Ordinary call: orientations and renunciation

Evaluation will be based on three points:

1) Attendance and participation in class. Class attendance is mandatory. Excused absences may be made up with the activity proposed by the professor in charge of the session. Unexcused attendance of less than 80% of the sessions will result in the failure of the course.

2) Presentation and discussion of scientific papers

3) Practical works on experimental data by bioinformatics methods.



The lack of delivery of the practical works will suppose resignation of the call for evaluation and will be recorded as Not Presented.

Extraordinary call: orientations and renunciation

The extraordinary call will involve the completion of an exam on the contents of the subject. The exam will consist of the development of a topic covered in the subject and it will be chosen from two topics elected at random.

Temary

THEORETICAL FRAMEWORK



Unit 1

Introduction to Genomics. Genomes sequencing. The human genome.



Unit 2

Annotation of genomes. Comparative genomics. The genome of model species in Biomedicine. Genes Ontology.



Unit 3

Bioinformatics analysis of sequences. Databases. Comparisons by similarity. Alignments of sequences ang genomes.



Unit 4

Analisis of the genomic variation. Single Nucleotide Polymorphisms (SNPs): Detection and genotyping technologies. Genomic variation in the human species and its relationship with health.



Unit 5

Linkage disequilibrium and Haplotype maps. SNPs technology applications: QTLs mapping and association studies with diseases.



Unit 6

Analysis of genomic expression. DNA microarrays and RNA sequencing. Experimental design and methodologies.Other tools: CGH, Chip on Chip.



Unit 7

Data mining.

Statistical analysis of microarray data.



Unit 8

Advanced topics in Genomics and Transcriptomics



COMPUTER PRACTICES



(1)Topic 1: Databases and tools for the analysis of sequences and genomes.

(2)Topic 2: Analysis of High Througput Sequencing data.

(3)Topic 3: SNPs: detection and genotyping.

(4)Topic 4: Statistical analysis of whole genome expression.

(5)Topic 4: Data mining: biological significance of whole expression results.

Bibliography

Compulsory materials

The graphic material used in the master classes by each professor will be stored in e-gela, or sent by e-mail to all students.

Basic bibliography

1. Malconm Campbell, A. & Heder Laurie J.A. 2003. Discovering Genomics, Proteomics and Bioinformatics. Pearson Education, Inc. Benjamin Cummings, San Francisco

2. Gibson G. and Muse, S.V. 2004. A primer of Genome Sciences. Sinauer Associates, Inc.

3. Azuaje, F.,Dopazo, J (Eds.).2005. Data analysis and visualization in Genomics and Proteomics. Wiley

4. Mount DW.2001. Bioinformatics. Sequence and Genome analysis. Applications in Biological Science and Medicine. CDR Press, Boca Raton

5. Baxevanis, A.D., Ouellette, B.F.F. 2001. Bioinformatics. A practical guide to the analysis of genes and proteins. 2nd ed. Wiley interscience.

6. Pevsner J. 2015. Bioinformatics and functional Genomics. Wiley Blackwell. 3rd. ed. ISBN 978-1-118-58178-0

7. Korpelainen E., Tumala J., Somervuo R., Huss M, Wong G. RNA-seq analysis: a practical approach. Chapman and Hall/CRC Computational Biology Series. 2014.ISBN-10:1466595000

In-depth bibliography

Specific bibliography for each unit will be provided through the course by each professor.

Journals

Other papers selected from important journals such as NATURE, SCIENCE, CELL, Molecular cell, EMBO J., NATURE GENETICS will be selected for reading and discussion.

Links

(1) NCBI databases https://www.ncbi.nlm.nih.gov



(2) EBI databases https://www.ebi.ac.uk/services



(3) USCS genome browser http://genome.ucsc.edu



(3.1.) UCSC Table Browser (within https://genome-euro.ucsc.edu/)



(4) Ensembl http://www.ensembl.org/



(5) Galaxy https://usegalaxy.org/



(6) SIFT, PolyPHEN (from within Galaxy) and wANNOVAR (wannovar.wglab.org/)



(7)PantherDB http://pantherdb.org/



(8)WebMeV (Multiple Experiment Viewer) http://mev.tm4.org/#/



(9)DAVID https://david.ncifcrf.gov/



(10)Babelomics http://www.babelomics.org/