Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender

Microfluidics-free single-cell genomics with templated emulsification

(2023) Iain C. Clark et al.   NATURE BIOTECHNOLOGY

Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

(2022) Marianna Zazhytska et al.   CELL

Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress

(2022) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

(2022) Gökcen Eraslan et al.   SCIENCE

Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy

(2022) Mark Chaffin et al.   NATURE

Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets

(2022) Emre Caglayan et al.   NEURON

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

(2021) Neil Dani et al.   CELL

Automated quality control and cell identification of droplet-based single-cell data using dropkick

(2021) Cody N Heiser et al.   GENOME RESEARCH

A molecular single-cell lung atlas of lethal COVID-19

(2021) Johannes C. Melms et al.   NATURE

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

(2021) Toni M. Delorey et al.   NATURE

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

(2021) Carly G.K. Ziegler et al.   CELL

Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids

(2021) Galina Popova et al.   Cell Stem Cell

Molecular logic of cellular diversification in the mouse cerebral cortex

(2021) Daniela J. Di Bella et al.   NATURE

Single-cell analysis enters the multiomics age

(2021) Jeffrey M. Perkel   NATURE

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

(2021) Zoe A. Clarke et al.   Nature Protocols

A single-cell transcriptomic landscape of the lungs of patients with COVID-19

(2021) Si Wang et al.   NATURE CELL BIOLOGY

Droplet scRNA-seq is not zero-inflated

(2020) Valentine Svensson   NATURE BIOTECHNOLOGY

A genome-wide transcriptomic analysis of protein-coding genes in human blood cells

(2020) Mathias Uhlen et al.   SCIENCE

scVAE: Variational auto-encoders for single-cell gene expression data

(2020) Christopher Heje Grønbech et al.   BIOINFORMATICS

Transcriptional and Cellular Diversity of the Human Heart

(2020) Nathan R. Tucker et al.   CIRCULATION

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Cells of the adult human heart

(2020) Monika Litviňuková et al.   NATURE

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

(2020) Gang Xu et al.   Cell Discovery

Mapping Development of the Human Intestinal Niche at Single-Cell Resolution

(2020) Emily M. Holloway et al.   Cell Stem Cell

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

(2020) Matthew D Young et al.   GigaScience

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

(2019) Gökcen Eraslan et al.   Nature Communications

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

(2019) Gianni Monaco et al.   Cell Reports

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

(2019) Longqi Liu et al.   Nature Communications

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

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

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Variational Inference: A Review for Statisticians

(2017) David M. Blei et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

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

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

(2016) Atray Dixit et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Regulation of CD45 Alternative Splicing by Heterogeneous Ribonucleoprotein, hnRNPLL

(2008) S. Oberdoerffer et al.   SCIENCE