02- 716: Cross species analysis of genomics data

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 part 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 part would 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.

Instructors

Ziv Bar-Joseph, GHC 8006, CMU, zivbj at cs.cmu.edu

Gerard (Jerry) Nau, W1157 BSTWR, Pitt, gjnau at pitt.edu

Course Information

Course requirements and grading

Lectures: Monday & Wednesday 15:00-16:20 Margaret Morrison A14

Office Hours, Bar-Joseph: Monday after class

Office Hours, Nau: By email appointment

Syllabus

Suggested papers for student lectures: See cross species paper list.

Lectures

08/29 Lecture 1: Introduction to cross species analysis and data

08/31 Lecture 2: Whole genome sequence alignment

09/12 Lecture 3: Alignment (cont.)

09/14 Lecture 4: Motifs

09/19 Lecture 5: Motifs (cont.)

09/21 Lecture 6: Micro RNAs

09/26 Lecture 7: Cell cycle expression

09/28 Lecture 8: Insights Based on Similarities

10/03 Lecture 9: Cross Species Analysis: Disease Susceptibility

10/12 Lecture 12: Systematic discovery of regulatory motifs in human promoters

10/17 Lecture 13: Graemlin: General and robust alignment of large interaction networks

10/19 Lecture 14: Leveraging Sequence Classification by Multitask Learning

10/24 Lecture 15: Inparanoid: a comprehensive database of eukaryotic orthologs

11/07 Lecture 19: A Gene Co-expression Network for Global Discovery of Conserved Genetic Modules

11/09 Lecture 20: pathBLAST: a tool for alignment of protein interaction networks

11/14 Lecture 21: properties of cross species interactions conservation