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Group: Motif Discovery - library [39 articles]

小组成员近期录入的文献 Motif Discovery 兴趣小组
  • Statistics review 13: receiver operating characteristic curves.
    Crit Care, Vol. 8, No. 6. (December 2004), pp. 508-512.
    by V Bewick, L Cheek, J Ball
    posted to statistics by nklee to the group Motif Discovery on 2008-05-09 03:21:51 as ** along with 1 person jyuh
  • 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 composite evaluation by nklee to the group Motif Discovery on 2008-04-16 08:25:34 as ** along with 7 people chad_davis maximilianh idonaldson xili03 csdhwang isimpson yoonk
  • An efficient method for statistical significance calculation of transcription factor binding sites.
    Bioinformation, Vol. 2, No. 5. (2007), pp. 169-174.
    by Z Qian, L Lu, L Qi, Y Li
    posted to significance statistical by nklee to the group Motif Discovery on 2008-04-14 02:23:24 as ** along with 3 people maximilianh idonaldson isimpson
  • Detecting cis-regulatory binding sites for cooperatively binding proteins
    Nucleic AcidsRes., Vol. 0, No. 0.
    by Liesbeth van Oeffelen1, Pierre Cornelis, Wouter Van Delm, Fedor De Ridder, Bart De Moor, Yves Moreau1
    posted to cis-regulatory composite discovery motif by nklee to the group Motif Discovery on 2008-04-10 06:45:32 as **
  • A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli
    PLoS Computational Biology, Vol. 4, No. 3. (2008), e1000044.
    by Jason Ernst, Qasim K Beg, Krin A Kay, Ga´bor B Zsi, Zolta´n N Oltvai, Ziv Bar-Joseph1
    posted to semi-supervised by nklee to the group Motif Discovery on 2008-04-03 06:44:20 as ** along with 1 person jjray
  • A Profile-Based Deterministic Sequential Monte Carlo Algorithm for Motif Discovery.
    Bioinformatics (17 November 2007)
    by Kuo-Ching C Liang, Xiaodong Wang, Dimitris Anastassiou
    posted to no-tag by nklee to the group Motif Discovery on 2008-04-01 08:23:44 as ** along with 5 people grahamc cjeans maximilianh idonaldson isimpson
  • JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by A Sandelin, W Alkema, P Engström, WW Wasserman, B Lenhard
    posted to database eukaryotic jaspar by nklee to the group Motif Discovery on 2008-04-01 02:08:44 as read along with 4 people and 1 group aalibes indigoviolet jguinney heliopais EisenLab
  • 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 deterministic discovery motif search by nklee to the group Motif Discovery on 2008-03-30 03:08:58 as ** along with 2 people dquest maximilianh
  • A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.
    Mol Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350.
    by O Elemento, N Slonim, S Tavazoie
    posted to discovery motif by nklee to the group Motif Discovery on 2008-03-25 21:12:01 as ** along with 12 people and 1 group ana brant cwbrown aswin cjeans zwang cabbagezs maximilianh idonaldson sb_journal_club kristen barwil EisenLab
  • Analysis of computational approaches for motif discovery
    Algorithms for Molecular Biology, Vol. 1, No. 1. (May 2006), 8.
    by Nan Li, Martin Tompa
    posted to analysis discovery motif tools by th2do to the group Motif Discovery on 2008-03-19 01:55:25 as **
  • Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (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, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to benchmarking binding discovery sites motif by th2do to the group Motif Discovery on 2008-03-19 01:55:25 as **
  • Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
    BMC Bioinformatics, Vol. 8 (August 2007), 283.
    by Xiangdong Liu, Walter J Jessen, Siva Sivaganesan, Bruce J Aronow, Mario Medvedovic
    posted to no-tag by th2do to the group Motif Discovery on 2008-03-19 01:55:25 as **
  • MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs
    BMC Bioinformatics, Vol. 8 (March 2007), 100.
    by Mamoru Kato, Tatsuhiko Tsunoda
    posted to algorithm genetic discovery motif by th2do to the group Motif Discovery on 2008-03-19 01:55:25 as **
  • Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
    Genome Biol, Vol. 5, No. 9. (2004)
    by BP Berman, BD Pfeiffer, TR Laverty, SL Salzberg, GM Rubin, MB Eisen, SE Celniker
    posted to enhancers discovery motif by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • Computational prediction of transcription-factor binding site locations.
    Genome Biol, Vol. 5, No. 1. (2003)
    by ML Bulyk
    posted to survey discovery motif by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • Self-organizing hierarchic networks for pattern recognition in protein sequence
    Protein Sci, Vol. 5, No. 1. (January 1996), pp. 72-82.
    by J Hanke, G Beckmann, P Bork, JG Reich
    posted to map motif organizing self discovery by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.
    J Comput Biol, Vol. 13, No. 4. (May 2006), pp. 929-945.
    by S Gunewardena, P Jeavons, Z Zhang
    posted to no-tag by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • 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 discovery discriminative motif by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • 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 no-tag by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • A novel ensemble learning method for de novo computational identification of DNA binding sites
    BMC Bioinformatics, Vol. 8 (July 2007), 249.
    by Arijit Chakravarty, Jonathan M Carlson, Radhika S Khetani, Robert H Gross
    posted to ensemble discovery motif by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • An algorithm for finding signals of unknown length in DNA sequences.
    Bioinformatics, Vol. 17 Suppl 1 (2001)
    by G Pavesi, G Mauri, G Pesole
    posted to length unknown discovery motif by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • Regulatory motif discovery using a population clustering evolutionary algorithm.
    IEEE/ACM Trans Comput Biol Bioinform, Vol. 4, No. 3. (2007), pp. 403-414.
    by MA Lones, AM Tyrrell
    posted to algorithm genetic discovery motif by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as ** along with 1 person csdhwang
  • Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Victor Levitsky, Elena Ignatieva, Elena Ananko, Igor Turnaev, Tatyana Merkulova, Nikolay Kolchanov, T Hodgman
    posted to algorithm genetic discovery motif by th2do to the group Motif Discovery on 2008-03-19 01:55:24 as **
  • Data Augmentation Algorithms for Detecting Conserved Domains in Protein Sequences: A Comparative Study
    J. Proteome Res. (December 2007)
    by Chengpeng Bi
    posted to no-tag by th2do to the group Motif Discovery on 2008-03-19 01:55:23 as **
  • Informative priors based on transcription factor structural class improve de novo motif discovery
    Bioinformatics, Vol. 22, No. 14. (July 2006), pp. e384-392.
    by Leelavati Narlikar, Raluca Gordan, Uwe Ohler, Alexander J Hartemink
    posted to bibtex-import discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:36:55 as **
  • TFBS Identification Based on Genetic Algorithm with Combined Representations and Adaptive Post-processing.
    Bioinformatics (December 2007)
    by Tak, Kwong, Kin
    posted to algorithm bibtex-import genetic discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:36:55 as **
  • iGibbs: Improving Gibbs motif sampler for proteins by sequence clustering and iterative pattern sampling
    Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 3. (2007), pp. 671-681.
    by Sun Kim, Zhiping Wang, Mehmet Dalkilic
    posted to bibtex-import clustering gibbs discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:36:55 as **
  • Prediction of transcription factor binding sites using ChIP-chip and phylogenetic footprinting data
    Journal of Bioinformatics and Computational Biology, Vol. 5, No. 1. (February 2007), pp. 105-116.
    by Markus T Friberg
    posted to bibtex-import chip comparative genomic discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:36:55 as **
  • Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.
    Nat Biotechnol, Vol. 21, No. 4. (April 2003), pp. 435-439.
    by ZS Qin, LA Mccue, W Thompson, L Mayerhofer, CE Lawrence, JS Liu
    posted to bibtex-import clustering discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:36:55 as **
  • A novel approach to identifying regulatory motifs in distantly related genomes
    Genome Biology, Vol. 6, No. 13. (2005)
    by Ruth Van Hellemont, Pieter Monsieurs, Gert Thijs, Bart De Moor, Yves Van de Peer, Kathleen Marchal
    posted to bibtex-import clustering comparative footprinting genomic discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:36:54 as **
  • Distinguishing Regulatory DNA From Neutral Sites
    Genome Res., Vol. 13, No. 1. (January 2003), pp. 64-72.
    by Laura Elnitski, Ross C Hardison, Jia Li, Shan Yang, Diana Kolbe, Pallavi Eswara, Michael J O'Connor, Scott Schwartz, Webb Miller, Francesca Chiaromonte
    posted to bibtex-import neutral site discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:36:54 as **
  • Efficient Detection of Network Motifs
    Computational Biology and Bioinformatics, IEEE/ACM Transactions on, Vol. 3, No. 4. (Oct.-Dec. 2006), pp. 347-359.
    by Sebastian Wernicke
    posted to algorithm bibtex-import biology computing design detection graphs methodsnetwork motif networks principles random sampling structural subgraphs discovery by th2do to the group Motif Discovery on 2008-03-18 23:18:05 as **
  • Regulatory Motif Discovery Using a Population Clustering Evolutionary Algorithm
    Computational Biology and Bioinformatics, IEEE/ACM Transactions on, Vol. 4, No. 3. (July-Sept. 2007), pp. 403-414.
    by MA Lones, AM Tyrrell
    posted to algorithm bibtex-import biology biophysics clustering computation computing data discovery diversity dna evolutionary frequency matrix models molecular motif population position processesdna promoter regulatory sequences sets solution stochastic synthetic by th2do to the group Motif Discovery on 2008-03-18 23:18:05 as **
  • Motif Search in Graphs: Application to Metabolic Networks
    Computational Biology and Bioinformatics, IEEE/ACM Transactions on, Vol. 3, No. 4. (Oct.-Dec. 2006), pp. 360-368.
    by Vincent Lacroix, Cristina G Fernandes, Marie F Sagot
    posted to bibtex-import biochemistry biology biophysicsbiochemical computing evolution features graphs metabolic metabolism molecular motif networks pathway reaction search structural discovery by th2do to the group Motif Discovery on 2008-03-18 23:18:04 as **
  • Motif discoveries in unaligned molecular sequences using self-organizing neural networks
    Neural Networks, IEEE Transactions on, Vol. 17, No. 4. (July 2006), pp. 919-928.
    by Derong Liu, Xiaoxu Xiong, B Dasgupta, Huaguang Zhang
    posted to algorithms bibtex-import biology biophysics classification complexity computational computing discoveries dna identification input molecular motif nets networks neural pattern patterns problems protein proteins search self-organizing sequence sequences unaligned discovery by th2do to the group Motif Discovery on 2008-03-18 23:18:04 as ** along with 1 person csdhwang
  • Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System
    Computational Biology and Bioinformatics, IEEE/ACM Transactions on, Vol. 4, No. 4. (Oct.-Dec. 2007), pp. 596-610.
    by S Michal, T Ivry, Schalit O Cohen, M Sipper, D Barash
    posted to algorithms bibtex-import biology biophysics compounds computing consensus genetic macromolecules molecular motif organic prediction programming rna sequences sequencesgernamo system discovery by th2do to the group Motif Discovery on 2008-03-18 23:18:04 as **
  • Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property
    NanoBioscience, IEEE Transactions on, Vol. 4, No. 3. (Sept. 2005), pp. 255-265.
    by Wei Zhong, G Altun, R Harrison, PC Tai, Yi Pan
    posted to activities algorithm algorithms analysis bibtex-import bioinformatics biology biophysics clustering common computing configurations conformation greedy improved initialization k-means local method molecular motifs property protein proteins sequence similarity statistical structural discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:18:04 as ** along with 1 person csdhwang
  • Computational Identification of Transcription Factor Binding Sites via a Transcription-factor-centric Clustering (TFCC) Algorithm
    Journal of Molecular Biology, Vol. 318, No. 1. (April 2002), pp. 71-81.
    by Zhou Zhu, Yitzhak Pilpel, George M Church
    posted to bibtex-import clustering discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:18:04 as **
  • A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
    Bioinformatics, Vol. 17, No. 12. (December 2001), pp. 1113-1122.
    by Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouze, Yves Moreau
    posted to background bibtex-import model discovery motif by th2do to the group Motif Discovery on 2008-03-18 23:18:03 as **
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