CALLR: a semi-supervised cell-type annotation method for single-cell RNA sequencing data

Single-Cell Mapping of Human Brain Cancer Reveals Tumor-Specific Instruction of Tissue-Invading Leukocytes

(2020) Ekaterina Friebel et al.   CELL

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

(2020) Maria Brbić et al.   NATURE METHODS

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

scMatch: a single-cell gene expression profile annotation tool using reference datasets

(2019) Rui Hou et al.   BIOINFORMATICS

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

(2019) Johanna Wagner et al.   CELL

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

(2019) Jurrian K de Kanter et al.   NUCLEIC ACIDS RESEARCH

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

(2019) Allen W. Zhang et al.   NATURE METHODS

A survey on semi-supervised learning

(2019) Jesper E. van Engelen et al.   MACHINE LEARNING

SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble

(2019) Ruth Huh et al.   NUCLEIC ACIDS RESEARCH

Spectral clustering based on learning similarity matrix

(2018) Seyoung Park et al.   BIOINFORMATICS

Single-cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma

(2018) Hongping Zheng et al.   HEPATOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell multi-omics sequencing of human early embryos

(2018) Lin Li et al.   NATURE CELL BIOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

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

(2018) Jiarui Ding et al.   Nature Communications

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

(2018) Yuchen Yang et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

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

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Single-cell transcriptomics to explore the immune system in health and disease

(2017) Michael J. T. Stubbington et al.   SCIENCE

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity

(2017) Renchao Chen et al.   Cell Reports

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

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

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

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

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Multiclass Data Segmentation Using Diffuse Interface Methods on Graphs

(2014) Cristina Garcia-Cardona et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Fast unfolding of communities in large networks

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