Computational Biology

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From: Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. A three-dimensional model of the yeast genome. Nature. 2010 May 20;465(7296):363-7. Epub 2010 May 2.

Computer Cluster. Click image to enlarge.
The computational biology component of the Yeast Resource Center develops and applies tools for both proteomics and genomics. On the proteomics side, we have existing software infrastructure for detection of remote protein homology and for characterizing the protein secondary and transmembrane structure on the basis of the primary amino acid sequence. We have also developed an extensive software toolkit for the analysis of shotgun proteomics mass spectrometry data sets, with application to peptide and protein identification from complex mixtures, as well as identification of cross-linked peptides.
On the genomics side, we are developing several methods for characterizing large-scale genome structure. These include methods that aggregate across a variety of functional genomics data sets defined along the genome, as well as a 3C-like assay that allows us to infer the 3D structure of the genome in the nucleus.