Carnegie Mellon University

Cross-Species Systems Modeling

Course Number: 02-716

Model organisms have longed played an important role in basic science studies and in the pharmaceutical industry. These organisms, ranging from yeast to worms to flies, share many processes that are similar to those active in humans which have made these and other animals the focus of many lab studies. Similarly, almost all drugs are initially tested on mice making cross species studies a key issue in drug development. However, many of the drugs that work well for mice fail in late stage human trials. Similarly, many interactions between highly conserved proteins in one species are not conserved, even between very close species. In this class we will discuss recent studies that try to compare and contrast genomics and functional genomics data across species with the goal of identifying the conserved and divergent processes that are active in each of the species being studied. The class will be divided into three parts. The first will focus on sequence analysis and comparative genomics covering issues related to whole genome sequence alignment, motif discovery using conservation data and miRNA identification using sequence data from multiple species. The second will focus on comparisons of a single type of functional genomics data including gene expression, protein interactions and protein-DNA interactions. This part will rely on recent studies regarding the integration of expression data across species, combining, comparing and aligning protein interaction networks in multiple species and experimental studies that compare protein-DNA interactions across species and in hybrids. In the final part of the class we will discuss methods that attempt to combine multiple functional genomics datasets for a systems biology comparison of interactions across species. Students would be required to present one or two papers and to complete a class project in which they compare or contrast genomics data across species.