Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity

Microglia and macrophages promote corralling, wound compaction and recovery after spinal cord injury via Plexin-B2

(2020) Xiang Zhou et al.   NATURE NEUROSCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies

(2018) Zhana Haimon et al.   NATURE IMMUNOLOGY

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

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

(2017) Susanne Krasemann et al.   IMMUNITY

Neurotoxic reactive astrocytes are induced by activated microglia

(2017) Shane A. Liddelow et al.   NATURE

A functional genomics predictive network model identifies regulators of inflammatory bowel disease

(2017) Lauren A Peters et al.   NATURE GENETICS

Sex-specific transcriptional signatures in human depression

(2017) Benoit Labonté et al.   NATURE MEDICINE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

HDAC3 inhibition ameliorates spinal cord injury by immunomodulation

(2017) Tomoharu Kuboyama et al.   Scientific Reports

TREM2-mediated early microglial response limits diffusion and toxicity of amyloid plaques

(2016) Yaming Wang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Origin, fate and dynamics of macrophages at central nervous system interfaces

(2016) Tobias Goldmann et al.   NATURE IMMUNOLOGY

TREM2 variants: new keys to decipher Alzheimer disease pathogenesis

(2016) Marco Colonna et al.   NATURE REVIEWS NEUROSCIENCE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

New tools for studying microglia in the mouse and human CNS

(2016) Mariko L. Bennett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling the brain’s neuroinflammatory and neurodegenerative transcriptional responses

(2016) Karpagam Srinivasan et al.   Nature Communications

ContextMap 2: fast and accurate context-based RNA-seq mapping

(2015) Thomas Bonfert et al.   BMC BIOINFORMATICS

Hematogenous macrophage depletion reduces the fibrotic scar and increases axonal growth after spinal cord injury

(2015) Y. Zhu et al.   NEUROBIOLOGY OF DISEASE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

TNF and Increased Intracellular Iron Alter Macrophage Polarization to a Detrimental M1 Phenotype in the Injured Spinal Cord

(2014) Antje Kroner et al.   NEURON

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Microglia Promote Learning-Dependent Synapse Formation through Brain-Derived Neurotrophic Factor

(2013) Christopher N. Parkhurst et al.   CELL

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Identification of a unique TGF-β–dependent molecular and functional signature in microglia

(2013) Oleg Butovsky et al.   NATURE NEUROSCIENCE

The microglial sensome revealed by direct RNA sequencing

(2013) Suzanne E Hickman et al.   NATURE NEUROSCIENCE

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

TGF-β signaling through SMAD2/3 induces the quiescent microglial phenotype within the CNS environment

(2012) Shai Abutbul et al.   GLIA

Fate Mapping Reveals Origins and Dynamics of Monocytes and Tissue Macrophages under Homeostasis

(2012) Simon Yona et al.   IMMUNITY

Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

(2012) Emmanuel L Gautier et al.   NATURE IMMUNOLOGY

GO-function: deriving biologically relevant functions from statistically significant functions

(2011) J. Wang et al.   BRIEFINGS IN BIOINFORMATICS

Physiology of Microglia

(2011) Helmut Kettenmann et al.   PHYSIOLOGICAL REVIEWS

Regeneration of axons in injured spinal cord by activation of bone morphogenetic protein/Smad1 signaling pathway in adult neurons

(2011) P. Parikh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative analysis of cellular inflammation after traumatic spinal cord injury: evidence for a multiphasic inflammatory response in the acute to chronic environment

(2010) Kevin D. Beck et al.   BRAIN

Histone Deacetylase Inhibitors Suppress Inflammatory Activation of Rheumatoid Arthritis Patient Synovial Macrophages and Tissue

(2010) Aleksander M. Grabiec et al.   JOURNAL OF IMMUNOLOGY

Ion channels in monocytes and microglia / brain macrophages: Promising therapeutic targets for neurological diseases

(2010) Claudia Eder   JOURNAL OF NEUROIMMUNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Identification of Two Distinct Macrophage Subsets with Divergent Effects Causing either Neurotoxicity or Regeneration in the Injured Mouse Spinal Cord

(2009) K. A. Kigerl et al.   JOURNAL OF NEUROSCIENCE

Indirect Macrophage Responses to Ionizing Radiation: Implications for Genotype-Dependent Bystander Signaling

(2008) P. J. Coates et al.   CANCER RESEARCH

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE