The evolution of lncRNA repertoires and expression patterns in tetrapods
暂无分享,去创建一个
Frank Grützner | Henrik Kaessmann | Anamaria Necsulea | Magali Soumillon | Maria Warnefors | Angélica Liechti | Tasman Daish | Ulrich Zeller | Julie C. Baker | H. Kaessmann | M. Soumillon | J. Baker | A. Necsulea | F. Grützner | Maria Warnefors | A. Liechti | U. Zeller | T. Daish | Tasman Daish
[1] Cole Trapnell,et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.
[2] Albert J. Vilella,et al. A high-resolution map of human evolutionary constraint using 29 mammals , 2011, Nature.
[3] Stijn van Dongen,et al. Using MCL to extract clusters from networks. , 2012, Methods in molecular biology.
[4] C. Ponting,et al. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes , 2010, Genome Biology.
[5] G. Elgar,et al. Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation , 2012, Nature.
[6] Michael F. Lin,et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.
[7] David Haussler,et al. The UCSC Genome Browser database: update 2010 , 2009, Nucleic Acids Res..
[8] D. Bartel,et al. Long noncoding RNAs in C. elegans , 2012, Genome research.
[9] S. Sunkin,et al. Specific expression of long noncoding RNAs in the mouse brain , 2008, Proceedings of the National Academy of Sciences.
[10] M. Kyba,et al. The H19 lincRNA is a developmental reservoir of miR-675 which suppresses growth and Igf1r , 2012, Nature Cell Biology.
[11] Hazel Sive,et al. Coherent but overlapping expression of microRNAs and their targets during vertebrate development. , 2009, Genes & development.
[12] S. Salzberg,et al. The Transcriptional Landscape of the Mammalian Genome , 2005, Science.
[13] Manolis Kellis,et al. Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions , 2012, Science.
[14] David Z. Chen,et al. Architecture of the human regulatory network derived from ENCODE data , 2012, Nature.
[15] D. Cacchiarelli,et al. A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA , 2011, Cell.
[16] A. Gylfason,et al. Fine-scale recombination rate differences between sexes, populations and individuals , 2010, Nature.
[17] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[18] David G. Knowles,et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.
[19] L. Duret,et al. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. , 2007, Trends in genetics : TIG.
[20] Chris P. Ponting,et al. Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome , 2012, Genome biology and evolution.
[21] J. Silberg,et al. A transposase strategy for creating libraries of circularly permuted proteins , 2012, Nucleic acids research.
[22] D. Haussler,et al. Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.
[23] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[24] Chris P. Ponting,et al. Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression , 2012, PLoS genetics.
[25] Damian Szklarczyk,et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..
[26] Bonnie Berger,et al. Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery , 2004, J. Comput. Biol..
[27] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[28] W. Stanford,et al. PCL2 modulates gene regulatory networks controlling self-renewal and commitment in embryonic stem cells , 2011, Cell cycle.
[29] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[30] Trey Ideker,et al. Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..
[31] Paulo P. Amaral,et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. , 2008, Genome research.
[32] Ana Kozomara,et al. miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..
[33] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[34] R. Nielsen,et al. Patterns of Positive Selection in Six Mammalian Genomes , 2008, PLoS genetics.
[35] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[36] Kenny Q. Ye,et al. An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.
[37] D. Haussler,et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.
[38] Albert J. Vilella,et al. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.
[39] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.
[40] D. Barlow,et al. Quantitative genetics: Turning up the heat on QTL mapping , 2002, Nature Reviews Genetics.
[41] Joel Dudley,et al. TimeTree: a public knowledge-base of divergence times among organisms , 2006, Bioinform..
[42] Carolyn J. Brown,et al. Silencing of the mammalian X chromosome. , 2005, Annual review of genomics and human genetics.
[43] T. Mikkelsen,et al. Cellular source and mechanisms of high transcriptome complexity in the mammalian testis. , 2013, Cell reports.
[44] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature biotechnology.
[45] Howard Y. Chang,et al. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.
[46] S. Bergmann,et al. The evolution of gene expression levels in mammalian organs , 2011, Nature.
[47] Joshua M. Stuart,et al. A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.
[48] T. Derrien,et al. Long Noncoding RNAs with Enhancer-like Function in Human Cells , 2010, Cell.
[49] Doron Lancet,et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification , 2005, Bioinform..
[50] A. J. Schroeder,et al. Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. , 2007, Genome research.
[51] J. Rinn,et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.
[52] Ian Chambers,et al. The transcriptional foundation of pluripotency , 2009, Development.
[53] D. Bartel,et al. Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution , 2011, Cell.
[54] Michael D. Wilson,et al. Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding , 2010, Science.
[55] Martin S. Taylor,et al. Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.
[56] C. Ponting,et al. Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness , 2009, Genome Biology.