Dysregulation of brain and choroid plexus cell types in severe COVID-19

Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages

(2021) Els Wauters et al.   CELL RESEARCH

Neuroinvasion of SARS-CoV-2 in human and mouse brain

(2021) Eric Song et al.   JOURNAL OF EXPERIMENTAL MEDICINE

White matter aging drives microglial diversity

(2021) Shima Safaiyan et al.   NEURON

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

A cellular and spatial map of the choroid plexus across brain ventricles and ages

(2021) Neil Dani et al.   CELL

Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain

(2021) Fabien Dachet et al.   Scientific Reports

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

Dendritic action potentials and computation in human layer 2/3 cortical neurons

(2020) Albert Gidon et al.   SCIENCE

Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study

(2020) Xiaobo Yang et al.   Lancet Respiratory Medicine

Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing

(2020) Tian Mou et al.   Frontiers in Genetics

Single-nucleus RNA-seq identifies Huntington disease astrocyte states

(2020) Osama Al-Dalahmah et al.   Acta Neuropathologica Communications

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

(2020) Pierre Bost et al.   CELL

Neurologic manifestations in hospitalized patients with COVID-19: The ALBACOVID registry

(2020) Carlos Manuel Romero-Sánchez et al.   NEUROLOGY

Neurologic Features in Severe SARS-CoV-2 Infection

(2020) Julie Helms et al.   NEW ENGLAND JOURNAL OF MEDICINE

GeneTrail 3: advanced high-throughput enrichment analysis

(2020) Nico Gerstner et al.   NUCLEIC ACIDS RESEARCH

Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model

(2020) Barry Rockx et al.   SCIENCE

Chitinase 3-like 1 is neurotoxic in primary cultured neurons

(2020) Clara Matute-Blanch et al.   Scientific Reports

Brain Endothelial Cells Are Exquisite Sensors of Age-Related Circulatory Cues

(2020) Michelle B. Chen et al.   Cell Reports

Neurologic Manifestations of Hospitalized Patients With Coronavirus Disease 2019 in Wuhan, China

(2020) Ling Mao et al.   JAMA Neurology

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

(2020) Jonas Schulte-Schrepping et al.   CELL

Persistent Symptoms in Patients After Acute COVID-19

(2020) Angelo Carfì et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Neurological associations of COVID-19

(2020) Mark A Ellul et al.   LANCET NEUROLOGY

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

Physiological blood–brain transport is impaired with age by a shift in transcytosis

(2020) Andrew C. Yang et al.   NATURE

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

(2020) Aaron J. Wilk et al.   NATURE MEDICINE

Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm

(2020) Chuang Guo et al.   Nature Communications

Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells

(2020) Mahmood Yaseen Hachim et al.   Frontiers in Immunology

Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19

(2020) Jeong Seok Lee et al.   Science Immunology

Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19

(2020) Benjamin J. Meckiff et al.   CELL

Effects of COVID-19 on the Nervous System

(2020) Costantino Iadecola et al.   CELL

Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium

(2020) Fadi Jacob et al.   Cell Stem Cell

SARS-CoV-2 infects the brain choroid plexus and disrupts the blood-CSF-barrier in human brain organoids

(2020) Laura Pellegrini et al.   Cell Stem Cell

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity

(2020) Ludovico Cantuti-Castelvetri et al.   SCIENCE

Frequent neurologic manifestations and encephalopathy‐associated morbidity in Covid‐19 patients

(2020) Eric M. Liotta et al.   Annals of Clinical and Translational Neurology

The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing

(2020) Gang Xu et al.   Cell Discovery

Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19

(2020) Yapeng Su et al.   CELL

Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19

(2020) Jenny Meinhardt et al.   NATURE NEUROSCIENCE

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

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

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

Microglial nodules provide the environment for pathogenic T cells in human encephalitis

(2019) Anna R. Tröscher et al.   ACTA NEUROPATHOLOGICA

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

Altered human oligodendrocyte heterogeneity in multiple sclerosis

(2019) Sarah Jäkel et al.   NATURE

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Single-cell genomics identifies cell type–specific molecular changes in autism

(2019) Dmitry Velmeshev et al.   SCIENCE

The Major Risk Factors for Alzheimer’s Disease: Age, Sex, and Genes Modulate the Microglia Response to Aβ Plaques

(2019) Carlo Sala Frigerio et al.   Cell Reports

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Single-cell analysis reveals T cell infiltration in old neurogenic niches

(2019) Ben W. Dulken et al.   NATURE

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Single-cell transcriptomic profiling of the aging mouse brain

(2019) Methodios Ximerakis et al.   NATURE NEUROSCIENCE

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

(2019) Alexandra Grubman et al.   NATURE NEUROSCIENCE

Long-Term Neuroinflammation Induced by Influenza A Virus Infection and the Impact on Hippocampal Neuron Morphology and Function

(2018) Shirin Hosseini et al.   JOURNAL OF NEUROSCIENCE

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

Necroptosis and RIPK1-mediated neuroinflammation in CNS diseases

(2018) Junying Yuan et al.   NATURE REVIEWS NEUROSCIENCE

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Modulators of microglial activation and polarization after intracerebral haemorrhage

(2017) Xi Lan et al.   Nature Reviews Neurology

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods

(2017) Alessandra Dal Molin et al.   Frontiers in Genetics

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

GABAergic Interneurons in the Neocortex: From Cellular Properties to Circuits

(2016) Robin Tremblay et al.   NEURON

Complement and microglia mediate early synapse loss in Alzheimer mouse models

(2016) S. Hong et al.   SCIENCE

viruSITE—integrated database for viral genomics

(2016) Matej Stano et al.   Database-The Journal of Biological Databases and Curation

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9

(2014) Lukasz Swiech et al.   NATURE BIOTECHNOLOGY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Aging-induced type I interferon response at the choroid plexus negatively affects brain function

(2014) K. Baruch et al.   SCIENCE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

IFITM-Family Proteins: The Cell's First Line of Antiviral Defense

(2014) Charles C. Bailey et al.   Annual Review of Virology

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Synaptic Computation and Sensory Processing in Neocortical Layer 2/3

(2013) Carl C.H. Petersen et al.   NEURON

Viral and Inflammatory Triggers of Neurodegenerative Diseases

(2012) M. Deleidi et al.   Science Translational Medicine

PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification

(2009) Athanasia Spandidos et al.   NUCLEIC ACIDS RESEARCH