SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation

A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data

(2019) Xiaoshu Zhu et al.   Genes

Network-based methods for predicting essential genes or proteins: a survey

(2019) Xingyi Li et al.   BRIEFINGS IN BIOINFORMATICS

Spectral clustering based on learning similarity matrix

(2018) Seyoung Park et al.   BIOINFORMATICS

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

dropClust: efficient clustering of ultra-large scRNA-seq data

(2018) Debajyoti Sinha et al.   NUCLEIC ACIDS RESEARCH

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

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks

(2018) Ruiqing Zheng et al.   BIOINFORMATICS

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar 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

Using neural networks for reducing the dimensions of single-cell RNA-Seq data

(2017) Chieh Lin et al.   NUCLEIC ACIDS RESEARCH

Robust classification of single-cell transcriptome data by nonnegative matrix factorization

(2016) Chunxuan Shao et al.   BIOINFORMATICS

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

(2016) Mubeen Goolam et al.   CELL

Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

(2016) Isaac Engel et al.   NATURE IMMUNOLOGY

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

BTG4 is a meiotic cell cycle–coupled maternal-zygotic-transition licensing factor in oocytes

(2016) Chao Yu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

BTG4 is a meiotic cell cycle–coupled maternal-zygotic-transition licensing factor in oocytes

(2016) Chao Yu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

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

(2015) Evan Z. Macosko et al.   CELL

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

(2015) P. Blakeley et al.   DEVELOPMENT

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) A. Zeisel et al.   SCIENCE

Interferon-Induced Transmembrane Protein 1 Regulates Endothelial Lumen Formation During Angiogenesis

(2014) Stephanie A. Popson et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein 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

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Low rank subspace clustering (LRSC)

(2013) René Vidal et al.   PATTERN RECOGNITION LETTERS

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

A Singular Value Thresholding Algorithm for Matrix Completion

(2010) Jian-Feng Cai et al.   SIAM JOURNAL ON OPTIMIZATION

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

(2008) J. D. Cahoy et al.   JOURNAL OF NEUROSCIENCE

Functional organization of the transcriptome in human brain

(2008) Michael C Oldham et al.   NATURE NEUROSCIENCE