Promoter prediction analysis on the whole human genome

Keywords

In silico, Genome, Promoter, CpG site, Computational biology

References

• Mechanisms of Gene Expression: Structure, Function and Evolution of the Basal Transcriptional MachineryRobert O. J. Weinzierl — 1999
• Large-scale human promoter mapping using CpG islandsIlya Ioshikhes, Michael Q. Zhang — 2000
• Pattern Recognition and Neural NetworksYann LeCun, Yoshua Bengio — 1995
• Diverse transcriptional initiation revealed by fine, large‐scale mapping of mRNA start sitesYutaka Suzuki, Hirotoshi Taira, Tatsuhiko Tsunoda — 2001
• Computational detection and location of transcription start sites in mammalian genomic DNA.Thomas A. Down, Tim Hubbard — 2002
• Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates.Vladimir B. Bajić, Seng Hong Seah, Allen Chong — 2003
• Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units.Vladimir B. Bajić, Seng Hong Seah — 2003
• Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling.Rongxiang Liu, David J. States — 2002
• Application of a Time-delay Neural Network to Promoter Annotation in the Drosophila Melanogaster GenomeMartin G. Reese — 2001
• Stochastic segment models of eukaryotic promoter regions.Uwe Ohler, Georg Stemmer, Stefan Harbeck — 1999
• Computational analysis of core promoters in the Drosophila genomeUwe Ohler, Guochun Liao, Heinrich Niemann — 2002
• The Biology of Eukaryotic Promoter Prediction - A ReviewAnders Gorm Pedersen, Pierre Baldi, Yves Chauvin — 1999
• Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach.Matthias Scherf, Andreas Klingenhoff, Thomas Werner — 2000
• Promoter2.0: for the recognition of PolII promoter sequencesSteen Knudsen — 1999
• CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequencesLoı̈c Ponger, Dominique Mouchiroud — 2002
• Dragon Gene Start Finder identifies approximate locations of the 5' ends of genesVladimir B. Bajić — 2003
• Promoter prediction in the human genomeSridhar Hannenhalli, Samuel Lévy — 2001
• First pass annotation of promoters on human chromosome 22.Matthias Scherf, Andreas Klingenhoff, Kornelie Frech — 2001
• Computational identification of promoters and first exons in the human genomeRamana V. Davuluri, Ivo Große, Michael Q. Zhang — 2001
• DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAsYasuhiro Suzuki — 2002

Cited by

• The procollagen type III, alpha 1 (COL3A1) gene first intron expresses poly‐A+ RNA corresponding to multiple ESTs and putative miRNAsShigeru Nakao — 2011
• Machine learning for genomic sequence analysisSonnenburg, Soeren — 2008
• Control of human gene expression: High abundance of divergent transcription in genes containing both INR and BRE elements in the core promoterPeter Wagstaff — 2018
• Computational analyses to identify and study cis-regulatory regions in eukaryotesKrishnakumar Sridharan — 2012
• Identification and characterization of transcriptional enhancers in the human genomeNathaniel D. Heintzman — 2007
• Regulatory modules discovery and mesenchymal stem cells characterization from high-throughput cancer genomics dataYari Ciani — 2015
• Human Promoter Prediction Using DNA Numerical RepresentationSwarna Bai Arniker — 2010
• Pulsing response of the cardiac transcriptomeRuben Martherus — 2011
• Human Promoter Recognition Based on Principal Component AnalysisXiaomeng Li — 2008
• The bystander effect : animal and plant modelsF. Zemp — 2008
• Overview Article: Identifying transcriptional cis-regulatory modules in animal genomesKushal Suryamohan, Marc S. Halfon — 2014
• Bayesian classification for promoter prediction in human DNA sequencesJean‐François Bercher, Patrick du Jardin, Bénédicte Duriez — 2006
• Non-Sparse Regularization for Multiple Kernel LearningMarius Kloft, Ulf Brefeld, Soeren Sonnenburg — 2010
• Robust machine learning algorithms predict microRNA genes and targets.Pål Sætrom, Ola Snøve — 2007
• Co-occurrence of transcription factor binding sites (Gemeinsames Auftreten von Transkriptionsfaktor-Bindungsstellen)Holger Klein — 2010
• Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairsVictor X. Jin, Gregory A. C. Singer, Francisco Agosto-Perez — 2006
• GC-compositional strand bias around transcription start sites in plants and fungiShigeo Fujimori, Takanori Washio, Masaru Tomita — 2005
• Generalizations of Markov model to characterize biological sequencesJunwen Wang, Sridhar Hannenhalli — 2005
• Analysis of n-Gram based Promoter Recognition Methods and Application to Whole Genome Promoter PredictionT. Sobha Rani, Raju S. Bapi — 2009
• ElemeNT: a computational tool for detecting core promoter elementsAnna Sloutskin, Yehuda M. Danino, Yaron Orenstein — 2015

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