Mikhail Shugay

Plot is not re-calculated correctly when uploading two chunks of samples with different max size

AD -> top panel, WS ->left panel

[Gupta T. Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis. Cancer Cell . 2024](https://pubmed.ncbi.nlm.nih.gov/38744246/) --- A convenient way to browse the data is by using...

[Zhang et al. Enhanced CD95 and interleukin 18 signalling accompany T cell receptor Vβ21.3+ activation in multi-inflammatory syndrome in children. Nat Comm 2024](https://pubmed.ncbi.nlm.nih.gov/38762592/)

See if our epitopes, linked to, say A*02, can be presented by other alleles based on NetMHCpan or other epitope presentation predictor. This functional may be transferred to downstream VDJdb...

Check for useful papers and studies in McPAS, IEDB and other databases and run association pipeline for them.

[subj.](https://podman-desktop.io/docs/migrating-from-docker)

[Kirk et al. DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma. Cell Rep Med 2024](https://pubmed.ncbi.nlm.nih.gov/38508137) --- Need more info on actual peptideTCR(?),...

[Roy P. et al. Identification of apolipoprotein B–reactive CDR3 motifs allows tracking of atherosclerosis-related memory CD4+T cells in multiple donors. Front Immunol 2024](https://pubmed.ncbi.nlm.nih.gov/38571941/)

Check [stcrdab](https://opig.stats.ox.ac.uk/webapps/stcrdab-stcrpred) and [PDB](https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22full_text%22%2C%22parameters%22%3A%7B%22value%22%3A%22%5C%22t-cell%5C%22%20receptor%20tcr%22%7D%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%5D%2C%22logical_operator%22%3A%22and%22%2C%22label%22%3A%22full_text%22%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22results_content_type%22%3A%5B%22experimental%22%5D%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%2C%22scoring_strategy%22%3A%22combined%22%7D%2C%22request_info%22%3A%7B%22query_id%22%3A%22f5de3657a14b81a1670b1252242e7a17%22%7D%7D) to update [PDB_Database.txt chunk](https://github.com/antigenomics/vdjdb-db/blob/master/chunks/PDB_Database.txt) and address #360.