T cell fate and clonality inference from single-cell transcriptomes

IMSEQ—a fast and error aware approach to immunogenetic sequence analysis

(2015) Leon Kuchenbecker et al.   BIOINFORMATICS

An atlas of mouse CD4+ T cell transcriptomes

(2015) Michael JT Stubbington et al.   Biology Direct

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

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

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

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

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) Arnold Han 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

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines

(2014) S. Becattini 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 Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

(2014) Bidesh Mahata et al.   Cell Reports

Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine

(2013) N. Thomas et al.   BIOINFORMATICS

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

(2013) Carsten Linnemann et al.   NATURE MEDICINE

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Analysis of the Paired TCR α- and β-chains of Single Human T Cells

(2012) Song-Min Kim et al.   PLoS One

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Quantitative tracking of T cell clones after haematopoietic stem cell transplantation

(2011) Ilgar Z. Mamedov et al.   EMBO Molecular Medicine

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Paired analysis of TCRα and TCRβ chains at the single-cell level in mice

(2010) Pradyot Dash et al.   JOURNAL OF CLINICAL INVESTIGATION

Antigen Receptor Allelic Exclusion: An Update and Reappraisal

(2010) B. L. Brady et al.   JOURNAL OF IMMUNOLOGY

Distinct regulation of effector and memory T-cell differentiation

(2008) Axel Kallies   IMMUNOLOGY AND CELL BIOLOGY

IMGT(R), the international ImMunoGeneTics information system(R)

(2008) M.-P. Lefranc et al.   NUCLEIC ACIDS RESEARCH