08:30 to 09:15 Registration for Gene Networks Meeting At the Isaac Newton InstituteSession: Vertical Integration in Biology: From Molecules to Organisms 09:20 to 09:30 Opening Remarks Meeting room 2 at Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 09:30 to 10:10 Reverse engineering of a developmental genetic regulatory network Meeting room 2 at the Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms I will give an overview of a collaborative project with Prof. Eric Davidson (Caltech) in which we have been reverse engineering the genetic regulatory network underlying endoderm-mesoderm specification in sea urchin embryos. To be able to carry out this work, we have developed - and are continuing to develop - a range of new software tools and an associated reverse engineering methodology which I will describe briefly. 10:10 to 10:50 J Jäger ([SUNY])Looking at the future of functional genomics from inside the Drosophila blastoderm -(Meeting Rm 2 at the Centre for Math. Sciences)Session: Vertical Integration in Biology: From Molecules to Organisms Functional genomics will ultimately involve the application of genomic methods to the full range of biological functions, including those that are properties of multicellular organisms. This includes areas such as neurobiology, development, macroevolution, and ecology. This talk will be concerned with the functional genomics of animal development. The central problem in animal development is the generation of body form. This problem was first considered by Aristotle, and in the nineteenth century is was shown that basic body form is determined by interactions among cells in a morphogenetic field. The determination of a morphogenetic field in development involves the expression of genes in spatial patterns. Spatially controlled gene expression cannot as yet be assayed in microarrays, but certain special properties of the fruit fly Drosophila which make it a premier system for developmental genetics also enable it to be used as a naturally grown differential display system for reverse engineering networks of genes. In this system we can approach fundamental scientific questions about development as well as certain computational questions that arise in the analysis of genomic level gene expression data. Our approach is called the gene circuit method'', and it consists of 4 components: (1) The formulation of a theoretical model for gene regulation. (2) The acquisition of gene expression data using fluorescently tagged antibodies. (3) The determination of the values of parameters in the model or the demonstration that no such values exist by numerical fits to data. The results of (1), (2), and (3) are used (4) to validate the model by comparison to the existing experimental data and by making further predictions. Recent progress in all 4 of these areas will be discussed. 10:50 to 11:10 Coffee At the Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 11:10 to 11:50 G Von Dassow ([Washington])Models of modules: putting the molecular parts together into genetic devices (Meeting rm 2 at the Centre for Mathematical Sciences)Session: Vertical Integration in Biology: From Molecules to Organisms Our research into mathematical models of gene networks began with a curiosity about the genetic architecture of development: to what extent can we say that gene networks are modular building blocks of developmental mechanisms? By "module" we mean a small conspiracy of genes that together exhibit some functional behavior, intrinsic to the network itself and related to the functional role of that network in the organism. I emphasize that modularity is a working assumption, rather than something we are trying to prove rigorously. We've made an extended study of two such putative modules, the Drosophila segment polarity network, and the Drosophila neurogenic network. Our approach has been to do the computer-modeling equivalent of a biochemical reconstitution: add known facts to the model until it begins to exhibit life-like behaviors. The segment polarity module's job is to maintain boundaries; the neurogenic network's job is to mediate lateral inhibition; for both modules, minimal in silico reconstitutions exhibit those behaviors robustly with respect to the kinds of variation that we would expect genetic networks to experience in real life. I'll discuss a handful of results from these models that we find provocative: first, I'll discuss what we've learned about what makes these modules' functional behaviors robust to parameter variation and other insults, and how we think these models shed light on the phenomenon of canalization; next, I'll describe some instances in which the failure of the segment polarity models to account for certain details led us to mechanistic questions about the real network; and finally, I'll talk about some ideas, stimulated by the models, about how these two networks arose, highlighting the hierarchical, nested nature of gene networks. Copyright © Isaac Newton Institute 11:50 to 12:30 Microarrays and yeast: insights into gene regulation Meeting room 2 at the Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 12:30 to 13:30 Lunch At the Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 13:50 to 14:00 K Vass ([Glasgow])Normalisation and local variation in microarrays Meeting room 2 at Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 14:00 to 14:40 A Brazma ([Euro Bioinformatics Institute])Reconstructing elements of gene networks from genome scale microarray data (Meeting rm 2 at the Centre for Mathematical Sciences)Session: Vertical Integration in Biology: From Molecules to Organisms 14:40 to 15:20 From gene expression to gene interaction Meeting room 2 at the Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 15:20 to 15:40 Tea At the Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 15:40 to 16:20 O Wolkenhauer ([UMIST])System theoretic models of gene expression and gene interactions Meeting room 2 at the Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 16:20 to 16:45 Funding opportunities in bioinformatics and theoretical biology Meeting room 2 at the Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 16:45 to 17:20 Discussion Session Meeting room 2 at The Centre for Mathematical SciencesSession: Vertical Integration in Biology: From Molecules to Organisms 19:00 to 00:00 Dinner at Wolfson Court (residents only)Session: Vertical Integration in Biology: From Molecules to Organisms