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Our group studies the large-scale organization of proteins, essentially trying to reconstruct the 'wiring diagrams' of cells by learning how all of the proteins encoded by a genome are associated into functional pathways, systems, and networks. We are interested both in discovering the functions of the proteins as well as in learning the underlying organizational principles of the networks. The work is evenly split between computational and experimental approaches, with the latter tending to be high-throughput functional genomics and proteomics approaches for studying thousands of genes/proteins in parallel.
Xenopus laevis is an essential model organism in several areas of biology. In addition to the key attributes of these embryos for in vivo imaging, cell-free extracts from Xenopus provide among the most powerful in vitro systems for studies of cell and molecular biology. A complete sequence of the X. laevis genome is an essential resource for accurate identification of peptides for mass-spec analyses, for cloning of an ORFeome, for identifying evolutionarily conserved regulatory regions, and for design of morpholino-oligonucleotides for gene knockdowns.
The Texas Xenopus Genome Project
The Wallingford and Marcotte labs have obtained funding from the Texas Institute for Drug and Diagnostic Development (TI3D) to begin sequencing of the X. laevis genome. We are primarily working with Scott Hunicke-Smith at the University of Texas Genome Sequencing and Analysis facility, with funding sufficient for ~20x coverage of the X. laevis genome using ABI SOLiD next-generation sequencing.