Elements of Genomics

Objectives

The curricular unit has the following objectives:

1. Recognize the differences between genetics and genomics;

2. To know different strategies of mass sequencing;

3. To know the main issues related to the sequencing of genomes (coverage, depth, etc.);

4. Review cases of application of massive sequencing to specific situations (eg Paleogenómica);

5. Recognize the importance of transcriptomics in various domains and identify their objectives;

6. Know the main methods for measuring gene expression;

7. Apply the knowledge to theoretical and practical situations, giving students skills to understand the potential of genomic tools to aid researchers and biomedical professionals.

Program

1. Genetics & Genomics: basic concepts;

2. Massive DNA Sequencing: importance, methods and derived information;

3. Sequencing strategies and information derived from the massive sequencing;

4. Application examples of massive sequencing: paleogenómica and the example of syphilis in human populations;

5. Main issues in massive sequencing (coverage, depth, assembly);

6. Functional genomics: the importance of transcriptomics;

7. Main objectives of transcriptomics;

8. Strategies for measuring gene expression: low yield techniques (Northern

blot, qPCR) and high performance techniques (ESTs; Serial Analysis of Gene Expression (SAGE); Microarrays; RNA-Seq).

Teaching Methodologies

The lecture sessions are limited to 4 hours, in the remaining hours is developed theoretical and practical nature learning activities, encouraging the discussion and active participation of the students. These practical theoretical oriented activities include activities related to) the analysis of results from a study of expression "Genome-Wide" (namely one "array" of expression with the Illumina platform, developed under a project in which the teacher is involved) (www.mesca3.uac.pt) and b) the monitoring and discussion of an analysis in Sillico, using Promo Prediction program of transcription factors binding sites (http: //alggen.lsi. upc.es/cgibin/ promo_v3/promo/promoinit.cgi?dirDB=TF_8.3.).

Bibliography

Introduction to Bioinformatics (Oxford UP), (2002), Arthur M. Lesk.

Current Protocols in Bioinformatics (Wiley), Vol. 1 (2005), A.D. Baxevanis et al.

Molecular Biology of the Cell (Garland Sci.), 4th Ed. (2002), Bruce Alberts et al.

Bioinformatics: A practical guide to the analyses of genes and genomes (Wiley), 3rd ed. (2005), Andreas D. Baxevanis & B.F. Francis Ouellette.

NCBI Books, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books

Hiperligações:

http://www.ncbi.nlm.nih.gov/

http://genome.ucsc.edu/

http://www.ensembl.org/

http://www3.oup.co.uk/nar/database/c/