Single-cell immune repertoire sequencing of B and T cells following viral infection, neurological disorders, cancer, immunizations, and ageing

Immune repertoires represent a vast and diverse collection of T and B cell receptors which are able to interact with a seemingly infinite number of foreign pathogens. Recent advances in high-throughput sequencing and microfluidics allow us to pair immune receptor sequence and gene expression at the single-cell resolution. This technology is instrumental both to quantify clonal selection of immune populations and to discover novel lymphocytes relevant in the context of disease, immunization, and infection. We are seeking master students for research projects or theses involving the computational analysis of single-cell immune repertoires sequencing data. Projects involve studying B and T cells from both human and mice, across experimental settings ranging viral infection, ageing, neuroimmunology (infections, multiple sclerosis, cancer), and immunizations. The projects aim to characterize the clonal selection of B and T cells in the aforementioned conditions and quantify how immune repertoire parameters (e.g. antigen specificity, mutational load, germline gene usage, clonal expansion) relate to transcriptional phenotypes (e.g. cell activation, exhaustion, dysfunction). This computational data will be used to later instruct experimental validation of candidate B and T cell receptors to uncover their contribution to disease. While the majority of the projects are computational, the opportunity to experimentally validate bioinformatic conclusions in the lab will be available towards the end of the project/thesis. All research infrastructure and future experiments will take place in the Lab for Systems and Synthetic Immunology at the ETH Zurich, Department of Biosystems Science and Engineering in Basel (https://bsse.ethz.ch/lsi) in the lab of Professor Sai Reddy. Given the current pandemic, it may be possible to largely work remotely or exclusively from Zurich. Students should have experience with programming (preferably in R) and a basic understanding of immunology. The project/thesis will preferably last at least 6 consecutive months. To apply please send a CV, your earliest possible start date, and brief cover letter to Alex Yermanos (ayermano@ethz.ch). Students can expect to obtain computational skills tailored to analyzing single-cell immune repertoire sequencing data and potentially can obtain experimental skills involving high-throughput sequencing library preparation, processing and phenotyping immune cells, antibody and T cell expression

Immune repertoires represent a vast and diverse collection of T and B cell receptors which are able to interact with a seemingly infinite number of foreign pathogens. Recent advances in high-throughput sequencing and microfluidics allow us to pair immune receptor sequence and gene expression at the single-cell resolution. This technology is instrumental both to quantify clonal selection of immune populations and to discover novel lymphocytes relevant in the context of disease, immunization, and infection.
We are seeking master students for research projects or theses involving the computational analysis of single-cell immune repertoires sequencing data. Projects involve studying B and T cells from both human and mice, across experimental settings ranging viral infection, ageing, neuroimmunology (infections, multiple sclerosis, cancer), and immunizations. The projects aim to characterize the clonal selection of B and T cells in the aforementioned conditions and quantify how immune repertoire parameters (e.g. antigen specificity, mutational load, germline gene usage, clonal expansion) relate to transcriptional phenotypes (e.g. cell activation, exhaustion, dysfunction). This computational data will be used to later instruct experimental validation of candidate B and T cell receptors to uncover their contribution to disease.

While the majority of the projects are computational, the opportunity to experimentally validate bioinformatic conclusions in the lab will be available towards the end of the project/thesis. All research infrastructure and future experiments will take place in the Lab for Systems and Synthetic Immunology at the ETH Zurich, Department of Biosystems Science and Engineering in Basel (https://bsse.ethz.ch/lsi) in the lab of Professor Sai Reddy. Given the current pandemic, it may be possible to largely work remotely or exclusively from Zurich. Students should have experience with programming (preferably in R) and a basic understanding of immunology. The project/thesis will preferably last at least 6 consecutive months. To apply please send a CV, your earliest possible start date, and brief cover letter to Alex Yermanos (ayermano@ethz.ch).
Students can expect to obtain computational skills tailored to analyzing single-cell immune repertoire sequencing data and potentially can obtain experimental skills involving high-throughput sequencing library preparation, processing and phenotyping immune cells, antibody and T cell expression

To investigate and understand the adaptive immune system in the context of immunization, neurological disorders, cancer, disease, and ageing. Example publications include: Gate,D. et al. (2020) Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease. Nature, 577, 399–404. Horns,F. et al. (2020) Memory B Cell Activation, Broad Anti-influenza Antibodies, and Bystander Activation Revealed by Single-Cell Transcriptomics. Cell Rep., 30, 905–913.e6. Ramesh,A. et al. (2020) A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis. Proc. Natl. Acad. Sci. U. S. A., 117, 22932–22943. Yermanos,A. et al. (2020) … immune repertoire and transcriptome sequencing reveals that clonally expanded and transcriptionally distinct lymphocytes populate the aged central nervous system …. bioRxiv.

To investigate and understand the adaptive immune system in the context of immunization, neurological disorders, cancer, disease, and ageing. Example publications include:
Gate,D. et al. (2020) Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease. Nature, 577, 399–404.
Horns,F. et al. (2020) Memory B Cell Activation, Broad Anti-influenza Antibodies, and Bystander Activation Revealed by Single-Cell Transcriptomics. Cell Rep., 30, 905–913.e6.
Ramesh,A. et al. (2020) A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis. Proc. Natl. Acad. Sci. U. S. A., 117, 22932–22943.
Yermanos,A. et al. (2020) … immune repertoire and transcriptome sequencing reveals that clonally expanded and transcriptionally distinct lymphocytes populate the aged central nervous system …. bioRxiv.

The project/thesis will preferably last at least 6 consecutive months. To apply please send a CV, your earliest possible start date, and brief cover letter to Alex Yermanos (ayermano@ethz.ch).

The project/thesis will preferably last at least 6 consecutive months. To apply please send a CV, your earliest possible start date, and brief cover letter to Alex Yermanos (ayermano@ethz.ch).