Schedule
For the Spring 2023 quarter we will meet twice a week on Monday and Wednesday at 4:30-6:20 pm in TATA 2501 (Map). Clicking on the topics below will take you to supporting class content in Google Drive, hands-on “lab session” sheets, walk-through screencasts, required reading material and homework assignments.
| # | Date | Topics for Spring 2023 |
|---|---|---|
| 1 | Monday 04/03/23 & Wednesday 04/05/23 | Barry Grant - Recap of foundations of bioinformatics. Topics: - Working with UNIX. - Sequence alignment. - Key online resources. - Data analysis and visualization with R and Bioconductor. - annotation of Gene lists (GO term and pathway enrichment). DriveFolder. |
| 2 | Monday 04/10/23 & Wednesday 04/12/23 | Ferhat Ay - Gene expression analysis. Topics: Gene expression, differential gene expression and relevant statistics. GO term enrichment and gene set enrichment analysis. Gene co-expression network analysis. Single-cell RNAseq and CITE-seq introduction. Hands on single-cell analysis exercise using Seurat. DriveFolder. |
| 3 | Monday 04/17/23 & Wednesday 04/19/23 | Graham McVicker - Human genetics Topics: - Intro. - Genome-wide association studies with a focus on immune-related diseases. - Identification of expression quantitative trait loci (eQTLs). - Identification of chromatin/histone quantitative trait loci. - (hQTLs). - CRISPR screens for enhancer regions of immune genes |
| 4 | Monday 04/24/23 & Wednesday 04/26/23 | Tiffany Amariuta - Advanced topics in human genetics Topics: - Multi-ancestry genetic association studies. - Prediction of disease-critical regulatory elements. - Transcriptome-wide association studies. - Fine-mapping. - Heritability estimation. |
| 5 | Monday 05/01/23 & Wednesday 05/03/23 | Ferhat Ay - Analysis of epigenomics data from immune cells Topics: - Analysis of ChIP-seq for histone modifications and transcription factor binding. - Analysis of chromatin accessibility using ATAC-seq data. - Analysis of 3D genome architecture and enhancer-promoter interactions using Hi-C and HiChIP data |
| 6 | Monday 05/08/23 & Wednesday 05/10/23 | Bjoern Peters - Prediction and analysis of epitope Topics: - Background: antibodies, T cell receptors, MHC molecules, epitopes. - The Immune Epitope Database (IEDB). - Machine learning approaches for peptide:MHC binding |
| 7 | Monday 05/15/23 & Wednesday 05/17/23 | Hannah Carter – Neoantigens Topics: - Brief review of HLA-antigen binding prediction. - HLA-typing from exome data. - Tumor neoantigens. - Analysis of immunoediting in tumors. - Tumor-immune infiltrates |
| 8 | Monday 05/22/23 & Wednesday 05/24/23 | Sam Myers & Pieter Dorrestein- Proteomics Topics: - Intro to liquid chromatography and mass spectrometer instrumentation. - Intro to data structure, spectral alignment, and a survey of bioinformatic tools for proteomic/metabolomic analyses. - Hands-on example of metabolomic data and/or proteomic/post-translational modification analysis. |
| 9 | Monday 05/29/23 | Holiday |
| 9 | Wednesday 05/31/23 | Pieter Dorrestein – Metabolomics Topics: |
| 10 | Monday 06/05/23 & Wednesday 06/07/23 | Sara McArdle and Zbigniew Mikulski Topics: - Introduction to 2D imaging of 4D objects and QuPath. - Cell classification with random forest. - Pixel classification with artificial neural networks. - Quantification of tumor-immune infiltrates. - Quantification of RNA molecules in cells with RNAscope. - Data export for Cytomap and spatial relationship analysis. |
