GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group
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Tzong-Yi Lee | Justin Bo-Kai Hsu | Tzu-Hao Chang | Wen-Chi Chang | Dray-Ming Shien | Tzong-Yi Lee | J. B. Hsu | Tzu-Hao Chang | W. Chang | Dray-Ming Shien | Wen-Chi Chang
[1] T. Hubbard,et al. Computational detection and location of transcription start sites in mammalian genomic DNA. , 2002, Genome research.
[2] Mattias Höglund,et al. Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs , 2010, BMC Genomics.
[3] Seng Hong Seah,et al. Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. , 2003, Genome research.
[4] G. Rubin,et al. Computational analysis of core promoters in the Drosophila genome , 2002, Genome Biology.
[5] K. Gardner,et al. Identification of new Rel/NFκB regulatory networks by focused genome location analysis , 2009, Cell cycle.
[6] E. Wingender,et al. MATCH: A tool for searching transcription factor binding sites in DNA sequences. , 2003, Nucleic acids research.
[7] Wyeth W. Wasserman,et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..
[8] L. Aravind,et al. Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. , 2006, Journal of molecular biology.
[9] Martin S. Taylor,et al. Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.
[10] B. De Moor,et al. Toucan: deciphering the cis-regulatory logic of coregulated genes. , 2003, Nucleic acids research.
[11] Hsien-Da Huang,et al. Identifying transcriptional regulatory sites in the human genome using an integrated system. , 2004, Nucleic acids research.
[12] Manju Bansal,et al. A novel method for prokaryotic promoter prediction based on DNA stability , 2005, BMC Bioinformatics.
[13] Victor V. Solovyev,et al. PromH: promoters identification using orthologous genomic sequences , 2003, Nucleic Acids Res..
[14] Manju Bansal,et al. Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes , 2005, Nucleic acids research.
[15] G. Benson,et al. Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.
[16] H. Karas,et al. TRANSFAC database as a bridge between sequence data libraries and biological function. , 1997, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[17] Kenta Nakai,et al. Modeling tissue-specific structural patterns in human and mouse promoters , 2009, Nucleic acids research.
[18] T. Curran,et al. Role of DNA 5-methylcytosine transferase in cell transformation by fos. , 1999, Science.
[19] Tao Liu,et al. CEAS: cis-regulatory element annotation system , 2009, Bioinform..
[20] Kenta Nakai,et al. DBTSS: DataBase of Human Transcription Start Sites, progress report 2006 , 2005, Nucleic Acids Res..
[21] Zhiping Weng,et al. PromoSer: a large-scale mammalian promoter and transcription start site identification service , 2003, Nucleic Acids Res..
[22] Chih-Jen Lin,et al. LIBSVM: A library for support vector machines , 2011, TIST.
[23] Xin Chen,et al. TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..
[24] Michael Ruogu Zhang,et al. Computational identification of promoters and first exons in the human genome , 2002, Nature Genetics.
[25] Xueping Yu,et al. Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae , 2006, Nucleic acids research.
[26] Kengo Kinoshita,et al. COXPRESdb: a database to compare gene coexpression in seven model animals , 2010, Nucleic Acids Res..
[27] Dominique Mouchiroud,et al. CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences , 2002, Bioinform..
[28] U. Ohler,et al. Promoter Prediction on a Genomic Scale – the Adh Experience , 2000 .
[29] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[30] Damian Smedley,et al. Ensembl 2005 , 2004, Nucleic Acids Res..
[31] M. Batzer,et al. Alu repeats and human genomic diversity , 2002, Nature Reviews Genetics.
[32] Elmar Nöth,et al. Interpolated markov chains for eukaryotic promoter recognition , 1999, Bioinform..
[33] J. SantaLucia,et al. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[34] R. Zhang,et al. Improving promoter prediction for the NNPP 2 . 2 algorithm : a case study using Escherichia coli DNA sequences , 2004 .
[35] S. Burden,et al. Sequence analysis Improving promoter prediction for the NNPP 2 . 2 algorithm : a case study using Escherichia coli DNA sequences , 2005 .
[36] P. Zimmermann,et al. GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1[w] , 2004, Plant Physiology.
[37] Alexander E. Kel,et al. MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..
[38] Michael Q. Zhang,et al. Identifying combinatorial regulation of transcription factors and binding motifs , 2004, Genome Biology.
[39] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[40] Ramakrishnan Srikant,et al. Mining generalized association rules , 1995, Future Gener. Comput. Syst..
[41] Ankush Mittal,et al. Computational modeling of oligonucleotide positional densities for human promoter prediction , 2005, Artif. Intell. Medicine.
[42] Martin Tompa,et al. Discovery of regulatory elements in vertebrates through comparative genomics , 2005, Nature Biotechnology.
[43] Jun Song,et al. CEAS: cis-regulatory element annotation system , 2006, Nucleic Acids Res..
[44] Sin Lam Tan,et al. Promoter prediction analysis on the whole human genome , 2004, Nature Biotechnology.
[45] Tzong-Yi Lee,et al. PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups , 2008, BMC Genomics.
[46] Yoshihide Hayashizaki,et al. [FANTOM-DB: database of functional annotation of RIKEN mouse cDNA clones]. , 2003, Seikagaku. The Journal of Japanese Biochemical Society.
[47] Michael Q. Zhang,et al. Genome-wide promoter extraction and analysis in human, mouse, and rat , 2005, Genome Biology.
[48] K. Chou,et al. Recent progress in protein subcellular location prediction. , 2007, Analytical biochemistry.
[49] C. Vinson,et al. Clustering of DNA sequences in human promoters. , 2004, Genome research.
[50] Martin G. Reese,et al. Application of a Time-delay Neural Network to Promoter Annotation in the Drosophila Melanogaster Genome , 2001, Comput. Chem..
[51] Jef D. Boeke,et al. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes , 2004, Nature.
[52] Kengo Kinoshita,et al. COXPRESdb: a database of coexpressed gene networks in mammals , 2007, Nucleic Acids Res..
[53] E. Birney,et al. The Ensembl core software libraries. , 2004, Genome research.