Coordinated networks of microRNAs and transcription factors with evolutionary perspectives.
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[1] Albertha J. M. Walhout,et al. The interplay between transcription factors and microRNAs in genome‐scale regulatory networks , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.
[2] Chung-I Wu,et al. Evolution under canalization and the dual roles of microRNAs: a hypothesis. , 2009, Genome research.
[3] Manolis Kellis,et al. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. , 2007, Genome research.
[4] Job Harms,et al. THE LANDSCAPE OF , 2010 .
[5] Srinka Ghosh,et al. Biological function of unannotated transcription during the early development of Drosophila melanogaster , 2006, Nature Genetics.
[6] Bing Su,et al. Rapid evolution of an X-linked microRNA cluster in primates. , 2007, Genome research.
[7] U. Alon. Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.
[8] C. Allis,et al. Translating the Histone Code , 2001, Science.
[9] Xin Li,et al. A microRNA Mediates EGF Receptor Signaling and Promotes Photoreceptor Differentiation in the Drosophila Eye , 2005, Cell.
[10] I. King Jordan,et al. A Family of Human MicroRNA Genes from Miniature Inverted-Repeat Transposable Elements , 2007, PloS one.
[11] Anjali J. Koppal,et al. Supplementary data: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites , 2010 .
[12] Wyeth W. Wasserman,et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..
[13] I. K. Jordan,et al. Origin and Evolution of Human microRNAs From Transposable Elements , 2007, Genetics.
[14] Guiliang Tang,et al. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region , 2004 .
[15] S. Shen-Orr,et al. Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.
[16] S. Batalov,et al. A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[17] T. Ishida,et al. Transcriptional double-autorepression feedforward circuits act for multicellularity and nervous system development , 2011, BMC Genomics.
[18] Wen-Hsiung Li,et al. Lowly expressed human microRNA genes evolve rapidly. , 2009, Molecular biology and evolution.
[19] Yitzhak Pilpel,et al. Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network , 2007, PLoS Comput. Biol..
[20] Yvonne Tay,et al. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation , 2008, Nature.
[21] M. Nei,et al. Concerted and birth-and-death evolution of multigene families. , 2005, Annual review of genetics.
[22] R. Milo,et al. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[23] Anton J. Enright,et al. MicroRNA targets in Drosophila , 2003, Genome Biology.
[24] M. Lynch. The frailty of adaptive hypotheses for the origins of organismal complexity , 2007, Proceedings of the National Academy of Sciences.
[25] E. Levanon,et al. Human housekeeping genes are compact. , 2003, Trends in genetics : TIG.
[26] N. Rajewsky. microRNA target predictions in animals , 2006, Nature Genetics.
[27] S. Shen-Orr,et al. Superfamilies of Evolved and Designed Networks , 2004, Science.
[28] D. Bartel,et al. The impact of microRNAs on protein output , 2008, Nature.
[29] G. Rubin,et al. Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[30] Yukio Hori,et al. ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences , 2008, BMC Bioinformatics.
[31] N. Rajewsky,et al. Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.
[32] Stijn van Dongen,et al. miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..
[33] Jason S. Cumbie,et al. High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes , 2007, PloS one.
[34] Holger Karas,et al. TRANSFAC: a database on transcription factors and their DNA binding sites , 1996, Nucleic Acids Res..
[35] T. Gojobori,et al. Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[36] D. Bartel. MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.
[37] Jian Lu,et al. Reply to “Evolutionary flux of canonical microRNAs and mirtrons in Drosophila” , 2010, Nature Genetics.
[38] Peter F Stadler,et al. Molecular evolution of a microRNA cluster. , 2004, Journal of molecular biology.
[39] Anton J. Enright,et al. Human MicroRNA Targets , 2004, PLoS biology.
[40] T. Ishida,et al. MicroRNA networks alter to conform to transcription factor networks adding redundancy and reducing the repertoire of target genes for coordinated regulation. , 2011, Molecular biology and evolution.
[41] S. Salzberg,et al. The Transcriptional Landscape of the Mammalian Genome , 2005, Science.
[42] Robert D. Finn,et al. InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..
[43] Kevin Kim,et al. Targets of microRNA regulation in the Drosophila oocyte proteome. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[44] D. Bartel,et al. Formation, Regulation and Evolution of Caenorhabditis elegans 3′UTRs , 2010, Nature.
[45] R. Aharonov,et al. Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.
[46] Noam Shomron,et al. Canalization of development by microRNAs , 2006, Nature Genetics.
[47] Lynn Doucette-Stamm,et al. A C . elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity , 2008 .
[48] M. Lynch. The evolution of genetic networks by non-adaptive processes , 2007, Nature Reviews Genetics.
[49] Michael Kertesz,et al. The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.
[50] G. Hannon,et al. Evolutionary flux of canonical microRNAs and mirtrons in Drosophila , 2010, Nature Genetics.
[51] D. Bartel. MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.
[52] C. Burge,et al. Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.
[53] Zhaolei Zhang,et al. Evolution of an X-linked primate-specific micro RNA cluster. , 2010, Molecular biology and evolution.
[54] Jan Krüger,et al. RNAhybrid: microRNA target prediction easy, fast and flexible , 2006, Nucleic Acids Res..
[55] Doron Betel,et al. The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..
[56] T. Masaki,et al. Abundance of microRNA target motifs in the 3′‐UTRs of 20 527 human genes , 2007, FEBS letters.
[57] Mary Goldman,et al. The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..
[58] E. Lai,et al. The Mirtron Pathway Generates microRNA-Class Regulatory RNAs in Drosophila , 2007, Cell.
[59] C. Burge,et al. Prediction of Mammalian MicroRNA Targets , 2003, Cell.
[60] Sarah A. Teichmann,et al. DBD: a transcription factor prediction database , 2005, Nucleic Acids Res..
[61] Alexander E. Kel,et al. TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes , 2005, Nucleic Acids Res..
[62] Scott B. Dewell,et al. Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.
[63] I. K. Jordan,et al. Dual coding of siRNAs and miRNAs by plant transposable elements. , 2008, RNA.
[64] Kai Zeng,et al. Adaptive evolution of newly emerged micro-RNA genes in Drosophila. , 2008, Molecular biology and evolution.
[65] Gi-Ho Sung,et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana , 2004, Nature Genetics.
[66] Michael T. McManus,et al. The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development , 2005, Nature.
[67] C. Burge,et al. The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution , 2005, Science.
[68] Oliver Hofmann,et al. miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements. , 2009, Molecular cell.
[69] Edgar Wingender,et al. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation , 2008, Briefings Bioinform..
[70] V. Kim,et al. The nuclear RNase III Drosha initiates microRNA processing , 2003, Nature.
[71] R. Shiekhattar,et al. Human RISC Couples MicroRNA Biogenesis and Posttranscriptional Gene Silencing , 2005, Cell.
[72] Jessica Treisman,et al. The Conserved microRNA MiR-8 Tunes Atrophin Levels to Prevent Neurodegeneration in Drosophila , 2007, Cell.
[73] C. Burge,et al. Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.
[74] Jian Lu,et al. The birth and death of microRNA genes in Drosophila , 2008, Nature Genetics.
[75] S. Nelson,et al. Molecular taxonomy of major neuronal classes in the adult mouse forebrain , 2006, Nature Neuroscience.
[76] Ana Kozomara,et al. miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..
[77] J. Lieberman,et al. Desperately seeking microRNA targets , 2010, Nature Structural &Molecular Biology.
[78] D. Bartel,et al. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. , 2005, RNA.
[79] Emile Zuckerkandl,et al. Neutral and Nonneutral Mutations: The Creative Mix—Evolution of Complexity in Gene Interaction Systems , 1997, Journal of Molecular Evolution.
[80] Colin N. Dewey,et al. A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans , 2006, Current Biology.
[81] Juan M. Vaquerizas,et al. A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.
[82] B. Reinhart,et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans , 2000, Nature.
[83] D. Zack,et al. Analysis of regulatory network topology reveals functionally distinct classes of microRNAs , 2008, Nucleic acids research.
[84] A. van Oudenaarden,et al. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. , 2007, Molecular cell.
[85] S. Shen-Orr,et al. Network motifs: simple building blocks of complex networks. , 2002, Science.
[86] A. Bradley,et al. Identification of mammalian microRNA host genes and transcription units. , 2004, Genome research.
[87] L. Lim,et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.
[88] N. Rajewsky,et al. A pancreatic islet-specific microRNA regulates insulin secretion , 2004, Nature.
[89] R. Giegerich,et al. Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.
[90] V. Ambros,et al. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.
[91] Ranit Aharonov,et al. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. , 2004, Genome research.
[92] Sebastian D. Mackowiak,et al. The Landscape of C. elegans 3′UTRs , 2010, Science.
[93] Paola Arlotta,et al. Neuronal Subtype-Specific Genes that Control Corticospinal Motor Neuron Development In Vivo , 2005, Neuron.
[94] 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..
[95] C. Allis,et al. The language of covalent histone modifications , 2000, Nature.
[96] R. Russell,et al. Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR Evolution , 2005, Cell.
[97] Angela N. Brooks,et al. Structural Basis for Double-Stranded RNA Processing by Dicer , 2006, Science.
[98] G. Ruvkun,et al. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans , 1993, Cell.
[99] D. Bartel,et al. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs , 2004, Nature Reviews Genetics.
[100] Sanghyuk Lee,et al. MicroRNA genes are transcribed by RNA polymerase II , 2004, The EMBO journal.
[101] N. Rajewsky,et al. Natural selection on human microRNA binding sites inferred from SNP data , 2006, Nature Genetics.
[102] H. Horvitz,et al. Most Caenorhabditis elegans microRNAs Are Individually Not Essential for Development or Viability , 2007, PLoS genetics.
[103] Sam Griffiths-Jones,et al. The microRNA Registry , 2004, Nucleic Acids Res..
[104] Jennifer McDowall,et al. InterPro protein classification. , 2011, Methods in molecular biology.
[105] Christian A. Grove,et al. A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks , 2005, Genome Biology.
[106] V. Ambros,et al. The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans. , 2008, Genes & development.
[107] Christian A. Grove,et al. A Gene-Centered C. elegans Protein-DNA Interaction Network , 2006, Cell.
[108] M. Newman,et al. Random graphs with arbitrary degree distributions and their applications. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.
[109] Alexander E. Kel,et al. TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..
[110] Kristin C. Gunsalus,et al. microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets , 2005, PLoS Comput. Biol..
[111] K. Gunsalus,et al. Combinatorial microRNA target predictions , 2005, Nature Genetics.
[112] A. Mele,et al. Ago HITS-CLIP decodes miRNA-mRNA interaction maps , 2009, Nature.
[113] Albert-László Barabási,et al. Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. , 2007, Genome research.
[114] Peter C. Hollenhorst,et al. Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. , 2007, Genes & development.
[115] Eugene Berezikov,et al. Mammalian mirtron genes. , 2007, Molecular cell.