Interpretable factor models of single-cell RNA-seq via variational autoencoders

Droplet scRNA-seq is not zero-inflated

(2020) Valentine Svensson   NATURE BIOTECHNOLOGY

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

(2019) Gökcen Eraslan et al.   Nature Communications

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

De novo gene signature identification from single‐cell RNA‐seq with hierarchical Poisson factorization

(2019) Hanna Mendes Levitin et al.   Molecular Systems Biology

Probabilistic Count Matrix Factorization for Single Cell Expression Data Analysis

(2019) G Durif et al.   BIOINFORMATICS

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

(2018) Valentine Svensson et al.   Nature Protocols

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

(2018) Davide Risso et al.   Nature Communications

Review: Transcriptional Regulation of CD4+ T Cell Differentiation in Experimentally Induced Arthritis and Rheumatoid Arthritis

(2018) Yuya Kondo et al.   Arthritis & Rheumatology

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Cell-Type-Specific Gene Programs of the Normal Human Nephron Define Kidney Cancer Subtypes

(2017) David Lindgren et al.   Cell Reports

Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states

(2017) Sumin Jang et al.   eLife

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

(2017) Xun Zhu et al.   PeerJ

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

(2015) Dawn Thompson et al.   Annual Review of Cell and Developmental Biology

Geometry of the Gene Expression Space of Individual Cells

(2015) Yael Korem et al.   PLoS Computational Biology

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL