Pseudocell Tracer—A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination

Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks

(2020) Mohamed Marouf et al.   Nature Communications

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

(2019) Gökcen Eraslan et al.   Nature Communications

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

(2019) Fan Zhang et al.   NATURE IMMUNOLOGY

Class-Switch Recombination Occurs Infrequently in Germinal Centers

(2019) Jonathan A. Roco et al.   IMMUNITY

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

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

Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells

(2019) Noa Bossel Ben-Moshe et al.   Nature Communications

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut

(2018) Charles A. Herring et al.   Cell Systems

Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination

(2018) Karlynn E. Neu et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2018) et al.   NATURE

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single-Cell Genomics: Approaches and Utility in Immunology

(2017) Karlynn E. Neu et al.   TRENDS IN IMMUNOLOGY

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

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

(2016) Atray Dixit et al.   CELL

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway

(2016) Yong Yu et al.   NATURE

Orchestration of plasma cell differentiation by Bach2 and its gene regulatory network

(2014) Kazuhiko Igarashi et al.   IMMUNOLOGICAL REVIEWS

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Mechanism and Regulation of Class Switch Recombination

(2008) Janet Stavnezer et al.   Annual Review of Immunology