SC3: consensus clustering of single-cell RNA-seq data

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

(2016) Mubeen Goolam et al.   CELL

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

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

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Effect of Mutation Order on Myeloproliferative Neoplasms

(2015) Christina A. Ortmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

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

(2015) A. Zeisel et al.   SCIENCE

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

(2015) Minzhe Guo et al.   PLoS Computational Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing

(2014) Fernando H. Biase et al.   GENOME RESEARCH

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

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

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

(2014) Simone Picelli et al.   Nature Protocols

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

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

(2014) Q. Deng et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin 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

Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

(2014) Bidesh Mahata et al.   Cell Reports

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

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

Somatic CALR Mutations in Myeloproliferative Neoplasms with Nonmutated JAK2

(2013) J. Nangalia et al.   NEW ENGLAND JOURNAL OF MEDICINE

Janus Kinase Deregulation in Leukemia and Lymphoma

(2012) Edwin Chen et al.   IMMUNITY

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

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS