ONCSC 7700 - 013 CANCER DATA SCIENCE JOURNAL CLUB WEBSITE

Course Director: Aik Choon Tan, Ph.D.

Course Teaching Assistant:
Min Hu

Class: Thursday 9:30am - 10:30am
Venue: HCI Research South Conference Room 4C

COURSE TOPICS

1. TOPIC 1 - GENE SET ANALYSIS

   Classic & Concept: (AC Tan - 9/4/2025)

   • GSEA Paper: Subramanian et al. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS. [PDF].
   • Mootha et al. (2003). PGC-1-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genetics. [PDF]
   • Liberzon et al. (2015). The Molecular Signature Database (MSigDB) hallmark gene set collection. Cell Systems. 1(6): 417-425. [PDF]

     Variations & Expansions:

   • Irizarry et al. (2009). Gene set enrichment analysis made simple. Stat Methods Med Res. 18(6): 565-575. [PDF]
   • Hanzelmann et al. (2013). GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics. 14: Article number: 7. [PDF]
   • Powers et al. (2018). GSEA-InContext: identifying novel and common patterns in expression experiments. Bioinformatics. 34(13): i555-i564. [PDF]
   • Cousins et al. (2023). Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19. Bioinformatics. 39(1): btac735. [PDF]
     

     Applications:

   • Ma et al. (2020). Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies. Nature Communications. 11: Article number: 1585. [PDF]
   • Franchini et al. (2023). Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data. NAR Genomics and Bioinformatics, 5(1): lqad024. [PDF]
   • Fan et al. (2024). irGSEA: the integration of single-cell rank-based gene set enrichment analysis. Briefings in Bioinformatics. 25)4_: bbae243. [PDF]
     

     AI:

   • Joachimiak et al. (2024). Gene Set Summarization using Large Language Models. ArXiv:2305.13338v3. [PDF]
   • Wang et al. (2025). GeneAgent: self-verification language agent for gene-set analysis using domain databases. Nature Methods. 22:1677-1685. [PDF]