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

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Seminar in Bioinformatics (236818)

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Seminar in bioinformatics 236818
Seminar in Bioinformatics (236818)

Ron Y. Pinter

Spring 2006


Seminar in bioinformatics 236818
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


Seminar in bioinformatics 236818
What?

  • PathwayandNetworkAnalysis

  • Genome Rearrangements

  • Protein and RNA Structure Prediction

  • Expression analysis (Zohar Yakhini)

  • Linkage analysis (Dan Geiger)

  • Phylogenetic analysis (Shlomo Moran)

  • Protein-protein Interactions (Golan Yona)



Analysis paradigms
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
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
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)

Interesting Dynamic Properties


When to use what
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
Topics

  • Static analysis of metabolic pathways

  • Flux balance analysis of metabolic pathways

  • Pathway modeling and simulation

  • Dynamic analysis of small networks

  • Analysis of genomewide networks

  • Network motifs: discovery and applications


When where and who
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


Seminar in bioinformatics 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)


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