Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

(2018) Amir Giladi et al.   CELL

Single-Cell Sequencing of the Healthy and Diseased Heart Reveals Cytoskeleton-Associated Protein 4 as a New Modulator of Fibroblasts Activation

(2018) Monika M. Gladka et al.   CIRCULATION

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

(2018) Roser Vento-Tormo et al.   NATURE

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

A Single-Cell Sequencing Guide for Immunologists

(2018) Peter See et al.   Frontiers in Immunology

Revealing allele-specific gene expression by single-cell transcriptomics

(2017) Julio Aguila Benitez et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

GSA: Genome Sequence Archive *

(2017) Yanqing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq

(2016) Björn Reinius et al.   NATURE GENETICS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells

(2016) Amit Grover et al.   Nature Communications

Single-cell analysis of transcription kinetics across the cell cycle

(2016) Samuel O Skinner et al.   eLife

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

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

(2015) Allon M. Klein et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

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

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

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

(2015) Matthew B Johnson et al.   NATURE NEUROSCIENCE

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek 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

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

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

(2014) Q. Deng et al.   SCIENCE

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS