Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules
暂无分享,去创建一个
Mireille Régnier | Julien Clément | Mikhail A. Roytberg | Vsevolod J. Makeev | Valentina Boeva | V. Makeev | M. Régnier | M. Roytberg | V. Boeva | J. Clément
[1] M. Régnier,et al. Mathematical Tools for Regulatory Signals Extraction , 2004 .
[2] G. K. Sandve,et al. A survey of motif discovery methods in an integrated framework , 2006, Biology Direct.
[3] J. Szostak,et al. In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.
[4] Mireille Régnier,et al. Rare Events and Conditional Events on Random Strings , 2004, Discret. Math. Theor. Comput. Sci..
[5] Mireille Régnier,et al. A unified approach to word occurrence probabilities , 2000, Discret. Appl. Math..
[6] William Stafford Noble,et al. Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.
[7] J. Fickett,et al. Identification of regulatory regions which confer muscle-specific gene expression. , 1998, Journal of molecular biology.
[8] Kathleen Marchal,et al. Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1 , 2003, Plant Physiology.
[9] Gesine Reinert,et al. Compound Poisson and Poisson Process Approximations for Occurrences of Multiple Words in Markov Chains , 1998, J. Comput. Biol..
[10] Nikolay A. Kolchanov,et al. Bioinformatics of Genome Regulation and Structure , 2013, Springer US.
[11] G. Kucherov,et al. Multiseed lossless filtration , 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[12] Files for Figures,et al. Genes Regulated Cooperatively By One or More Transcription Factors and Their Identification in Whole Eukaryotic Genomes , 1998 .
[13] Nicola J. Rinaldi,et al. Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.
[14] Richard Arratia,et al. Central Limit Theorem from Renewal Theory for Several Patterns , 1997, J. Comput. Biol..
[15] Martha L Bulyk,et al. DNA microarray technologies for measuring protein-DNA interactions. , 2006, Current opinion in biotechnology.
[16] Yuh-Jyh Hu,et al. Combinatorial motif analysis and hypothesis generation on a genomic scale , 2000, Bioinform..
[17] J. Lengyel,et al. Control of tailless expression by bicoid, dorsal and synergistically interacting terminal system regulatory elements , 1993, Mechanisms of Development.
[18] Jean-Jacques Daudin,et al. Exact distribution of word occurrences in a random sequence of letters , 1999, Journal of Applied Probability.
[19] Philippe Flajolet,et al. Motif statistics , 1999, Theor. Comput. Sci..
[20] Pierre Nicodème,et al. Regexpcount, a symbolic package for counting problems on regular expressions and words , 2000, Fundam. Informaticae.
[21] Thomas Werner,et al. Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach , 2000, Silico Biol..
[22] Anna G. Nazina,et al. Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. , 2003, Nucleic acids research.
[23] Ernest Fraenkel,et al. Practical Strategies for Discovering Regulatory DNA Sequence Motifs , 2006, PLoS Comput. Biol..
[24] James W Carman,et al. Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately controlled genes. , 2002, Genome research.
[25] L. Gold,et al. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.
[26] A. Mikaelyan,et al. Constructive Synergism of Regulatory Genes Expressed in the Course of Eye and Muscle Development and Regeneration , 2001, Biology Bulletin of the Russian Academy of Sciences.
[27] Donald E. Knuth,et al. The art of computer programming: sorting and searching (volume 3) , 1973 .
[28] S. Salzberg,et al. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura , 2004, Genome Biology.
[29] O. Berg,et al. Selection of DNA binding sites by regulatory proteins. Functional specificity and pseudosite competition. , 1988, Journal of biomolecular structure & dynamics.
[30] O. Chrysaphinou,et al. The Occurrence of Sequence Patterns in Repeated Dependent Experiments , 1991 .
[31] Maude Pupin,et al. Detecting Localized Repeats in Genomic Sequences: A New Strategy and Its Application to Bacillus Subtilis and Arabidopsis Thaliana Sequences , 2000, Comput. Chem..
[32] Leonidas J. Guibas,et al. String Overlaps, Pattern Matching, and Nontransitive Games , 1981, J. Comb. Theory A.
[33] Eric H Davidson,et al. New computational approaches for analysis of cis-regulatory networks. , 2002, Developmental biology.
[34] Peter W. Markstein,et al. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[35] Peter W. Markstein,et al. A regulatory code for neurogenic gene expression in the Drosophila embryo , 2004, Development.
[36] P. V. von Hippel,et al. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. , 1987, Journal of molecular biology.
[37] Donald E. Knuth,et al. The Art of Computer Programming: Volume 3: Sorting and Searching , 1998 .
[38] C. Desplan,et al. Cooperative interactions between paired domain and homeodomain. , 1996, Development.
[39] William Krivan. Searching for Transcription Factor Binding Site Clusters: How True Are True Positives? , 2004, J. Bioinform. Comput. Biol..
[40] Mireille Régnier,et al. Assessing the Significance of Sets of Words , 2005, CPM.
[41] Dmitri A. Papatsenko,et al. ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors , 2007, Bioinform..
[42] Bart De Moor,et al. Computational detection of cis-regulatory modules , 2003, ECCB.
[43] William Stafford Noble,et al. Searching for statistically significant regulatory modules , 2003, ECCB.
[44] 加藤 護. Identifying combinatorial regulation of transcription factors and binding motifs , 2004 .
[45] A. Wagner,et al. A computational genomics approach to the identification of gene networks. , 1997, Nucleic acids research.
[46] Yunlong Liu,et al. Modeling Transcriptional Regulation in Chondrogenesis Using Particle Swarm Optimization , 2005, 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
[47] Dmitri Papatsenko,et al. A self-organizing system of repressor gradients establishes segmental complexity in Drosophila , 2003, Nature.
[48] John L. Spouge,et al. Searching for Multiple Words in a Markov Sequence , 2004, INFORMS J. Comput..
[49] Eytan Domany,et al. Finding Motifs in Promoter Regions , 2005, J. Comput. Biol..
[50] Gregory Kucherov,et al. Multi-seed Lossless Filtration (Extended Abstract) , 2004, CPM.
[51] J. Shendure,et al. Discovering functional transcription-factor combinations in the human cell cycle. , 2005, Genome research.
[52] Wojciech Szpankowski,et al. Average Case Analysis of Algorithms on Sequences: Szpankowski/Average , 2001 .
[53] W. Szpankowski. Average Case Analysis of Algorithms on Sequences , 2001 .
[54] Martin C. Frith,et al. Cluster-Buster: finding dense clusters of motifs in DNA sequences , 2003, Nucleic Acids Res..
[55] M. Levine,et al. Regulation of even‐skipped stripe 2 in the Drosophila embryo. , 1992, The EMBO journal.
[56] Alfred V. Aho,et al. Efficient string matching , 1975, Commun. ACM.
[57] Julien Clément,et al. Counting occurrences for a finite set of words: an inclusion-exclusion approach , 2007 .
[58] Mathieu Blanchette,et al. Separating real motifs from their artifacts , 2001, ISMB.
[59] Marc S Halfon,et al. Exploring genetic regulatory networks in metazoan development: methods and models. , 2002, Physiological genomics.
[60] A. Philippakis,et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities , 2006, Nature Biotechnology.
[61] Anna G. Nazina,et al. Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. , 2002, Genome research.
[62] Michael Q. Zhang,et al. BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btl662 Sequence analysis Computing exact P-values for DNA motifs , 2022 .
[63] Eric D Siggia,et al. Identification of the binding sites of regulatory proteins in bacterial genomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[64] Anna G. Nazina,et al. Homotypic regulatory clusters in Drosophila. , 2003, Genome research.
[65] Martin C. Frith,et al. Detection of cis -element clusters in higher eukaryotic DNA , 2001, Bioinform..
[66] Barry Honig,et al. Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors , 2003, Nucleic Acids Res..
[67] Mark Rebeiz,et al. SCORE: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[68] Mireille Régnier,et al. Comparison of Statistical Significance Criteria , 2006, J. Bioinform. Comput. Biol..
[69] Rodger Staden,et al. Methods for calculating the probabilities of finding patterns in sequences , 1989, Comput. Appl. Biosci..