Repository associated with the paper "Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals" (https://www.biorxiv.org/content/10.1101/2021.12.17.473105v1). Each figure, except Figure 4, is generated using the Jupyter notebook file Figure(n)_all.ipynb. The Figure(n).pdf is the resulting figure after modification on Inkscape. Sketch shown in Figure 1 was designed using MacBook's default Keynote.
Datasets used for the analysis are obtained from:
(i) Briney B, Inderbitzin A, Joyce C, Burton DR (2019) Commonality despite exceptional diversity in the baseline human antibody repertoire. Nature 566:393–397.
(ii) Emerson RO, et al. (2017) Immunosequencing identifies signatures of cytomegalovirus exposure history and hla-mediated effects on the t cell repertoire. Nature Genetics 49:659– 665.
(iii) Nielsen SC, et al. (2020) Human b cell clonal expansion and convergent antibody responses to sars-cov-2. Cell Host & Microbe 28:516 – 525.e5.
(iv) Montague Z, et al. (2021) Dynamics of b cell repertoires and emergence of cross-reactive responses in patients with different severities of covid-19. Cell Reports 35:109173.
(v) Galson JD, et al. (2020) Deep sequencing of b cell receptor repertoires from covid-19 patients reveals strong convergent immune signatures. Frontiers in Immunology 11:3283.
(vi) Nolan S, et al. (2020) A large-scale database of t-cell receptor beta sequences and binding associations from natural and synthetic exposure to sars-cov-2. Research Square.