1. MERFISHing for spatial context.

    Trends in Immunology 36(7):390 (2015) PMID 26013647

    A new paper in Science by Zhuang and colleagues introduces multiplexed error-robust FISH (MERFISH). MERFISH extends single-molecule imaging techniques to profile the copy number and localization patterns of thousands of genes, representing a major advance for spatial transcriptomics, with exciti...
  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. 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...
  5. 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 ...
  6. 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 ...
  7. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

    Cell 159(1):148 (2014) PMID 25219674 PMCID PMC4180118

    Pseudouridine is the most abundant RNA modification, yet except for a few well-studied cases, little is known about the modified positions and their function(s). Here, we develop Ψ-seq for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with spike-ins and de novo iden...
  8. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

    Cell 159(1):148 (2014) PMID 25219674 PMCID PMC4180118

    Pseudouridine is the most abundant RNA modification, yet except for a few well-studied cases, little is known about the modified positions and their function(s). Here, we develop Ψ-seq for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with spike-ins and de novo iden...
  9. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

    Cell Reports 8(1):284 (2014) PMID 24981863 PMCID PMC4142486

    N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429) are req...
  10. Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

    Cell Reports 8(1):284 (2014)

    N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA142...
  11. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

    Cell Reports 8(1):284 (2014) PMID 24981863 PMCID PMC4142486

    N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429) are req...
  12. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

    Cell Reports 8(1):284 (2014) PMID 24981863 PMCID PMC4142486

    N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429) are req...
  13. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

    Cell Reports 8(1):284 (2014) PMID 24981863 PMCID PMC4142486

    N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429) are req...
  14. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

    Nature 510(7505):363 (2014) PMID 24919153 PMCID PMC4193940

    High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendr...
  15. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

    Nature 510(7505):363 (2014) PMID 24919153 PMCID PMC4193940

    High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendr...
  16. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

    Nature 510(7505):363 (2014) PMID 24919153 PMCID PMC4193940

    High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendr...
  17. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

    Nature 510(7505):363 (2014) PMID 24919153 PMCID PMC4193940

    High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendr...
  18. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

    Nature 510(7505):363 (2014) PMID 24919153 PMCID PMC4193940

    High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendr...
  19. Heterogeneity in immune responses: from populations to single cells.

    Trends in Immunology 35(5):219 (2014) PMID 24746883 PMCID PMC4035247

    The mammalian immune system is tasked with protecting the host against a broad range of threats. Understanding how immune populations leverage cellular diversity to achieve this breadth and flexibility, particularly during dynamic processes such as differentiation and antigenic response, is a co...
  20. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.

    Nature Biotechnology 32(5):479 (2014) PMID 24752078 PMCID PMC4034575

    Comprehensive analyses of cancer genomes promise to inform prognoses and precise cancer treatments. A major barrier, however, is inaccessibility of metastatic tissue. A potential solution is to characterize circulating tumor cells (CTCs), but this requires overcoming the challenges of isolating ...