Germinal Center Replay Analysis & Results

Here we present some useful reference materials for the analysis of the GC Replay data.

For complete computational pipeline see our GitHub repository

Key Files outlines the source code for figures seen in our manuscript, as well as descriptions of the pipeline input, intermediate, and results files that are available to download.
Mutation heatmaps for browsing mutational effects as measured both across both Deep Mutational Scanning (DMS), and replay data.
Tree Visualizations for browsing the phylogenetic trees generated from the B-cell receptor sequences.
Analysis (Notebooks) for a summary of the analysis performed downstream from BCR isolation, and phylogenetic inference.
Supplementary for the results we generated with different parameters to the gctree inference step
Nextflow Pipeline for a description of the pipeline used to process the data, and generate the results.

Citation

Preprint

Replaying germinal center evolution on a quantified affinity landscape. William S. DeWitt, Ashni A. Vora, Tatsuya Araki, Jared G. Galloway, Tanwee Alkutkar, Juliana Bortolatto, Tiago B.R. Castro, Will Dumm, Chris Jennings-Shaffer, Tongqiu Jia, Luka Mesin, Gabriel Ozorowski, Juhee Pae, Duncan K. Ralph, Jesse D. Bloom, Armita Nourmohammad, Yun S. Song, Andrew B. Ward, Tyler N. Starr, Frederick A. Matsen IV, Gabriel D. Victora. bioRxiv 2025.06.02.656870; doi: https://doi.org/10.1101/2025.06.02.656870

bibtex

@article {DeWitt2025.06.02.656870,
    author = {DeWitt, William S. and Vora, Ashni A. and Araki, Tatsuya and Galloway, Jared G. and Alkutkar, Tanwee and Bortolatto, Juliana and Castro, Tiago B.R. and Dumm, Will and Jennings-Shaffer, Chris and Jia, Tongqiu and Mesin, Luka and Ozorowski, Gabriel and Pae, Juhee and Ralph, Duncan K. and Bloom, Jesse D. and Nourmohammad, Armita and Song, Yun S. and Ward, Andrew B. and Starr, Tyler N. and Matsen, Frederick A. and Victora, Gabriel D.},
    title = {Replaying germinal center evolution on a quantified affinity landscape},
    year = {2025},
    doi = {10.1101/2025.06.02.656870},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2025/06/05/2025.06.02.656870},
    journal = {bioRxiv}
}

License

                GNU GENERAL PUBLIC LICENSE
                   Version 3, 29 June 2007