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Seminar in Bioinformatics (236818)

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

  2. 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

  3. 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)

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

  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 • 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

  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-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

  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)

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