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Ключевое слово motif-discovery [32 articles]

Recent papers classified by the tag motif-discovery.
  • Computational identification of transcriptional regulatory elements in DNA sequence
    Nucl. Acids Res., Vol. 34, No. 12. (19 July 2006), pp. 3585-3598.
    by Debraj Guhathakurta
    posted to transcription-regulation review must-read motifs motif-discovery gene by isimpson on 2008-09-01 16:35:53 as ***** along with 9 people and 1 group tmmurali jfr johncumbers reidy giovanni cabbagezs ankur_iitg vietanh0 xili03 GeschwindLab
  • Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model.
    Genome Res, Vol. 12, No. 7. (July 2002), pp. 1019-1028.
    by MS Halfon, Y Grad, GM Church, AM Michelson
    posted to transcription-regulation must-read motifs motif-discovery database by isimpson on 2008-10-09 10:50:50 as ***** along with 1 person maximilianh
  • DNA binding sites: representation and discovery.
    Bioinformatics, Vol. 16, No. 1. (January 2000), pp. 16-23.
    by GD Stormo
    posted to transcription-regulation review must-read motifs motif-discovery by isimpson on 2008-09-01 16:41:35 as ***** along with 7 people emptyhb kaarsinogen mbj dquest lusk ezralanglois xili03
  • CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.
    Proc Natl Acad Sci U S A, Vol. 101, No. 33. (17 August 2004), pp. 12114-12119.
    by Q Zhou, WH Wong
    posted to transcription-regulation must-read motifs motif-discovery database by isimpson on 2008-10-09 10:52:02 as ***** along with 3 people and 1 group indigoviolet dpollard ep161302 EisenLab
  • Homotypic regulatory clusters in Drosophila.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 579-588.
    by AP Lifanov, VJ Makeev, AG Nazina, DA Papatsenko
    posted to transcription-regulation must-read motifs motif-discovery database by isimpson on 2008-10-09 10:51:42 as ***** along with 2 people and 1 group indigoviolet tresch EisenLab
  • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
    BMC Bioinformatics, Vol. 3 (24 October 2002)
    by N Rajewsky, M Vergassola, U Gaul, ED Siggia
    posted to transcription-regulation must-read motifs motif-discovery database by isimpson on 2008-10-09 10:51:16 as ***** along with 6 people and 1 group ansobol indigoviolet adepace koller Stew csdhwang EisenLab
  • Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets.
    Genome research (14 April 2008)
    by Chaim Linhart, Yonit Halperin, Ron Shamir
    posted to motif-discovery by isimpson on 2008-06-04 09:56:52 as ***** along with 7 people and 1 group jfr ealloza idonaldson maralena fpattyn tmmurali maximilianh BergmanLab
  • 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 motif-discovery tool by idonaldson on 2007-10-29 10:38:59 as *** along with 6 people eckart_bindewald zwang GeeSharpMinor ppark hpaces isimpson
  • 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 motif-discovery tfbs tool by idonaldson on 2007-10-29 11:42:16 as ** along with 3 people maximilianh isimpson nuin
  • W-AlignACE: An improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data.
    Bioinformatics (5 March 2008)
    by Xin Chen, Lingqiong Guo, Zhaocheng Fan, Tao Jiang
    posted to chip-chip chip-on-chip motif-discovery tool by idonaldson on 2008-04-25 14:11:01 as ** along with 2 people maximilianh isimpson
  • How does DNA sequence motif discovery work?
    Nature Biotechnology, Vol. 24, No. 8., pp. 959-961.
    by Patrik D'Haeseleer
    posted to cis-regulation motif-discovery primer tfbs by idonaldson on 2007-10-26 14:26:18 as *** along with 7 people and 1 group bryankr okarsligil Evangelia antonkratz xi03 isimpson chad_davis Bioinformatics
  • HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing
    BMC Bioinformatics, Vol. 8 (28 October 2007), 418.
    by Erik Larsson, Per Lindahl, Petter Mostad
    posted to motif-discovery spacing tfbs tool by idonaldson on 2007-11-06 09:18:26 as read along with 2 people maximilianh isimpson
  • Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells
    Genome Res. (15 May 2008), gr.072769.107.
    by Dan Xie, Jun Cai, Na-Yu Chia, Huck Ng, Sheng Zhong
    posted to cis-regulation crm motif-discovery tool by idonaldson on 2008-05-27 09:53:11 as *** along with 5 people maximilianh isimpson GustavoLacerda phoenixzxl yoonk
  • fdrMotif: Identifying cis-elements by an EM Algorithm Coupled with False Discovery Rate Control.
    Bioinformatics (22 February 2008)
    by Leping Li, Robert L L Bass, Yu Liang
    posted to motif-discovery tool by idonaldson on 2008-02-28 16:05:34 as *** along with 3 people maximilianh csdhwang isimpson
  • Discovering motifs with transcription factor domain knowledge.
    Pac Symp Biocomput (2007), pp. 472-483.
    by HC Leung, FY Chin, BM Chan
    posted to motif-discovery tfbs tool by idonaldson on 2007-11-12 08:50:57 as **** along with 1 person maximilianh
  • Regulatory motif discovery using a population clustering evolutionary algorithm.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (p 2007), pp. 403-414.
    by MA Lones, AM Tyrrell
    posted to motif-discovery tool by idonaldson on 2007-10-22 09:26:24 as **** along with 4 people nklee xili03 csdhwang isimpson
  • GIMSAN: a Gibbs motif finder with significance analysis
    Bioinformatics, Vol. 24, No. 19. (1 October 2008), pp. 2256-2257.
    by Patrick Ng, Uri Keich
    posted to tool motif-discovery by idonaldson on 2008-09-29 09:48:40 as *** along with 2 people nuin GeeSharpMinor
  • 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 conserved motif-discovery tfbs tool by idonaldson on 2007-10-29 10:39:49 as read along with 12 people and 3 groups druvus ana postrational dquest AaronDarling nickluscombe noano adsmitty lusk lilou yevishere isimpson structural_bioinformatics Bioinformatics EBI-regulation
  • Motif discovery in tissue-specific regulatory sequences using directed information.
    EURASIP J Bioinform Syst Biol (2007)
    by A Rao, AO Hero Iii, DJ States, JD Engel
    posted to motif-discovery tissue-specific by idonaldson on 2008-03-17 11:03:58 as *** along with 2 people maximilianh isimpson
  • Discriminative motif discovery in DNA and protein sequences using the DEME Algorithm
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Emma Redhead, Timothy Bailey
    posted to motif-discovery tool by idonaldson on 2007-10-22 09:25:28 as **** along with 5 people and 1 group dpollard cjeans nklee niallhaslam maximilianh EisenLab
  • MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders.
    Bioinformatics (Oxford, England) (12 August 2008)
    by Edward Wijaya, Siu-Ming M Yiu, Ngo Thanh T Son, Rajaraman Kanagasabai, Wing-Kin K Sung
    posted to motif-discovery tool by idonaldson on 2008-08-18 14:20:17 as *** along with 3 people nuin chad_davis maximilianh
  • CoMoDis: composite motif discovery in mammalian genomes.
    Nucleic Acids Res, Vol. 35, No. 1. (2007)
    by IJ Donaldson, B Göttgens
    posted to cis-regulation me motif-discovery tfbs tool by idonaldson on 2007-10-18 16:41:50 as read along with 1 person and 1 group csdhwang Bioinformatics
  • NestedMICA as an ab initio protein motif discovery tool
    BMC Bioinformatics, Vol. 9 (14 January 2008), 19.
    by Mutlu Dogruel, Thomas A Down, Tim JP Hubbard
    posted to motif-discovery protein tool by idonaldson on 2008-01-21 10:44:04 as **
  • A survey of motif discovery methods in an integrated framework
    Biology Direct, Vol. 1, No. 1. (06 April 2006), 11.
    by Geir K Sandve, Finn Drabløs
    posted to motif-discovery review tools by idonaldson on 2008-07-08 09:03:38 as *** along with 6 people and 1 group aprasad dpollard samal yevishere csdhwang yoonk EisenLab
  • Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules
    Algorithms for Molecular Biology, Vol. 2 (10 October 2007), 13.
    by Valentina Boeva, Julien Clement, Mireille Regnier, Mikhail A Roytberg, Vsevolod J Makeev
    posted to crm motif-discovery statistics by idonaldson on 2007-11-06 09:14:45 as ** along with 3 people and 1 group beete guos isimpson csb_journal_club_public
  • Assessment of composite motif discovery methods
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Kjetil Klepper, Geir Sandve, Osman Abul, Jostein Johansen, Finn Drablos
    posted to analysis motif-discovery tool by idonaldson on 2008-03-03 09:19:03 as *** along with 7 people and 1 group chad_davis nklee maximilianh xili03 csdhwang isimpson yoonk Motif Discovery
  • A Hybrid Model for Robust Detection of Transcription Factor Binding Sites.
    Bioinformatics (9 January 2008)
    by Sumedha Gunewardena, Zhaolei Zhang
    posted to motif-discovery tfbs tool by idonaldson on 2008-01-14 09:30:49 as *** along with 2 people jyuh maximilianh
  • TFBS Identification Based on Genetic Algorithm with Combined Representations and Adaptive Post-processing.
    Bioinformatics (6 December 2007)
    by Tak-Ming M Chan, Kwong-Sak S Leung, Kin-Hong H Lee
    posted to motif-discovery tfbs tool by idonaldson on 2008-01-31 11:07:05 as *** along with 5 people nklee maximilianh xili03 csdhwang isimpson
  • 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 motif-discovery structural tfbs by idonaldson on 2007-10-29 10:42:19 as ** along with 3 people dquest nklee yevishere
  • Seeder: Discriminative Seeding DNA Motif Discovery.
    Bioinformatics (Oxford, England) (21 August 2008)
    by François Fauteux, Mathieu Blanchette, Martina V V Strömvik
    posted to motif-discovery tool by idonaldson on 2008-08-26 10:37:49 as ** along with 4 people nuin brant maximilianh isimpson
  • Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets.
    Bioinformatics, Vol. 21, No. 3. (1 February 2005), pp. 314-324.
    by H Li, J Li
    posted to motif-discovery ppi-database by bicko on 2006-06-27 11:57:09 as **
  • Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e178.
    by Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A Marti-Renom, Baldo Oliva
    posted to motif-discovery protein-networks by bicko on 2008-01-09 16:11:45 as ** along with 1 person zwang
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