Junior AG Systems Infection Biology
Our lab develops computational methods to analyze single-cell omics datasets (RNA-seq, ATAC-seq, spatial transcriptomics) in the context of infection biology. The growing availability of single-cell atlases across species and organs enables the discovery of previously unrecognized cell types in both healthy and diseased tissues. However, rare or transient cell populations are often overlooked by standard analysis approaches, despite their importance in many biological processes, from development to cancer and infection biology.
We build tools for the detection and characterization of rare cell states across diverse models and conditions. By comparing new data with well-annotated reference atlases, we aim to define transcriptomic identities, uncover functional roles, and better understand how rare cell populations shape biological outcomes.
Join our team:
Motivated students are very welcome to apply at any time for Master’s and PhD thesis projects per mail: gabriele.lubatti@uniklinik-freiburg.de
Dr. Gabriele Lubatti
Bioinformatician
Selected Publications
- Jitesh Neupane*, Gabriele Lubatti*, Theresa Gross-Thebing, Mayra Luisa Ruiz Tejada Segura, Richard Butler, Sargon Gross-Thebing, Sabine Dietmann, Antonio Scialdone, M Azim Surani (2025). The emergence of human primordial germ cell–like cells in stem cell–derived gastruloids. Science Advances. doi:10.1126/sciadv.ado1350
- Gabriele Lubatti, Marco Stock, Ane Iturbide, Mayra L Ruiz Tejada Segura, Melina Riepl, Richard CV Tyser, Anna Danese, Maria Colomé-Tatché, Fabian J Theis, Shankar Srinivas, Maria-Elena Torres-Padilla, Antonio Scialdone (2023). CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data. Development. doi: 10.1242/dev.201264
- Ana Lima*, Gabriele Lubatti*, Jorg Burgstaller, Di Hu, Alistair Green, Aida Di Gregorio, Tamzin Zawadzki, Barbara Pernaute, Elmir Mahammadov, Salvador Perez Montero, Marian Dore, Juan Miguel Sanchez, Sarah Bowling, Margarida Sancho, Mohammed Karimi, David Carling, Nick Jones, Shankar Srinivas, Antonio Scialdone, Tristan A Rodriguez (2021). Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development. Nature Metabolism. doi: 10.1038/s42255-021-00422-7
* joint authorship
