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Published June 1, 2002 | public
Journal Article

New Computational Approaches for Analysis of cis-Regulatory Networks


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.

Additional Information

© 2002 Elsevier Science (USA). Received for publication December 21, 2001. Revised February 7, 2002. Accepted February 7, 2002. We thank Drs. Rod Adams, Henry Brzeski, and Jonathan Rast for numerous discussions and helpful feedback. Data for Fig. 3 were generated by Toni Snow and Yinjian Xiong. We also thank the robotics macroarraying facility, supported by NIH Grant RR15044 (to E.H.D.) and by the Caltech Beckman Institute. The software development work reported in this paper was supported in part by UK BBSRC Grant 310/BI012024 to HB, and US NIH Grant GM61005 (to E.H.D. and H.B.). C.T.B. is a participant in the Initiative in Computational Molecular Biology, which is funded by an award from the Burroughs Wellcome Fund Interfaces program.

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