Self-supervised contrastive learning for integrative single cell RNA-seq data analysis

Fast and precise single-cell data analysis using a hierarchical autoencoder

(2021) Duc Tran et al.   Nature Communications

Model-based deep embedding for constrained clustering analysis of single cell RNA-seq data

(2021) Tian Tian et al.   Nature Communications

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

(2021) Juexin Wang et al.   Nature Communications

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces

(2021) Jiarui Ding et al.   Nature Communications

Contrastive self-supervised clustering of scRNA-seq data

(2021) Madalina Ciortan et al.   BMC BIOINFORMATICS

HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data

(2021) Xiao Wang et al.   BIOINFORMATICS

SMILE: mutual information learning for integration of single-cell omics data

(2021) Yang Xu et al.   BIOINFORMATICS

scRAE: Deterministic Regularized Autoencoders With Flexible Priors for Clustering Single-Cell Gene Expression Data

(2021) Arnab Kumar Mondal et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019

(2020) Juanjuan Zhao et al.   CLINICAL INFECTIOUS DISEASES

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

(2020) Jonas Schulte-Schrepping et al.   CELL

The cytokine storm and COVID‐19

(2020) Biying Hu et al.   JOURNAL OF MEDICAL VIROLOGY

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

A single-cell atlas of the peripheral immune response in patients with severe COVID-19

(2020) Aaron J. Wilk et al.   NATURE MEDICINE

Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm

(2020) Chuang Guo et al.   Nature Communications

Comprehensive mapping of immune perturbations associated with severe COVID-19

(2020) Leticia Kuri-Cervantes et al.   Science Immunology

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

(2020) Ashley Maynard et al.   CELL

MARS: discovering novel cell types across heterogeneous single-cell experiments

(2020) Maria Brbić et al.   NATURE METHODS

The interplay between inflammatory pathways and COVID-19: A critical review on pathogenesis and therapeutic options

(2020) Shalki Choudhary et al.   MICROBIAL PATHOGENESIS

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

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

(2019) Gökcen Eraslan et al.   Nature Communications

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

(2019) Yue Deng et al.   NATURE METHODS

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

(2019) Peter van Galen et al.   CELL

Data denoising with transfer learning in single-cell transcriptomics

(2019) Jingshu Wang et al.   NATURE METHODS

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Spectral clustering based on learning similarity matrix

(2018) Seyoung Park et al.   BIOINFORMATICS

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

(2018) Kelly Street et al.   BMC GENOMICS

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

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

(2018) Jiarui Ding 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

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez 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

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

(2017) Sinisa Hrvatin et al.   NATURE NEUROSCIENCE

A Single-Cell Transcriptome Atlas of the Human Pancreas

(2016) Mauro J. Muraro et al.   Cell Systems

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

(2015) Jacob H. Levine et al.   CELL

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

(2015) Minzhe Guo et al.   PLoS Computational Biology

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY