Fall/Herbst-semester 2020
Mondays 9.00-9.45 (remote), 10.00-10.45 (remote)
Monday 11.00-11.45 (remote)
Dr. Hubert Rehrauer, Group Leader of Genome Informatics at FGCZ
Prof. Dr. Mark Robinson, Associate Professor of Statistical Genomics, IMLS, UZH
Ahmadreza Yousefkhani, M.Sc. student in Computational Biology and Bioinformatics
| Date | Lecturer | Topic | Exercise | JC1 | JC2 | Tutorial |
|---|---|---|---|---|---|---|
| 14.09.2020 | Mark + Hubert | admin; mol. bio. basics | R markdown; git(hub) | |||
| 21.09.2020 | Mark | interactive technology/statistics session | group exercise: technology pull request | Exploratory data analysis and visualization with ggplot2 and dplyr | ||
| 28.09.2020 | Hubert | NGS intro; exploratory data analysis | EDA in R | PCA - concept and pitfalls | ||
| 05.10.2020 | Hubert | mapping | Rsubread | Linear regression, diagnostic plots and residual analysis | ||
| 12.10.2020 | Mark | limma + friends | linear model simulation + design matrices | Linear regression, tests and confidence regions, F-value analysis | ||
| 19.10.2020 | Hubert | RNA-seq quantification | RSEM | R-squared and model selection in linear models, Mallow Cp statistic, AIC, BIC criterion | ||
| 26.10.2020 | Mark | edgeR+friends 1 | basic edgeR/voom | DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data (TK, SS, TE) | From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL (DC, LM) | Bayesian linear regression |
| 02.11.2020 | Mark | edgeR+friends 2 | GLM/DEXSeq | Redefining CpG islands using hidden Markov models (Zhiwei Dou, Huixin Jin, Peiying Cai) | Causal Inference in Genetic Trio Studies (ZS, GW, LN) | Empirical Bayes |
| 09.11.2020 | Kathi | hands-on session #1: RNA-seq | FASTQC/Salmon/etc. | Statistical significance for genomewide studies (RA, HH, JR) | Identifying signaling genes in spatial single cell expression data (YM, KD, GJ) | MLE, Fisher information, assymptotic efficiency |
| 16.11.2020 | Hubert | single-cell 1: preprocessing, dim. reduction, clustering | Testing hypotheses about the microbiome using the linear decomposition model (FS,BO,SA) | Generalizing RNA velocity to transient cell states through dynamical modeling (DP, EH) | Likelihood ratio statistics, profile likelihood | |
| 23.11.2020 | Stephany | hands-on session #2: cytometry | cytof null comparison | Genome-wide detection of intervals of genetic heterogeneity associated with complex traits (Richard Affolter, Philip Hartout, Martin Emons) | Empirical Bayes Analysis of a Microarray Experiment (Jennifer Probst, Eljas Röllin, Lisa Herzog) | Validation of models, sequential cross validation |
| 30.11.2020 | Mark | single-cell 2: clustering, marker gene DE | marker gene DE | A Bayesian mixture model for the analysis of allelic expression in single cells (Sneha-Sundar,SmaragdaDimitrakopoulou,marinapanteli) | scMET: Bayesian modelling of DNA methylation heterogeneity at single-cell resolution (MW, RM, DW) | Managing your projects with workflowr |
| 07.12.2020 | Pierre-Luc | hands-on session #3: single-cell RNA-seq (cell type definition, differential state) | full scRNA-seq pipeline | ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling (Leonor Schubert, Jonathan Haab, Flavio Rump) | Detection of differentially abundant cell subpopulations discriminates biological states in scRNA-seq data (TE, RB, AB) | |
| 14.12.2020 | Mark | loose ends: HMM, EM, robustness | segmentation, peak finding | NEBULA: a fast negative binomial mixed model for differential expression and co-expression analyses of large-scale multi-subject single-cell data (HML, SCD, SW) | A test metric for assessing single-cell RNA-seq batch correction (Dimitri Schmid, Lola Kouroma, Jonas Bucher); AUC-RF: A New Strategy for Genomic Profiling with Random Forest (Jonas Meirer, Dominique Paul) |
Assuming you have git installed locally, you can check out the entire set of course materials with the following command (from command line):
git clone https://github.com/sta426hs2020/material.git
Alternatively, for a ZIP file of the repository, you can click on the (green) 'Clone or download' (top right) and then click 'Download ZIP'.