Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

(2020) Alison D. Tang et al.   Nature Communications

Signatures of selection in the human antibody repertoire: Selective sweeps, competing subclones, and neutral drift

(2019) Felix Horns et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

arcasHLA: high resolution HLA typing from RNAseq

(2019) R Orenbuch et al.   BIOINFORMATICS

Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (Ursus maritimus)

(2019) Ashley Byrne et al.   Frontiers in Genetics

Analysis of the B cell receptor repertoire in six immune-mediated diseases

(2019) R. J. M. Bashford-Rogers et al.   NATURE

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Nanopore native RNA sequencing of a human poly(A) transcriptome

(2019) Rachael E. Workman et al.   NATURE METHODS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

(2018) Manuel Tardaguila et al.   GENOME RESEARCH

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA

(2018) Roger Volden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Posttranscriptional Regulation of HLA-A Protein Expression by Alternative Polyadenylation Signals Involving the RNA-Binding Protein Syncrip

(2017) Smita Kulkarni et al.   JOURNAL OF IMMUNOLOGY

CD19 Isoforms Enabling Resistance to CART-19 Immunotherapy Are Expressed in B-ALL Patients at Initial Diagnosis

(2017) Jeannette Fischer et al.   JOURNAL OF IMMUNOTHERAPY

Antigen receptor repertoire profiling from RNA-seq data

(2017) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

CD22-targeted CAR T cells induce remission in B-ALL that is naive or resistant to CD19-targeted CAR immunotherapy

(2017) Terry J Fry et al.   NATURE MEDICINE

Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging

(2017) Charles F. A. de Bourcy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer

(2016) Lisle E. Mose et al.   BIOINFORMATICS

Highly Accurate Sequencing of Full-Length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier–Guided Amplicon Assembly

(2016) Charles Cole et al.   JOURNAL OF IMMUNOLOGY

IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing

(2016) Benjamin Deonovic et al.   NUCLEIC ACIDS RESEARCH

Likelihood-Based Inference of B Cell Clonal Families

(2016) Duncan K. Ralph et al.   PLoS Computational Biology

Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching

(2016) Felix Horns et al.   eLife

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

(2016) Spyros Oikonomopoulos et al.   Scientific Reports

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1.

(2015) Namita T. Gupta et al.   BIOINFORMATICS

Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy

(2015) E. Sotillo et al.   Cancer Discovery

Monitoring Pharmacologically Induced Immunosuppression by Immune Repertoire Sequencing to Detect Acute Allograft Rejection in Heart Transplant Patients: A Proof-of-Concept Diagnostic Accuracy Study

(2015) Christopher Vollmers et al.   PLOS MEDICINE

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

(2014) Jason A. Vander Heiden et al.   BIOINFORMATICS

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

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

(2014) Simone Picelli et al.   Nature Protocols

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

Genetic measurement of memory B-cell recall using antibody repertoire sequencing

(2013) C. Vollmers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimal Residual Disease Monitoring with High-Throughput Sequencing of T Cell Receptors in Cutaneous T Cell Lymphoma

(2013) W.-K. Weng et al.   Science Translational Medicine

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

High-throughput, high-fidelity HLA genotyping with deep sequencing

(2012) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HLA typing from RNA-Seq sequence reads

(2012) Sebastian Boegel et al.   Genome Medicine

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment

(2011) A. C. Logan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding

(2011) J. F. Scheid et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The HLA genomic loci map: expression, interaction, diversity and disease

(2009) Takashi Shiina et al.   JOURNAL OF HUMAN GENETICS

High-Throughput Sequencing of the Zebrafish Antibody Repertoire

(2009) J. A. Weinstein et al.   SCIENCE