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  1. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans.

    Nature structural & molecular biology · 2010 · 17(2): 173-9

    MicroRNAs (miRNAs) regulate gene expression by guiding Argonaute proteins to specific target mRNA sequences. Identification of bona fide miRNA target sites in animals is challenging because of uncertainties regarding the base-pairing requirements between miRNA and target as well as the …

    PMID 20062054 DOI ↗

  2. Transcriptional signature and memory retention of human-induced pluripotent stem cells.

    PloS one · 2009 · 4(9): e7076

    Genetic reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells or iPSCs) by over-expression of specific genes has been accomplished using mouse and human cells. However, it is still unclear how similar human iPSCs are to human …

    PMID 19763270 DOI ↗

  3. Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea.

    RNA (New York, N.Y.) · 2009 · 15(8): 1483-91

    MicroRNAs (miRNAs) play important roles in directing the differentiation of cells down a variety of cell lineage pathways. The planarian Schmidtea mediterranea can regenerate all lost body tissue after amputation due to a population of pluripotent somatic stem cells called …

    PMID 19553344 DOI ↗

  4. L1 retrotransposition in human neural progenitor cells.

    Nature · 2009 · 460(7259): 1127-31

    Long interspersed element 1 (LINE-1 or L1) retrotransposons have markedly affected the human genome. L1s must retrotranspose in the germ line or during early development to ensure their evolutionary success, yet the extent to which this process affects somatic cells …

    PMID 19657334 DOI ↗

  5. Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice.

    Hippocampus · 2009 · 19(7): 658-69

    The hippocampus is involved in declarative memory and produces new neurons throughout adulthood. Numerous experiments have been aimed at testing the possibility that adult neurogenesis is required for learning and memory. However, progress has been encumbered by the fact that …

    PMID 19140178 DOI ↗

  6. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells.

    Nature structural & molecular biology · 2009 · 16(2): 130-7

    The elucidation of a code for regulated splicing has been a long-standing goal in understanding the control of post-transcriptional gene expression events that are crucial for cell survival, differentiation and development. We decoded functional RNA elements in vivo by constructing …

    PMID 19136955 DOI ↗

  7. 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 ↗

  8. Divergent transcription from active promoters.

    Science (New York, N.Y.) · 2008 · 322(5909): 1849-51

    Transcription initiation by RNA polymerase II (RNAPII) is thought to occur unidirectionally from most genes. Here, we present evidence of widespread divergent transcription at protein-encoding gene promoters. Transcription start site-associated RNAs (TSSa-RNAs) nonrandomly flank active promoters, with peaks of antisense …

    PMID 19056940 DOI ↗

  9. The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians.

    RNA (New York, N.Y.) · 2008 · 14(6): 1174-86

    PIWI proteins are expressed in germ cells in a wide variety of metazoans, where they participate in the synthesis and function of a novel class of small RNAs called PIWI associated RNAs (piRNAs). One function of piRNAs is to preserve …

    PMID 18456843 DOI ↗

  10. Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells.

    Human molecular genetics · 2008 · 17(R1): R67-75

    Elucidating the molecular changes that arise during neural differentiation and fate specification is crucial for building accurate in vitro models of neurodegenerative diseases using human embryonic stem cells (hESCs). Here we review the importance of hESCs and derived progenitors in …

    PMID 18632700 DOI ↗

  11. A regulator of Dscam mutually exclusive splicing fidelity.

    Nature structural & molecular biology · 2007 · 14(12): 1134-40

    The Down syndrome cell adhesion molecule (Dscam) gene has essential roles in neural wiring and pathogen recognition in Drosophila melanogaster. Dscam encodes 38,016 distinct isoforms via extensive alternative splicing. The 95 alternative exons in Dscam are organized into clusters that …

    PMID 21188797 DOI ↗

  12. 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 ↗

  13. 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 ↗

  14. The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression.

    Cell · 2007 · 130(1): 179-91

    Proper neuronal function and several forms of synaptic plasticity are highly dependent on precise control of mRNA translation, particularly in dendrites. We find that eIF4AIII, a core exon junction complex (EJC) component loaded onto mRNAs by pre-mRNA splicing, is associated …

    PMID 17632064 DOI ↗

  15. Plant-derived flavanol (-)epicatechin enhances angiogenesis and retention of spatial memory in mice.

    The Journal of neuroscience : the official journal of the Society for Neuroscience · 2007 · 27(22): 5869-78

    Diet and exercise have a profound impact on brain function. In particular, natural nutrients found in plants may influence neuronal survival and plasticity. Here, we tested whether consumption of a plant-derived flavanol, (-)epicatechin, enhances cognition in sedentary or wheel-running female …

    PMID 17537957 DOI ↗

  16. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.

    PLoS genetics · 2007 · 3(5): e85

    Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs). Our …

    PMID 17530930 DOI ↗

  17. 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 ↗

  18. Splicing regulators: targets and drugs.

    Genome biology · 2005 · 6(12): 240

    Silencing of splicing regulators by RNA interference, combined with splicing-specific microarrays, has revealed a complex network of distinct alternative splicing events in Drosophila, while a high-throughput screen of more than 6,000 compounds has identified drugs that interfere specifically and directly …

    PMID 16356274 DOI ↗

  19. 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 ↗

  20. 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 ↗