Discriminative motif optimization based on perceptron training
暂无分享,去创建一个
[1] Saurabh Sinha,et al. Discriminative motifs , 2002, RECOMB '02.
[2] G. Stormo,et al. Determining the specificity of protein–DNA interactions , 2010, Nature Reviews Genetics.
[3] J. Söding,et al. P-value-based regulatory motif discovery using positional weight matrices , 2013, Genome research.
[4] R. Shamir,et al. Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. , 2008, Genome research.
[5] J. Younger,et al. Statistical methodology: III. Receiver operating characteristic (ROC) curves. , 1997, Academic emergency medicine : official journal of the Society for Academic Emergency Medicine.
[6] Viv Bewick,et al. Statistics review 13: Receiver operating characteristic curves , 2004, Critical care.
[7] Mithat Gönen,et al. Receiver Operating Characteristic (ROC) Curves , 2006 .
[8] Olivier Elemento,et al. DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices , 2009, BMC Bioinformatics.
[9] Atina G. Coté,et al. Evaluation of methods for modeling transcription factor sequence specificity , 2013, Nature Biotechnology.
[10] T. Furey. ChIP – seq and beyond : new and improved methodologies to detect and characterize protein – DNA interactions , 2012 .
[11] Vsevolod J. Makeev,et al. Deep and wide digging for binding motifs in ChIP-Seq data , 2010, Bioinform..
[12] Rahul Siddharthan,et al. PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling , 2008, PLoS Comput. Biol..
[13] Roded Sharan,et al. A motif-based framework for recognizing sequence families , 2005, ISMB.
[14] Saurabh Sinha,et al. On counting position weight matrix matches in a sequence, with application to discriminative motif finding , 2006, ISMB.
[15] Jun S. Liu,et al. An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments , 2002, Nature Biotechnology.
[16] Ziv Bar-Joseph,et al. DECOD: fast and accurate discriminative DNA motif finding , 2011, Bioinform..
[17] Michael Q. Zhang,et al. Identifying tissue-selective transcription factor binding sites in vertebrate promoters. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[18] Qing Zhou,et al. Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data , 2010, Bioinform..
[19] Francis Y. L. Chin,et al. Finding motifs from all sequences with and without binding sites , 2006, Bioinform..
[20] J. Helden,et al. A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs , 2012, Nature Protocols.
[21] Timothy L. Bailey,et al. Gene expression Advance Access publication May 4, 2011 DREME: motif discovery in transcription factor ChIP-seq data , 2011 .
[22] R. A. Lejk. Statistical methodology II , 1974, WSC '74.
[23] Weixiong Zhang,et al. WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar , 2005, Nucleic Acids Res..
[24] Philip N. Benfey,et al. POWRS: Position-Sensitive Motif Discovery , 2012, PloS one.
[25] T. D. Schneider,et al. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. , 1982, Nucleic acids research.
[26] T. Bailey,et al. Inferring direct DNA binding from ChIP-seq , 2012, Nucleic acids research.
[27] Frank Rosenblatt,et al. PRINCIPLES OF NEURODYNAMICS. PERCEPTRONS AND THE THEORY OF BRAIN MECHANISMS , 1963 .
[28] Wenjie Fu,et al. DISCOVER: a feature-based discriminative method for motif search in complex genomes , 2009, Bioinform..
[29] Mathieu Blanchette,et al. Seeder: discriminative seeding DNA motif discovery , 2008, Bioinform..
[30] Timothy L. Bailey,et al. Discriminative motif discovery in DNA and protein sequences using the DEME algorithm , 2007, BMC Bioinformatics.
[31] N. Slonim,et al. A universal framework for regulatory element discovery across all genomes and data types. , 2007, Molecular cell.
[32] Yanzhi Du,et al. AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses , 2011, PloS one.
[33] J. van Helden,et al. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets , 2011, Nucleic acids research.
[34] Yu Liang,et al. BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm080 Sequence analysis , 2022 .