Towards a complete map of the human long non-coding RNA transcriptome
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[1] Zixiang Wang,et al. Ontological function annotation of long non‐coding RNAs through hierarchical multi‐label classification , 2018, Bioinform..
[2] Michael Q. Zhang,et al. NONCODEV5: a comprehensive annotation database for long non-coding RNAs , 2017, Nucleic Acids Res..
[3] Rory Johnson,et al. Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs , 2017, bioRxiv.
[4] I. Ulitsky,et al. Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells , 2017, Nature.
[5] Daniel R. Garalde,et al. Highly parallel direct RNA sequencing on an array of nanopores , 2016, Nature Methods.
[6] Mathieu Blanchette,et al. CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells , 2018, RNA.
[7] J. Mattick,et al. Intergenic disease-associated regions are abundant in novel transcripts , 2017, Genome Biology.
[8] I. Ulitsky,et al. The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element , 2017, Genome Biology.
[9] Guang-Rong Yan,et al. A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth. , 2017, Molecular cell.
[10] R. Guigó,et al. Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC) , 2017, bioRxiv.
[11] Guangyuan Fu,et al. BRWLDA: bi-random walks for predicting lncRNA-disease associations , 2017, Oncotarget.
[12] P. Stadler,et al. Rare Splice Variants in Long Non-Coding RNAs , 2017, Non-coding RNA.
[13] Roderic Guigo,et al. LncATLAS database for subcellular localization of long noncoding RNAs , 2017, bioRxiv.
[14] J. Rinn,et al. Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking , 2017, bioRxiv.
[15] Lennart Martens,et al. Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products. , 2017, Journal of proteome research.
[16] Jin-Wu Nam,et al. High-confidence coding and noncoding transcriptome maps. , 2017, Genome research.
[17] Ira W. Deveson,et al. Universal alternative splicing of noncoding exons , 2017, bioRxiv.
[18] Jan Gorodkin,et al. The identification and functional annotation of RNA structures conserved in vertebrates , 2017, Genome research.
[19] S. Arron,et al. Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin , 2017, Scientific Reports.
[20] Mark Akeson,et al. Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing , 2017, bioRxiv.
[21] Hugh E. Olsen,et al. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells , 2017, Nature Communications.
[22] Mingfu Shao,et al. Scallop enables accurate assembly of transcripts through phasing-preserving graph decomposition , 2017, bioRxiv.
[23] Tobias Madsen,et al. Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate , 2017, eLife.
[24] R. Guigó,et al. LncATLAS database for subcellular localisation of long noncoding RNAs , 2017, bioRxiv.
[25] Jordan A. Ramilowski,et al. An atlas of human long non-coding RNAs with accurate 5′ ends , 2017, Nature.
[26] Z. Kutalik,et al. cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture. , 2017, Cell reports.
[27] Jennifer Harrow,et al. High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing , 2017, Nature Genetics.
[28] M. Boutros,et al. The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its extremely low abundance , 2017, Nucleic acids research.
[29] Paolo Piazza,et al. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis , 2017, F1000Research.
[30] Howard Y. Chang,et al. NONCODING RNA: CRISPRi‐based genome‐scale identification of functional long noncoding RNA loci in human cells , 2017 .
[31] K. Lindblad-Toh,et al. FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome , 2017, Nucleic acids research.
[32] Alex Bateman,et al. RNAcentral: a comprehensive database of non-coding RNA sequences , 2016, Nucleic acids research.
[33] The RNAcentral Consortium. RNAcentral: a comprehensive database of non-coding RNA sequences , 2016, Nucleic Acids Res..
[34] J. Rinn,et al. Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs , 2016, bioRxiv.
[35] B. Langmead,et al. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive , 2016, Genome Biology.
[36] Zhongzheng Cao,et al. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library , 2016, Nature Biotechnology.
[37] D. Duboule,et al. Hotair Is Dispensible for Mouse Development , 2016, PLoS genetics.
[38] Hugh E. Olsen,et al. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community , 2016, Genome Biology.
[39] L. Boyer,et al. A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. , 2016, Molecular cell.
[40] Karissa Y Sanbonmatsu,et al. COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures. , 2016, Cell reports.
[41] Z. Lu,et al. Critical roles of long noncoding RNAs in Drosophila spermatogenesis , 2016, Genome research.
[42] Ira W. Deveson,et al. Spliced synthetic genes as internal controls in RNA sequencing experiments , 2016, Nature Methods.
[43] Kaoru Inoue,et al. SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells , 2016, Proceedings of the National Academy of Sciences.
[44] Dave T. Gerrard,et al. An integrative transcriptomic atlas of organogenesis in human embryos , 2016, eLife.
[45] Ferran Reverter,et al. Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features , 2016, Scientific Reports.
[46] Toni Gabaldón,et al. Secondary structure impacts patterns of selection in human lncRNAs , 2016, BMC Biology.
[47] James C. Wright,et al. Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow , 2016, Nature Communications.
[48] B. Blencowe,et al. Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine , 2016, Scientific Reports.
[49] Jiang Chang,et al. A functional polymorphism in lnc-LAMC2-1:1 confers risk of colorectal cancer by affecting miRNA binding. , 2016, Carcinogenesis.
[50] Lior Pachter,et al. Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.
[51] Anton J. Enright,et al. Improved definition of the mouse transcriptome via targeted RNA sequencing , 2016, Genome research.
[52] Roderic Guigó,et al. Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells , 2016, RNA.
[53] Max A. Horlbeck,et al. Single-cell analysis of long non-coding RNAs in the developing human neocortex , 2016, Genome Biology.
[54] Jiannis Ragoussis,et al. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations , 2016, Scientific Reports.
[55] T. Pan,et al. N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding. , 2016, Journal of molecular biology.
[56] F. Pauler,et al. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans , 2016, Genome Biology.
[57] Daniel J. Gaffney,et al. A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.
[58] Stephen C. Cannon,et al. A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle , 2016, Science.
[59] Tsung-Cheng Chang,et al. Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins , 2016, Cell.
[60] Panayiotis Tsanakas,et al. DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts , 2015, Nucleic Acids Res..
[61] Wen J. Li,et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..
[62] Peng Wang,et al. Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers , 2015, Nucleic Acids Res..
[63] Piero Carninci,et al. Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine. , 2016, Current topics in microbiology and immunology.
[64] Jennifer Harrow,et al. Devising a Consensus Framework for Validation of Novel Human Coding Loci. , 2015, Journal of proteome research.
[65] R. Guigó,et al. CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis. , 2015, Journal of molecular and cellular cardiology.
[66] Walter N. Moss,et al. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq , 2015, PLoS genetics.
[67] Alfonso Valencia,et al. The potential clinical impact of the release of two drafts of the human proteome , 2015, Expert review of proteomics.
[68] Latarsha J. Carithers,et al. The Genotype-Tissue Expression (GTEx) Project. , 2015, Biopreservation and biobanking.
[69] Sebastian D. Mackowiak,et al. Extensive identification and analysis of conserved small ORFs in animals , 2015, Genome Biology.
[70] Mihaela Zavolan,et al. Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data , 2015, Genome Biology.
[71] Dmitri D. Pervouchine,et al. The human transcriptome across tissues and individuals , 2015, Science.
[72] D. Bartel,et al. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. , 2015, Cell reports.
[73] Igor Ulitsky,et al. Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs , 2015, bioRxiv.
[74] Anton J. Enright,et al. Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing , 2015, Nature Methods.
[75] J. Vandesompele,et al. An update on LNCipedia: a database for annotated human lncRNA sequences , 2015, Nucleic Acids Res..
[76] Retinoic acid-independent expression of Meis2 during autopod patterning in the developing bat and mouse limb , 2015, EvoDevo.
[77] Scott D. Brown,et al. Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma , 2015, Genome Medicine.
[78] S. Salzberg,et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.
[79] C. Ponting,et al. Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci , 2015, RNA.
[80] S. Dhanasekaran,et al. The landscape of long noncoding RNAs in the human transcriptome , 2015, Nature Genetics.
[81] John M. Shelton,et al. A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance , 2015, Cell.
[82] Michael Q. Zhang,et al. Integrative analysis of 111 reference human epigenomes , 2015, Nature.
[83] J. Rinn,et al. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution , 2015, Genome Biology.
[84] Leonardo Collado-Torres,et al. Developmental regulation of human cortex transcription and its clinical relevance at base resolution , 2014, Nature Neuroscience.
[85] Jun Yu,et al. LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs , 2014, Nucleic Acids Res..
[86] Gang Fu,et al. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data , 2014, Nucleic Acids Res..
[87] Marcel E. Dinger,et al. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs , 2014, Nucleic Acids Res..
[88] David R. Kelley,et al. Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions , 2014, Genome Biology.
[89] Vladimir B. Bajic,et al. Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes , 2014, PloS one.
[90] Howard Y. Chang,et al. Physiological roles of long noncoding RNAs: insight from knockout mice. , 2014, Trends in cell biology.
[91] Donald Sharon,et al. Defining a personal, allele-specific, and single-molecule long-read transcriptome , 2014, Proceedings of the National Academy of Sciences.
[92] J. Harrow,et al. Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes , 2014, Human molecular genetics.
[93] M. Albà,et al. Long non-coding RNAs as a source of new peptides , 2014, eLife.
[94] Marcel E Dinger,et al. Targeted sequencing for gene discovery and quantification using RNA CaptureSeq , 2014, Nature Protocols.
[95] F. Niazi,et al. A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA , 2014, Molecular and Cellular Biology.
[96] Jiao Ma,et al. Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue , 2014, Journal of proteome research.
[97] Hui Zhou,et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data , 2013, Nucleic Acids Res..
[98] Melissa J. Landrum,et al. RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..
[99] Susumu Goto,et al. Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..
[100] Michael Morse,et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development , 2013, eLife.
[101] Monika S. Kowalczyk,et al. Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs , 2013, Genome Biology.
[102] J. Harrow,et al. Assessment of transcript reconstruction methods for RNA-seq , 2013, Nature Methods.
[103] Donald Sharon,et al. A single-molecule long-read survey of the human transcriptome , 2013, Nature Biotechnology.
[104] Fabian A. Buske,et al. Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci , 2013, Bioinform..
[105] J. Mattick,et al. A meta-analysis of the genomic and transcriptomic composition of complex life , 2013, Cell cycle.
[106] Nicholas T. Ingolia,et al. Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins , 2013, Cell.
[107] Zev N. Kronenberg,et al. Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs , 2013, PLoS genetics.
[108] J. Kocher,et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model , 2013, Nucleic acids research.
[109] Xing Chen,et al. LncRNADisease: a database for long-non-coding RNA-associated diseases , 2012, Nucleic Acids Res..
[110] Xiaoke Ma,et al. Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks , 2012, Nucleic acids research.
[111] John S. Mattick,et al. Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes , 2012, Bioinform..
[112] David R. Kelley,et al. Transposable elements reveal a stem cell-specific class of long noncoding RNAs , 2012, Genome Biology.
[113] Piero Carninci,et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat , 2012, Nature.
[114] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[115] 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.
[116] James B. Brown,et al. Long noncoding RNAs are rarely translated in two human cell lines , 2012, Genome research.
[117] David G. Knowles,et al. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs , 2012, Genome research.
[118] Nadav S. Bar,et al. Landscape of transcription in human cells , 2012, Nature.
[119] Bronwen L. Aken,et al. GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.
[120] Thomas Lengauer,et al. BLUEPRINT to decode the epigenetic signature written in blood , 2012, Nature Biotechnology.
[121] R. Guigó,et al. Estimation of alternative splicing variability in human populations. , 2012, Genome research.
[122] J. Rinn,et al. Modular regulatory principles of large non-coding RNAs , 2012, Nature.
[123] Rory Johnson,et al. Human long non‐coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors , 2012, The EMBO journal.
[124] Martin Renqiang Min,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[125] Cole Trapnell,et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome , 2011, Nature Biotechnology.
[126] Nicholas T. Ingolia,et al. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.
[127] Cole Trapnell,et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.
[128] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[129] L. Maquat,et al. lncRNAs transactivate Staufen1-mediated mRNA decay by duplexing with 3'UTRs via Alu elements , 2010, Nature.
[130] D. Bartel,et al. Formation, Regulation and Evolution of Caenorhabditis elegans 3′UTRs , 2010, Nature.
[131] Li Yang,et al. Genomewide characterization of non-polyadenylated RNAs , 2011, Genome Biology.
[132] J. Rinn,et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells , 2010, Nature Genetics.
[133] Michael F. Lin,et al. PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions , 2010 .
[134] Leonard Lipovich,et al. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. , 2010, RNA.
[135] J. Rinn,et al. A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response , 2010, Cell.
[136] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[137] Elias Campo Guerri,et al. International network of cancer genome projects , 2010, Nature.
[138] K. Hansen,et al. Biases in Illumina transcriptome sequencing caused by random hexamer priming , 2010, Nucleic acids research.
[139] M. Gerstein,et al. Variation in Transcription Factor Binding Among Humans , 2010, Science.
[140] P. Robson,et al. Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. , 2010, RNA.
[141] 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.
[142] Michael F. Lin,et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.
[143] Tim R. Mercer,et al. Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities , 2008, PLoS Comput. Biol..
[144] Anton J. Enright,et al. Genomic analysis of human microRNA transcripts , 2007, Proceedings of the National Academy of Sciences.
[145] Yong Zhang,et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine , 2007, Nucleic Acids Res..
[146] C. Ponting,et al. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. , 2007, Genome research.
[147] Enrique Blanco,et al. Using geneid to Identify Genes , 2002, Current protocols in bioinformatics.
[148] D. Gautheret,et al. The disparate nature of "intergenic" polyadenylation sites. , 2006, RNA.
[149] S. Salzberg,et al. The Transcriptional Landscape of the Mammalian Genome , 2005, Science.
[150] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[151] M. Fagiolini,et al. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. , 2003, Genome research.
[152] S. P. Fodor,et al. Large-Scale Transcriptional Activity in Chromosomes 21 and 22 , 2002, Science.
[153] L. Kiemeney,et al. DD3(PCA3), a very sensitive and specific marker to detect prostate tumors. , 2002, Cancer research.
[154] A. Chenchik,et al. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. , 2001, BioTechniques.
[155] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[156] Sean R. Eddy,et al. Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..
[157] Piero Carninci,et al. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. , 1996, Genomics.