| Study programme competencies |
| Code | Study programme competences |
| A1 | Skills of using usual techniques and instruments in the cellular, biological and molecular research: that are able to use techniques and instruments as well as understanding potentials of their uses and applications. |
| A3 | Skills of understanding the functioning of cells through the structural organization, biochemistry, gene expression and genetic variability. |
| A11 | Skills of understanding the structure, dynamics and evolution of genomes and to apply tools necessary to his study. |
| B1 | Analysis skills to understand biological problems in connection with the Molecular and Cellular Biology and Genetics. |
| B2 | Skills of decision making for the problem solving: that are able to apply theoretical knowledges and practical acquired in the formulation of biological problems and the looking for solutions. |
| B3 | Skills of management of the information: that are able to gather and to understand relevant information and results, obtaining conclusions and to prepare reasoned reports on scientific and biotechnological questions |
| B5 | Correct oral and written communication on scientific topics in the native language and at least in another International diffusion language. |
| B9 | Skills of preparation, show and defense of a work. |
| C3 | Skills of Using basic tools of the information technologies and communications (ICT) necessary to the exercise of his profession and for the apprenticeship over his life. |
| C8 | Considering the importance that the investigation has, the innovation and the technological development in the socioeconomic advance and cultural of the society. |
| Learning aims | |||
| Learning outcomes | Study programme competences | ||
| To learn the basics of the different molecular techniques used in genomics, with particular emphasis in NGS | AR1 |
BR1 BR5 |
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| To acquire an updated view about the current scope and future perspectives of structural, functional and evolutionary genomics | AR1 |
BR1 BR5 BR9 |
CC8 |
| To understand how genomes evolve and how molecular and bioinformatic tools are used for that purpose | AR1 AR3 AR11 |
BR1 BR2 BR9 |
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| DNA microarrays: experimental set up and data analysis. | AR3 |
BR1 BR2 BR3 |
CC3 |
| Contents |
| Topic | Sub-topic |
| Structural Genomics | Mapping, sequencing, annotation and databases The Human Genome Project Next Generation Sequencing (NGS) |
| Comparative Genomics | How do genomes evolve? |
| Genomes of Prokaryotes | Metagenomics |
| Genomes of Eukaryotes | Taxonomy Paleogenomics Medicine |
| Functional Genomics | DNA microarrays: methodology, types of platforms, experimental set up, data analysis |
| Computer lab | 1. Exploring databases (e.g. ENSEMBL) and large-scale genomic projects (ENCODE, EXOME, 1000Genomes) 2. Using GENEIOUS to assemble an organelle genome from NGS-generated data 3. Gene expression analysis and microarrays |
| Planning | ||||
| Methodologies / tests | Competencies | Ordinary class hours | Student’s personal work hours | Total hours |
| Guest lecture / keynote speech | A1 A11 B1 | 10 | 18.62 | 28.62 |
| Oral presentation | B5 B9 | 5 | 3 | 8 |
| Events academic / information | C8 | 1 | 3 | 4 |
| ICT practicals | A3 C3 | 10 | 20 | 30 |
| Objective test | B2 B3 | 2 | 0 | 2 |
| Personalized attention | 2.38 | 0 | 2.38 | |
| (*)The information in the planning table is for guidance only and does not take into account the heterogeneity of the students. | ||||
| Methodologies |
| Methodologies | Description |
| Guest lecture / keynote speech | Active lecturing. |
| Oral presentation | Each student will have to summarize in up to 15 minutes the content of a review paper. Readings assignments will be made available three weeks in advance via MOODLE. |
| Events academic / information | During the term, a seminar speaker, with expertise in Genomics, is invited as a guest lecturer. Students are required to attend this seminar and read the paper assigned (via MOODLE) for this activity. |
| ICT practicals | OUr 10-hour, computer lab curriculum was developed to accompany the lecture course in Genomics. The students work on their own web-based investigations and present their results to each other (active learnning). |
| Objective test | Written exam. |
| Personalized attention |
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| Assessment | |||
| Methodologies | Competencies | Description | Qualification |
| Guest lecture / keynote speech | A1 A11 B1 | Attendance and active learning. |
10 |
| Oral presentation | B5 B9 | Summarising and communication skills. |
20 |
| ICT practicals | A3 C3 | Attendance and active learning. Distance learning students will be required to submit a report, so that comprehension and performance may be assessed. |
10 |
| Objective test | B2 B3 | The exam will evaluate items discussed in the aforementioned activities. | 50 |
| Events academic / information | C8 | Attendance and participation in the final discussion. |
10 |
| Assessment comments | |||
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Mark "A with distinction" will only be awarded to outstanding students passing the subject in June. |
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| Sources of information |
| Basic |
McLachlan, G. J., Do, K-A., Ambroise, C (2004). Analyzing Microarray Gene Expression Data. Wiley-Interscience. John Wiley & Sons
Campbell, A.M & Heyer, L.J. (2007). Discovering Genomics, Proteomics & Bioinformatics. Pearson Benjamin Cummings
Bowtell, D., Sambrook, J. (2003). DNA Microarrays. Cold Spring Harbor Laboratory Press.
Allison, David B., et al (2006). DNA microarrays and related genomics techniques design, analysis, and interpretation of experiments. Chapman & Hall/CRC
E. Rinaldis, A. Lahm. (2007). DNA microarrays: current applications. Wymondham: Horizon Bioscience
Lesk, Arthur M. (2012). Introduction to Genomics. Oxford University Press |
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| Complementary |
Straalen, Nico M. van (2006). An introduction to ecological genomics. Oxford University Press
Zhanjiang, Liu (2007). Aquaculture genome techonologies. Blackwell
Futuyama, Douglas J. (2006). Evolution. Sinauer Associates
Dale Jeremy (2008). From genes to genomes: concepst and applications of DNA technology. John Wiley & Sons
Sensen, Christoph W. (2005). Handbook of genome research genomics, proteomics, metabolism, bioinformatics, ethical & legal issues . Wiley-VCH |
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RECURSOS EN INTERNET:
DOE Joint Genome Institut. Why sequence them? EMBL (European Molecular BIology Laboratory), Bioinformatics. ExPASy (Expert Protein Analysis System). GeneMark: GenomeNet (Kyoto University Bioinformatics Center). Genoscope. Le séquençage des génomes. GOLD (Genomes Online Database). Human genome: advanced annotation tutorial. http://www.mad-cow.org/00/annotation_tutorial.html Human Genome Project Information. http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml Iañez Pareja, E. (1997). Introducción a los Proyectos Genoma. KEGG (Kyoto Encyclopedia of Genes and Genomes). Nacional Human Genome Research Institute: NCBI (National Center for Biotechnology Information). The Sanger Institute. TIGR (The Institute for Genomic Research). tRNAscan-SE 1.21. The WWW Virtual Library: Model Organisms: ALGUNAS BASES DE DATOS DE MICROARRAYS DE ADN ArrayExpress http://www.ebi.ac.uk/arrayexpress/ ChipDB http://staffa.wi.mit.edu/chipdb/public/ ExpressDB http://twod.med.harvard.edu/ExpressDB/ Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/geo/ READ (RIKEN cDNA Expression Array Database) http://read.gsc.riken.go.jp/ Saccharomyces Genome Database (SGD) http://genome-www4.Stanford.EDU/cgi-bin/SGD/expression/expressionConnection.pl Standford Microarray Database ( SMD) http://genome-www5.stanford.edu/ The Yale Microarray Database http://www.med.yale.edu/microarray/ yeast Microarray Global Viewer (yMGV) http://www.transcriptome.ens.fr/ymgv/ |
| Recommendations | |||||
| Subjects that it is recommended to have taken before | |||||
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| Subjects that are recommended to be taken simultaneously | ||||
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| Subjects that continue the syllabus | |
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| Other comments | |