Modeling Biological Networks

IV.1 Coordinators
IV.2 Participants
IV.3 Introduction
IV.4 Background and Significance
IV.5 Research Plan

• 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 Specific Subprojects
IV.7 Connection to Specific Projects 2 (cytoskeleton) and 3 (organogenesis)
IV.8 Timeline

< Previous | Page 3 of 35 | Next >

IV.5 RESEARCH PLAN:

The proposed research merges two truly interdisciplinary efforts: (i) The ongoing well-established collaboration among theoretical physicists with experience in characterizing the structure and dynamics of complex networks; biophysicists with experience in studying the dynamics of cytoskeleton formation and reaction-diffusion processes; cell biologists with experience in studying the topology of metabolic and regulatory networks; computer scientists with expertise in clustering algorithms, graph theory, and algorithm complexity; and applied mathematicians with experience in reaction-diffusion equations and stochastic dynamical systems as well as topological characterization of networks; and (ii) the emerging collaboration among biologists who study developmental phenomena using genetics, comparative embryology, and functional genomics; bioinformaticists with expertise in high throughput searches and data-mining; and applied mathematicians with well-established interests in the analysis of complex patterns in biology and linguistics.

IV.5.i Specific Subprojects:

We structure our modeling effort into the following Specific Subprojects:

• Subproject 1 - Topological analysis of selected metabolic and regulatory networks to uncover and model their large-scale structure.
• Subproject 2 - Topology of signaling protein networks and the cytoskeleton.
• Subproject 3 - Regulatory words in eukaryotic genomes.
• Subproject 4 - Modeling the regulation and function of metabolism.
• Subproject 5 - Gene complexes in the evolution of development.
• Subproject 6 - Transcription factor responses and regulatory networks in Drosophila development.
• Subproject 7 - Identification and characterization of transcriptional networks in early cardiovascular development