Ordinary call: orientations and renunciation

Evaluation will be based on three points:

1) Attendance and participation in class (Class attendance will be mandatory)

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.



In the event that the sanitary conditions prevent the realization of a face-to-face evaluation, a non-face-to-face evaluation will be activated, of which the students will be informed promptly.

Extraordinary call: orientations and renunciation

In the extraordinary call, the final grade will be established in the same way as in the Ordinary Call.



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



In the event that the sanitary conditions prevent the realization of a face-to-face evaluation, a non-face-to-face evaluation will be activated, of which the students will be informed promptly.

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

Introduction to Proteomics. Methods of protein separation and quantification.



Unit 9

Mass spechtometry. Strategies for protein identification.



Unit 10

Bioinformatics in Proteomics.



COMPUTER PRACTICES



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

(2)Analysis of High Througput Sequencing data.

(3)SNPs: detection and genotyping.

(4)Statistical analysis of whole genome expression.

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

(6)Research in Proteomics.

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) A. MALCON CAMPBELL & LAURIE J. HEDER (2003): DISCOVERING GENOMICS, PROTEOMICS AND BIOINFORMATICS.. PEARSON EDUCATION, INC. BENJAMIN CUMMINGS, SAN FRANCISCO.

2) G. GIBSON AND S.V. MUSE. A PRIMER OF GENOME SCIENCE. (2004). SINAUER ASSOCIATES, INC.

3) AZUAJE, F., DOPAZO, J (EDS.). DATA ANALYSIS AND VISUALIZATION IN GENOMICS AND PROTEOMICS. (2005) 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) DC. LIEBLER. (2002): INTRODUCTION TO PROTEOMICS. TOOLS FOR THE NEW BIOLOGY.. HUMAN PRESS, TOTOWA, NEW YORK,

7) JAMES P. (2001): PROTEOME RESEARCH: MASS SPECTROMETRY. SPRINGER, BERLIN.

8) E. DE HOFFMANN & V. STROOBANT (2002): MASS SPECTROMETRY: PRINCIPLES AND APPLICATIONS. WILEY, CHICHESTER

In-depth bibliography

Specific bibliography 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/