Hotspot identifies informative gene modules across modalities of single-cell genomics

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

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

(2019) Joshua D. Welch et al.   CELL

Simulating multiple faceted variability in single cell RNA sequencing

(2019) Xiuwei Zhang et al.   Nature Communications

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

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

(2018) Valentine Svensson et al.   Nature Protocols

A comprehensive evaluation of module detection methods for gene expression data

(2018) Wouter Saelens et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Population snapshots predict early haematopoietic and erythroid hierarchies

(2018) Betsabeh Khoramian Tusi et al.   NATURE

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

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

(2016) P. L. Stahl et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

(2013) Jong Kim et al.   GENOME BIOLOGY

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans

(2011) Maxime Rotival et al.   PLoS Genetics

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS