Computers and Biology
Instructor: Patrice Koehl, Department of Computer Science, College of Engineering
Description: Most living organisms are complex assemblies of cells, the building blocks for life. Each cell can be seen as a small chemical factory, involving thousands of different players with a large range of size and function. Among them biological macro-molecules hold a special place. These usually large molecules serve as storage for the genetic information (the nucleic acids such as DNA and RNA), and as key actors of cellular functions (the proteins). Biochemistry, the field that studies these biomolecules, is currently experiencing a major revolution. In hope of deciphering the rules that define cellular functions, large scale experimental projects are performed as collaborative efforts involving many laboratories in many countries. The main aims of these projects are to provide maps of the genetic information of different organisms (the genome projects), to derive as much structural information as possible on the products of the corresponding genes (the structural genomics projects), and to relate these genes to the function of their products, usually deduced from their structure (the functional genomics projects). The success of these projects is completely changing the landscape of research in biology. As of September 2006, more than 400 whole genomes have been sequenced, corresponding to a database of over forty million gene sequences. The need to store this data efficiently and to analyze its contents has led to the emergence of a collaborative effort between computer science and biology, referred to as bio-informatics. In parallel, the repository of bio-molecular structures contains more than 37,000 structures of proteins and nucleic acids. The similar need to organize and analyze the structural information contained in this database is leading to the emergence of another partnership between computer science and biology, namely bio-geometry.
Format: The seminar will meet for one hour each week. This series of seminar will focus on the benefits of applying computing technology and science to biological research. Some of the topics we will cover include: genome projects, bio-molecules, biological databases, bioinformatics and computational structural biology. "Information technology" usually does not mean much to biologists, and reversely, "biology" does not mean much to a computer professional. Our goal in this seminar series is to bring awareness to the students of the critical need of interdisciplinary approaches to study biological problems, focusing on the possibilities that computers create for biologists. Students will have to read a scientific paper every week. Grading: Grading will be based on Pass/Fail. The grade will be based on participation in class (20%), some homework (20%), and a final written project (60%).
About the Instructor: Professor Koehl is a member of the Department of Computer Science and of the Genome Center. He is interested in understanding the role of shape on biomolecular evolution, and on predicting the structure of a protein from its sequence. He develops algorithms and computational tools to analyze, predict and represent biomolecules. His current project include rational drug design and predicting protein-protein interactions.