Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 2016)

Likelihood-Based Inference of B Cell Clonal Families. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 2016)

Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 2019)

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis. - Amrit Dhar; Duncan K. Ralph; Vladimir N. Minin; Frederick A. Matsen IV (PLoS Comput. Biol., 2020)

Using B cell receptor lineage structures to predict affinity. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 2020)

Inference of B cell clonal families using heavy/light chain pairing information. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 2022)