WM7 Computational Systems Biology
Lecturer
Zlatko Trajanoski, Anne Krogsdam, Giorgia Lamberti, Dietmar Rieder, Michael Schubert, Hubert Hackl
Notes
Introduction into RNAseq data analysis
RNAseq data analysis practical part notes
RNAseq data anlysis with DESeq2
Functional Annotation of Differential Expression Results
Schedule
| Date | Room | Topic | Lecturer |
| 08.06 (9-14) | M.01.392 | VO Functionmal precision oncology VO Integrative multiomics analyses | Zlatko Trajanoski |
| 09.06 (9-14) | M.01.392 | VO Single cell and spatial analyses VO Systems biology and pharmacology | Zlatko Trajanoski |
| 10.06 (9-12) 10.06 (12-16) | M.01.392 wet lab | VO Cancer models PR Cancer cell line cultures | Giorgia Lamberti, Anne Krogsdam |
| 11.06 (9-12) 11.06 (12-16) | M.01.392 wet lab | VO Precision therapy PR Kinase inhibitor treatment | Giorgia Lamberti, Anne Krogsdam |
| 15.06 (9-12) 15.06 (12-16) | M.01.392 wet lab | VO NGS PR RNA isolation | Anne Krogsdam, Giorgia Lamberti |
| 16.06 (9-12) 16.06 (12-16) | M.01.392 wet lab | VO RNA sequencing PR Library generation, sequencing | Anne Krogsdam, Giorgia Lamberti |
| 17.06 (9-16) | FP3 C3 | VO|PR RNA sequencing data processing | Dietmar Rieder |
| 18.06 (9-16) | FP3 C3 | VO|PR Differential expression analyses | Dietmar Rieder |
| 19.06 (9-16) | FP3 C3 | VO|PR Functional analyses | Michael Schubert |
| 22.06 (9-16) | FP3 C3 | VO|PR Pathway and network modeling | Michael Schubert |
| 24.06 (9-16) | FP3 C1 | VO|PR Drug sensitivity | Hubert Hackl |
| 25.06 (9-16) | FP3 C1 | VO|PR Tumor sample analyses | Hubert Hackl |
| 29.06 (9-16) | M.01.392 | JC Journal club of relevant publications | ZT, AK,GL, DR, MS, HH |
| 30.06 (9-16) | M.01.392 | SE Seminar, presentation of results | ZT, AK,GL, DR, MS, HH |
Publications
Heimberg G, Kuo T, DePianto DJ et al. A cell atlas foundation model for scalable search of similar human cells. Nature 638, 1085–1094 (2025). https://doi.org/10.1038/s41586-024-08411-y
Betge J, Rindtorff N, Sauer J et al. The drug-induced phenotypic landscape of colorectal cancer organoids. Nat Commun 13, 3135 (2022). https://doi.org/10.1038/s41467-022-30722-9
Roelands J, Kuppen PJK, Ahmed EI et al. An integrated tumor, immune and microbiome atlas of colon cancer. Nat Med 29, 1273–1286 (2023). https://doi.org/10.1038/s41591-023-02324-5
Aissa AF, Islam ABMMK, Ariss MM et al. Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer. Nat Commun 12, 1628 (2021). https://doi.org/10.1038/s41467-021-21884-z
Tan CL, Lindner K, Boschert T et al. Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy. Nat Biotechnol 43, 134–142 (2025). https://doi.org/10.1038/s41587-024-02161-y
Woolston A, Khan K, Spain G et al. Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer. Cancer Cell 36, 35-50 (2019). https://doi.org/10.1016/j.ccell.2019.05.013
Zhang J, Ubas AA, de Borja R et al. Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling. bioRxiv 2025.02.20.639398 (2025). https://doi.org/10.1101/2025.02.20.639398
Qi, X., Zhao, L., Tian, C. et al. Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery. Nat Commun 15, 9256 (2024). https://doi.org/10.1038/s41467-024-53457-1