1. CISC667, S07, Lec25, Liao1 CISC 467/667 Intro to Bioinformatics (Spring 2007) Review Session

2. CISC667, S07, Lec25, Liao2 Basics of Molecular biology Central dogma –Transcription –Translation Genetic code DNA –Double helix –Watson-Crick binding RNA –Secondary structures Genes –Compositional Structure –Reading frames Proteins –Secondary structure: alpha helices, beta sheets, and coils –3-d structure Gene Regulations (Operons) DNA Microarray Cloning PCR Gel electrophoresis Yeast 2 hybrid system

3. CISC667, S07, Lec25, Liao3 Computational methods Dynamic programming –Problems can be dissect to sub-problems –Recurrence equations –DP Table –Traceback Maximum Likelihood Pairwise alignments Multiple alignments Hidden Markov models - viterbi, forward, and viterbi training Phylogenetic trees - distance-based, character-based, and probability-based - Bootstrap Structural predictions - secondary - lattice model Clustering Profiles and inferring genetic networks - K-means - Boolean networks

4. CISC667, F05, Lec17, Liao4 Phylogenetic Trees Motivations Concepts and assumptions –Gene trees versus species trees –Rooted v.s. unrooted Mothods –Character-based Maximum Parsimony: conventional and weighted Traceback –Distance-based UWPGA Neighbor-joining Metric distance, ultrametric distance, molecular clock, additive distance –Probability-based Evolution models: Jukes-Cantor, Kimura.

5. CISC667, S07, Lec25, Liao5 RNA secondary structures Concepts –Single strand –Intramolecular pairings –Structural categories Hairpins, bulge loops, interior loops, and multi loops Pseudo knots –Similarity in secondary structure plays a more important role than primary sequence in determining homology for RNAs Algorithms for predicting structures –Nussinov’s Maximum base pairing –Zuker’s Minimum energy

6. CISC667, S07, Lec25, Liao6 Protein structures Concepts –Anfinsen hypothesis –Primary, secondary, tertiary, and quaternary Algorithms for predicting structures –Secondary structure encoding Artificial neural networks –3-dimensional Lattice models –HP models: Monte Carlo, Genetic algorithm, and hybrid

7. CISC667, S07, Lec25, Liao7 Genetic networks Concepts –Regulation, protein-protein interactions, … –Operons Clustering and Modeling –K-mean –Boolean networks Acyclic Truth tables 3 steps predictor Maximum entropy chooser

8. CISC667, S07, Lec25, Liao8 About the Final Exam –Time and Place: May 22, 1:00PM-3:00PM Purnell Hall 325 –closed-book –Four parts Primary sequence analysis [30 points] Phylogenetic trees [30 points] Structural prediction [25 points] Clustering gene expression profiles (K-means) and inferring genetic network [15 points]

9. CISC667, S07, Lec25, Liao9 Thank you and hope to see you in CISC841