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

A practical solution to pseudoreplication bias in single-cell studies

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

Modular, efficient and constant-memory single-cell RNA-seq preprocessing

(2021) Páll Melsted et al.   NATURE BIOTECHNOLOGY

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

TooManyCells identifies and visualizes relationships of single-cell clades

(2020) Gregory W. Schwartz et al.   NATURE METHODS

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Transcriptional and Spatial Resolution of Cell Types in the Mammalian Habenula

(2020) Yoshiko Hashikawa et al.   NEURON

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

(2020)   NATURE

Neurons that regulate mouse torpor

(2020) Sinisa Hrvatin et al.   NATURE

Cell type prioritization in single-cell data

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

Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remission

(2020) Marie A. Bentsen et al.   Nature Communications

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

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Evaluating measures of association for single-cell transcriptomics

(2019) Michael A. Skinnider et al.   NATURE METHODS

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

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

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

(2019) Christopher S. Smillie et al.   CELL

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

(2019) Joshua D. Welch et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

scSLAM-seq reveals core features of transcription dynamics in single cells

(2019) Florian Erhard et al.   NATURE

Neuronal vulnerability and multilineage diversity in multiple sclerosis

(2019) Lucas Schirmer et al.   NATURE

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

A cellular census of human lungs identifies novel cell states in health and in asthma

(2019) Felipe A. Vieira Braga et al.   NATURE MEDICINE

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

(2019) Mark A. Rossi et al.   SCIENCE

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

(2019) Allen W. Zhang et al.   NATURE METHODS

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

(2019) Dong-Wook Kim et al.   CELL

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

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

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

(2019) Aritra Bhattacherjee et al.   Nature Communications

Orchestrating single-cell analysis with Bioconductor

(2019) Robert A. Amezquita et al.   NATURE METHODS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Charlotte Soneson et al.   NATURE METHODS

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

(2018) Valentine Svensson et al.   Nature Protocols

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

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

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

(2018) Luke Zappia et al.   GigaScience

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

(2018) Denis Avey et al.   Cell Reports

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Gene expression variability across cells and species shapes innate immunity

(2018) Tzachi Hagai et al.   NATURE

Targeted neurotechnology restores walking in humans with spinal cord injury

(2018) Fabien B. Wagner et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Electrical spinal cord stimulation must preserve proprioception to enable locomotion in humans with spinal cord injury

(2018) Emanuele Formento et al.   NATURE NEUROSCIENCE

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

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

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius 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

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

What Is Your Conceptual Definition of “Cell Type” in the Context of a Mature Organism?

(2017)   Cell Systems

Microglial TNF-α Suppresses Cocaine-Induced Plasticity and Behavioral Sensitization

(2016) Gil M. Lewitus et al.   NEURON

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

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

(2012) Andrew McDavid et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

(2010) Belinda Phipson et al.   Statistical Applications in Genetics and Molecular Biology

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS