Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.
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Diego Miranda-Saavedra | Berthold Göttgens | Marc S. Halfon | Saurabh Sinha | Gene E. Robinson | Majid Kazemian | Qiyun Zhu | Miriam R. Kantorovitz | Sarah Kinston | G. Robinson | B. Göttgens | S. Kinston | S. Sinha | D. Miranda-Saavedra | M. Kazemian | M. Halfon | M. R. Kantorovitz | Qiyun Zhu | Diego Miranda-Saavedra | S. Sinha
[1] Z. Weng,et al. Detection of functional DNA motifs via statistical over-representation. , 2004, Nucleic acids research.
[2] E. Davidson,et al. The hardwiring of development: organization and function of genomic regulatory systems. , 1997, Development.
[3] Dmitri A. Papatsenko,et al. Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency , 2003, BMC Bioinformatics.
[4] M. Noyes,et al. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system , 2008, Nucleic acids research.
[5] R. Maeda,et al. An optimized transgenesis system for Drosophila using germ-line-specific φC31 integrases , 2007, Proceedings of the National Academy of Sciences.
[6] Walter R. Gilks,et al. Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test , 2004, BMC Bioinformatics.
[7] Steven M. Gallo,et al. REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila , 2007, Nucleic Acids Res..
[8] G. Benson,et al. Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.
[9] Marc S Halfon,et al. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. , 2002, Genome research.
[10] Martin C. Frith,et al. Cluster-Buster: finding dense clusters of motifs in DNA sequences , 2003, Nucleic Acids Res..
[11] Massimo Vergassola,et al. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo , 2002, BMC Bioinformatics.
[12] Ivan Ovcharenko,et al. ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes , 2007, Bioinform..
[13] G. Rubin,et al. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[14] G. Stormo,et al. Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. , 2002, Genome research.
[15] Jiang Qian,et al. Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors , 2007, BMC Bioinformatics.
[16] Saurabh Sinha,et al. A probabilistic method to detect regulatory modules , 2003, ISMB.
[17] E. Davidson. The Regulatory Genome: Gene Regulatory Networks In Development And Evolution , 2006 .
[18] Marc S Halfon,et al. Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs , 2008, Genome Biology.
[19] M. Busslinger,et al. Lineage commitment in lymphopoiesis. , 2000, Current opinion in immunology.
[20] William Stafford Noble,et al. Assessing computational tools for the discovery of transcription factor binding sites , 2005, Nature Biotechnology.
[21] Dennis F. Kibler,et al. Using hexamers to predict cis-regulatory motifs in Drosophila , 2005, BMC Bioinformatics.
[22] N. Gostling,et al. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design , 2002, Heredity.
[23] Alan M. Moses,et al. In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.
[24] Berthold Göttgens,et al. TFBScluster: a resource for the characterization of transcriptional regulatory networks , 2005, Bioinform..
[25] Marc S Halfon,et al. Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses , 2007, Genome Biology.
[26] B. Göttgens,et al. Endoglin expression in the endothelium is regulated by Fli-1, Erg, and Elf-1 acting on the promoter and a -8-kb enhancer. , 2006, Blood.
[27] S. Carroll,et al. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design , 2000 .
[28] M. Laubichler. Review of: Carroll, Sean B., Jennifer K. Grenier and Scott D. Weatherbee: From DNA to diversity : molecular genetics and the evolution of animal design. Malden, Mass [u.a.]: Blackwell Science 2001 , 2003 .
[29] Xiaoyu Chen,et al. Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees , 2007, BMC Bioinformatics.
[30] Marc S. Halfon,et al. Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura , 2004, Bioinform..
[31] Subhajyoti De,et al. BloodExpress: a database of gene expression in mouse haematopoiesis , 2008, Nucleic Acids Res..
[32] A. Philippakis,et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities , 2006, Nature Biotechnology.
[33] Saurabh Sinha,et al. A statistical method for alignment-free comparison of regulatory sequences , 2007, ISMB/ECCB.
[34] A. Visel,et al. ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.
[35] J. Skeath,et al. Characterization of a novel subset of cardiac cells and their progenitors in the Drosophila embryo. , 2000, Development.
[36] E. Ukkonen,et al. Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity , 2006, Cell.
[37] Alexander E. Kel,et al. TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..
[38] Saurabh Sinha,et al. A Statistical Method for Finding Transcription Factor Binding Sites , 2000, ISMB.
[39] Piero Carninci,et al. The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. , 2002, Genome research.
[40] Anthony A. Philippakis,et al. ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules , 2004, Pacific Symposium on Biocomputing.
[41] Ivan Ovcharenko,et al. Predicting tissue-specific enhancers in the human genome. , 2006, Genome research.
[42] B. Göttgens,et al. Fli1, Elf1, and Ets1 regulate the proximal promoter of the LMO2 gene in endothelial cells. , 2005, Blood.
[43] 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..
[44] D. W. Knowles,et al. Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm , 2008, PLoS biology.
[45] Andrea Califano,et al. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting , 2007, Proceedings of the National Academy of Sciences.
[46] Michael Q. Zhang,et al. Tissue-specific Regulatory Elements in Mammalian Promoters: Supplementary Information 1 Transcripts and Promoters under Tissue-specific Regulation , 2022 .
[47] J. Fak,et al. Transcriptional Control in the Segmentation Gene Network of Drosophila , 2004, PLoS biology.
[48] J. Reinitz,et al. Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins , 1998, Development Genes and Evolution.