Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies

(2022) Katia de Paiva Lopes et al.   NATURE GENETICS

Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease

(2021) Kun Leng et al.   NATURE NEUROSCIENCE

Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation

(2021) Léo Machado et al.   Cell Stem Cell

Iterative single-cell multi-omic integration using online learning

(2021) Chao Gao et al.   NATURE BIOTECHNOLOGY

Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization

(2021) Ana Rita Pombo Antunes et al.   NATURE NEUROSCIENCE

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

(2021) Eleni P. Mimitou et al.   NATURE BIOTECHNOLOGY

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

(2021) Zizhen Yao et al.   NATURE

Confronting false discoveries in single-cell differential expression

(2021) Jordan W. Squair et al.   Nature Communications

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

(2020) Yingyue Zhou et al.   NATURE MEDICINE

Single-cell biology: beyond the sum of its parts

(2020) Alexander F. Schier   NATURE METHODS

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Microglia response following acute demyelination is heterogeneous and limits infiltrating macrophage dispersion

(2020) Jason R. Plemel et al.   Science Advances

Microglia Require CD4 T Cells to Complete the Fetal-to-Adult Transition

(2020) Emanuela Pasciuto et al.   CELL

Integrative genomics approach identifies conserved transcriptomic networks in Alzheimer’s disease

(2020) Samuel Morabito et al.   HUMAN MOLECULAR GENETICS

Microglia and Astrocytes in Disease: Dynamic Duo or Partners in Crime?

(2020) Shane A. Liddelow et al.   TRENDS IN IMMUNOLOGY

muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

(2020) Helena L. Crowell et al.   Nature Communications

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

Single-Cell Analysis of Regional Differences in Adult V-SVZ Neural Stem Cell Lineages

(2019) Dogukan Mizrak et al.   Cell Reports

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

(2019) Deanne M. Taylor et al.   DEVELOPMENTAL CELL

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

(2019) Hannah Van Hove et al.   NATURE NEUROSCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Mapping microglia states in the human brain through the integration of high-dimensional techniques

(2019) Roman Sankowski et al.   NATURE NEUROSCIENCE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

A Combination of Ontogeny and CNS Environment Establishes Microglial Identity

(2018) F. Chris Bennett et al.   NEURON

Induction of (Ubiquitin C ) UBC gene transcription is mediated by HSF1: role of proteotoxic and oxidative stress

(2018) Marzia Bianchi et al.   FEBS Open Bio

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Microglial translational profiling reveals a convergent APOE pathway from aging, amyloid, and tau

(2018) Silvia S. Kang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Best Practices for Preparing a Single Cell Suspension from Solid Tissues for Flow Cytometry

(2018) Andrew Reichard et al.   CYTOMETRY PART A

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

(2018) Timothy R. Hammond et al.   IMMUNITY

High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NK Cell Subsets in Humans and Mice

(2018) Adeline Crinier et al.   IMMUNITY

Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing

(2018) Qingyun Li et al.   NEURON

Single-Cell Transcriptomics Characterizes Cell Types in the Subventricular Zone and Uncovers Molecular Defects Impairing Adult Neurogenesis

(2018) Vera Zywitza et al.   Cell Reports

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases

(2017) Susanne Krasemann et al.   IMMUNITY

Quantitative comparison of human intestinal mononuclear leukocyte isolation techniques for flow cytometric analyses

(2017) R.R.C.E. Schreurs et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Phenotypic and functional consequences of different isolation protocols on skin mononuclear phagocytes

(2017) Rachel A. Botting et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

(2017) Sinisa Hrvatin et al.   NATURE NEUROSCIENCE

Detecting Activated Cell Populations Using Single-Cell RNA-Seq

(2017) Ye Emily Wu et al.   NEURON

Diverse Requirements for Microglial Survival, Specification, and Function Revealed by Defined-Medium Cultures

(2017) Christopher J. Bohlen et al.   NEURON

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

Single-cell transcriptomics to explore the immune system in health and disease

(2017) Michael J. T. Stubbington et al.   SCIENCE

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution

(2017) Hansruedi Mathys et al.   Cell Reports

Neuropathological and transcriptomic characteristics of the aged brain

(2017) Jeremy A Miller et al.   eLife

Postmortem human brain genomics in neuropsychiatric disorders—how far can we go?

(2016) Andrew E Jaffe   CURRENT OPINION IN NEUROBIOLOGY

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

(2016) S. Marques et al.   SCIENCE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Phenotypic characterization and functional analysis of human tumor immune infiltration after mechanical and enzymatic disaggregation

(2011) Cécile Grange et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Effects of Antemortem and Postmortem Variables on Human Brain mRNA Quality: A BrainNet Europe Study

(2009) Pascal F. Durrenberger et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

pH measurement as quality control on humanpost mortembrain tissue: a study of the BrainNet Europe consortium

(2009) C. M. Monoranu et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY