Quantifying evolutionary constraints on B-cell affinity maturation

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

(2014) Filip Bielejec et al.   BMC BIOINFORMATICS

Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences

(2014) Alexander Mirsky et al.   MOLECULAR BIOLOGY AND EVOLUTION

A predictive fitness model for influenza

(2014) Marta Łuksza et al.   NATURE

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

(2014) George Georgiou et al.   NATURE BIOTECHNOLOGY

Predicting evolution from the shape of genealogical trees

(2014) Richard A Neher et al.   eLife

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

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

High-throughput sequencing of B- and T-lymphocyte antigen receptors in hematology

(2013) E. H. Warren et al.   BLOOD

Immunosequencing: applications of immune repertoire deep sequencing

(2013) Harlan Robins   CURRENT OPINION IN IMMUNOLOGY

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

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

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

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Hua-Xin Liao et al.   NATURE

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

(2013) Brandon J DeKosky et al.   NATURE BIOTECHNOLOGY

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

Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination

(2013) N. Jiang et al.   Science Translational Medicine

Using synthetic templates to design an unbiased multiplex PCR assay

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

Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation

(2013) Haipeng Li et al.   PLoS Computational Biology

The Past, Present, and Future of Immune Repertoire Biology – The Rise of Next-Generation Repertoire Analysis

(2013) Adrien Six et al.   Frontiers in Immunology

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

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

(2012) Philippe Lemey et al.   BIOINFORMATICS

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

(2012) Ramit Mehr et al.   IMMUNOLOGY LETTERS

Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing

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

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantifying selection in high-throughput Immunoglobulin sequencing data sets

(2012) Gur Yaari et al.   NUCLEIC ACIDS RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

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

(2010) Y.-C. Wu et al.   BLOOD

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

(2009) H. S. Robins et al.   BLOOD

Structure of IL-17A in Complex with a Potent, Fully Human Neutralizing Antibody

(2009) Stefan Gerhardt et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolutionary Fingerprinting of Genes

(2009) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

A coming-of-age story: activation-induced cytidine deaminase turns 10

(2009) Rebecca K Delker et al.   NATURE IMMUNOLOGY

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

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

Dinucleotide repeat polymorphism in Fms-like tyrosine kinase-1 (Flt-1) gene is not associated with preeclampsia

(2008) Shin-Young Kim et al.   BMC Medical Genetics

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

Antigen-driven selection in germinal centers as reflected by the shape characteristics of immunoglobulin gene lineage trees: A large-scale simulation study

(2008) Gitit Shahaf et al.   JOURNAL OF THEORETICAL BIOLOGY

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

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

“compositions”: A unified R package to analyze compositional data

(2007) K. Gerald van den Boogaart et al.   COMPUTERS & GEOSCIENCES