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

Capturing needles in haystacks: a comparison of B-cell receptor sequencing methods

(2014) Rachael JM Bashford-Rogers et al.   BMC IMMUNOLOGY

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 depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

(2014) Claire T. Deakin et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Ulrike Menzel et al.   PLoS One

Immunoglobulin Gene Repertoire Diversification and Selection in the Stomach – From Gastritis to Gastric Lymphomas

(2014) Miri Michaeli et al.   Frontiers in Immunology

Convergent Antibody Signatures in Human Dengue

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

Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations

(2013) Rachael J.M. Bashford-Rogers et al.   GENOME RESEARCH

Calculating Sample Size Estimates for RNA Sequencing Data

(2013) Steven N. Hart et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Novel Approach to Tracking Antigen-Experienced CD4 T Cells into Functional Compartments via Tandem Deep and Shallow TCR Clonotyping

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

Plasma Cell Homeostasis: The Effects of Chronic Antigen Stimulation and Inflammation

(2013) T. Slocombe et al.   JOURNAL OF IMMUNOLOGY

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

(2013) Hua-Xin Liao et al.   NATURE

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen 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

MiTCR: software for T-cell receptor sequencing data analysis

(2013) Dmitriy A Bolotin et al.   NATURE METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

The role of replicates for error mitigation in next-generation sequencing

(2013) Kimberly Robasky et al.   NATURE REVIEWS GENETICS

Correlation of Gene Expression and Genome Mutation in Single B-Cells

(2013) Joshua A. Weinstein et al.   PLoS One

Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response

(2013) Y. Wine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains

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

The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops

(2013) Vered Kunik et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Using synthetic templates to design an unbiased multiplex PCR assay

(2013) Christopher S. Carlson et al.   Nature Communications

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

The Structural Basis of Antibody-Antigen Recognition

(2013) Inbal Sela-Culang et al.   Frontiers in Immunology

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

A minimal model of peptide binding predicts ensemble properties of serum antibodies

(2012) Victor Greiff et al.   BMC GENOMICS

The establishment of the plasma cell survival niche in the bone marrow

(2012) Van T. Chu et al.   IMMUNOLOGICAL REVIEWS

Germinal center selection and the development of memory B and plasma cells

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

Models and methods for analysis of lymphocyte repertoire generation, development, selection and evolution

(2012) Ramit Mehr et al.   IMMUNOLOGY LETTERS

Methods for diversity and overlap analysis in T-cell receptor populations

(2012) Grzegorz A. Rempala et al.   JOURNAL OF MATHEMATICAL BIOLOGY

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

(2012) Wan Cheung Cheung et al.   NATURE BIOTECHNOLOGY

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibody isolation from immunized animals: comparison of phage display and antibody discovery via V gene repertoire mining

(2012) I. Saggy et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Structural Consensus among Antibodies Defines the Antigen Binding Site

(2012) Vered Kunik et al.   PLoS Computational Biology

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Systems analysis of adaptive immunity by utilization of high-throughput technologies

(2011) Sai T Reddy et al.   CURRENT OPINION IN BIOTECHNOLOGY

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

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

(2011) Jennifer Benichou et al.   IMMUNOLOGY

Systems immunology: Complexity captured

(2011) Charlotte Schubert   NATURE

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

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

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

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

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

(2010) Y.-C. Wu et al.   BLOOD

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

(2010) Sai T Reddy et al.   NATURE BIOTECHNOLOGY

Maximum entropy models for antibody diversity

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

Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1

(2010) X. Wu et al.   SCIENCE

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models

(2009) Nuno Sepúlveda et al.   JOURNAL OF IMMUNOLOGICAL METHODS

High-Throughput Sequencing of the Zebrafish Antibody Repertoire

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

Blood-borne human plasma cells in steady state are derived from mucosal immune responses

(2008) H. E. Mei et al.   BLOOD

IgTree©: Creating Immunoglobulin variable region gene lineage trees

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

Rapid cloning of high-affinity human monoclonal antibodies against influenza virus

(2008) Jens Wrammert et al.   NATURE

IMGT(R), the international ImMunoGeneTics information system(R)

(2008) M.-P. Lefranc et al.   NUCLEIC ACIDS RESEARCH

Method for assessing the similarity between subsets of the T cell receptor repertoire

(2007) Vanessa Venturi et al.   JOURNAL OF IMMUNOLOGICAL METHODS