Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes
暂无分享,去创建一个
Ian T. Fiddes | D. Haussler | S. Salama | Sol Katzman | J. L. Rosenkrantz | F. Jacobs | Alex P. R. Phillips | A. Field | Mari N. Olsen | Erin LaMontagne | Lila Whitehead | A. M. Reyes-Ortiz | Vincent Meng | M. Hauessler | A. Reyes-Ortiz | M. Olsen
[1] David Haussler,et al. Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation , 2017, bioRxiv.
[2] Alex A. Pollen,et al. Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex , 2017, Science.
[3] Kathleen M Jagodnik,et al. Massive mining of publicly available RNA-seq data from human and mouse , 2017, Nature Communications.
[4] Jordan A. Ramilowski,et al. An atlas of human long non-coding RNAs with accurate 5′ ends , 2017, Nature.
[5] Jennifer Harrow,et al. High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing , 2017, Nature Genetics.
[6] Howard Y. Chang,et al. NONCODING RNA: CRISPRi‐based genome‐scale identification of functional long noncoding RNA loci in human cells , 2017 .
[7] S. Pääbo,et al. Author response: Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development , 2016 .
[8] Igor Ulitsky,et al. Evolution to the rescue: using comparative genomics to understand long non-coding RNAs , 2016, Nature Reviews Genetics.
[9] Mario Stanke,et al. Simultaneous gene finding in multiple genomes , 2016, Bioinform..
[10] A. Kriegstein,et al. A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA , 2016, Neuron.
[11] Andrew D. Rouillard,et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update , 2016, Nucleic Acids Res..
[12] Max A. Horlbeck,et al. Single-cell analysis of long non-coding RNAs in the developing human neocortex , 2016, Genome Biology.
[13] F. Gage,et al. 2D and 3D Stem Cell Models of Primate Cortical Development Identify Species-Specific Differences in Progenitor Behavior Contributing to Brain Size , 2016, Cell stem cell.
[14] Nick Barker,et al. Organoids as an in vitro model of human development and disease , 2016, Nature Cell Biology.
[15] Madeline A. Lancaster,et al. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development , 2015, Proceedings of the National Academy of Sciences.
[16] Alexandro E. Trevino,et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.
[17] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[18] Madeline A. Lancaster,et al. Cerebral organoids model human brain development and microcephaly , 2013, Nature.
[19] B. Finlay,et al. Modeling Transformations of Neurodevelopmental Sequences across Mammalian Species , 2013, The Journal of Neuroscience.
[20] 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.
[21] Chris P. Ponting,et al. Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression , 2012, PLoS genetics.
[22] M. Ritchie,et al. Faculty Opinions recommendation of Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. , 2012 .
[23] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[24] Michael F. Lin,et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. , 2012, Genome research.
[25] Thomas R. Gingeras,et al. Molecular biology: RNA discrimination , 2012, Nature.
[26] D. Bartel,et al. Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution , 2011, Cell.
[27] Cole Trapnell,et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.
[28] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[29] J. Rinn,et al. lincRNAs act in the circuitry controlling pluripotency and differentiation , 2011, Nature.
[30] David Haussler,et al. Cactus: Algorithms for genome multiple sequence alignment. , 2011, Genome research.
[31] Yasuko Matsumura,et al. A more efficient method to generate integration-free human iPS cells , 2011, Nature Methods.
[32] Howard Y. Chang,et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression , 2011, Nature.
[33] Albert J. Vilella,et al. Comparative and demographic analysis of orang-utan genomes , 2011, Nature.
[34] Sibum Sung,et al. Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA , 2011, Science.
[35] J. Rinn,et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells , 2010, Nature Genetics.
[36] T. Derrien,et al. Long Noncoding RNAs with Enhancer-like Function in Human Cells , 2010, Cell.
[37] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[38] T. Borodina,et al. Transcriptome analysis by strand-specific sequencing of complementary DNA , 2009, Nucleic acids research.
[39] 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.
[40] Moustapha Kassem,et al. Teratoma formation by human embryonic stem cells is site dependent and enhanced by the presence of Matrigel. , 2009, Stem cells and development.
[41] Jennifer A. Mitchell,et al. The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin , 2008, Science.
[42] Yoshiki Sasai,et al. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. , 2008, Cell stem cell.
[43] Jeannie T. Lee,et al. Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome , 2008, Science.
[44] J. Komorowski,et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. , 2008, Molecular cell.
[45] Paulo P. Amaral,et al. Noncoding RNA in development , 2008, Mammalian Genome.
[46] David Haussler,et al. Using native and syntenically mapped cDNA alignments to improve de novo gene finding , 2008, Bioinform..
[47] B. Horsthemke,et al. C15orf2 and a novel noncoding transcript from the Prader-Willi/Angelman syndrome region show monoallelic expression in fetal brain. , 2007, Genomics.
[48] C. Ponting,et al. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. , 2007, Genome research.
[49] K. Struhl. Transcriptional noise and the fidelity of initiation by RNA polymerase II , 2007, Nature Structural &Molecular Biology.
[50] C. Dehay,et al. Cell Cycle Features of Primate Embryonic Stem Cells , 2006, Stem cells.
[51] T. Hughes,et al. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription , 2005, BMC Genomics.
[52] 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.
[53] J A Thomson,et al. Clonally derived human embryonic stem cell lines maintain pluripotency and proliferative potential for prolonged periods of culture. , 2000, Developmental biology.
[54] S. Rastan,et al. Requirement for Xist in X chromosome inactivation , 1996, Nature.
[55] S. Tilghman,et al. Disruption of imprinting caused by deletion of the H19 gene region in mice , 1995, Nature.
[56] R. Lacy,et al. Patience is a virtue. , 1994, Caring : National Association for Home Care magazine.
[57] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[58] Ira M. Hall,et al. BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..
[59] J. Mattick,et al. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. , 2006, Trends in genetics : TIG.