A5051555132- Single-cell and spatial transcriptomics
- Retinal Development and Disorders
- Neuroinflammation and Neurodegeneration Mechanisms
- Cell Image Analysis Techniques
- Immune Cell Function and Interaction
- HIV Research and Treatment
- T-cell and B-cell Immunology
- Zebrafish Biomedical Research Applications
- Evolution and Genetic Dynamics
- Glaucoma and retinal disorders
- Advanced Fluorescence Microscopy Techniques
- vaccines and immunoinformatics approaches
- Parasites and Host Interactions
- Neural dynamics and brain function
- Cancer Cells and Metastasis
- Retinal Diseases and Treatments
- Zoonotic diseases and public health
- Photoreceptor and optogenetics research
- Neurobiology and Insect Physiology Research
- Circadian rhythm and melatonin
- interferon and immune responses
- Genetics and Neurodevelopmental Disorders
- Epigenetics and DNA Methylation
- Spectroscopy and Quantum Chemical Studies
- Microfluidic and Bio-sensing Technologies
University of California, Berkeley
2020-2025
Lawrence Berkeley National Laboratory
2021-2025
QB3
2020-2025
Neuroscience Institute
2021-2024
Broad Institute
2015-2023
University of California System
2023
Center for Pain and the Brain
2021-2022
Harvard University
2017-2022
Howard Hughes Medical Institute
2020
Massachusetts Institute of Technology
2012-2020
What's in a drop of blood? Blood contains many types cells, including immune system components. Immune cells used to be characterized by marker-based assays, but now classification relies on the genes that express. Villani et al. deep sequencing at single-cell level and unbiased clustering define six dendritic cell four monocyte populations. This refined analysis has identified, among others, previously unknown population potently activates T cells. Further culture revealed possible...
Mapping the brain, one neuron at a time Spatial transcriptomics can link molecularly described cell types to their anatomical positions and functional roles. Moffitt et al. used combination of single-cell RNA-sequencing MERFISH (multiplexed error-robust fluorescence in situ hybridization) map identity location specific within mouse preoptic hypothalamus surrounding areas brain (see Perspective by Tasic Nicovich). They related these behaviors via gene activity. The approach provides an...
During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these trajectories during zebrafish we sequenced 38,731 and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the of 25 cell types early somitogenesis, gene expression along them, their spatial origin in blastula. Analysis Nodal signaling mutants revealed that transcriptomes were canalized into subset wild-type trajectories. Some...
Abstract Most irreversible blindness results from retinal disease. To advance our understanding of the etiology blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze transcriptomes ~85,000 cells fovea and peripheral retina seven adult human donors. Utilizing computational methods, identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, ganglion non-neuronal cells. Nearly all are shared between two regions, but there notable differences...
Significance Mass cytometry enables the measurement of nearly 40 different proteins at single-cell level, providing an unprecedented level multidimensional information. Because complexity these datasets across diverse populations cells, new computational tools are needed to glean useful biological insights. Here we describe ACCENSE (Automatic Classification Cellular Expression by Nonlinear Stochastic Embedding), a tool that computes two-dimensional nonlinear distillation raw data, and...
Increased intraocular pressure (IOP) represents a major risk factor for glaucoma, prevalent eye disease characterized by death of retinal ganglion cells; lowering IOP is the only proven treatment strategy to delay progression. The main determinant equilibrium between production and drainage aqueous humor, with compromised generally viewed as primary contributor dangerous elevations. Drainage occurs through two pathways in anterior segment called conventional uveoscleral. To gain insights...
Classification and characterization of neuronal types are critical for understanding their function dysfunction. Neuronal classification schemes typically rely on measurements electrophysiological, morphological, molecular features, but aligning such datasets has been challenging. Here, we present a unified mouse retinal ganglion cells (RGCs), the sole output neurons. We use visually evoked responses to classify 1,859 RGCs into 42 types. also obtain morphological or transcriptomic data from...
Abstract The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs 1 . Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, reptile, teleost fish lamprey. We found high molecular conservation...
Cellular immune control of HIV is mediated, in part, by induction single amino acid mutations that reduce viral fitness, but compensatory limit this effect. Here, we sought to determine if higher order constraints on evolution exist, because some coordinately linked combinations may hurt viability. Immune targeting multiple sites such a multidimensionally conserved region might render the virus particularly vulnerable, viable escape pathways would be greatly restricted. We analyzed available...
Significance The human immune system consists of many different white blood cells that coordinate their actions to fight infections. balance between these cell populations is determined by direct interactions and soluble factors such as cytokines, which serve messengers cells. Understanding how the influence function a whole will allow us better distinguish patients most at risk for specific infections or immune-mediated diseases inform vaccination strategies. Here, we determine key...