Modeling Biological Networks

• IV.5.i Specific Subprojects
• IV.5.ii Preliminary Results
  • IV.5.ii.a The Topology of Cellular Networks
  • IV.5.ii.b Metabolic Networks
  • IV.5.ii.c Protein Interaction Networks
  • IV.5.ii.d Synopsis

• IV.6.i Subproject 1 – Topological Analysis of Selected Metabolic and Regulatory Networks for Large-scale Structure
  • IV.6.i.a Datasources
  • IV.6.i.b Methodology
  • IV.6.i.c Large-Scale Statistical Characterization of Pathways
  • IV.6.i.d Clustering
    • IV.6.i.d.1 Clustering algorithms
      • IV.6.i.d.1.i Spatial clustering algorithms
      • IV.6.i.d.1.ii Clustering by thermal annealing
      • IV.6.i.d.1.iii Network clustering

• IV.6.ii Subproject 2 – Topology of Signaling Protein Networks and the Cytoskeleton
  • IV.6.ii.a Datasources
  • IV.6.ii.b Overview
  • IV.6.ii.c Hypotheses
  • IV.6.ii.d Specific Aims
  • IV.6.ii.e Preliminary Results and Research Plan
    • IV.6.ii.e.1 Aim 1
    • IV.6.ii.e.2 Aim 2
    • IV.6.ii.e.3 Aim 3
    • IV.6.ii.e.4 Aim 4

• IV.6.iii Subproject 3 – Regulatory Words in Eukaryotic Genomes:
  • IV.6.iii.a Introduction
  • IV.6.iii.b Methodology
  • IV.6.iii.c Research Plan

• IV.6.iv Subproject 4 – Modeling the Regulation and Function of Metabolism
  • IV.6.iv.a Datasources
  • IV.6.iv.b Methods
  • IV.6.iv.c Methodology
    • IV.6.iv.c.1 Cluster analysis
    • IV.6.iv.c.2 Uncovering dynamical constraints using Singular Value Decomposition
  • IV.6.iv.d Research Plan
    • IV.6.iv.d.1 Model construction
    • IV.6.iv.d.2 Model validation
      • IV.6.iv.d.2.i Phenotypic validation
      • IV.6.iv.d.2.ii Molecular validation
      • IV.6.iv.d.2.iii Experimental validation

• IV.6.v Subproject 5 – Gene Complexes in the Evolution of Development
  • IV.6.v.a Background and Overview
  • IV.6.v.b Preliminary Results
  • IV.6.v.c Specific Aims

• IV.6.vi Subproject 6 – Transcription Factor Responses and Regulatory Networks in Drosophila Development
  • IV.6.vi.a Introduction
  • IV.6.vi.b Advantages of the Drosophila Model
  • IV.6.vi.c Datasources
  • IV.6.vi.d Microarray Methodology
  • IV.6.vi.e Specific Aims
  • IV.6.vi.f Research Plan
    • IV.6.vi.f.1 Aim 1
    • IV.6.vi.f.2 Aim 2
    • IV.6.vi.f.3 Aim 3
  • IV.6.vi.g Significance

• IV.6.vii Subproject 7 – The Identification and Characterization of Transcriptional Networks in Early Cardiovascular Development
  • IV.6.vii.a Introduction
  • IV.6.vii.b Background and Significance
  • IV.6.vii.c Preliminary Result
    • IV.6.vii.c.1 Clones for in vitro RNA synthesis
    • IV.6.vii.c.2 Xenopis laevis embryonic heart microarray
  • IV.6.vii.d Specific Aims
  • IV.6.vii.e Research Plan
    • IV.6.vii.e.1 Aim 1
    • IV.6.vii.e.2 Aim 2
    • IV.6.vii.e.3 Aim 3