Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire

(2017) Ryan O Emerson et al.   NATURE GENETICS

Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires

(2017) Simon Friedensohn et al.   TRENDS IN BIOTECHNOLOGY

The Individual and Population Genetics of Antibody Immunity

(2017) Corey T. Watson et al.   TRENDS IN IMMUNOLOGY

Novel Approaches to Analyze Immunoglobulin Repertoires

(2017) Hedda Wardemann et al.   TRENDS IN IMMUNOLOGY

Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development

(2017) Victor Greiff et al.   Cell Reports

T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences

(2017) Asaf Madi et al.   eLife

Specificity, Privacy, and Degeneracy in the CD4 T Cell Receptor Repertoire Following Immunization

(2017) Yuxin Sun et al.   Frontiers in Immunology

Deep sequencing and human antibody repertoire analysis

(2016) Scott D Boyd et al.   CURRENT OPINION IN IMMUNOLOGY

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen

(2016) J. G. Jardine et al.   SCIENCE

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

(2016) Florian Rubelt et al.   Nature Communications

Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity

(2016) Martin M. Corcoran et al.   Nature Communications

System-wide Analysis of the T Cell Response

(2016) Ruxandra Covacu et al.   Cell Reports

Statistical inference of a convergent antibody repertoire response to influenza vaccine

(2016) Nicolas B. Strauli et al.   Genome Medicine

Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting

(2016) T. A. Khan et al.   Science Advances

A Public Database of Memory and Naive B-Cell Receptor Sequences

(2016) William S. DeWitt et al.   PLoS One

KeBABS: an R package for kernel-based analysis of biological sequences: Fig. 1.

(2015) Johannes Palme et al.   BIOINFORMATICS

IgSimulator: a versatile immunosequencing simulator: Fig. 1.

(2015) Yana Safonova et al.   BIOINFORMATICS

BatchJobsandBatchExperiments: Abstraction Mechanisms for UsingRin Batch Environments

(2015) Bernd Bischl et al.   Journal of Statistical Software

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

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

Inferring processes underlying B-cell repertoire diversity

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

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

(2015) Bryan Howie et al.   Science Translational Medicine

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

(2015) Victor Greiff et al.   TRENDS IN IMMUNOLOGY

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

(2015) Victor Greiff et al.   Genome Medicine

Practical guidelines for B-cell receptor repertoire sequencing analysis

(2015) Gur Yaari et al.   Genome Medicine

Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires

(2015) Yang Yang et al.   eLife

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

Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence

(2014) Niclas Thomas et al.   BIOINFORMATICS

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice

(2014) Victor Greiff et al.   BMC IMMUNOLOGY

T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity

(2014) Asaf Madi et al.   GENOME RESEARCH

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

(2014) George Georgiou et al.   NATURE BIOTECHNOLOGY

Unifying immunology with informatics and multiscale biology

(2014) Brian A Kidd et al.   NATURE IMMUNOLOGY

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

Comprehensive Evaluation and Optimization of Amplicon Library Preparation Methods for High-Throughput Antibody Sequencing

(2014) Ulrike Menzel et al.   PLoS One

Quantifying selection in immune receptor repertoires

(2014) Yuval Elhanati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterizing immune repertoires by high throughput sequencing: strategies and applications

(2014) Jorg J.A. Calis et al.   TRENDS IN IMMUNOLOGY

Differences in the Composition of the Human Antibody Repertoire by B Cell Subsets in the Blood

(2014) Eva Szymanska Mroczek et al.   Frontiers in Immunology

Convergent Antibody Signatures in Human Dengue

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

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

(2013) Brandon J DeKosky et al.   NATURE BIOTECHNOLOGY

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

The Shape of the Lymphocyte Receptor Repertoire: Lessons from the B Cell Receptor

(2013) Katherine J. L. Jackson et al.   Frontiers in Immunology

Recombinatorial Biases and Convergent Recombination Determine Interindividual TCR  Sharing in Murine Thymocytes

(2012) H. Li et al.   JOURNAL OF IMMUNOLOGY

Genome-Wide Chromatin Remodeling Identified at GC-Rich Long Nucleosome-Free Regions

(2012) Karin Schwarzbauer et al.   PLoS One

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

Structural Consensus among Antibodies Defines the Antigen Binding Site

(2012) Vered Kunik et al.   PLoS Computational Biology

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

Complex Networks Govern Coiled-Coil Oligomerization – Predicting and Profiling by Means of a Machine Learning Approach

(2011) Carsten C. Mahrenholz et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Determinism and stochasticity during maturation of the zebrafish antibody repertoire

(2011) N. Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maximum entropy models for antibody diversity

(2010) T. Mora et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire

(2009) J. Glanville et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA