Cell type prioritization in single-cell data

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

(2019) Vasilis Ntranos et al.   NATURE METHODS

Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures

(2019) Miguel Reyes et al.   Science Advances

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

(2019) Florian Erhard et al.   NATURE

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

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

Sensory lesioning induces microglial synapse elimination via ADAM10 and fractalkine signaling

(2019) Georgia Gunner et al.   NATURE NEUROSCIENCE

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

(2019) Mark A. Rossi et al.   SCIENCE

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

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data

(2018) Shun H Yip et al.   BRIEFINGS IN BIOINFORMATICS

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

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

(2018) Leonie Asboth et al.   NATURE NEUROSCIENCE

Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types

(2018) Martin Häring et al.   NATURE NEUROSCIENCE

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

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

(2018) Jonathan A. Griffiths 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

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

(2018) Luke Zappia et al.   GigaScience

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

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

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

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

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

(2018) Jordan W Squair et al.   eLife

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

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

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink 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

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity

(2017) Renchao Chen et al.   Cell Reports

Parsing the Interferon Transcriptional Network and Its Disease Associations

(2016) Sara Mostafavi et al.   CELL

Astrocyte scar formation aids central nervous system axon regeneration

(2016) Mark A. Anderson et al.   NATURE

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing

(2016) Graham Heimberg et al.   Cell Systems

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

V1 and V2b Interneurons Secure the Alternating Flexor-Extensor Motor Activity Mice Require for Limbed Locomotion

(2014) Jingming Zhang et al.   NEURON

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

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

RNAscope

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

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

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

Genetic Ablation of V2a Ipsilateral Interneurons Disrupts Left-Right Locomotor Coordination in Mammalian Spinal Cord

(2008) Steven A. Crone et al.   NEURON