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

netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis

(2020) Rebecca Elyanow et al.   GENOME RESEARCH

Putative cell type discovery from single-cell gene expression data

(2020) Zhichao Miao et al.   NATURE METHODS

IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq

(2020) Anjun Ma et al.   NUCLEIC ACIDS RESEARCH

Integrative Methods and Practical Challenges for Single-Cell Multi-omics

(2020) Anjun Ma et al.   TRENDS IN BIOTECHNOLOGY

scIGANs: single-cell RNA-seq imputation using generative adversarial networks

(2020) Yungang Xu et al.   NUCLEIC ACIDS RESEARCH

An entropy-based metric for assessing the purity of single cell populations

(2020) Baolin Liu et al.   Nature Communications

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

(2019) Gökcen Eraslan et al.   Nature Communications

Single-cell transcriptomic analysis of Alzheimer’s disease

(2019) Hansruedi Mathys et al.   NATURE

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

(2019) Luyi Tian et al.   NATURE METHODS

A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases

(2019) Danuta R. Gawel et al.   Genome Medicine

QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data

(2019) Juan Xie et al.   BIOINFORMATICS

Data denoising with transfer learning in single-cell transcriptomics

(2019) Jingshu Wang et al.   NATURE METHODS

LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data

(2019) Changlin Wan et al.   NUCLEIC ACIDS RESEARCH

Exploring single-cell data with deep multitasking neural networks

(2019) Matthew Amodio et al.   NATURE METHODS

Revealing dynamics of gene expression variability in cell state space

(2019) Dominic Grün   NATURE METHODS

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

(2019) Alexandra Grubman et al.   NATURE NEUROSCIENCE

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

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

SAVER: gene expression recovery for single-cell RNA sequencing

(2018) Mo Huang et al.   NATURE METHODS

An accurate and robust imputation method scImpute for single-cell RNA-seq data

(2018) Wei Vivian Li 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

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

The Transcription Factor Sp3 Cooperates with HDAC2 to Regulate Synaptic Function and Plasticity in Neurons

(2017) Hidekuni Yamakawa et al.   Cell Reports

Alzheimer’s Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci

(2016) Celeste M. Karch et al.   PLoS One

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

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

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

(2015) A. Zeisel et al.   SCIENCE

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

The Genetics of Alzheimer Disease

(2013) R. E. Tanzi   Cold Spring Harbor Perspectives in Medicine

Oxidative Stress Signaling in Alzheimers Disease

(2008) B. Su et al.   Current Alzheimer Research

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT