SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement

An Adaptive Sparse Subspace Clustering for Cell Type Identification

(2020) Ruiqing Zheng et al.   Frontiers in Genetics

ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets

(2020) Hong-Dong Li et al.   Journal of Bioinformatics and Computational Biology

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

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

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

(2019) Ruiqing Zheng et al.   BIOINFORMATICS

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization

(2019) Zhanying Feng et al.   BIOINFORMATICS

Spectral clustering based on learning similarity matrix

(2018) Seyoung Park et al.   BIOINFORMATICS

Random forest based similarity learning for single cell RNA sequencing data

(2018) Maziyar Baran Pouyan et al.   BIOINFORMATICS

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

ELF: Extract Landmark Features by optimizing topology maintenance, redundancy, and specificity

(2018) Zhanying Feng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

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

(2018) Debajyoti Sinha et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

(2018) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

(2018) Yuchen Yang et al.   BIOINFORMATICS

Enhancing subspace clustering based on dynamic prediction

(2018) Ratha Pech et al.   Frontiers of Computer Science

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation

(2017) Yan Song et al.   MOLECULAR CELL

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber 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

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

(2016) Chunxuan Shao et al.   BIOINFORMATICS

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

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

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

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

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

(2014) Barbara Treutlein et al.   NATURE

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

Differences in Gene Expression between Mouse and Human for Dynamically Regulated Genes in Early Embryo

(2014) Elo Madissoon et al.   PLoS One

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

(2014) Q. Deng et al.   SCIENCE

Single-Cell RNA Sequencing Identifies Extracellular Matrix Gene Expression by Pancreatic Circulating Tumor Cells

(2014) David T. Ting et al.   Cell Reports

Sparse Subspace Clustering: Algorithm, Theory, and Applications

(2013) E. Elhamifar et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

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

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

Low rank subspace clustering (LRSC)

(2013) René Vidal et al.   PATTERN RECOGNITION LETTERS

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

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

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

(2010) Fuchou Tang et al.   Nature Protocols