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タグ: motifpaper [152 articles]

Recent papers classified by the tag motifpaper.
  • notes Tsukuba BB: a branch and bound algorithm for local multiple alignment of DNA and protein sequences.
    J Comput Biol, Vol. 8, No. 3. (2001), pp. 283-303.
    by P Horton
    posted to motifpaper by dquest on 2006-09-29 22:07:06 as **
  • SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics
    BMC Bioinformatics, Vol. 9 (31 January 2008), 73.
    by Fabrice Touzain, Sophie Schbath, Isabelle Debled-Rennesson, Bertrand Aigle, Gregory Kucherov, Pierre Leblond
    posted to motifpaper motifsampling by dquest on 2008-02-01 15:23:42 as ** along with 2 people chad_davis xili03
  • notes Over- and underrepresentation of short DNA words in herpesvirus genomes.
    J Comput Biol, Vol. 3, No. 3. (1996), pp. 345-360.
    by MY Leung, GM Marsh, TP Speed
    posted to motifpaper by dquest on 2006-09-29 20:39:15 as **
  • notes Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.
    Pac Symp Biocomput (2004), pp. 324-335.
    by AM Moses, DY Chiang, MB Eisen
    posted to motifpaper by dquest on 2006-09-28 21:52:42 as ** along with 3 people eckart_bindewald lusk wenhan
  • LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731.
    by M Brudno, CB Do, GM Cooper, MF Kim, E Davydov, ED Green, A Sidow, S Batzoglou,
    posted to motifpaper by dquest on 2007-11-23 20:55:06 as ** along with 13 people and 1 group operon balajis dpollard xwbcn adepace hdopazo lusk Garamonfok adijr natstreet nklee Neeperando kcrawlik EisenLab
  • notes Detecting seeded motifs in DNA sequences.
    Nucleic Acids Res, Vol. 33, No. 15. (2005)
    by C Pizzi, S Bortoluzzi, A Bisognin, A Coppe, GA Danieli
    posted to motifpaper by dquest on 2006-10-02 17:30:25 as ** along with 2 people Cortel imouthesmp
  • MTAP: The Motif Tool Assessment Platform
    BMC Bioinformatics, Vol. 9, No. Suppl 9. (2008)
    by Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola, Hesham Ali
    posted to motifpaper by dquest on 2008-08-31 18:39:26 as read along with 1 person Stew
  • notes A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements
    Genome Biology, Vol. 7 (20 June 2006), R49.
    by Guandong Wang, Weixiong Zhang
    posted to motifpaper by dquest on 2006-10-02 19:24:55 as ** along with 2 people and 1 group indigoviolet ale EisenLab
  • notes Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by P Ng, N Nagarajan, N Jones, U Keich
    posted to motifpaper by dquest on 2006-10-02 19:34:44 as ** along with 2 people eckart_bindewald nedwards
  • notes A bi-dimensional regression tree approach to the modeling of gene expression regulation.
    Bioinformatics, Vol. 22, No. 3. (1 February 2006), pp. 332-340.
    by J Ruan, W Zhang
    posted to motifpaper by dquest on 2006-10-02 18:26:22 as **
  • notes Informative priors based on transcription factor structural class improve de novo motif discovery
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e384-392.
    by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J Hartemink
    posted to motifpaper by dquest on 2007-08-17 07:25:41 as ** along with 3 people nklee idonaldson yevishere
  • notes Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
    Science, Vol. 301, No. 5629. (4 July 2003), pp. 71-76.
    by P Cliften, P Sudarsanam, A Desikan, L Fulton, B Fulton, J Majors, R Waterston, BA Cohen, M Johnston
    posted to motifpaper by dquest on 2006-09-28 22:36:30 as **** along with 4 people and 1 group evaf chad_davis Eonwe cisevol cis-regulatory-evolution
  • KEGG: kyoto encyclopedia of genes and genomes.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 27-30.
    by M Kanehisa, S Goto
    posted to motifpaper by dquest on 2007-11-23 20:49:45 as ** along with 13 people namunet csanford j3xucite fisherp koerner ruvido noby naegele katerinakal grottenolm Evangelia natstreet jerome_ucsf_slb
  • MotifViz: an analysis and visualization tool for motif discovery.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (1 July 2004)
    by Y Fu, MC Frith, PM Haverty, Z Weng
    posted to motifpaper motifsampling visualization by dquest on 2007-11-11 20:34:10 as **
  • notes Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
    Bioinformatics, Vol. 14, No. 4. (1998), pp. 317-325.
    by T Yada, Y Totoki, M Ishikawa, K Asai, K Nakai
    posted to motifpaper by dquest on 2006-09-29 21:02:06 as **
  • notes From the Cover: Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis
    PNAS, Vol. 97, No. 18. (29 August 2000), pp. 10096-10100.
    by Harmen J Bussemaker, Hao Li, Eric D Siggia
    posted to motifpaper by dquest on 2006-09-29 21:33:35 as ** along with 3 people and 2 groups ana johncumbers ep161302 structural_bioinformatics Bioinformatics
  • Identification of DNA-binding proteins using support vector machines and evolutionary profiles
    BMC Bioinformatics, Vol. 8 (27 November 2007), 463.
    by Manish Kumar, Michael M Gromiha, Gajendra PS Raghava
    posted to motifpaper motifsampling proteinmotiffinding by dquest on 2007-11-28 17:59:06 as read
  • Transcription factor binding site identification using the self-organizing map.
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1807-1814.
    by S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar
    posted to motifpaper by dquest on 2006-09-28 19:27:09 as **
  • notes Combining frequency and positional information to predict transcription factor binding sites.
    Bioinformatics, Vol. 17, No. 11. (November 2001), pp. 1019-1026.
    by SM Kiełbasa, JO Korbel, D Beule, J Schuchhardt, H Herzel
    posted to motifpaper by dquest on 2006-09-29 22:08:35 as **
  • notes cWINNOWER algorithm for finding fuzzy dna motifs.
    J Bioinform Comput Biol, Vol. 2, No. 1. (March 2004), pp. 47-60.
    by S Liang, MP Samanta, BA Biegel
    posted to motifpaper by dquest on 2006-10-02 15:52:31 as **
  • notes A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2240-2245.
    by AV Favorov, MS Gelfand, AV Gerasimova, DA Ravcheev, AA Mironov, VJ Makeev
    posted to motifpaper by dquest on 2007-05-12 23:31:21 as **
  • notes Identifying protein-binding sites from unaligned DNA fragments.
    Proc Natl Acad Sci U S A, Vol. 86, No. 4. (February 1989), pp. 1183-1187.
    by GD Stormo, GW Hartzell
    posted to motifpaper by dquest on 2006-09-28 20:27:16 as read
  • notes A statistical method for finding transcription factor binding sites.
    Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 344-354.
    by S Sinha, M Tompa
    posted to motifpaper by dquest on 2006-09-29 21:17:52 as **
  • notes Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers.
    Genome Res, Vol. 12, No. 3. (March 2002), pp. 470-481.
    by DA Papatsenko, VJ Makeev, AP Lifanov, M Régnier, AG Nazina, C Desplan
    posted to motifpaper by dquest on 2006-09-29 22:41:40 as **
  • notes Regulatory element detection using a probabilistic segmentation model.
    Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 67-74.
    by HJ Bussemaker, H Li, ED Siggia
    posted to motifpaper by dquest on 2006-09-29 21:33:05 as **
  • notes Supervised detection of regulatory motifs in DNA sequences.
    Stat Appl Genet Mol Biol, Vol. 2, No. 1. (2003)
    by S Keles, MJ van der Laan, S Dudoit, B Xing, MB Eisen
    posted to motifpaper by dquest on 2006-10-02 18:46:41 as ** along with 1 person postrational
  • notes Recognition of characteristic patterns in sets of functionally equivalent DNA sequences.
    Comput Appl Biosci, Vol. 3, No. 3. (September 1987), pp. 223-227.
    by G Mengeritsky, TF Smith
    posted to motifpaper by dquest on 2006-09-29 20:15:22 as **
  • Microarray-Based Analysis of the Staphylococcus aureus sigmaB Regulon
    J. Bacteriol., Vol. 186, No. 13. (1 July 2004), pp. 4085-4099.
    by Markus Bischoff, Paul Dunman, Jan Kormanec, Daphne Macapagal, Ellen Murphy, William Mounts, Brigitte Berger-Bachi, Steven Projan
    posted to motifpaper by dquest on 2007-05-12 21:54:56 as ** along with 1 person daniel_quest
  • Discovering Motifs in Ranked Lists of DNA Sequences
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39.
    by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini
    posted to motifpaper motifsampling by dquest on 2007-11-23 13:58:08 as ** along with 3 people and 1 group dpollard yevishere chad_davis EisenLab
  • notes Finding motifs with insufficient number of strong binding sites.
    J Comput Biol, Vol. 12, No. 6. (g 2005), pp. 686-701.
    by HC Leung, FY Chin, SM Yiu, R Rosenfeld, WW Tsang
    posted to motifpaper by dquest on 2006-09-28 19:21:40 as *
  • notes Detecting localized repeats in genomic sequences: a new strategy and its application to Bacillus subtilis and Arabidopsis thaliana sequences.
    Comput Chem, Vol. 24, No. 1. (January 2000), pp. 57-70.
    by M Klaerr-Blanchard, H Chiapello, E Coward
    posted to motifpaper by dquest on 2006-10-02 16:01:48 as **
  • notes A deterministic motif finding algorithm with application to the human genome
    Bioinformatics, Vol. 22, No. 9. (1 May 2006), pp. 1047-1054.
    by Lawrence S Hon, Ajay N Jain
    posted to motifpaper by dquest on 2006-10-02 18:40:51 as ** along with 3 people and 1 group idonaldson nklee maximilianh Motif Discovery
  • notes PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
    PLoS Comput Biol, Vol. 1, No. 7. (December 2005)
    by R Siddharthan, ED Siggia, E van Nimwegen
    posted to motifpaper by dquest on 2006-09-28 19:34:13 as read along with 12 people and 3 groups druvus ana postrational AaronDarling nickluscombe noano adsmitty lusk lilou idonaldson yevishere isimpson structural_bioinformatics Bioinformatics EBI-regulation
  • notes Bounded search for de novo identification of degenerate cis-regulatory elements.
    BMC Bioinformatics, Vol. 7 (2006)
    by JM Carlson, A Chakravarty, RS Khetani, RH Gross
    posted to motifpaper by dquest on 2006-10-02 19:23:14 as ** along with 1 person and 1 group indigoviolet EisenLab
  • notes A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
    Bioinformatics, Vol. 17, No. 12. (1 December 2001), pp. 1113-1122.
    by Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouze, Yves Moreau
    posted to motifpaper by dquest on 2006-09-28 19:18:57 as read along with 5 people chad_davis lyongu natstreet nklee xili03
  • 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 motifpaper by dquest on 2006-09-28 21:13:38 as read along with 5 people and 2 groups chad_davis balajis lyongu dpollard csdhwang EisenLab cis-regulatory-evolution
  • notes Finding subtle motifs with variable gaps in unaligned DNA sequences.
    Comput Methods Programs Biomed, Vol. 70, No. 1. (January 2003), pp. 11-20.
    by YJ Hu
    posted to motifpaper by dquest on 2006-09-29 22:49:05 as **
  • notes ANN-Spec: a method for discovering transcription factor binding sites with improved specificity.
    Pac Symp Biocomput (2000), pp. 467-478.
    by CT Workman, GD Stormo
    posted to motifpaper by dquest on 2006-10-04 18:30:20 as ** along with 1 person ezralanglois
  • 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 motifpaper by dquest on 2007-05-12 23:02:17 as ** along with 2 people GustavoLacerda nuin
  • notes Finding functional sequence elements by multiple local alignment.
    Nucleic Acids Res, Vol. 32, No. 1. (2004), pp. 189-200.
    by MC Frith, U Hansen, JL Spouge, Z Weng
    posted to motifpaper by dquest on 2006-09-29 23:09:23 as ** along with 2 people and 1 group kengg nklee Plantandetc
  • notes BioOptimizer: a Bayesian scoring function approach to motif discovery.
    Bioinformatics, Vol. 20, No. 10. (10 July 2004), pp. 1557-1564.
    by ST Jensen, JS Liu
    posted to motifpaper by dquest on 2006-10-02 15:33:42 as **
  • notes 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 motifpaper by dquest on 2006-09-29 22:10:42 as ** along with 3 people xiaobeizhao dandaman bryankr
  • notes Bipartite pattern discovery by entropy minimization-based multiple local alignment.
    Nucleic Acids Res, Vol. 32, No. 17. (2004), pp. 4979-4991.
    by C Bi, PK Rogan
    posted to motifpaper by dquest on 2006-10-02 16:13:59 as **
  • notes PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.
    BMC Bioinformatics, Vol. 5 (28 October 2004)
    by S Sinha, M Blanchette, M Tompa
    posted to motifpaper by dquest on 2006-09-28 21:17:45 as read along with 4 people eckart_bindewald adsmitty lusk xili03
  • notes BEAM: a beam search algorithm for the identification of cis-regulatory elements in groups of genes.
    J Comput Biol, Vol. 13, No. 3. (April 2006), pp. 686-701.
    by JM Carlson, A Chakravarty, RH Gross
    posted to motifpaper by dquest on 2006-10-02 19:27:26 as ** along with 1 person maximilianh
  • notes Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.
    J Comput Biol, Vol. 7, No. 3-4. (2000), pp. 345-362.
    by L Marsan, MF Sagot
    posted to motifpaper by dquest on 2006-09-29 21:35:59 as **
  • CoMoDis: composite motif discovery in mammalian genomes
    Nucleic Acids Research, Vol. 35, No. 1. (January 2007), pp. e1-e1.
    by Donaldson, J Ian, Gottgens, Berthold
    posted to motifpaper motifsampling by dquest on 2007-11-11 20:32:00 as **
  • notes From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles
    (2004), pp. 115-124.
    by Eleazar Eskin
    posted to motifpaper by dquest on 2006-09-29 22:43:08 as **
  • notes 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 motifpaper by dquest on 2006-09-29 22:26:39 as ** along with 2 people eckart_bindewald nuin
  • notes Efficient detection of unusual words.
    J Comput Biol, Vol. 7, No. 1-2. (r 2000), pp. 71-94.
    by A Apostolico, ME Bock, S Lonardi, X Xu
    posted to motifpaper by dquest on 2006-09-29 21:07:09 as ** along with 1 person suizan
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