Introduction to Computational Biology

1
Introduction to Computational Biology

• Topics

2
Molecular Data

• Definition of data
• DNA/RNA
• Protein
• Expression
• Basics of programming in Matlab
• Vectors
• Matrices
• Loops
• Conditions
• Functions

3
Sequence Alignment

• Dot Plots
• Dynamic Programming
• global alignment
• local alignment
• K-tuple Methods
• Fasta
• Blast

4
Molecular Evolution

• Patterns of substitutions
• Synonymous vs. nonsynonymous
• Estimation of substitutions
• Jukes-Cantor model
• Kimuras two-parameter model
• Molecular clock
• Relative rate test

5
Phylogenetics

• Homology orthologs vs. paralogs
• Phylogenetic Trees
• Distance-based methods
• UPGMA
• Neighbor-joining
• Character-based methods
• Parsimony
• Tree confidence
• Bootstrapping

6
Genomics

• Genomic content
• Hidden Markov Models (HMMs)
• CpG islands
• Motif finding
• Gibbs Sampling
• Transcriptional factor binding sites
• Phylogenetic footprinting
• Vista Plot

7
Microarray Technology

• cDNA vs. oligo arrays
• Labeling
• Hybridization
• Scanning
• Analysis

8
Normalization and Quality Control

• Array normalization methods
• Global normalization
• Lowess normalization
• Quantile normalization
• Quality control
• Data distributions
• Histograms
• boxplots

9
Differential Gene Expression

• Experimental Design
• Replication
• Pooling
• Two-sample Comparisons
• Case-studies
• Single slides
• Replicate slides
• T-test and ANOVA
• P-values
• Adjusted p-values

10
Clustering Microarray Data

• Dissimilarity Measures
• Clustering Methods
• Hierarchical methods
• Partitioning methods
• K-means
• Self-organizing maps (SOMs)

11
Clustering Microarray Data

• Multivariate analysis
• Principal Components Analysis
• Singular Value Decomposition

12
Genetic Variation

• Alleles, frequencies, inheritance
• Population genetics HWE
• SNPs Single Nucleotide Polymorphisms
• Databases
• Patterns
• Analysis

13
QTL Quantitative Trait Loci

• Complex diseases
• Haplotype Analysis
• Linkage
• Association