Practical guidelines for B-cell receptor repertoire sequencing analysis

Single B-cell deconvolution of peanut-specific antibody responses in allergic patients

(2016) Ramona A. Hoh et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

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

(2015) Leon Kuchenbecker 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

Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing

(2015) D. M. Kurtz et al.   BLOOD

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Equine immunoglobulins and organization of immunoglobulin genes

(2015) Stefanie Walther et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

MSPrecise: A molecular diagnostic test for multiple sclerosis using next generation sequencing

(2015) William H. Rounds et al.   GENE

V genes in primates from whole genome sequencing data

(2015) D. N. Olivieri et al.   IMMUNOGENETICS

Immunoglobulin genomics in the prairie vole (Microtus ochrogaster)

(2015) Tong Qin et al.   IMMUNOLOGY LETTERS

Peanut oral immunotherapy transiently expands circulating Ara h 2–specific B cells with a homologous repertoire in unrelated subjects

(2015) Sarita U. Patil et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Analysis of Celiac Disease Autoreactive Gut Plasma Cells and Their Corresponding Memory Compartment in Peripheral Blood Using High-Throughput Sequencing

(2015) Omri Snir et al.   JOURNAL OF IMMUNOLOGY

Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells

(2015) Wei Shi et al.   NATURE IMMUNOLOGY

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Restricted, canonical, stereotyped and convergent immunoglobulin responses

(2015) Carole J. Henry Dunand et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The analysis of clonal expansions in normal and autoimmune B cell repertoires

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

Assigning and visualizing germline genes in antibody repertoires

(2015) Simon D. W. Frost et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Quantifying evolutionary constraints on B-cell affinity maturation

(2015) Connor O. McCoy et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales

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

Ageing of the B-cell repertoire

(2015) Victoria Martin 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

A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status

(2015) Victor Greiff et al.   Genome Medicine

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire

(2015) Jacob D. Galson et al.   Frontiers in Immunology

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

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

Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing

(2014) Mathieu Giraud et al.   BMC GENOMICS

Immunoglobulin Gene Insertions and Deletions in the Affinity Maturation of HIV-1 Broadly Reactive Neutralizing Antibodies

(2014) Thomas B. Kepler et al.   Cell Host & Microbe

Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements

(2014) Katherine J.L. Jackson et al.   Cell Host & Microbe

Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis

(2014) Yu-Chang B. Wu et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

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

(2014) George Georgiou et al.   NATURE BIOTECHNOLOGY

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

(2014) Brandon J DeKosky et al.   NATURE MEDICINE

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing

(2014) Richard H. Liang et al.   NUCLEIC ACIDS RESEARCH

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

Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis

(2014) A. Palanichamy et al.   Science Translational Medicine

B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes

(2014) J. N. H. Stern et al.   Science Translational Medicine

OMICtools: an informative directory for multi-omic data analysis

(2014) V. J. Henry et al.   Database-The Journal of Biological Databases and Curation

Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding

(2014) Linling He et al.   Scientific Reports

Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation

(2014) Thomas B. Kepler et al.   Frontiers in Immunology

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Convergent Antibody Signatures in Human Dengue

(2013) Poornima Parameswaran et al.   Cell Host & Microbe

Immunosequencing: applications of immune repertoire deep sequencing

(2013) Harlan Robins   CURRENT OPINION IN IMMUNOLOGY

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes

(2013) J. L. Duke et al.   JOURNAL OF IMMUNOLOGY

Integrating B Cell Lineage Information into Statistical Tests for Detecting Selection in Ig Sequences

(2013) M. Uduman et al.   JOURNAL OF IMMUNOLOGY

Deep Sequencing of the Murine Igh Repertoire Reveals Complex Regulation of Nonrandom V Gene Rearrangement Frequencies

(2013) N. M. Choi et al.   JOURNAL OF IMMUNOLOGY

Cerebrospinal-fluid-derived Immunoglobulin G of Different Multiple Sclerosis Patients Shares Mutated Sequences in Complementarity Determining Regions

(2013) Vaibhav Singh et al.   MOLECULAR & CELLULAR PROTEOMICS

Prize-based contests can provide solutions to computational biology problems

(2013) Karim R Lakhani et al.   NATURE BIOTECHNOLOGY

High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire

(2013) Brandon J DeKosky 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

De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts

(2013) J. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Effects of Somatic Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies

(2013) Devin Sok et al.   PLoS Pathogens

Targeting B cells in the treatment of multiple sclerosis: recent advances and remaining challenges

(2013) Klaus Lehmann-Horn et al.   Therapeutic Advances in Neurological Disorders

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

Multi Step Selection in Ig H Chains is Initially Focused on CDR3 and Then on Other CDR Regions

(2013) Gilad Liberman et al.   Frontiers in Immunology

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

The immunoglobulin heavy chain locus: genetic variation, missing data and implications for human disease

(2012) C T Watson et al.   GENES AND IMMUNITY

Germinal centers

(2012) Mark J. Shlomchik et al.   IMMUNOLOGICAL REVIEWS

B cell exchange across the blood-brain barrier in multiple sclerosis

(2012) H.-Christian von Büdingen et al.   JOURNAL OF CLINICAL INVESTIGATION

Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing

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

Skewed Primary Ig  Repertoire and V-J Joining in C57BL/6 Mice: Implications for Recombination Accessibility and Receptor Editing

(2012) M. Aoki-Ota et al.   JOURNAL OF IMMUNOLOGY

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

(2012) Wan Cheung Cheung et al.   NATURE BIOTECHNOLOGY

Quantifying selection in high-throughput Immunoglobulin sequencing data sets

(2012) Gur Yaari et al.   NUCLEIC ACIDS RESEARCH

Vaccination-induced changes in human B-cell repertoire and pneumococcal IgM and IgA antibody at different ages

(2011) Alexander Ademokun et al.   AGING CELL

Genomic screening by 454 pyrosequencing identifies a new human IGHV gene and sixteen other new IGHV allelic variants

(2011) Yan Wang et al.   IMMUNOGENETICS

Rep-Seq: uncovering the immunological repertoire through next-generation sequencing

(2011) Jennifer Benichou et al.   IMMUNOLOGY

The Inference of Phased Haplotypes for the Immunoglobulin H Chain V Region Gene Loci by Analysis of VDJ Gene Rearrangements

(2011) M. J. Kidd et al.   JOURNAL OF IMMUNOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Preliminary Analysis of the Immunoglobulin Genes in the African Elephant (Loxodonta africana)

(2011) Yongchen Guo et al.   PLoS One

High-Resolution Description of Antibody Heavy-Chain Repertoires in Humans

(2011) Ramy Arnaout et al.   PLoS One

Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation

(2011) J. Glanville et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

(2011) X. Wu et al.   SCIENCE

SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements

(2010) S. Munshaw et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations

(2010) Y.-C. Wu et al.   BLOOD

B cell repertoire and ageing

(2010) Deborah K Dunn-Walters et al.   CURRENT OPINION IN IMMUNOLOGY

Somatic hypermutation and antigen-driven selection of B cells are altered in autoimmune diseases

(2010) Neta S. Zuckerman et al.   JOURNAL OF AUTOIMMUNITY

Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements

(2010) S. D. Boyd et al.   JOURNAL OF IMMUNOLOGY

Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells

(2010) Sai T Reddy et al.   NATURE BIOTECHNOLOGY

A consistent terminology for quantifying species diversity? Yes, it does exist

(2010) Hanna Tuomisto   OECOLOGIA

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

Potential of a unique antibody gene signature to predict conversion to clinically definite multiple sclerosis☆

(2009) Elizabeth M. Cameron et al.   JOURNAL OF NEUROIMMUNOLOGY

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment

(2009) T. MacCarthy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

B-cell diversity decreases in old age and is correlated with poor health status

(2008) Kate L. Gibson et al.   AGING CELL

The Biochemistry of Somatic Hypermutation

(2008) Jonathan U. Peled et al.   Annual Review of Immunology

B-cell clonal diversification and gut-lymph node trafficking in ulcerative colitis revealed using lineage tree analysis

(2008) Hilla Tabibian-Keissar et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Improved methods for detecting selection by mutation analysis of Ig V region sequences

(2008) Uri Hershberg et al.   INTERNATIONAL IMMUNOLOGY

IgTree©: Creating Immunoglobulin variable region gene lineage trees

(2008) Michal Barak et al.   JOURNAL OF IMMUNOLOGICAL METHODS