UZH BIO390 - Learning Goals
This page indicates some of the learning goals, as emphasised by the different lecturers. Some points will have been discussed in different lectures; accordingly, exam questions may not refer to information of one specific presentation.
Cave: Please be aware that some of the "Learning Goals" may reflect aspects not necessarily captured by the lectures in the current semester - The ones reelevant for the current semester's exam are related to the given lectures. Also, updates may occurr at any time.
Bioinformatics: Definition & Concepts
- definition of "Bioinformatics" (cf. Anna Tramontano)
- categories of informatics tools used in bioinformatics
- hypothesis versus data driven science
- areas of bioinformatics/bioinformaticians, (in contrast to "pure" modelling, statistics etc.)
- 3 main categories of biological data, and example resources
- definition of API
- common sequence related file formats
- hierarchies and relationships as 2 main principles of ontologies
- areas of "not-bioinformatics", and why
- bioinformatics tools (programming languages, libraries, online resources) and their specific use cases
Bioinformatics tools & resources
- common programming/analysis languages in bioinformatics and their preferred use
- components of bioinformatics online resources
Sequence Analysis
- substitution matrices
- BLAST
Statistical Bioinformatics
- usage of gene expression profiling
- multiple testing correction
- parameters for hierarchical clustering
- statistical evidence for a change in the mean
- dimensionality reduction
- central limit theorem
- hierarchical clustering
- clustering coefficient
Regulatory Genomics and Epigenomics
- secondary/tertiary human genome structure
- functional genome content
- transcription factors & genome interaction
- chemical genome modifications, their effectors and results
- Chip-Seq
- read mapping
- peak calling
- sequence compression algorithms
Metagenomics
- concept of taxonomic diversity
- concept microbial community dissimilarity
- how are sequences used to derive an adopted species concept for prokaryotes
- principle steps for 16S rRNA-based taxonomic composition analysis
- essential steps of short sequencing read assembly into contigs and scaffolds
- basic steps of metagenomic analysis: from raw reads to the reconstruction of genomic scaffolds
Proteomics
- principles of proteome organization in the cell
- key experimental and computational concepts for the collection and analysis of high confidence protein-protein interaction data
- peptide fragmentation
- target-decoy approach
- protein quantification
Clinical Bioinformatics & Personalized Medicine
- genomic variants (types, numbers)
- genomic privacy and re-identification (concepts)
- reference genome(s)
- main bottlenecks of molecular diagnostics in the clinical setting
- goals of many personalized health initiatives
- direct-to-consumer genetic testing -> what, how
- currently favoured clinical NGS technology
- clinical trial participation
- genotype-phenotype (G2P) (ab-)use
Text Mining
- text mining pipelines & (current) common programs/applications
- article/literature repositories (with focus on accessibility)
- processing steps in text mining
- common problems in text mining
- search engine precision metrics
- benchmarking
Semantic web, RDF, Ontologies
- semantic web and its benefits
- stack of standards in semantic web and their functions
- RDF for modeling data
- OWL/OBO for modeling a biomedical domain
- querying knowledge graphs for answering biomedical questions
Biological Networks
- Protein interaction and metabolic networks
- the two-hybrid assay and its limitations
- detection of protein complexes
- graphs, nodes, edges, paths
- geodesics, graph diameter
- common types of degree distributions
- adjacency matrix
- shortest path matrix
- assortative and disassortative graphs
- community (module) detection
- cliques
- motifs, graph representations of metabolic networks
Genomic data & provacy
- reasons for needing many genomes
- principle of re-identification attacks over the Beacon protocol
- long range familial searches
- opinions about risk vs. opportunities
- technical and regulatory solutions against privacy breaches & data abuse