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

iWAS – A novel approach to analyzing Next Generation Sequence data for immunology

(2016) Benjamin Vincent et al.   CELLULAR IMMUNOLOGY

CRISPR Detection From Short Reads Using Partial Overlap Graphs

(2016) Ilan Ben-Bassat et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

The prognostic landscape of genes and infiltrating immune cells across human cancers

(2015) Andrew J Gentles et al.   NATURE MEDICINE

Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia

(2015) James S. Blachly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput pairing of T cell receptor α and β sequences

(2015) Bryan Howie et al.   Science Translational Medicine

Peptide/MHC Tetramer-Based Sorting of CD8+ T Cells to a Leukemia Antigen Yields Clonotypes Drawn Nonspecifically from an Underlying Restricted Repertoire

(2015) S. A. Hunsucker et al.   Cancer Immunology Research

ABRA: improved coding indel detection via assembly-based realignment

(2014) Lisle E. Mose et al.   BIOINFORMATICS

Immunoglobulin and T Cell Receptor Gene High-Throughput Sequencing Quantifies Minimal Residual Disease in Acute Lymphoblastic Leukemia and Predicts Post-Transplantation Relapse and Survival

(2014) Aaron C. Logan et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Prognostic B-cell Signatures Using mRNA-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer

(2014) M. D. Iglesia et al.   CLINICAL CANCER RESEARCH

In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire

(2014) Brandon J DeKosky et al.   NATURE MEDICINE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing

(2012) K. Larimore et al.   JOURNAL OF IMMUNOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

(2011) R. L. Warren et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Profiling model T-cell metagenomes with short reads

(2009) René L. Warren et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cloning and expression of murine Ig genes from single B cells

(2009) Thomas Tiller et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing

(2009) S. D. Boyd et al.   Science Translational Medicine