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nuin motifs [48 articles]

最近 nuin さんのライブラリに追加された論文の中から タグ motifs. You can also see everyone's motifs.
  • Efficient representation and P-value computation for high-order Markov motifs.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by PG da Fonseca, KS Guimarães, MF Sagot
    posted to motifs markov by nuin on 2008-08-12 18:10:09 as **
  • Identification of transcription factor binding sites with variable-order Bayesian networks
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2657-2666.
    by I Ben-Gal, A Shani, A Gohr, J Grau, S Arviv, A Shmilovici, S Posch, I Grosse
    posted to motifs identification bayes by nuin on 2008-06-26 18:22:34 as ** along with 1 person lyongu
  • AthaMap: from in silico data to real transcription factor binding sites.
    In silico biology, Vol. 6, No. 3. (2006), pp. 243-252.
    by L Bülow, NO Steffens, C Galuschka, M Schindler, R Hehl
    posted to software motifs identification by nuin on 2008-06-26 18:21:36 as **
  • STOP: searching for Transcription Factor motifs using gene expression.
    Bioinformatics (8 May 2007)
    by Libi Hertzberg, Shai Izraeli, Eytan Domany
    posted to software motifs by nuin on 2008-06-26 18:20:54 as ** along with 1 person and 1 group dpollard EisenLab
  • WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences
    BMC Bioinformatics, Vol. 8 (07 February 2007), 46.
    by Giulio Pavesi, Federico Zambelli, Graziano Pesole
    posted to software motifs by nuin on 2008-06-26 18:19:56 as ** along with 2 people dquest GustavoLacerda
  • dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2619-2621.
    by Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, Sun Kim
    posted to motifs identification by nuin on 2008-06-26 18:19:25 as ** along with 3 people isimpson maximilianh idonaldson
  • Long-range upstream and downstream enhancers control distinct subsets of the complex spatiotemporal Sox9 expression pattern
    Developmental Biology, Vol. 291, No. 2. (15 March 2006), pp. 382-397.
    by Stefan Bagheri-Fam, Francisco Barrionuevo, Ulrike Dohrmann, Thomas Günther, Roland Schüle, Rolf Kemler, Moisés Mallo, Benoit Kanzler, Gerd Scherer
    posted to motifs by nuin on 2008-06-26 18:17:57 as **
  • Condition-specific coregulation with cis-regulatory motifs and modules in the mouse genome.
    Genomics, Vol. 87, No. 4. (April 2006), pp. 500-508.
    by D Choi, Y Fang, WD Mathers
    posted to mouse motifs by nuin on 2008-06-26 18:16:46 as **
  • Integrating regulatory motif discovery and genome-wide expression analysis
    Proceedings of the National Academy of Sciences, Vol. 100, No. 6. (18 March 2003), pp. 3339-3344.
    by Erin M Conlon, Shirley X Liu, Jason D Lieb, Jun S Liu
    posted to motifs identification by nuin on 2008-06-26 18:15:38 as ** along with 2 people maximilianh danish_punter
  • Method for identifying transcription factor binding sites in yeast
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. 1675-1681.
    by Huai-Kuang Tsai, Grace T Huang, Meng-Yuan Chou, Henry H Lu, Wen-Hsiung Li
    posted to motifs methods identification by nuin on 2008-06-26 18:14:44 as ** along with 1 person dquest
  • Finding motifs from all sequences with and without binding sites*
    Bioinformatics (26 July 2006)
    by Henry C M C Leung, Francis Y L Y Chin
    posted to motifs identification by nuin on 2008-06-26 18:13:32 as ** along with 2 people eckart_bindewald dquest
  • Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
    PLoS Computational Biology, Vol. 2, No. 10. (1 October 2006), e130.
    by Alan M Moses, Daniel A Pollard, David A Nix, Venky N Iyer, Xiao-Yong Li, Mark D Biggin, Michael B Eisen
    posted to motifs identification by nuin on 2008-06-26 18:10:10 as ** along with 1 person and 1 group nickluscombe EBI-regulation
  • Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes
    BMC Genomics, Vol. 7 (01 June 2006), 133.
    by Paz Polak, Eytan Domany
    posted to motifs alu by nuin on 2008-06-26 18:08:35 as ** along with 1 person dquest
  • Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes.
    Nucleic acids research, Vol. 32, No. 9. (2004), pp. 2889-2900.
    by G Kreiman
    posted to motifs identification by nuin on 2008-06-26 18:07:38 as **
  • Analysis of promoter regions of co-expressed genes identified by microarray analysis
    BMC Bioinformatics, Vol. 7 (17 August 2006), 384.
    by Srinivas Veerla, Mattias Hoglund
    posted to motifs identification by nuin on 2008-06-26 15:39:05 as ** along with 5 people and 1 group heliopais jfr gpalidwor giovanni SeungjoonOh GeschwindLab
  • 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 software motifs comparison by nuin on 2008-06-26 15:36:36 as ** along with 23 people and 6 groups ep161302 icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs
    BMC Bioinformatics, Vol. 5, No. 1. (2004)
    by Davide Cora, Ferdinando Di Cunto, Paolo Provero, Lorenzo Silengo, Michele Caselle
    posted to motifs identification by nuin on 2008-06-26 15:35:05 as ** along with 1 person nklee
  • Ab initio identification of putative human transcription factor binding sites by comparative genomics.
    BMC bioinformatics, Vol. 6 (2005)
    by D Corà, C Herrmann, C Dieterich, F Di Cunto, P Provero, M Caselle
    posted to motifs identification by nuin on 2008-06-26 15:34:27 as **
  • Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions
    BMC Bioinformatics, Vol. 8 (24 May 2007), 174.
    by Davide Cora', Ferdinando Di Cunto, Michele Caselle, Paolo Provero
    posted to motifs identification by nuin on 2008-06-26 15:34:09 as ** along with 4 people and 2 groups bertelsen andersbj mtagaya GustavoLacerda Bioinformatics microRNA
  • Assessing Clusters and Motifs from Gene Expression Data
    Genome Res., Vol. 11, No. 1. (1 January 2001), pp. 112-123.
    by Lars M Jakt, Liang Cao, Kathryn S Cheah, David K Smith
    posted to motifs enhancing clusters by nuin on 2008-06-26 15:32:48 as **
  • Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
    Nucl. Acids Res., Vol. 35, No. 10. (11 May 2007), pp. 3203-3213.
    by Saran Vardhanabhuti, Junwen Wang, Sridhar Hannenhalli
    posted to position motifs evolution by nuin on 2008-06-26 15:31:17 as ** along with 3 people cjeans ankur_iitg csdhwang
  • A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1789-1796.
    by M Stepanova, T Tiazhelova, M Skoblov, A Baranova
    posted to motifs comparison by nuin on 2008-06-26 15:25:15 as ** along with 1 person troels_marstrand
  • notes Eukaryotic transcription factor binding sites - modeling and integrative search methods
    Bioinformatics, Vol. 24 (Jun 2008)
    posted to motifs by nuin on 2008-06-26 12:54:52 as **
  • notes Statistical significance of cis-regulatory modules
    BMC Bioinformatics, Vol. 8 (xx 2007)
    posted to motifs by nuin on 2008-06-26 12:54:46 as **
  • notes CisML: an XML-based format for sequence motif detection software
    Bioinformatics, Vol. 20 (Jul 2004)
    by Peter Haverty, Zhiping Weng
    posted to motifs by nuin on 2008-06-26 12:54:45 as **
  • notes One Billion Years of bZIP Transcription Factor Evolution: Conservation and Change in Dimerization and DNA-Binding Site Specificity
    Molecular Biology and Evolution, Vol. 24 (xx 2006)
    posted to motifs by nuin on 2008-06-26 12:54:42 as **
  • notes The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates
    Genome Biology, Vol. 6 (Dec 2005)
    by Laurence Ettwiller, Benedict Paten, Marcel Souren, Felix Loosli, Jochen Wittbrodt, Ewan Birney
    posted to motifs by nuin on 2008-06-26 12:54:39 as **
  • notes Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
    BMC Bioinformatics, Vol. 9 (Jun 2008)
    by Nak K Kim, Kannan Tharakaraman, Leonardo M Ramirez, John L Spouge
    posted to motifs by nuin on 2008-06-26 12:54:36 as **
  • CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing
    posted to motifs by nuin on 2008-06-26 12:54:33 as **
  • notes STOP: searching for transcription factor motifs using gene expression
    Bioinformatics, Vol. 23 (May 2007)
    by Libi Hertzberg, Shai Izraeli, Eytan Domany
    posted to motifs by nuin on 2008-06-26 12:54:24 as **
  • notes Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation
    Genome Research, Vol. 14 (Jan 2004), pp. 99-108.
    posted to motifs by nuin on 2008-06-26 12:54:20 as **
  • notes Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
    Genome Biol, Vol. 8 (Jun 2007)
    by Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc Halfon
    posted to motifs by nuin on 2008-06-26 12:54:20 as **
  • notes SwissRegulon: a database of genome-wide annotations of regulatory sites
    Nucleic Acids Research, Vol. 35 (xx 2007)
    posted to motifs by nuin on 2008-06-26 12:54:19 as **
  • notes ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
    Nucleic acids research., Vol. 34 (Jan 2006), pp. D63-7.
    by Enrique Blanco, Domènec Farré, Mar M Albà, Xavier Messeguer, Roderic Guigó
    posted to motifs by nuin on 2008-06-26 12:54:18 as **
  • notes Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
    Proceedings of the National Academy of Sciences, Vol. 102 (Nov 2005), pp. 17400-17405.
    by Ting Wang, Gary Stormo
    posted to motifs by nuin on 2008-06-26 12:54:18 as **
  • notes MotifCut: regulatory motifs finding with maximum density subgraphs
    Bioinformatics, Vol. 22 (Jul 2006)
    by Eugene Fratkin, Brian Naughton, Douglas Brutlag, Serafim Batzoglou
    posted to motifs by nuin on 2008-06-26 12:54:16 as **
  • Combining phylogenetic data with co-regulated genes to identify regulatory motifs -- Wang and Stormo 19 (18): 2369 -- Bioinformatics
    posted to motifs by nuin on 2008-06-26 12:54:08 as **
  • DNA binding sites: representation and discovery.
    Bioinformatics (Oxford, England), Vol. 16 (Jan 2000), pp. 16-23.
    by GD Stormo
    posted to motifs by nuin on 2008-06-26 12:54:08 as **
  • ANN-Spec: a method for discovering transcription factor binding sites with improved specificity.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (xx 2000), pp. 467-478.
    by CT Workman, GD Stormo
    posted to motifs by nuin on 2008-06-26 12:54:07 as **
  • notes Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals.
    Journal of molecular biology, Vol. 297 (Mar 2000), pp. 335-353.
    by A Vanet, L Marsan, A Labigne, MF Sagot
    posted to motifs by nuin on 2008-06-26 12:54:06 as **
  • notes Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.
    Journal of molecular biology, Vol. 281 (Sep 1998), pp. 827-842.
    by J van Helden, B André, Collado J Vides
    posted to motifs by nuin on 2008-06-26 12:54:06 as **
  • notes Applications and Statistics for Multiple High-Scoring Segments in Molecular Sequences
    Proceedings of the National Academy of Sciences, Vol. 90 (Jun 1993), pp. 5873-5877.
    by S Karlin, S Altschul
    posted to motifs by nuin on 2008-06-26 12:54:06 as **
  • notes TFBS: Computational framework for transcription factor binding site analysis
    Bioinformatics, Vol. 18 (Aug 2002)
    by Boris Lenhard, Wyeth Wasserman
    posted to motifs by nuin on 2008-06-26 12:54:06 as **
  • notes A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome.
    Journal of molecular biology, Vol. 284 (Nov 1998), pp. 241-254.
    by K Robison, AM Mcguire, GM Church
    posted to motifs by nuin on 2008-06-26 12:54:05 as **
  • notes Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.
    Journal of molecular biology., Vol. 296 (Mar 2000), pp. 1205-1214.
    by JD Hughes, PW Estep, S Tavazoie, GM Church
    posted to motifs by nuin on 2008-06-26 12:54:05 as **
  • notes Identifying Protein-Binding Sites from Unaligned DNA Fragments
    Proceedings of the National Academy of Sciences, Vol. 86 (Feb 1989), pp. 1183-1187.
    by Gary Stormo, George Hartzell
    posted to motifs by nuin on 2008-06-26 12:54:05 as **
  • notes Separating real motifs from their artifacts
    Bioinformatics, Vol. 17 (Jun 2001)
    by Mathieu Blanchette, Saurabh Sinha
    posted to motifs by nuin on 2008-06-26 12:54:05 as **
  • notes An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences.
    Proteins, Vol. 7 (xx 1990), pp. 41-51.
    by CE Lawrence, AA Reilly
    posted to motifs by nuin on 2008-06-26 12:54:05 as **
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