Center for Computational Regulatory Genomics

Eric Davidson, PI
Andrew Cameron, Center Director

The Center for Computational Regulatory Biology and its subsidiary, the Genomics Technology Facility, provides information and materials to support research with echinoderm models. It is the home of the sea urchin web system, SpBase.

The Center focuses on three areas of activity: macro-array libraries, echinoderm molecular biology and computational support of echinoderm molecular biology and genomics.

  1. A high-throughput operation that arrays and prints macroarray libraries and provides clones to the community. These materials formed the basis of a number of echinoderm genome projects and continue to be useful to the laboratory scientist.
  2. The center designs, produces and tests reagents such as recombineered BAC clones used as gene transfer constructs. These reporter constructs carry a fluorescent protein coding region inserted into the coding region of a gene of interest and thus provide a genomically correct substrate in which cis-regulatory modules (CRM) can be deleted or mutated. All of the recombineered BAC clones once tested are listed on the SpBase website and made available to the community.
  3. A computational branch supplies software to the sea urchin developmental biologist and maintains databases fundamental to the Sea Urchin Genome Project. Many of these tools were specifically designed to aaugment experimental work that uses iterative cycles of experimentation and computation. One example is the Java-based software package, Bio-Tapestry, which is used to draw, visualize and analyze gene regulatory networks (http://sugp.caltech.edu/endomes/).

For more information, visit the website.

Contact

Eric Davidson, PI
Room 84 - Alles
Mail Code 156-29
E-mail:
Tel: (626) 395-4937
Andrew Cameron, Center Director
Room 224 - Beckman Institute
Mail Code 139-74
Email:
Tel: (626) 395-8421