Gene expression info-gibbs : a motif discovery algorithm that directly optimizes information content during sampling
暂无分享,去创建一个
[1] M. Tompa,et al. Discovery of novel transcription factor binding sites by statistical overrepresentation. , 2002, Nucleic acids research.
[2] J. Collado-Vides,et al. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. , 2000, Nucleic acids research.
[3] Gary D. Stormo,et al. Identification of consensus patterns in unaligned DNA sequences known to be functionally related , 1990, Comput. Appl. Biosci..
[4] Jacques van Helden,et al. RSAT: regulatory sequence analysis tools , 2008, Nucleic Acids Res..
[5] Douglas L. Brutlag,et al. BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes , 2000, Pacific Symposium on Biocomputing.
[6] Shane T. Jensen,et al. BioOptimizer: a Bayesian scoring function approach to motif discovery , 2004, Bioinform..
[7] Kwong-Sak Leung,et al. TFBS identification based on genetic algorithm with combined representations and adaptive post-processing , 2008, Bioinform..
[8] Saurabh Sinha,et al. YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation , 2003, Nucleic Acids Res..
[9] G. Stormo. Information content and free energy in DNA--protein interactions. , 1998, Journal of theoretical biology.
[10] Graziano Pesole,et al. An algorithm for finding signals of unknown length in DNA sequences , 2001, ISMB.
[11] Jun S. Liu,et al. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. , 1993, Science.
[12] G. Church,et al. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.
[13] Zhi Wei,et al. GAME: detecting cis-regulatory elements using a genetic algorithm , 2006, Bioinform..
[14] T. D. Schneider,et al. Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.
[15] Kazuhito Shida,et al. GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima , 2006, BMC Bioinformatics.
[16] Shane T. Jensen,et al. Computational Discovery of Gene Regulatory Binding Motifs: A Bayesian Perspective , 2004 .
[17] Nicola J. Rinaldi,et al. Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.
[18] Pavel A. Pevzner,et al. Combinatorial Approaches to Finding Subtle Signals in DNA Sequences , 2000, ISMB.
[19] Jacques van Helden,et al. Regulatory Sequence Analysis Tools , 2003, Nucleic Acids Res..
[20] Jun S. Liu,et al. Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies , 1995 .
[21] Kathleen Marchal,et al. A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling , 2001, Bioinform..
[22] Michael Q. Zhang,et al. SCPD: a promoter database of the yeast Saccharomyces cerevisiae , 1999, Bioinform..
[23] Gary D. Stormo,et al. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences , 1999, Bioinform..
[24] T. D. Schneider,et al. Information content of binding sites on nucleotide sequences. , 1986, Journal of molecular biology.
[25] Jun S. Liu,et al. Gibbs motif sampling: Detection of bacterial outer membrane protein repeats , 1995, Protein science : a publication of the Protein Society.
[26] Julio Collado-Vides,et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation , 2007, Nucleic Acids Res..
[27] Kazuhito Shida,et al. Hybrid Gibbs-sampling algorithm for challenging motif discovery: GibbsDST. , 2006, Genome informatics. International Conference on Genome Informatics.
[28] G. Crooks,et al. WebLogo: a sequence logo generator. , 2004, Genome research.
[29] J. Collado-Vides,et al. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. , 1998, Journal of molecular biology.
[30] Kathleen Marchal,et al. A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes , 2001, RECOMB.
[31] Charles Elkan,et al. Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.
[32] Martin Vingron,et al. Natural similarity measures between position frequency matrices with an application to clustering , 2008, Bioinform..
[33] G. Church,et al. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation , 1998, Nature Biotechnology.
[34] William Stafford Noble,et al. Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.