BiocenterMedical University of Innsbruck
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WM7 Computational and Systems Biology



LECTURER

Hubert Hackl, Anne Krogsdam, Dietmar Rieder,
Michael Schubert, Giorgia Lamberti, Zlatko Trajanoski


NOTES

Introduction
Introduction into RNAseq data analysis
RNAseq data anlysis practical part notes
Unix mini tutorial
RNAseq data anlysis with DESeq2
Notes


SCHEDULE

DateRoomTopicLecturer
04.06 (9-17)M.01.392VO Functional precision oncology
VO Integrative multiomics analyses
ZT
05.06 (9-17)M.01.392VO Single cell and spatial analyses
VO Systems biology and pharmacology
ZT
10.06 (9-12)
10.06 (12-16)
M.01.392
wet lab
VO Cancer models
PR Cancer cell line culture
GL,AK
11.06 (9-12)
11.06 (12-16)
M.01.392
wet lab
VO Precision therapy
PR Kinase inhibtor treatment
GL,AK
12.06 (9-12)
12.06 (12-16)
M.01.392
wet lab
VO NGS
PR RNA isolation
AK,GL
13.06 (9-12)
13.06 (12-16)
M.01.392
wet lab
VO RNA sequencing
PR Library generation, sequencing
AK,GL
16.06 (9-16)FP3 C3VO|PR RNA sequencing data preprocessing DR
17.06 (9-16)FP3 C2VO|PR Differential expression analyses DR
18.06 (9-16)FP3 C2VO|PR Drug sensitivityHH
23.06 (9-16)FP3 C3VO|PR Functional analysesMS
24.06 (9-16)FP3 C3VO|PR Pathway and network modelingMS
25.06 (9-16)FP3 C3VO|PR Tumor sample analysesHH
26.06 (9-16)M.01.392JC Journal club of relevant publicationsZT,AK,GL,DR,MS,HH
27.06 (9-16)M.01.392SE Seminar, Presentation of resultsZT,AK,GL,DR,MS,HH



FILES & SCRIPTS

GDSC1.txt
CCLE_TPM.txt
GDSC.R
CACO2_OXO_DEG.txt
VENN.R
CRC_scaled_estimate.txt
COADREAD.clin.merged.picked.txt
CRC_PRIM_LOG2TPM1_2.txt
CRC_CLIN_2_CMS_MSI_TMB.txt
GSVA_CRC.txt
GENESETS.gmt
get_PRIM_TPM2.R
get_CLIN.R
BOXPLOT.R
GSVA.R
GSEA.R
deconv.R
OS.R
OS2.R





PUBLICATIONS FOR JOURNAL CLUB

Heimberg et al. A cell atlas foundation model for scalable search of similar human cells.
Nature. 2025. 638:1085-1094. PMID:39566551
Betge et al. The drug-induced phenotypic landscape of colorectal cancer organoids.
Nat Commun. 2022. 13:3135. PMID:35668108
Roelands et al. An integrated tumor, immune and microbiome atlas of colon cancer.
Nat Med. 2023. 29:1273-1286. PMID:37202560
Aissa et al. Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer.
Nat Commun. 2021. 12:1628. PMID:33712615
Tan et al. Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy.
Nat Biotechnol. 2024. 524:47-53. PMID:38454173
Woolston et al. Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer.
Cancer Cell. 2019. 36:35-50. PMID:31287991
Zhang et al. Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling.
bioRxiv. 2025. doi: 10.1101/2025.02.20.639398
Qi et al. Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery.
Nat Commun. 2025. 15:9256. PMID:39462106



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