Neuronal–glial communication perturbations in murine SOD1G93A spinal cord

Clusterin secreted from astrocyte promotes excitatory synaptic transmission and ameliorates Alzheimer’s disease neuropathology

(2021) Fading Chen et al.   Molecular Neurodegeneration

A practical solution to pseudoreplication bias in single-cell studies

(2021) Kip D. Zimmerman et al.   Nature Communications

Rare variant burden analysis within enhancers identifies CAV1 as an ALS risk gene

(2021) Johnathan Cooper-Knock et al.   Cell Reports

Multiple sclerosis risk gene Mertk is required for microglial activation and subsequent remyelination

(2021) Kimberle Shen et al.   Cell Reports

Oligodendrocyte Dysfunction in Amyotrophic Lateral Sclerosis: Mechanisms and Therapeutic Perspectives

(2021) Stefano Raffaele et al.   Cells

Non-neuronal cells in amyotrophic lateral sclerosis — from pathogenesis to biomarkers

(2021) Björn F. Vahsen et al.   Nature Reviews Neurology

Non-cell-autonomous pathogenic mechanisms in amyotrophic lateral sclerosis

(2021) Alexandra C.M. Van Harten et al.   TRENDS IN NEUROSCIENCES

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Amyloid beta increases ABCA1 and HMGCR protein expression, and cholesterol synthesis and accumulation in mice neurons and astrocytes

(2021) Shirin Azizidoost et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Neurotoxic reactive astrocytes induce cell death via saturated lipids

(2021) Kevin A. Guttenplan et al.   NATURE

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

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

Knockout of reactive astrocyte activating factors slows disease progression in an ALS mouse model

(2020) Kevin A. Guttenplan et al.   Nature Communications

Trial of Sodium Phenylbutyrate–Taurursodiol for Amyotrophic Lateral Sclerosis

(2020) Sabrina Paganoni et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

The dark side of HDAC inhibition in ALS

(2019) Anne-Laurence Boutillier et al.   EBioMedicine

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

(2019) Bérénice A. Benayoun et al.   GENOME RESEARCH

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

(2019) Jellert T. Gaublomme et al.   Nature Communications

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

NF‐κB activation in astrocytes drives a stage‐specific beneficial neuroimmunological response in ALS

(2018) Najwa Ouali Alami et al.   EMBO JOURNAL

Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors

(2018) Jay H. Kalin et al.   Nature Communications

Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Neurons and Their Activity during Behavior

(2018) Anupama Sathyamurthy et al.   Cell Reports

Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis

(2018) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

(2018) Trygve E. Bakken et al.   PLoS One

FRMPD4 mutations cause X-linked intellectual disability and disrupt dendritic spine morphogenesis

(2017) Juliette Piard et al.   HUMAN MOLECULAR GENETICS

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

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

The multifaceted role of astrocytes in regulating myelination

(2016) Hülya Kıray et al.   EXPERIMENTAL NEUROLOGY

Activation of oligodendroglial Stat3 is required for efficient remyelination

(2016) Andrew J. Steelman et al.   NEUROBIOLOGY OF DISEASE

Possibility of a sex-specific role for a genetic variant in FRMPD4 in schizophrenia, but not cognitive function

(2016) Natalie Matosin et al.   NEUROREPORT

CSF1R blockade slows the progression of amyotrophic lateral sclerosis by reducing microgliosis and invasion of macrophages into peripheral nerves

(2016) Anna Martínez-Muriana et al.   Scientific Reports

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

α-Synuclein, a chemoattractant, directs microglial migration via H2O2-dependent Lyn phosphorylation

(2015) Shijun Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational profiling identifies a cascade of damage initiated in motor neurons and spreading to glia in mutant SOD1-mediated ALS

(2015) Shuying Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Astrocyte-Derived TGF-β1 Accelerates Disease Progression in ALS Mice by Interfering with the Neuroprotective Functions of Microglia and T Cells

(2015) Fumito Endo et al.   Cell Reports

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Microglia Induce Motor Neuron Death via the Classical NF-κB Pathway in Amyotrophic Lateral Sclerosis

(2014) Ashley E. Frakes et al.   NEURON

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

(2013) Y. Liao et al.   BIOINFORMATICS

State of play in amyotrophic lateral sclerosis genetics

(2013) Alan E Renton et al.   NATURE NEUROSCIENCE

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Copy Number Variation in Sporadic Amyotrophic Lateral Sclerosis in the Turkish Population: Deletion of EPHA3 Is a Possible Protective Factor

(2013) Özgün Uyan et al.   PLoS One

A Neurodegeneration-Specific Gene-Expression Signature of Acutely Isolated Microglia from an Amyotrophic Lateral Sclerosis Mouse Model

(2013) Isaac M. Chiu et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Preso1 dynamically regulates group I metabotropic glutamate receptors

(2012) Jia-Hua Hu et al.   NATURE NEUROSCIENCE

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

Astrocytes Control Glutamate Receptor Levels at Developing Synapses through SPARC- -Integrin Interactions

(2011) E. V. Jones et al.   JOURNAL OF NEUROSCIENCE

Astrocytes from familial and sporadic ALS patients are toxic to motor neurons

(2011) Amanda M Haidet-Phillips et al.   NATURE BIOTECHNOLOGY

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

REST and CoREST are transcriptional and epigenetic regulators of seminal neural fate decisions

(2010) Irfan A. Qureshi et al.   CELL CYCLE

Effects of gender in amyotrophic lateral sclerosis

(2010) Pamela A. McCombe et al.   Gender Medicine

The P2X7-Egr pathway regulates nucleotide-dependent inflammatory gene expression in microglia

(2010) S. A. Friedle et al.   GLIA

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

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

Synapse formation regulated by protein tyrosine phosphatase receptor T through interaction with cell adhesion molecules and Fyn

(2009) So-Hee Lim et al.   EMBO JOURNAL

A role for motoneuron subtype–selective ER stress in disease manifestations of FALS mice

(2009) Smita Saxena et al.   NATURE NEUROSCIENCE

REST and CoREST Modulate Neuronal Subtype Specification, Maturation and Maintenance

(2009) Joseph J. Abrajano et al.   PLoS One

Essential role of B-Raf in oligodendrocyte maturation and myelination during postnatal central nervous system development

(2008) Gergana Galabova-Kovacs et al.   JOURNAL OF CELL BIOLOGY

Neuron-Specific Expression of Mutant Superoxide Dismutase Is Sufficient to Induce Amyotrophic Lateral Sclerosis in Transgenic Mice

(2008) D. Jaarsma et al.   JOURNAL OF NEUROSCIENCE

Astrocytes as determinants of disease progression in inherited amyotrophic lateral sclerosis

(2008) Koji Yamanaka et al.   NATURE NEUROSCIENCE

Restricted expression of mutant SOD1 in spinal motor neurons and interneurons induces motor neuron pathology

(2007) Lijun Wang et al.   NEUROBIOLOGY OF DISEASE