Seminar in Bioinformatics (236818)

Ron Y. Pinter

Spring 2006

Why?

• Really … Advanced Algorithmsin 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

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)

Some Networks and Pathways

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)

Modeling and Analysis Methods

• Labeled graphs

• Networks – Boolean, discrete, continuous

• [Hybrid Functional] Petri Nets (HFPN)

• ODEs/PDEs

• Various calculi

• Flux Balance Analysis (FBA)

Interesting Static Properties

• Structural similarity

• Label similarity (nodes and edges)

• Basic (small) building blocks and how they are composed

• …

Interesting Dynamic Properties

• Quantitative– kinetics– concentrations– expression levels– …

• Qualitative– robustness

– stability

– convergence

– oscillation

– transient expression

– fail-safety (sensitivity)

– …

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

Topics

1. Static analysis of metabolic pathways2. Flux balance analysis of metabolic

pathways3. Pathway modeling and simulation4. Dynamic analysis of small networks5. Analysis of genomewide networks6. Network motifs: discovery and

applications

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-12noon– Oleg Rokhlenko, olegro@cs.technion.ac.il, x4877,

Taub 740; Office hours: Sunday, 16:30-17:30, with appointment in advance

• Site – http://webcourse.cs.technion.ac.il/236818

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)