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35 results for “Sequence analysis”

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  1. A novel splice-site mutation in ALS2 establishes the diagnosis of juvenile amyotrophic lateral sclerosis in a family with early onset anarthria and generalized dystonias.

    PloS one · 2014 · 9(12): e113258

    The diagnosis of childhood neurological disorders remains challenging given the overlapping clinical presentation across subgroups and heterogeneous presentation within subgroups. To determine the underlying genetic cause of a severe neurological disorder in a large consanguineous Pakistani family presenting with severe …

    PMID 25474699 DOI ↗

  2. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.

    Cell reports · 2012 · 1(2): 167-78

    Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate …

    PMID 22574288 DOI ↗

  3. High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection.

    Journal of virology · 2012 · 86(1): 226-35

    Human cytomegalovirus (HCMV) contributes its own set of microRNAs (miRNAs) during lytic infection of cells, likely fine-tuning conditions important for viral replication. To enhance our understanding of this component of the HCMV-host transcriptome, we have conducted deep-sequencing analysis of small …

    PMID 22013051 DOI ↗

  4. RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy.

    Methods in molecular biology (Clifton, N.J.) · 2011 · 729: 247-55

    Transcriptome analysis by deep sequencing, more commonly known as RNA-seq is, becoming the method of choice for gene discovery and quantitative splicing detection. We published a double-random priming RNA-seq approach capable of generating strand-specific information [Li et al., Proc Natl …

    PMID 21365495 DOI ↗

  5. Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model.

    Proceedings of the National Academy of Sciences of the United States of America · 2008 · 105(51): 20179-84

    High-throughput sequencing has rapidly gained popularity for transcriptome analysis in mammalian cells because of its ability to generate digital and quantitative information on annotated genes and to detect transcripts and mRNA isoforms. Here, we described a double-random priming method for …

    PMID 19088194 DOI ↗

  6. RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.

    Proceedings of the National Academy of Sciences of the United States of America · 2007 · 104(46): 18097-102

    Short RNA expression was analyzed from Dicer-positive and Dicer-knockout mouse embryonic [corrected] stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can …

    PMID 17989215 DOI ↗

  7. Alternative splicing events identified in human embryonic stem cells and neural progenitors.

    PLoS computational biology · 2007 · 3(10): 1951-67

    Human embryonic stem cells (hESCs) and neural progenitor (NP) cells are excellent models for recapitulating early neuronal development in vitro, and are key to establishing strategies for the treatment of degenerative disorders. While much effort had been undertaken to analyze …

    PMID 17967047 DOI ↗

  8. Inference of splicing regulatory activities by sequence neighborhood analysis.

    PLoS genetics · 2006 · 2(11): e191

    Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with activity in regulating a biochemical process based on the local density of known …

    PMID 17121466 DOI ↗

  9. Identification and analysis of alternative splicing events conserved in human and mouse.

    Proceedings of the National Academy of Sciences of the United States of America · 2005 · 102(8): 2850-5

    Alternative pre-mRNA splicing affects a majority of human genes and plays important roles in development and disease. Alternative splicing (AS) events conserved since the divergence of human and mouse are likely of primary biological importance, but relatively few of such …

    PMID 15708978 DOI ↗

  10. RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons.

    Nucleic acids research · 2004 · 32(Web Server issue): W187-90

    A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much attention has been focused on the effects …

    PMID 15215377 DOI ↗

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GSE9306 Processing Pipeline

GSE9306 · 2 steps · GSE · code_examples

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. (2007)