New computational approaches for analysis of cis-regulatory networks

Charles Brown, Alistair G. Rust, Peter J.C. Clarke, Zhengjun Pan, Maria J. Schilstra, Tristan De Buysscher, Gareth Griffin, Barbara J. Wold, R. Andrew Cameron, Eric H. Davidson, Hamid Bolouri

Research output: Contribution to journalArticlepeer-review

93 Scopus citations


The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and computational investigation. They include: BioArray, a macroarray spot processing program; SUGAR, a system to display and correlate large-BAC sequence analyses; SeqComp and FamilyRelations, programs for comparative sequence analysis; and NetBuilder, an environment for creating and analyzing models of gene networks. We also present an overview of the process used to build our model of the Strongylocentrotus purpuratus endomesoderm gene network. Several of the tools discussed in this paper are still in active development and some are available as open source.

Original languageEnglish (US)
Pages (from-to)86-102
Number of pages17
JournalDevelopmental Biology
Issue number1
StatePublished - Jun 1 2002
Externally publishedYes


  • Comparative analysis
  • Computational tools
  • Gene network modeling
  • Macroarrays
  • Sequence annotation

ASJC Scopus subject areas

  • Molecular Biology
  • Developmental Biology
  • Cell Biology


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