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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

Seminar in Bioinformatics (236818)

Ron Y. Pinter

Spring 2006

slide2
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
slide3
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, [email protected], x4955, Taub 705; Office hours: Tuesday, 10am-12noon
    • Oleg Rokhlenko, [email protected], x4877, Taub 740; Office hours: Sunday, 16:30-17:30, with appointment in advance
  • Site – http://webcourse.cs.technion.ac.il/236818
slide12
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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