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Group: EisenLab - with tag binding_site [26 articles]

Недавние статьи, отправленные по почте членами EisenLab группы with tag binding_site
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 **
  • 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 to the group EisenLab on 2007-10-29 01:04:01 as **** along with 4 people and 1 group dpollard djkt Garamonfok maximilianh cis-regulatory-evolution
  • 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
  • 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
  • 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 ***
  • 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
  • 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 7 people and 1 group emptyhb brant sebastien_vigneau zwang maximilianh cisevol xili03 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 **
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
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