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Tag binding_site [47 articles]

Recent papers classified by the tag binding_site.
  • Anatomy of Escherichia coli 70 promoters
    Nucleic Acids Research, Vol. 35, No. 3. (February 2007), pp. 771-788.
    by Ryan K Shultzaberger, Zehua Chen, Karen A Lewis, Thomas D Schneider
    posted to bacteria binding_site bioinformatics promotor by stajich on 2007-11-27 01:29:39 as **
  • Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation
    PLoS Genet, Vol. 4, No. 6. (27 June 2008), e1000106.
    by Emily E Hare, Brant K Peterson, Venky N Iyer, Rudolf Meier, Michael B Eisen
    posted to transcription_factor promotor evolution evodevo even-skipped drosophila binding_site by stajich on 2008-06-28 18:16:38 as ** along with 5 people and 2 groups emptyhb pradiptaray cisevol caseybrown djkt cis-regulatory-evolution Berkeley Mycology
  • Phylogenetic Simulation of Promoter Evolution: Estimation and Modeling of Binding Site Turnover Events and Assessing Their Impact on Alignment Tools
    Genome Biology, Vol. 8 (24 October 2007), R225.
    by Weichun Huang, Joseph R Nevins, Uwe Ohler
    posted to binding_site promotor turnover by stajich on 2007-10-29 01:04:01 as **** along with 4 people and 2 groups dpollard djkt Garamonfok maximilianh EisenLab cis-regulatory-evolution
  • Automated prediction of ligand-binding sites in proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Rodney Harris, Arthur J Olson, David S Goodsell
    posted to binding_site ligand qualifier by RamuAnandakrishnan on 2007-10-25 01:05:21 as ** along with 2 people tjimenez carlescorbi
  • Characterization of local geometry of protein surfaces with the visibility criterion
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani, Daisuke Kihara
    posted to binding_site qualifier by RamuAnandakrishnan on 2007-11-03 20:36:13 as **
  • Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: Implications for the channel potentiation mechanism
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Mary H Cheng, Rob D Coalson, Michael Cascio
    posted to binding_site ligand md by RamuAnandakrishnan on 2007-11-15 19:08:17 as **
  • Computational prediction of the binding site of proteinase 3 to the plasma membrane
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Eric Hajjar, Maja Mihajlovic, Véronique Witko-Sarsat, Themis Lazaridis, Nathalie Reuter
    posted to binding_site electrostatics implicit_solvent ligand md by RamuAnandakrishnan on 2008-01-07 14:43:43 as **
  • Natural selection on human microRNA binding sites inferred from SNP data.
    Nat Genet (29 October 2006)
    by Kevin Chen, Nikolaus Rajewsky
    posted to binding_site mirna natural_selection by plofje on 2006-11-04 06:17:07 as ** along with 8 people and 3 groups bpcusack jfr tardigrade andersbj mtagaya ealloza Garamonfok heliopais Bioinformatics microRNA BioinfoCIPF
  • 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 brant troels_marstrand kaspermunch adepace lusk Stew Bioinformatics
  • Conserved sequences and the evolution of gene regulatory signals.
    Curr Opin Genet Dev, Vol. 15, No. 6. (December 2005), pp. 628-633.
    by MD Adams
    posted to binding_site evolution regulatory_sequence transcription_factor turnover variation by dpollard to the group EisenLab on 2007-03-15 00:22:24 as *** along with 2 people cconboy lusk
  • Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
    Nucleic Acids Res (30 January 2007)
    by Trevor W W Siggers, Barry Honig
    posted to affinity binding_site dan_presented eisen_journal_club prediction round_robin structure transcription_factor by dpollard to the group EisenLab on 2007-02-09 01:34:13 as read along with 1 person aalibes
  • Frequent Gain and Loss of Functional Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e99.
    by Scott W Doniger, Justin C Fay
    posted to yeast turnover round_robin rich_presented eisen_journal_club dynamics binding_site by dpollard to the group EisenLab on 2007-06-04 22:33:14 as *** along with 6 people and 1 group brant sebastien_vigneau zwang maximilianh cisevol xili03 cis-regulatory-evolution
  • Dorsal gradient networks in the Drosophila embryo.
    Dev Biol, Vol. 246, No. 1. (1 June 2002), pp. 57-67.
    by A Stathopoulos, M Levine
    posted to gradient binding_site affinity by dpollard to the group EisenLab on 2007-02-05 20:05:59 as ** along with 1 person dquest
  • Incorporating evolution of transcription factor binding sites into annotated alignments.
    J Biosci, Vol. 32, No. 5. (August 2007), pp. 841-850.
    by AS Bais, S Grossmann, M Vingron
    posted to alignment binding_site conserved method prediction by dpollard to the group EisenLab on 2007-10-25 02:20:56 as ** along with 1 person and 1 group maximilianh 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
  • 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 **
  • Using DNA duplex stability information for transcription factor binding site discovery.
    Pac Symp Biocomput (2008), pp. 453-464.
    by R Gordân, AJ Hartemink
    posted to binding_site biophysical_model method motif_detection prediction transcription_factor by dpollard to the group EisenLab on 2008-02-01 06:21:42 as ** along with 1 person bootsy
  • A stochastic model for the evolution of transcription factor binding site abundance.
    J Theor Biol (7 March 2007)
    by Günter P P Wagner, Wolfgang Otto, Vincent Lynch, Peter F F Stadler
    posted to turnover model binding_site by dpollard to the group EisenLab on 2007-05-23 01:02:56 as ***** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • A SNP in a half-binding site creates p53 and estrogen receptor control of VEGFR-1.
    Mol Cell Biol (22 January 2007)
    by Daniel Menendez, Alberto Inga, Joyce Snipe, Oliver Krysiak, Gilbert Schönfelder, Michael A A Resnick
    posted to transcription polymorphism binding_site by dpollard to the group EisenLab on 2007-02-01 19:55:01 as ** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast.
    Pac Symp Biocomput (2008), pp. 489-500.
    by RW Lusk, MB Eisen
    posted to affinity binding_site transcription_factor variation yeast by dpollard to the group EisenLab on 2008-02-01 06:19:09 as read along with 1 person and 1 group maximilianh cis-regulatory-evolution
  • 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
  • PhyloScan: Identification of transcription factor binding sites using cross-species evidence
    Algorithms for Molecular Biology, Vol. 2 (23 January 2007), 1.
    by Steven C Carmack, Lee A Mccue, Lee A Newberg, Charles E Lawrence
    posted to prediction phylogeny comparative binding_site by dpollard to the group EisenLab on 2007-02-01 19:41:57 as ** along with 3 people dquest lusk nklee
  • 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
  • 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 yeast venky_presented round_robin motif method eisen_journal_club binding_site ab_initio by dpollard to the group EisenLab on 2007-06-14 23:38:43 as ** along with 5 people aalibes medic0747 GustavoLacerda mircea marti
  • 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
  • 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
  • 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 **
  • Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting
    Genome Res., Vol. 12, No. 5. (1 May 2002), pp. 739-748.
    by Mathieu Blanchette, Martin Tompa
    posted to ab_initio binding_site conservation method prediction by dpollard to the group EisenLab on 2007-11-01 00:41:11 as read along with 5 people and 1 group chad_davis balajis lyongu dquest csdhwang 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 ***
  • Regulatory element detection using correlation with expression.
    Nat Genet, Vol. 27, No. 2. (February 2001), pp. 167-171.
    by HJ Bussemaker, H Li, ED Siggia
    posted to ab_initio binding_site gene_expression prediction by dpollard to the group EisenLab on 2007-11-01 00:10:36 as read along with 4 people and 1 group isimpson tvdbulck nickluscombe heliopais EBI-regulation
  • Mining of putative cis-acting elements for chromatin mediated regulation of Hox genes in mammals by in-silico analysis.
    J Exp Zoolog B Mol Dev Evol (14 March 2007)
    by Hemant Bengani, Mythily Ganapathi, Gajinder Pal P Singh, Vani Brahmachari
    posted to vertibrates hox drosophila conserved binding_site by dpollard to the group EisenLab on 2007-03-22 23:14:58 as * along with 1 person blobbybirdman
  • 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
  • Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification.
    J Comput Biol, Vol. 11, No. 1. (2004), pp. 1-14.
    by H Huang, MC Kao, X Zhou, JS Liu, WH Wong
    posted to stuart_presented round_robin motif method markov eisen_journal_club binding_site ab_initio by dpollard to the group EisenLab on 2007-06-04 22:47:45 as * along with 1 person jguinney
  • Binding site for Robo receptors revealed by dissection of the leucine-rich repeat region of Slit.
    EMBO J, Vol. 23, No. 22. (10 November 2004), pp. 4406-4412.
    by JA Howitt, NJ Clout, E Hohenester
    posted to binding binding_site robo slit by Evangelia on 2007-10-24 09:22:22 as read
  • Binding specificity and in vivo targets of the EH domain, a novel protein-protein interaction module
    Genes Dev., Vol. 11, No. 17. (1 September 1997), pp. 2239-2249.
    by Anna E Salcini, Stefano Confalonieri, Margherita Doria, Elisa Santolini, Elena Tassi, Olga Minenkova, Gianni Cesareni, Pier G Pelicci, Pier P Di Fiore
    posted to binding binding_site domains eh motifs peptides protein protein-protein specificity by Evangelia on 2007-10-01 17:55:50 as read
  • Automatic generation of 3D motifs for classification of protein binding sites
    BMC Bioinformatics, Vol. 8 (30 August 2007), 321.
    by Jean-Christophe Nebel, Pawel Herzyk, David R Gilbert
    posted to computational motifs patterns prediction structure algorithm binding binding_site by Evangelia on 2007-10-01 18:45:14 as read along with 3 people shadowman carlescorbi Minty
  • Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces.
    J Mol Biol, Vol. 351, No. 2. (12 August 2005), pp. 309-326.
    by A Ben-Shimon, M Eisenstein
    posted to binding binding_site enzyme interaction prediction structure by Evangelia on 2007-10-01 16:44:24 as * along with 3 people and 1 group baaden Einat nickolay structural_bioinformatics
  • Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans.
    PLoS Biol, Vol. 3, No. 12. (15 November 2005)
    by Matthew V V Rockman, Matthew W W Hahn, Nicole Soranzo, Fritz Zimprich, David B B Goldstein, Gregory A A Wray
    posted to binding_site cis_regulatory_elements human regulatory_evolution regulatory_polymorphism regulatory_sequence_evolution turnover by dpollard on 2007-12-05 22:55:41 as read along with 8 people and 3 groups jphekman imouthesmp indigoviolet Archaeogenetics happy_manatee djkt mgaldzic cisevol EisenLab CHIP cis-regulatory-evolution
  • Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster
    PLoS Computational Biology, Vol. 3, No. 1. (1 January 2007), e7.
    by Thomas A Down, Casey M Bergman, Jing Su, Tim J Hubbard
    posted to binding_site cis_regulatory_elements drosophila motif_detection by dpollard on 2007-11-14 21:19:05 as read along with 6 people and 1 group isimpson indigoviolet dquest SeungjoonOh nklee emptyhb EisenLab
  • 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 binding_site cis_regulatory_elements drosophila pigmentation regulatory_evolution regulatory_sequence_evolution turnover by dpollard on 2007-12-05 22:48:37 as read along with 5 people and 2 groups pradiptaray emilyhare adepace cisevol emptyhb EisenLab cis-regulatory-evolution
  • Systematic detection of statistically overrepresented DNA motif association rules.
    Genome Inform, Vol. 17, No. 1. (2006), pp. 124-133.
    by JM Lin, Z Weng
    posted to ab_initio binding_site eisen_journal_club method motif_detection prediction round_robin rules venky_presented by dpollard on 2007-06-15 00:04:13 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution
    Cell, Vol. 125, No. 7. (30 June 2006), pp. 1387-1399.
    by Sangyun Jeong, Antonis Rokas, Sean B Carroll
    posted to binding_site cis_regulatory_elements pigmentation regulatory_evolution regulatory_sequence_evolution turnover by dpollard on 2007-12-05 22:44:47 as read along with 1 person and 2 groups emilyhare EisenLab cis-regulatory-evolution
  • Simultaneous alignment and annotation of cis-regulatory regions.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by AS Bais, S Grossmann, M Vingron
    posted to prediction binding_site alignment by dpollard on 2007-02-01 19:45:23 as ** along with 2 people and 1 group indigoviolet bluto EisenLab
  • Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by G Pavesi, P Mereghetti, G Mauri, G Pesole
    posted to binding_site prediction by dandaman on 2008-02-11 15:40:16 as ** along with 2 people dquest xiaobeizhao
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart D De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James J Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques v van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to binding_site prediction by dandaman on 2008-02-11 15:39:26 as ** along with 23 people and 6 groups nuin ep161302 icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon vietanh0 structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Predicting DNA-binding sites of proteins from amino acid sequence.
    BMC Bioinformatics, Vol. 7 (2006)
    by C Yan, M Terribilini, F Wu, RL Jernigan, D Dobbs, V Honavar
    posted to binding_site transcription_factor by dandaman on 2008-01-08 11:55:33 as ** along with 3 people kaarsinogen ameetsoni ezralanglois
  • A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
    Science, Vol. 315, No. 5809. (12 January 2007), pp. 233-237.
    by Sebastian J Maerkl, Stephen R Quake
    posted to in_vitro binding_site by brant on 2008-04-24 09:32:08 as ** along with 8 people and 2 groups jjray dpollard emilyhare adepace aswin skoch3 blobbybirdman emptyhb EisenLab Koch_Lab
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