De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference
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Jens Keilwagen | Marc Strickert | Ivo Grosse | Stefan Posch | Jan Grau | Ivan A. Paponov | J. Keilwagen | S. Posch | Jan Grau | I. Grosse | M. Strickert | I. Paponov
[1] Klaus Palme,et al. Comprehensive transcriptome analysis of auxin responses in Arabidopsis. , 2008, Molecular plant.
[2] Vijay V. Raghavan,et al. A critical investigation of recall and precision as measures of retrieval system performance , 1989, TOIS.
[3] Hongyu Zhao,et al. Protein–DNA interaction mapping using genomic tiling path microarrays in Drosophila , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[4] Matthew W. Hahn,et al. The evolution of transcriptional regulation in eukaryotes. , 2003, Molecular biology and evolution.
[5] R. Shamir,et al. Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. , 2008, Genome research.
[6] Christoph Plass,et al. ChIP-chip comes of age for genome-wide functional analysis. , 2006, Cancer research.
[7] Gunnar Rätsch,et al. Accurate splice site prediction using support vector machines , 2007, BMC Bioinformatics.
[8] William Stafford Noble,et al. Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.
[9] Ramón López de Mántaras,et al. Robust Bayesian Linear Classifier Ensembles , 2005, ECML.
[10] Timothy L. Bailey,et al. Discriminative motif discovery in DNA and protein sequences using the DEME algorithm , 2007, BMC Bioinformatics.
[11] Graziano Pesole,et al. An algorithm for finding signals of unknown length in DNA sequences , 2001, ISMB.
[12] Jun S. Liu,et al. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. , 1993, Science.
[13] L. Hellman,et al. Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions , 2007, Nature Protocols.
[14] Ole Winther,et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update , 2007, Nucleic Acids Res..
[15] G. Hagen,et al. Auxin Response Factors , 2001, Journal of Plant Growth Regulation.
[16] A. Mortazavi,et al. Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.
[17] M F Hoylaerts,et al. Nonisotopic quantitative analysis of protein-DNA interactions at equilibrium. , 1997, Analytical biochemistry.
[18] Lee Aaron Newberg,et al. The Gibbs Centroid Sampler , 2007, Nucleic Acids Res..
[19] W. J. Kent,et al. Environmentally Induced Foregut Remodeling by PHA-4/FoxA and DAF-12/NHR , 2004, Science.
[20] N. Slonim,et al. A universal framework for regulatory element discovery across all genomes and data types. , 2007, Molecular cell.
[21] Alexander E. Kel,et al. TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes , 2005, Nucleic Acids Res..
[22] T. D. Schneider,et al. Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.
[23] G. Hagen,et al. Dimerization and DNA binding of auxin response factors. , 1999, The Plant journal : for cell and molecular biology.
[24] Eric C. Rouchka,et al. Gibbs Recursive Sampler: finding transcription factor binding sites , 2003, Nucleic Acids Res..
[25] E. Winzeler,et al. Genomics, gene expression and DNA arrays , 2000, Nature.
[26] Charles Elkan,et al. Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.
[27] Mark Goadrich,et al. The relationship between Precision-Recall and ROC curves , 2006, ICML.
[28] Hans-Peter Mock,et al. Seed-specific transcription factors ABI3 and FUS3: molecular interaction with DNA , 2004, Planta.
[29] David J. C. MacKay,et al. Choice of Basis for Laplace Approximation , 1998, Machine Learning.
[30] G. Hagen,et al. ARF1, a transcription factor that binds to auxin response elements. , 1997, Science.
[31] D. Galas,et al. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. , 1978, Nucleic acids research.
[32] Holger Karas,et al. TRANSFAC: a database on transcription factors and their DNA binding sites , 1996, Nucleic Acids Res..
[33] G. Church,et al. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.
[34] Nak-Kyeong Kim,et al. Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites , 2008, BMC Bioinformatics.
[35] Gunnar Rätsch,et al. ARTS: accurate recognition of transcription starts in human , 2006, ISMB.
[36] Hanna M. Wallach,et al. Conditional Random Fields: An Introduction , 2004 .
[37] Klaus Palme,et al. Auxin in action: signalling, transport and the control of plant growth and development , 2006, Nature Reviews Molecular Cell Biology.
[38] 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.
[39] Nicola J. Rinaldi,et al. Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.
[40] Henry Tirri,et al. On Supervised Learning of Bayesian Network Parameters , 2002 .
[41] Finn Drabløs,et al. Improved benchmarks for computational motif discovery , 2007, BMC Bioinformatics.