1. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.

    Science 353(6299):aaf5573 (2016) PMID 27256883

    The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated genes (Cas) adaptive immune system defends microbes against foreign genetic elements via DNA or RNA-DNA interference. We characterize the class 2 type VI CRISPR-Cas effector C2c2 and demonstrate its RNA-guide...
  2. 142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis.

    Neurosurgery 63 Suppl 1:158 (2016) PMID 27399421

    Gliomas are among the most lethal malignancies and their histogenesis in humans remains unresolved. IDH1 mutational status and co-occurring genetic alterations define major clinical and prognostic classes of gliomas that closely mirror their histologic classification into astrocytic or oligodend...
  3. RBPJ Controls Development of Pathogenic Th17 Cells by Regulating IL-23 Receptor Expression.

    Cell Reports 16(2):392 (2016) PMID 27346359 PMCID PMC4984261

    Interleukin-17 (IL-17)-producing helper T cells (Th17 cells) play an important role in autoimmune diseases. However, not all Th17 cells induce tissue inflammation or autoimmunity. Th17 cells require IL-23 receptor (IL-23R) signaling to become pathogenic. The transcriptional mechanisms controllin...
  4. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.

    Science 352(6282):189 (2016) PMID 27124452 PMCID PMC4944528

    To explore the distinct genotypic and phenotypic states of melanoma tumors, we applied single-cell RNA sequencing (RNA-seq) to 4645 single cells isolated from 19 patients, profiling malignant, immune, stromal, and endothelial cells. Malignant cells within the same tumor displayed transcriptional...
  5. Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML.

    Cell 165(2):303 (2016) PMID 27058663 PMCID PMC4826477

    Leukemia stem cells (LSCs) have the capacity to self-renew and propagate disease upon serial transplantation in animal models, and elimination of this cell population is required for curative therapies. Here, we describe a series of pooled, in vivo RNAi screens to identify essential transcriptio...
  6. Transcriptome-scale RNase-footprinting of RNA-protein complexes.

    Nature Biotechnology 34(4):410 (2016) PMID 26900662 PMCID PMC4824641

    Ribosome profiling is widely used to study translation in vivo, but not all sequence reads correspond to ribosome-protected RNA. Here we describe Rfoot, a computational pipeline that analyzes ribosomal profiling data and identifies native, nonribosomal RNA-protein complexes. We use Rfoot to prec...
  7. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes.

    Science 351(6278):1192 (2016) PMID 26912365

    The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi iso...
  8. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.

    Nature Methods 13(3):245 (2016) PMID 26780094 PMCID PMC4767623

    Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined int...
  9. Voices of biotech.

    Nature Biotechnology 34(3):270 (2016) PMID 26963549

  10. Parsing the Interferon Transcriptional Network and Its Disease Associations.

    Cell 164(3):564 (2016) PMID 26824662 PMCID PMC4743492

    Type 1 interferon (IFN) is a key mediator of organismal responses to pathogens, eliciting prototypical "interferon signature genes" that encode antiviral and inflammatory mediators. For a global view of IFN signatures and regulatory pathways, we performed gene expression and chromatin analyses o...
  11. Mitochondrial dysfunction remodels one-carbon metabolism in human cells.

    eLife 5 (2016) PMID 27307216 PMCID PMC4911214

    Mitochondrial dysfunction is associated with a spectrum of human disorders, ranging from rare, inborn errors of metabolism to common, age-associated diseases such as neurodegeneration. How these lesions give rise to diverse pathology is not well understood, partly because their proximal conseque...
  12. Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs.

    Genome Biology 17(1):19 (2016) PMID 26838501 PMCID PMC4739325

    Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. ...
  13. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.

    Genome Biology 17(1):77 (2016) PMID 27121950 PMCID PMC4848782

    Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its...
  14. A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians.

    Developmental Cell 35(5):632 (2015) PMID 26651295 PMCID PMC4817857

    Regeneration starts with injury. Yet how injuries affect gene expression in different cell types and how distinct injuries differ in gene expression remain unclear. We defined the transcriptomes of major cell types of planarians--flatworms that regenerate from nearly any injury--and identified 1...
  15. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation.

    Molecular Cell 60(5):816 (2015) PMID 26638175 PMCID PMC4720255

    A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovere...
  16. Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.

    Cell 163(6):1400 (2015) PMID 26607794 PMCID PMC4671824

    Extensive cellular heterogeneity exists within specific immune-cell subtypes classified as a single lineage, but its molecular underpinnings are rarely characterized at a genomic scale. Here, we use single-cell RNA-seq to investigate the molecular mechanisms governing heterogeneity and pathogeni...
  17. CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity.

    Cell 163(6):1413 (2015) PMID 26607793 PMCID PMC4671820

    Th17 cells play a critical role in host defense against extracellular pathogens and tissue homeostasis but can induce autoimmunity. The mechanisms implicated in balancing "pathogenic" and "non-pathogenic" Th17 cell states remain largely unknown. We used single-cell RNA-seq to identify CD5L/AIM a...
  18. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells.

    Genome Research 25(12):1860 (2015) PMID 26430063 PMCID PMC4665007

    Both intrinsic cell state changes and variations in the composition of stem cell populations have been implicated as contributors to aging. We used single-cell RNA-seq to dissect variability in hematopoietic stem cell (HSC) and hematopoietic progenitor cell populations from young and old mice fr...
  19. Oct1 and OCA-B are selectively required for CD4 memory T cell function.

    Journal of Experimental Medicine 212(12):2115 (2015) PMID 26481684 PMCID PMC4647264

    Epigenetic changes are crucial for the generation of immunological memory. Failure to generate or maintain these changes will result in poor memory responses. Similarly, augmenting or stabilizing the correct epigenetic states offers a potential method of enhancing memory. Yet the transcription f...
  20. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.

    Cell 163(3):759 (2015) PMID 26422227 PMCID PMC4638220

    The microbial adaptive immune system CRISPR mediates defense against foreign genetic elements through two classes of RNA-guided nuclease effectors. Class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characteriz...