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Tag motifsampling [29 articles]

Recent papers classified by the tag motifsampling.
  • Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
    BMC Bioinformatics, Vol. 8 (03 August 2007), 283.
    by Xiangdong Liu, Walter J Jessen, Siva Sivaganesan, Bruce J Aronow, Mario Medvedovic
    posted to motifpaper motifsampling by dquest on 2007-11-22 13:59:46 as ** along with 2 people and 1 group nklee naegele ic4
  • 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 **
  • 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 **
  • Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Yuji Zhang, Jianhua Xuan, Benildo, Robert Clarke, Habtom Ressom
    posted to motifsampling motifpaper by dquest on 2008-04-23 15:14:39 as ** along with 4 people bertelsen bootsy kengg robertvandenberg
  • A survey of DNA motif finding algorithms
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Modan Das, Ho K Dai
    posted to motifpaper motifsampling by dquest on 2007-11-22 13:55:32 as ** along with 6 people xili03 brant nklee maximilianh yevishere csdhwang
  • Ab initio prediction of transcription factor targets using structural knowledge.
    PLoS Comput Biol, Vol. 1, No. 1. (June 2005)
    by T Kaplan, N Friedman, H Margalit
    posted to motifpaper motifsampling by dquest on 2008-04-17 16:48:46 as ** along with 1 person bpb
  • notes 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 motifsampling by dquest on 2006-10-16 23:23:07 as read along with 23 people and 6 groups nuin ep161302 icases ana barry aalibes aprasad jfr tuck chad_davis lyongu tabu neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Analysis of computational approaches for motif discovery
    Algorithms for Molecular Biology, Vol. 1, No. 1. (19 May 2006), 8.
    by Nan Li, Martin Tompa
    posted to motifsampling by dquest on 2006-05-22 14:36:03 as ***** along with 9 people and 2 groups ana barry tuck chad_davis lusk nklee maximilianh xi03 csdhwang structural_bioinformatics Bioinformatics
  • notes Limitations and potentials of current motif discovery algorithms
    Nucleic Acids Research, Vol. 33, No. 15. (2005), pp. 4899-4913.
    by Jianjun Hu, Bin Li, Daisuke Kihara
    posted to motifsampling by dquest on 2006-10-16 23:21:05 as read along with 1 person gpalidwor
  • REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3487-3490.
    by C Roven, HJ Bussemaker
    posted to motifpaper motifsampling by dquest on 2007-11-23 14:25:46 as ** along with 3 people and 1 group mariakmejia nickluscombe heliopais EBI-regulation
  • Discovering sequence motifs with arbitrary insertions and deletions.
    PLoS computational biology, Vol. 4, No. 4. (April 2008)
    by MC Frith, NF Saunders, B Kobe, TL Bailey
    posted to motifsampling motifpaper by dquest on 2008-05-14 19:38:39 as ** along with 5 people Ema Stew gjuggler neils cabbagesofdoom
  • notes Identification of the binding sites of regulatory proteins in bacterial genomes.
    Proc Natl Acad Sci U S A, Vol. 99, No. 18. (3 September 2002), pp. 11772-11777.
    by H Li, V Rhodius, C Gross, ED Siggia
    posted to motifsampling motifpaper by dquest on 2007-01-24 06:45:17 as ** along with 1 person kaarsinogen
  • notes 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 motifsampling motifpaper by dquest on 2007-01-23 14:08:16 as ** along with 6 people and 1 group isimpson indigoviolet dpollard SeungjoonOh nklee emptyhb EisenLab
  • Improved benchmarks for computational motif discovery
    BMC Bioinformatics, Vol. 8 (08 June 2007), 193.
    by Geir K Sandve, Osman Abul, Vegard Walseng, Finn Drablos
    posted to motifpaper motifsampling by dquest on 2007-11-23 15:52:44 as read
  • notes Discovering transcriptional modules from motif, chip-chip and microarray data.
    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2005), pp. 483-494.
    by T De Bie, P Monsieurs, K Engelen, B De Moor, N Cristianini, K Marchal
    posted to motifsampling motifpaper by dquest on 2008-05-07 23:04:45 as read
  • BLISS: biding site level identification of shared signal-modules in DNA regulatory sequences
    BMC Bioinformatics, Vol. 7 (07 June 2006), 287.
    by Hailong Meng, Arunava Banerjee, Lei Zhou
    posted to motifsampling by dquest on 2006-06-12 16:41:13 as ** along with 2 people and 1 group dpollard uz_labu_laimi EisenLab
  • Evolutionary approaches for the reverse-engineering of gene regulatory networks: a study on a biologically realistic dataset
    BMC Bioinformatics, Vol. 9 (08 February 2008), 91.
    by Cedric Auliac, Vincent Frouin, Xavier Gidrol, Florence D'alche-Buc
    posted to baysian motifpaper motifsampling regulatorynetworks by dquest on 2008-02-11 18:38:01 as read along with 1 person thomaskelder
  • Visual setup of logical models of signaling and regulatory networks with ProMoT
    BMC Bioinformatics, Vol. 7 (17 November 2006), 506.
    by Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst D Gilles, Martin Ginkel
    posted to motifpaper motifsampling proteinnetworks regulatorynetworks by dquest on 2006-11-22 01:43:12 as read along with 1 person wnpx
  • 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 chad_davis dpollard yevishere EisenLab
  • Using local gene expression similarities to discover regulatory binding site modules
    BMC Bioinformatics, Vol. 7 (17 November 2006), 505.
    by Bartek Wilczynski, Torgeir R Hvidsten, Andriy Kryshtafovych, Jerzy Tiuryn, Jan Komorowski, Krzysztof Fidelis
    posted to motifpaper motifsampling by dquest on 2006-11-22 01:40:42 as ** along with 2 people jfr smiddha
  • notes Statistical significance of cis-regulatory modules
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Dustin Schones, Andrew Smith, Michael Zhang
    posted to motifsampling motifpaper by dquest on 2007-01-23 14:02:15 as ** along with 9 people and 1 group sconlan indigoviolet dpollard sebastien_vigneau shigepong SeungjoonOh GustavoLacerda nklee xili03 EisenLab
  • notes TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs
    Bioinformatics, Vol. 21, No. 14. (15 July 2005), pp. 3164-3165.
    by Benjamin D Gordon, Lena Nekludova, Scott Mccallum, Ernest Fraenkel
    posted to motifsampling by dquest on 2006-10-16 22:53:11 as read
  • notes Modeling within-motif dependence for transcription factor binding site predictions.
    Bioinformatics, Vol. 20, No. 6. (12 April 2004), pp. 909-916.
    by Q Zhou, JS Liu
    posted to motifsampling by dquest on 2006-09-29 23:02:10 as ** along with 1 person xili03
  • Approaches to the automatic discovery of patterns in biosequences.
    J Comput Biol, Vol. 5, No. 2. (1998), pp. 279-305.
    by A Brazma, I Jonassen, I Eidhammer, D Gilbert
    posted to motifpaper motifsampling by dquest on 2007-11-23 13:48:37 as ** along with 1 person treangen
  • BEST: Binding-site Estimation Suite of Tools
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2909-2911.
    by Dongsheng Che, Shane Jensen, Liming Cai, Jun S Liu
    posted to motifpaper motifsampling by dquest on 2006-06-07 20:04:09 as *
  • CoXpress: differential co-expression in gene expression data
    BMC Bioinformatics, Vol. 7 (20 November 2006), 509.
    by Michael Watson
    posted to motifpaper motifsampling by dquest on 2006-11-22 01:38:02 as ** along with 4 people jfr shigepong waszak dps
  • 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
  • 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
  • notes Gibbs Recursive Sampler: finding transcription factor binding sites
    Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3580-3585.
    by William Thompson, Eric C Rouchka, Charles E Lawrence
    posted to motifsampling by daniel_quest on 2006-02-09 23:38:26 as read along with 4 people lyongu dquest johncumbers xiaobeizhao
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