Bioinformatics and Genomics in Biomedical Research

PHYS 245: Bioinformatics and Genomics in Biomedical Research

INTRODUCTION

This course provides information and in-depth training in the use of bioinformatics and genomics-related tools and resources that are becoming increasing important in biomedical research. The course is offered as a Sackler School elective in the spring semester and extends over a period of 13 weeks. The class size is limited to 15 students. The course is intended for students who already have computer experience and who wish to apply concepts and techniques of bioinformatics and genomics to their research. Familiarity with genetic approaches is also required for the course.

The class meets twice a week. The first meeting is used to introduce the topic for the week and provide basic training in the use of tools related to the topic. A problem set for the topic is given at this time for students to work on during the week. At the second meeting, selected students present projects related to the topic of the week. As can be seen in the syllabus, the course covers most aspects of bioinformatics and genomics and involves didactic as well as practical training.

Computer Facility:

The course is taught in the Health Sciences Library computer lab on the fifth floor of the Health Sciences Library in the Sackler Building on Harrison Avenue.

Grading:

The course will be graded on the basis of student performance in problem sets (40%), projects (40%) and class participation (20%). No written exam is given in the course.

Topics:

Course Introduction (G. Sahagian) - The nuts and bolts of the course are described. Included is an overview of course content, a tour of the course website and other websites that will be used in the course, and information regarding assignments and grading.

Computer and Web-based Technologies (G .Sahagian) – This is an optional workshop that will be carried out in the computer lab to bring students with minimal computer experience up to speed in computer-based tasks that will be required throughout the course.

Genomes and Databases (A. Schroeder) – Dr. Andrew Schroeder, Flybase Curator at Harvard, gives a insider’s view of the vast amount of information provided by sequencing and annotating the genomes of model organisms and man.

Analysis of Nucleic Acid Sequences (Ortiz) – This topic covers approaches and tools for analyzing DNA and RNA sequences. Included are methods for gene identification, characterization and prediction of promoters and RNA structure.

Sequence Alignment/BLAST (G. Sahagian) – Approaches for comparison of protein and nucleic acid sequences using sequence alignment algorithms are discussed along with their practical use in retrieving sequences and related information from protein and nucleic acid databases.

Analysis of Protein Sequences (Liscum) – Approaches and tools for predicting protein structure and function from protein sequences are covered. Included are methods for prediction of secondary structure, solvent accessibility, transmembrane segments, motifs and patterns and subcellular location.

Protein Structure - Determination and Analysis (G. Sahagian) – Approaches and tools for determining and analyzing protein structure for drug discovery and research purposes are discussed and demonstrated.

Genetic Variation and Molecular Evolution (D. Ortiz) – Mechanisms for the generation of genetic variation are discussed along with sequence comparison tools for the study of evolutionary relationships among sequences from different organisms.

Microarray/Chip Technology (B. Cochran) – A discussion of microarray/chip technology and how it is revolutionizing the field of Genetics. Included is a discussion of cDNA, SNP, CGH, chip on chip and other array technologies.

Genome-wide Analysis of Gene Expression (B. Cochran) – Approaches for analysis of gene expression using microarrays and other technologies are discussed and demonstrated.

Analysis of Gene Expression Data (Slonim) – This topic covers clustering, expression signatures and other methods for analysis of gene expression data.

Proteomics and Functional Genomics (D. Jay/J. DeGnore) – This topic includes discussion of the newly emerging fields of proteomics and functional genomics along with a description of tools and emerging technologies that are being used by researchers in these areas.

Website Reviews (B. Cochran) - An interesting and informative topic on which to end the course, in which newly developed websites of interest to biomedical researcher are identified and evaluated by the students.