Master Thesis - Development of a Bayesian Framework for T-cell Receptor
Antigen Pairing from Single-cells Data
30.01.2023, Studentische Hilfskräfte, Praktikantenstellen, Studienarbeiten
If you are interested in single-cell data analysis and have a neck for
statistical modeling, contact us!
Goals : Development of a Bayesian framework to assign T-/B-cells to
cognate antigens based on single-cell immune profiling data.
Methods : Bayesian hierarchical models (pymc, NumPyro, TensorFlow-
Probability), Single-cell analysis (Scanpy, Scirpy)
Literature : - 10x Genomics. Tech. rep (2019).
Minervina, A. A., Pogorelyy, M. V., Kirk, A. M., Crawford, J. C., Allen,
E. K., Chou, C. H., ... & Thomas, P. G. (2022). SARS-CoV-2 antigen
exposure history shapes phenotypes and specificity of memory CD8+ T cells.
Nature immunology, 23(5), 781-790.
Zhang, W., Hawkins, P. G., He, J., Gupta, N. T., Liu, J., Choonoo, G., ...
& Atwal, G. S. (2021). A framework for highly multiplexed dextramer
mapping and prediction of T cell receptor sequences to antigen
specificity. Science Advances, 7(20), eabf5835.
Francis, J. M., Leistritz-Edwards, D., Dunn, A., Tarr, C., Lehman, J.,
Dempsey, C., ... & Pregibon, D. C. (2021). Allelic variation in class I
HLA determines CD8+ T cell repertoire shape and cross-reactive memory
responses to SARS-CoV-2. Science immunology, 7(67), eabk3070.
Povlsen, H. R., Bentzen, A. K., Kadivar, M., Jessen, L. E., Hadrup, S. R.,
& Nielsen, M. (2022). ATRAP-Accurate T cell Receptor Antigen Pairing
through data-driven filtering of sequencing information from single-cells.
bioRxiv, 2022-08.
Howitt, G., Feng, Y., Tobar, L., Vassiliadis, D., Hickey, P., Dawson, M.
A., ... & Oshlack, A. (2022). Benchmarking single-cell hashtag oligo
demultiplexing methods. bioRxiv, 2022-12.
Sturm, G. Tamas, GS, ..., Finotello, F. Scirpy: A Scanpy extension for
analyzing single-cell T-cell receptor sequencing data. Bioinformatics
(2020).
Milestones :
Benchmark threshold-based assignment and demultiplexing methods
Develop your own statistical assignment model accounting for biological
and technical aspects
Contacts Please send a CV and transcript of records of your Bachelor and
Master to [email protected]
Kontakt: [email protected]