JingleBells: A Repository of Immune-Related Single-Cell RNA–Sequencing Datasets

Genetics and immunity in the era of single-cell genomics

(2016) Felipe A. Vieira Braga et al.   HUMAN MOLECULAR GENETICS

Visualization and cellular hierarchy inference of single-cell data using SPADE

(2016) Benedict Anchang et al.   Nature Protocols

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

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

(2015) Nicola K. Wilson et al.   Cell Stem Cell

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

Aire controls gene expression in the thymic epithelium with ordered stochasticity

(2015) Matthew Meredith et al.   NATURE IMMUNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Each cell counts: Hematopoiesis and immunity research in the era of single cell genomics

(2015) Diego Adhemar Jaitin et al.   SEMINARS IN IMMUNOLOGY

Population and single-cell genomics reveal theAiredependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

(2014) Stephen N. Sansom et al.   GENOME RESEARCH

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

(2014) Alex K. Shalek et al.   NATURE

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

(2014) D. A. Jaitin et al.   SCIENCE

A novel splice variant of folate receptor 4 predominantly expressed in regulatory T cells

(2012) Yi Tian et al.   BMC IMMUNOLOGY

ArrayExpress update—trends in database growth and links to data analysis tools

(2012) Gabriella Rustici et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS