Gene Ontology (GO) provides a controlled vocabulary and hierarchy of terms to facilitate the annotation of gene functions and molecular attributes. Given a set of genes, a Gene Ontology Network (GON) can be constructed from the corresponding GO annotations and semantic relations among GO terms. Transitive rules can be applied to GO semantic relations to infer transitive regulations among genes....

Regulatory networks of transcription factors and signaling molecules lie at the heart of development. Their architecture implements logic functions whose execution propels cells from one regulatory state to the next, thus driving development forward. As an example of a subcircuit that translates transcriptional input into developmental output, we consider a particularly simple case, the regulat...

Animal development is an elaborate process programmed by genomic regulatory instructions. Regulatory genes encode transcription factors and signal molecules, and their expression is under the control of cis-regulatory modules that define the logic of transcriptional responses to the inputs of other regulatory genes. The functional linkages among regulatory genes constitute the gene regulatory n...

Design and implementation of robust network modules is essential for construction of complex biological systems through hierarchical assembly of 'parts' and 'devices'. The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology. The automatic designing capability of GRN topology that can exhibit robust behavior can dramatically change the current practice in...

In the past year, great strides have been made in our understanding of the regulatory networks that control gene expression in the model eukaryote Saccharomyces cerevisiae. The development and use of a number of genomic tools, including genome-wide location and expression analysis, has fueled this progress. In addition, a variety of computational algorithms have been devised to mine genomic seq...

The genomic program for development operates primarily by the regulated expression of genes encoding transcription factors and components of cell signaling pathways. This program is executed by cis-regulatory DNAs (e.g., enhancers and silencers) that control gene expression. The regulatory inputs and functional outputs of developmental control genes constitute network-like architectures. In thi...

Gene regulatory networks (GRNs) represent dependencies between genes and their products during protein synthesis at the molecular level. At the present there exist many inference methods that infer GRNs form observed data. However, gene expression data sets have in general considerable noise that make understanding and learning even simple regulatory patterns difficult. Also, there is no well-k...

Complex gene regulatory networks, not individual genes, control cellular function. Genes and gene products act together to determine cellular phenotypes. Estimation of these networks is necessary to understand cellular mechanisms, detect differences in gene regulation between cell types, and predict cellular response to interventions. A plethora of algorithms have been developed to infer networ...

I have been assisting Professor Jacques Cohen at Brandeis University to explore and compare the the many available representations and interpretations of genetic regulatory networks. The term regulatory network usually refers to the complex system of interactions that controls gene transcription and translation. A simplified description of the transcription-translation process is as follows: Fi...