Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

αβ T cell receptors as predictors of health and disease

(2015) Meriem Attaf et al.   Cellular & Molecular Immunology

Transmitted/Founder Viruses Rapidly Escape from CD8+T Cell Responses in Acute Hepatitis C Virus Infection

(2015) Rowena A. Bull et al.   JOURNAL OF VIROLOGY

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

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

A prospective study of hepatitis C incidence in Australian prisoners

(2014) Fabio Luciani et al.   ADDICTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Recognition of Distinct Cross-Reactive Virus-Specific CD8+ T Cells Reveals a Unique TCR Signature in a Clinical Setting

(2014) T. H. O. Nguyen et al.   JOURNAL OF IMMUNOLOGY

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells

(2014) Evan W Newell 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

Single-cell technologies for monitoring immune systems

(2014) Pratip K Chattopadhyay et al.   NATURE IMMUNOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

High-throughput identification of antigen-specific TCRs by TCR gene capture

(2013) Carsten Linnemann et al.   NATURE MEDICINE

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

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

Disparate Individual Fates Compose Robust CD8+ T Cell Immunity

(2013) V. R. Buchholz et al.   SCIENCE

Heterogeneous Differentiation Patterns of Individual CD8+ T Cells

(2013) C. Gerlach et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

T Cell Receptor    Diversity Inversely Correlates with Pathogen-Specific Antibody Levels in Human Cytomegalovirus Infection

(2012) G. C. Wang et al.   Science Translational Medicine

Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination

(2011) John J Miles et al.   IMMUNOLOGY AND CELL BIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Functional implications of T cell receptor diversity

(2009) Stephen J Turner et al.   CURRENT OPINION IN IMMUNOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS