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

Developmental diversification of cortical inhibitory interneurons

(2018) Christian Mayer et al.   NATURE

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson 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 RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation

(2017) Benjamin Lacar et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Single-Cell Resolution of Temporal Gene Expression during Heart Development

(2016) Daniel M. DeLaughter et al.   DEVELOPMENTAL CELL

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

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

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

(2015) Chen Xu et al.   BIOINFORMATICS

GOplot: an R package for visually combining expression data with functional analysis: Fig. 1.

(2015) Wencke Walter et al.   BIOINFORMATICS

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

(2015) Allon M. Klein et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

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) Paul Blakeley et al.   DEVELOPMENT

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex

(2015) Matthew B Johnson et al.   NATURE NEUROSCIENCE

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

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

Computing and Visualizing Dynamic Time Warping Alignments inR: ThedtwPackage

(2015) Toni Giorgino   Journal of Statistical Software

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

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

(2014) Sean C. Bendall et al.   CELL

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

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

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

Comprehensive literature review and statistical considerations for microarray meta-analysis

(2012) George C. Tseng et al.   NUCLEIC ACIDS RESEARCH

Super-resolution of human face image using canonical correlation analysis

(2010) Hua Huang et al.   PATTERN RECOGNITION

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Sparse canonical methods for biological data integration: application to a cross-platform study

(2009) Kim-Anh Lê Cao et al.   BMC BIOINFORMATICS

The Unfolded Protein Response: A Pathway That Links Insulin Demand with β-Cell Failure and Diabetes

(2008) Donalyn Scheuner et al.   ENDOCRINE REVIEWS

CD56brightnatural killer (NK) cells: an important NK cell subset

(2008) Aurélie Poli et al.   IMMUNOLOGY

Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis

(2008) Sandra Waaijenborg et al.   Statistical Applications in Genetics and Molecular Biology