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5,144 results found
    1. Computational and Systems Biology

    Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

    Christopher A Jackson et al.
    Single cell expression data can be used to determine how regulatory transcription factors and target genes are connected, and is especially useful when studying transcription factors controlling heterogeneous cell states.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq

    Dylan Kotliar et al.
    A novel algorithm, consensus non-negative matrix factorization (cNMF), accurately identifies gene expression programs underlying cell-type identity and cellular activities from single-cell RNA-Seq data.
    1. Neuroscience

    Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons

    Mark S Cembrowski et al.
    Gene expression was analyzed in hippocampal principal cells, enabling cellular phenotyping and revealing novel organizational principles; complementing this, a publicly available website is released to provide outside analysis and visualization of hippocampal RNA-seq data in an accessible fashion.
    1. Cell Biology
    2. Evolutionary Biology

    tRNA genes rapidly change in evolution to meet novel translational demands

    Avihu H Yona et al.
    Experimental evolution and systematic sequence analysis of transfer RNA genes reveal that anticodon mutations provide adaptive plasticity to the translation machinery.
    1. Chromosomes and Gene Expression

    Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

    Ava C Carter et al.
    A long noncoding RNA uses viral mimicry to achieve developmental gene silencing across a chromosome.
    1. Chromosomes and Gene Expression
    2. Cancer Biology

    Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

    Ana R Grosso et al.
    Transcription beyond annotated gene boundaries expands the diversity of the cancer transcriptome with overexpressed oncogenes and RNA chimeras.
    1. Chromosomes and Gene Expression

    A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans

    Kevin I Manage et al.
    SIMR-1 acts downstream of the piRNA pathway to promote siRNA amplification by the Mutator complex and localizes to perinuclear foci distinct from Mutator foci, P granules and Z granules.
    1. Chromosomes and Gene Expression
    2. Stem Cells and Regenerative Medicine

    SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program

    Madara Ratnadiwakara et al.
    RNA-binding protein SRSF3 mediates critical changes in RNA processing of pluripotency genes, which reveals functional consequences of regulated RNA processing during stem cell self-renewal and early development.
    1. Evolutionary Biology

    The birth of a bacterial tRNA gene by large-scale, tandem duplication events

    Gökçe B Ayan et al.
    A bacterial tRNA gene set rapidly evolves, compensating the loss of one tRNA type by large duplication events that increase the gene copy number of a second, different tRNA type.
    1. Computational and Systems Biology

    The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture

    Athma A Pai et al.
    Surprising connections between gene architecture and splicing kinetics are illuminated using short, progressive metabolic labeling/RNA sequencing and novel computational modeling approaches in Drosophila cells.

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