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Tag noalignment [15 articles]

Recent papers classified by the tag noalignment.
  • Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
    Genome Res. (10 December 2007), gr.6929408.
    by David M Mcgaughey, Ryan M Vinton, Jimmy Huynh, Amr Al-Saif, Michael A Beer, Andrew S Mccallion
    posted to application cns discovery enhancer noalignment notconserved rennes by maximilianh on 2007-12-13 09:33:28 as ** along with 2 people brant djkt
  • BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences.
    Bioinformatics (27 July 2007)
    by Hailong Meng, Arunava Banerjee, Lei Zhou
    posted to noalignment by maximilianh on 2007-11-27 12:35:05 as ** along with 2 people and 1 group grahamc GustavoLacerda ParkinsonLab_at_MaRS
  • Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i165-171.
    by Lucas D Ward, Harmen J Bussemaker
    posted to noalignment by maximilianh on 2008-06-27 15:59:14 as ** along with 1 person xili03
  • Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2738-2750.
    by YH Grad, FP Roth, MS Halfon, GM Church
    posted to noalignment by maximilianh on 2007-10-23 17:39:34 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation.
    Methods Mol Biol, Vol. 395 (2007), pp. 349-366.
    by O Elemento, S Tavazoie
    posted to noalignment by maximilianh on 2007-11-29 14:58:38 as **
  • MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs
    Nucl. Acids Res. (7 July 2008), gkn407.
    by Jianfei Hu, Haiyan Hu, Xiaoman Li
    posted to scanning noalignment motif combination cns-similarity by maximilianh on 2008-07-07 17:15:10 as **
  • Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.
    Proc Natl Acad Sci U S A (29 March 2007)
    by Alona Sosinsky, Barry Honig, Richard S S Mann, Andrea Califano
    posted to noalignment by maximilianh on 2007-10-23 17:39:16 as ** along with 4 people and 2 groups isimpson dpollard Stew cisevol EisenLab cis-regulatory-evolution
  • Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity
    Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59.
    by Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen, Jussi Taipale
    posted to enhancerprediction noalignment by maximilianh on 2008-01-14 16:04:36 as ** along with 13 people and 5 groups emptyhb Terkko kaarsinogen tuck brant xwbcn dchughes nickluscombe olympos cabbagezs karfunkel heliopais oelemento Bioinformatics EisenLab G4ID EBI-regulation Genetics-of-Gambling
  • A statistical method for alignment-free comparison of regulatory sequences
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i249-255.
    by Miriam R Kantorovitz, Gene E Robinson, Saurabh Sinha
    posted to cns-differences cns-similarity noalignment by maximilianh on 2007-09-25 15:13:07 as ** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Studying the functional conservation of cis-regulatory modules and their transcriptional output
    BMC Bioinformatics, Vol. 9 (29 April 2008), 220.
    by Denis C Bauer, Timothy L Bailey
    posted to notconserved noalignment enhancerprediction by maximilianh on 2008-05-01 09:16:32 as ** along with 2 people and 1 group xili03 cisevol cis-regulatory-evolution
  • Prediction of synergistic transcription factors by function conservation
    Genome Biology, Vol. 8, No. 12. (2007)
    by Zihua Hu, Boyu Hu, James Collins
    posted to cluster factors noalignment tfsynergy transcription by maximilianh on 2007-12-08 15:12:16 as ** along with 3 people and 1 group cjeans nklee ale cis-regulatory-evolution
  • Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e7.
    by Daniela Raijman, Ron Shamir, Amos Tanay
    posted to conserved cross-species-enhancer evoluation noalignment by maximilianh on 2008-01-17 08:14:34 as ** along with 7 people and 1 group aalibes chad_davis sebastien_vigneau lusk Garamonfok nklee emptyhb BioinfoCIPF
  • Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements.
    Bioinformatics (18 March 2008)
    by R Satija, L Pachter, J Hein
    posted to noalignment footprinting alignment by maximilianh on 2008-05-07 15:29:24 as ** along with 4 people Stew Ema gjuggler eckart_bindewald
  • Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.
    Molecular biology and evolution, Vol. 23, No. 6. (June 2006), pp. 1293-1303.
    by S De Bodt, G Theissen, Y Van de Peer
    posted to promoter noalignment composition comparison by maximilianh on 2008-04-30 15:54:45 as **
  • Transcriptional Regulation of Pituitary POMC Is Conserved at the Vertebrate Extremes Despite Great Promoter Sequence Divergence
    Mol Endocrinol, Vol. 21, No. 11. (1 November 2007), pp. 2738-2749.
    by Viviana F Bumaschny, Flavio S de Souza, Lopez, Andrea M Santangelo, Manfred Baetscher, Diego H Levi, Malcolm J Low, Marcelo Rubinstein
    posted to cross-species-enhancer enhancer noalignment pituitary by maximilianh on 2007-10-27 12:07:13 as * along with 1 person and 1 group cisevol cis-regulatory-evolution
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