 2006)
    by Amos Tanay
    posted to cis_regulatory_elements motif_searching statistical_method by emptyhb on 2008-01-21 23:32:43 as ** along with 6 people and 1 group devin indigoviolet dpollard balicea koller lusk EisenLab
  • Rapid restructuring of bicoid-dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution
    Evolution & Development, Vol. 3, No. 6. (2001), pp. 397-407.
    by Alistair P Mcgregor, Philip J Shaw, John M Hancock, Daniel Bopp, Monika Hediger, Naomi S Wratten, Gabriel A Dover
    posted to binding_sites_turnover cis_regulatory_elements drosophila by emptyhb on 2007-12-31 03:36:29 as **
  • A two-step mode of stripe formation in the Drosophila blastoderm requires interactions among primary pair rule genes
    Mechanisms of Development, Vol. 45, No. 1. (January 1994), pp. 3-13.
    by Christine Hartmann, Heike Taubert, Herbert Jackle, Michael J Pankratz
    posted to cis_regulatory_elements drosophila function_study by emptyhb on 2007-12-20 18:04:18 as **
  • The Drosophila even-skipped promoter is transcribed in a stage-specific manner in vitro and contains multiple, overlapping factor-binding sites.
    Mol. Cell. Biol., Vol. 10, No. 8. (1 August 1990), pp. 4334-4344.
    by D Read, T Nishigaki, JL Manley
    posted to cis_regulatory_elements drosophila even-skipped_enhancer by emptyhb on 2008-02-28 17:24:23 as **
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