Eukaryotic and prokaryotic promoter prediction using hybrid approach
暂无分享,去创建一个
[1] R. Laxton. The measure of diversity. , 1978, Journal of theoretical biology.
[2] G. Rubin,et al. Computational analysis of core promoters in the Drosophila genome , 2002, Genome Biology.
[3] R. Zhang,et al. Improving Promoter Prediction for the NNPP 2 . 2 Algorithm : A Case Study Using EColi DNA Sequences , 2004 .
[4] A. Sandelin,et al. Applied bioinformatics for the identification of regulatory elements , 2004, Nature Reviews Genetics.
[5] Manju Bansal,et al. Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability , 2007, Journal of Biosciences.
[6] Hao Lin,et al. The recognition and prediction of σ70 promoters in Escherichia coli K-12 , 2006 .
[7] James M. Hogan,et al. Improved prediction of bacterial transcription start sites , 2006 .
[8] Gunnar Rätsch,et al. ARTS: accurate recognition of transcription starts in human , 2006, ISMB.
[9] Manju Bansal,et al. Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition. , 2009, Molecular bioSystems.
[10] Martin G. Reese,et al. Application of a Time-delay Neural Network to Promoter Annotation in the Drosophila Melanogaster Genome , 2001, Comput. Chem..
[11] A. Kassim,et al. Digital signal processing for potential promoter prediction , 2004, IEEE International Workshop on Biomedical Circuits and Systems, 2004..
[12] Heinrich Niemann,et al. Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition , 2001, ISMB.
[13] U. Ohler. Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction , 2006, Nucleic acids research.
[14] K. Chou,et al. Prediction and classification of domain structural classes , 1998, Proteins.
[15] S. Durga Bhavani,et al. Analysis of E.coli promoter recognition problem in dinucleotide feature space , 2007, Bioinform..
[16] M Kanehisa,et al. An assessment of neural network and statistical approaches for prediction of E. coli promoter sites. , 1992, Nucleic acids research.
[17] Liaofu Luo,et al. Splice site prediction with quadratic discriminant analysis using diversity measure. , 2003, Nucleic acids research.
[18] Michael Q. Zhang,et al. Using CorePromoter to Find Human Core Promoters , 2005, Current protocols in bioinformatics.
[19] Julio Collado-Vides,et al. RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 , 2004, Nucleic Acids Res..
[20] Ray Walshe,et al. Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach , 2008, BMC Bioinformatics.
[21] Vladimir B. Bajic,et al. Content analysis of the core promoter region of human genes , 2003, Silico Biol..
[22] Michael Q. Zhang,et al. Computational identification of promoters and first exons in the human genome , 2001, Nature Genetics.
[23] D. K. Hawley,et al. Compilation and analysis of Escherichia coli promoter DNA sequences. , 1983, Nucleic acids research.
[24] Stefan Maetschke,et al. Genome-wide analysis of chlamydiae for promoters that phylogenetically footprint. , 2007, Research in microbiology.
[25] Yu Zhou,et al. Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides , 2007, BMC Bioinformatics.
[26] Yves Moreau,et al. Comprehensive analysis of the base composition around the transcription start site in Metazoa , 2004, BMC Genomics.
[27] R. Zhang,et al. Improving promoter prediction for the NNPP 2 . 2 algorithm : a case study using Escherichia coli DNA sequences , 2004 .
[28] A. J. Gammerman,et al. Plant promoter prediction with confidence estimation , 2005, Nucleic acids research.
[29] Vladimir B. Bajic,et al. Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters , 2002, Bioinform..
[30] Yvan Saeys,et al. ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles , 2008, ISMB.
[31] Modesto Orozco,et al. Determining promoter location based on DNA structure first-principles calculations , 2007, Genome Biology.
[32] Pierre Baldi,et al. The Biology of Eukaryotic Promoter Prediction - A Review , 1999, Comput. Chem..
[33] Victor G. Levitsky,et al. Recognition of eukaryotic promoters using a genetic algorithm based on iterative discriminant analysis , 2003, Silico Biol..
[34] Dennis F. Kibler,et al. Using hexamers to predict cis-regulatory motifs in Drosophila , 2005, BMC Bioinformatics.
[35] Valery Shepelev,et al. Advances in the Exon-Intron Database (EID) , 2006, Briefings Bioinform..
[36] Lior Pachter,et al. Combining statistical alignment and phylogenetic footprinting to detect regulatory elements , 2008, Bioinform..
[37] Philipp Bucher,et al. EPD in its twentieth year: towards complete promoter coverage of selected model organisms , 2005, Nucleic Acids Res..
[38] K. Chou. A novel approach to predicting protein structural classes in a (20–1)‐D amino acid composition space , 1995, Proteins.
[39] Victor V. Solovyev,et al. PromH: promoters identification using orthologous genomic sequences , 2003, Nucleic Acids Res..
[40] Szymon M. Kielbasa,et al. Measuring similarities between transcription factor binding sites , 2005, BMC Bioinformatics.
[41] T. Hubbard,et al. Computational detection and location of transcription start sites in mammalian genomic DNA. , 2002, Genome research.
[42] Peter Timms,et al. Phylogenetic comparison of the known Chlamydia trachomatis sigma(66) promoters across to Chlamydia pneumoniae and Chlamydia caviae identifies seven poorly conserved promoters. , 2008, Research in microbiology.
[43] Alexander Gammerman,et al. Sequence alignment kernel for recognition of promoter regions , 2003, Bioinform..
[44] D. S. Prestridge. Predicting Pol II promoter sequences using transcription factor binding sites. , 1995, Journal of molecular biology.
[45] Yvan Saeys,et al. Generic eukaryotic core promoter prediction using structural features of DNA. , 2008, Genome research.
[46] Panos Deloukas,et al. DNA sequence and structural properties as predictors of human and mouse promoters , 2008, Gene.
[47] Anders Gorm Pedersen,et al. Investigations of Escherichia coli Promoter Sequences with Artificial Neural Networks: New Signals Discovered Upstream of the Transcriptional Startpoint , 1995, ISMB.
[48] Kenta Nakai,et al. BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics , 2004, Nucleic Acids Res..
[49] Huiquan Wang,et al. Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress , 2006, BMC Bioinformatics.
[50] Elmar Nöth,et al. Interpolated markov chains for eukaryotic promoter recognition , 1999, Bioinform..
[51] G. B. Hutchinson,et al. The prediction of vertebrate promoter regions using differential hexamer frequency analysis , 1996, Comput. Appl. Biosci..
[52] Eric C. Rouchka,et al. RBF-TSS: Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies , 2009, PloS one.
[53] Michael Ruogu Zhang,et al. Identification of protein coding regions in the human genome by quadratic discriminant analysis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[54] Julio Collado-Vides,et al. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. , 2003, Journal of molecular biology.
[55] R. Gangal,et al. Human pol II promoter prediction: time series descriptors and machine learning , 2005, Nucleic acids research.
[56] Dominique Mouchiroud,et al. CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences , 2002, Bioinform..
[57] Jacques van Helden,et al. Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution , 2008, BMC Bioinformatics.
[58] Liaofu Luo,et al. Use of tetrapeptide signals for protein secondary-structure prediction , 2008, Amino Acids.
[59] Steen Knudsen,et al. Promoter2.0: for the recognition of PolII promoter sequences , 1999, Bioinform..
[60] Pierre Baldi,et al. Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models , 1996, ISMB.