Confronting false discoveries in single-cell differential expression

A practical solution to pseudoreplication bias in single-cell studies

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

Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

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

Single-Cell Transcriptomic Atlas of Primate Ovarian Aging

(2020) Si Wang et al.   CELL

Single cell transcriptome profiling of the human alcohol-dependent brain

(2020) Eric Brenner et al.   HUMAN MOLECULAR GENETICS

Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus

(2020) Yuri Kotliarov et al.   NATURE MEDICINE

An immune-cell signature of bacterial sepsis

(2020) Miguel Reyes et al.   NATURE MEDICINE

Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis

(2020) David Schafflick et al.   Nature Communications

Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons

(2020) Corina Nagy et al.   NATURE NEUROSCIENCE

Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines

(2020) Eddie Cano-Gamez et al.   Nature Communications

Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium

(2020) Katherine C. Goldfarbmuren et al.   Nature Communications

Cell type prioritization in single-cell data

(2020) Michael A. Skinnider et al.   NATURE BIOTECHNOLOGY

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

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

Single nuclei RNA sequencing assessment of the hepatic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin

(2020) Rance Nault et al.   Cellular and Molecular Gastroenterology and Hepatology

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

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

A discriminative learning approach to differential expression analysis for single-cell RNA-seq

(2019) Vasilis Ntranos et al.   NATURE METHODS

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

(2019) Ilias Angelidis et al.   Nature Communications

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

Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways

(2019) Evan Der et al.   NATURE IMMUNOLOGY

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

Identification of a regeneration-organizing cell in the Xenopus tail

(2019) C. Aztekin et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner

(2019) Diego Adhemar Jaitin et al.   CELL

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Neuronal vulnerability and multilineage diversity in multiple sclerosis

(2019) Lucas Schirmer et al.   NATURE

Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis

(2019) Robert C. Wirka et al.   NATURE MEDICINE

Sensory lesioning induces microglial synapse elimination via ADAM10 and fractalkine signaling

(2019) Georgia Gunner et al.   NATURE NEUROSCIENCE

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

Obesity remodels activity and transcriptional state of a lateral hypothalamic brake on feeding

(2019) Mark A. Rossi et al.   SCIENCE

Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet

(2019) Chia-Wei Cheng et al.   CELL

The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue

(2019) Fabian F. Voigt et al.   NATURE METHODS

Single-cell transcriptomic profiling of the aging mouse brain

(2019) Methodios Ximerakis et al.   NATURE NEUROSCIENCE

Valid Post-clustering Differential Analysis for Single-Cell RNA-Seq

(2019) Jesse M. Zhang et al.   Cell Systems

Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

(2019) Dong-Wook Kim et al.   CELL

Mucosal Profiling of Pediatric-Onset Colitis and IBD Reveals Common Pathogenics and Therapeutic Pathways

(2019) Bing Huang et al.   CELL

Cortical Foxp2 Supports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression

(2019) Marissa Co et al.   CEREBRAL CORTEX

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

Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians

(2019) Kosuke Hashimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction

(2019) Aritra Bhattacherjee et al.   Nature Communications

Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes

(2019) Nicholas M. Tran et al.   NEURON

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

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

(2018) Charlotte Soneson et al.   NATURE METHODS

Cortico–reticulo–spinal circuit reorganization enables functional recovery after severe spinal cord contusion

(2018) Leonie Asboth et al.   NATURE NEUROSCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

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

(2018) Anupama Sathyamurthy et al.   Cell Reports

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Allergic inflammatory memory in human respiratory epithelial progenitor cells

(2018) Jose Ordovas-Montanes et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Required growth facilitators propel axon regeneration across complete spinal cord injury

(2018) Mark A. Anderson et al.   NATURE

Single cell molecular alterations reveal target cells and pathways of concussive brain injury

(2018) Douglas Arneson et al.   Nature Communications

Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia

(2018) Denis Avey et al.   Cell Reports

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

(2018) Paul A Reyfman et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Gene expression variability across cells and species shapes innate immunity

(2018) Tzachi Hagai et al.   NATURE

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury

(2018) Jordan W Squair et al.   eLife

Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq

(2017) Peng Hu et al.   MOLECULAR CELL

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Pericytes impair capillary blood flow and motor function after chronic spinal cord injury

(2017) Yaqing Li et al.   NATURE MEDICINE

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

Maintenance of redox homeostasis by hypoxia-inducible factors

(2017) Debangshu Samanta et al.   Redox Biology

Batch effects and the effective design of single-cell gene expression studies

(2017) Po-Yuan Tung et al.   Scientific Reports

Astrocyte scar formation aids central nervous system axon regeneration

(2016) Mark A. Anderson et al.   NATURE

Spatiotemporal neuromodulation therapies engaging muscle synergies improve motor control after spinal cord injury

(2016) Nikolaus Wenger et al.   NATURE MEDICINE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Untangling the brain’s neuroinflammatory and neurodegenerative transcriptional responses

(2016) Karpagam Srinivasan et al.   Nature Communications

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

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

Muscle Spindle Feedback Directs Locomotor Recovery and Circuit Reorganization after Spinal Cord Injury

(2014) Aya Takeoka et al.   CELL

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

(2014) Raju Tomer et al.   Nature Protocols

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Undirected compensatory plasticity contributes to neuronal dysfunction after severe spinal cord injury

(2013) Janine Beauparlant et al.   BRAIN

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

Versatile robotic interface to evaluate, enable and train locomotion and balance after neuromotor disorders

(2012) Nadia Dominici et al.   NATURE MEDICINE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Restoring Voluntary Control of Locomotion after Paralyzing Spinal Cord Injury

(2012) R. van den Brand et al.   SCIENCE

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

IGF binding protein-6 expression in vascular endothelial cells is induced by hypoxia and plays a negative role in tumor angiogenesis

(2011) Chunyang Zhang et al.   INTERNATIONAL JOURNAL OF CANCER

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

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

Transformation of nonfunctional spinal circuits into functional states after the loss of brain input

(2009) Grégoire Courtine et al.   NATURE NEUROSCIENCE

In Vitro and In Vivo Gene Therapy Vector Evolution via Multispecies Interbreeding and Retargeting of Adeno-Associated Viruses

(2008) D. Grimm et al.   JOURNAL OF VIROLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS