Master Thesis - Development of a Bayesian Framework for T-cell Receptor Antigen Pairing from Single-cells Data

Technische Universität München
March 04, 2023
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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]

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