Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads

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

Secreted autoantibody repertoires in Sjögren's syndrome and systemic lupus erythematosus: A proteomic approach

(2016) Mahmood A. Al Kindi et al.   AUTOIMMUNITY REVIEWS

Identification of antigen-specific human monoclonal antibodies using high-throughput sequencing of the antibody repertoire

(2016) Ju Liu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data

(2016) Bram Gerritsen et al.   BIOINFORMATICS

rnaQUAST: a quality assessment tool forde novotranscriptome assemblies: Table 1.

(2016) Elena Bushmanova 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

Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination

(2016) Ali H Ellebedy et al.   NATURE IMMUNOLOGY

High-quality full-length immunoglobulin profiling with unique molecular barcoding

(2016) M A Turchaninova et al.   Nature Protocols

Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells

(2016) Florian Rubelt et al.   Nature Communications

Clonify: unseeded antibody lineage assignment from next-generation sequencing data

(2016) Bryan Briney et al.   Scientific Reports

B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation

(2016) Jacob D. Galson et al.   Genome Medicine

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

(2015) Leon Kuchenbecker et al.   BIOINFORMATICS

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

(2015) Yana Safonova et al.   BIOINFORMATICS

IgSimulator: a versatile immunosequencing simulator: Fig. 1.

(2015) Yana Safonova et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

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

(2015) Namita T. Gupta et al.   BIOINFORMATICS

Next-generation sequencing and protein mass spectrometry for the comprehensive analysis of human cellular and serum antibody repertoires

(2015) Jason J Lavinder et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Inferring processes underlying B-cell repertoire diversity

(2015) Yuval Elhanati et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

(2015) Daniel Gadala-Maria et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

(2015) Victor Greiff et al.   TRENDS IN IMMUNOLOGY

Practical guidelines for B-cell receptor repertoire sequencing analysis

(2015) Gur Yaari et al.   Genome Medicine

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

(2015) Mikhail Shugay et al.   PLoS Computational Biology

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

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

The promise and challenge of high-throughput sequencing of the antibody repertoire

(2014) George Georgiou et al.   NATURE BIOTECHNOLOGY

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery

(2014) William H. Robinson   Nature Reviews Rheumatology

High-resolution antibody dynamics of vaccine-induced immune responses

(2014) Uri Laserson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Barcode-Enabled Sequencing of Plasmablast Antibody Repertoires in Rheumatoid Arthritis

(2014) Yann-Chong Tan et al.   Arthritis & Rheumatology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

(2013) Tilo Buschmann et al.   BMC BIOINFORMATICS

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

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

IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling

(2013) Shuo Li et al.   Nature Communications

Models of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data

(2013) Gur Yaari et al.   Frontiers in Immunology

Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms

(2012) Dmitry A. Bolotin et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A proteomics approach for the identification and cloning of monoclonal antibodies from serum

(2012) Wan Cheung Cheung et al.   NATURE BIOTECHNOLOGY

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

(2012) A. Murugan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error correction of high-throughput sequencing datasets with non-uniform coverage

(2011) P. Medvedev et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Barcodes for DNA sequencing with guaranteed error correction capability

(2011) A.R. Krishnan et al.   ELECTRONICS LETTERS

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

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reptile: representative tiling for short read error correction

(2010) X. Yang et al.   BIOINFORMATICS

Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire

(2010) H. S. Robins et al.   Science Translational Medicine

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

(2009) J. D. Freeman et al.   GENOME RESEARCH

High-Throughput Sequencing of the Zebrafish Antibody Repertoire

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

ZOOM! Zillions of oligos mapped

(2008) H. Lin et al.   BIOINFORMATICS

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS