1. The MicroRNA-132 and MicroRNA-212 Cluster Regulates Hematopoietic Stem Cell Maintenance and Survival with Age by Buffering FOXO3 Expression.

    Immunity 42(6):1021 (2015) PMID 26084022 PMCID PMC4471877

    MicroRNAs are critical post-transcriptional regulators of hematopoietic cell-fate decisions, though little remains known about their role in aging hematopoietic stem cells (HSCs). We found that the microRNA-212/132 cluster (Mirc19) is enriched in HSCs and is upregulated during aging. Both overex...
  2. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

    Cell 161(5):1202 (2015) PMID 26000488 PMCID PMC4481139

    Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thous...
  3. Spatial reconstruction of single-cell gene expression data.

    Nature Biotechnology 33(5):495 (2015) PMID 25867923 PMCID PMC4430369

    Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures...
  4. Pluripotency transcription factor oct4 mediates stepwise nucleosome demethylation and depletion.

    Molecular and Cellular Biology 35(6):1014 (2015) PMID 25582194 PMCID PMC4333097

    The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes the accumulation of local H3K9me2 and subsequent Dnmt3a-...
  5. Pluripotency transcription factor oct4 mediates stepwise nucleosome demethylation and depletion.

    Molecular and Cellular Biology 35(6):1014 (2015) PMID 25582194 PMCID PMC4333097

    The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes the accumulation of local H3K9me2 and subsequent Dnmt3a-...
  6. Pluripotency transcription factor oct4 mediates stepwise nucleosome demethylation and depletion.

    Molecular and Cellular Biology 35(6):1014 (2015) PMID 25582194 PMCID PMC4333097

    The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes the accumulation of local H3K9me2 and subsequent Dnmt3a-...
  7. Pluripotency transcription factor oct4 mediates stepwise nucleosome demethylation and depletion.

    Molecular and Cellular Biology 35(6):1014 (2015) PMID 25582194

    The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes the accumulation of local H3K9me2 and subsequent Dnmt3a-...
  8. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

    Science 347(6226):1259038 (2015) PMID 25745177 PMCID PMC4506746

    Protein expression is regulated by the production and degradation of messenger RNAs (mRNAs) and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics so as to build a quantitative genomic model of the differenti...
  9. ImmVar project: Insights and design considerations for future studies of "healthy" immune variation.

    Seminars in Immunology 27(1):51 (2015) PMID 25819567

    The Immune Variation (ImmVar) project is one of a series of recent efforts to map the extent of variation in immune function in healthy human subjects. The focus of our initial studies involved a careful mapping of the genetic architecture of the adaptive and innate immunologic transcriptomes. O...
  10. The evolution of drug resistance in clinical isolates of Candida albicans.

    eLife 4:e00662 (2015) PMID 25646566 PMCID PMC4383195

    Candida albicans is both a member of the healthy human microbiome and a major pathogen in immunocompromised individuals. Infections are typically treated with azole inhibitors of ergosterol biosynthesis often leading to drug resistance. Studies in clinical isolates have implicated multiple mecha...
  11. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.

    Genome biology 16(1):20 (2015) PMID 25630241 PMCID PMC4369099

    Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization and cell-to-cell variability. Addressing this requires systematic, direct visuali...
  12. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.

    Cell 159(7):1698 (2014) PMID 25497548

    Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing...
  13. High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

    Cell 159(7):1698 (2014)

    Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the leve...
  14. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.

    Cell 159(7):1698 (2014) PMID 25497548 PMCID PMC4272607

    Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing...
  15. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.

    Cell 159(7):1698 (2014) PMID 25497548

    Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing...
  16. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.

    Cell 159(7):1698 (2014) PMID 25497548 PMCID PMC4272607

    Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing...
  17. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.

    Cell 159(7):1698 (2014) PMID 25497548 PMCID PMC4272607

    Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing...
  18. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.

    Cell 159(7):1698 (2014) PMID 25497548 PMCID PMC4272607

    Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing...
  19. Deconstructing transcriptional heterogeneity in pluripotent stem cells.

    Nature 516(7529):56 (2014) PMID 25471879 PMCID PMC4256722

    Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates; however, the regulatory circuits specifying these states and enabling transitions between them are not well understood. Here we set out to characterize transcriptional heterogeneity in mouse PSCs by ...
  20. Deconstructing transcriptional heterogeneity in pluripotent stem cells.

    Nature 516(7529):56 (2014) PMID 25471879 PMCID PMC4256722

    Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates; however, the regulatory circuits specifying these states and enabling transitions between them are not well understood. Here we set out to characterize transcriptional heterogeneity in mouse PSCs by ...