1. Seminar in Bioinformatics (236818) Ron Y. Pinter Spring 2006

2. Why? Really … Advanced Algorithms in Computational Biology II –Can’t fit everything in one term –Not just sequence alignment, HMMs, and Bayesian networks Ever evolving and changing needs and ideas Still, trying to focus on some specific area

3. What? Pathway and Network Analysis Genome Rearrangements Protein and RNA Structure PredictionProtein and RNA Structure Prediction Expression analysis (Zohar Yakhini)Expression analysis (Zohar Yakhini) Linkage analysis (Dan Geiger)Linkage analysis (Dan Geiger) Phylogenetic analysis (Shlomo Moran)Phylogenetic analysis (Shlomo Moran) Protein-protein Interactions (Golan Yona)Protein-protein Interactions (Golan Yona)

4. Some Networks and Pathways

5. Analysis Paradigms Static –Integrative Analyses of Interaction Networks Underlying the Cellular Circuitry in Yeast (Yeger-Lotem et al., PNAS, 2004) –Alignment of Metabolic Pathways (Pinter et al., Bioinformatics, 2005) Dynamic –HFPN-based Simulation of the Reduced Folates Metabolic Pathway (Assaraf et al., to appear, JTB 2006) –Faithful Modeling of Transient Behavior in Developmental Pathways (Rubinstein et al., submitted)

6. Modeling and Analysis Methods Labeled graphs Networks – Boolean, discrete, continuous [Hybrid Functional] Petri Nets (HFPN) ODEs/PDEs Various calculi Flux Balance Analysis (FBA)

7. Interesting Static Properties Structural similarity Label similarity (nodes and edges) Basic (small) building blocks and how they are composed …

8. Interesting Dynamic Properties Quantitative –kinetics –concentrations –expression levels –… Qualitative –robustness –stability –convergence –oscillation –transient expression –fail-safety (sensitivity) –…

9. When to use what? For static analysis –Graph algorithms –Algebraic methods –Statistical tests For dynamic analysis –Detailed behavior – ODEs –Qualitative behavior – networks –Some specific properties – various calculi

10. Topics 1.Static analysis of metabolic pathways 2.Flux balance analysis of metabolic pathways 3.Pathway modeling and simulation 4.Dynamic analysis of small networks 5.Analysis of genomewide networks 6.Network motifs: discovery and applications

11. When, where and who? Time and Place –Monday, 16:30am-18:30pm, Taub 4 Staff –Prof. Ron Pinter, pinter@cs.technion.ac.il, x4955, Taub 705; Office hours: Tuesday, 10am-12noonpinter@cs.technion.ac.il –Oleg Rokhlenko, olegro@cs.technion.ac.il, x4877, Taub 740; Office hours: Sunday, 16:30-17:30, with appointment in advanceolegro@cs.technion.ac.il Site – http://webcourse.cs.technion.ac.il/236818 http://webcourse.cs.technion.ac.il/236818

12. How? References –Bernhard Ø. Palsson: Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, 2006 –papers (ISMB, RECOMB, WABI; journals) –websites Duties –attendance (10%) –presentation (30%) –term paper (60%) Prereqs –course in algorithms (234246 or 234247) –background in bioinformatics (236522 or 236523)