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Integrating Biology – The “Omics” World
October 31 - November 4
Isabel Marques Carreira (i_marques@hotmail.com)

Joana Barbosa de Melo (mmelo@fmed.uc.pt)
Ph.D. Programme in Experimental Biology and Biomedicine 2011/2012
Center for Neuroscience and Cell Biology (CNC)
University of Coimbra, Coimbra, Portugal

Course: Integrating Biology – The “Omics” World

Date: October 31- November 4, 2011

Isabel Marques Carreira (i_marques@hotmail.com)
Joana Barbosa de Melo (mmelo@fmed.uc.pt)

Isabel Marques Carreira, Faculdade de Medicina da Universidade de Coimbra
Joana Barbosa de Melo, Faculdade de Medicina da Universidade de Coimbra
Iola Duarte, CICECO, Universidade de Aveiro
Laura Carreto, CESAM, Universidade de Aveiro
José Pereira Leal, Instituto Gulbenkian de Ciência, Lisboa
Miguel Castelo-Branco, Faculdade de Medicina da Universidade de Coimbra
Carlos Fontes Ribeiro, Faculdade de Medicina da Universidade de Coimbra
Jildau Bouwman, TNO Quality of Life, the Netherlands

Laboratory Tutors:
Eunice Matoso, Faculdade de Medicina da Universidade de Coimbra
Luís Miguel Pires, Faculdade de Medicina da Universidade de Coimbra
José Ferrão, Faculdade de Medicina da Universidade de Coimbra
Susana I Ferreira, Faculdade de Medicina da Universidade de Coimbra

Topics to be addressed:
The complete sequencing of the human genome has lead to a new era of systems biology referred to as omics. The term omics refers to the comprehensive analysis of biological systems. A variety of omics subdisciplines have begun to emerge, each with their own set of instruments, techniques and software. Omics will not only have an impact on our understanding of biological processes, but the prospect of more accurately diagnosing and treating disease will soon become a reality.
This course will focus on different omics subdisciplines concerning human health issues, and how they could be integrated for an “Integrative Biology”.

Practical Day:
The students will perform a small experience in the Cytogenetics and Genomic Laboratory, at the Faculty of Medicine of University of Coimbra. At the end of the day, the students will discuss the results with colleagues, lecturers, tutors and coordinators.

Student’s Evaluation
Student’s Evaluation depends on 3 components:
1) At the end of each module, students will be asked brief fundamental questions (mini-exam).

2) The students, distributed in very small groups, will have to discuss an article (one article for student/course week) suggested by the coordinators/lecturers mentioning:
-    State of the art
-    Aims
-    Relevant Findings
-    Postulate the directions that the research presented in the article should take.

Each group has 20 minutes for presentation, followed by 10 minutes of discussion. All students must be prepared to ask questions to the presenting group. Both presentation (clarity, time, critical thinking) and discussion will be evaluated.

3) The performance of students during practical day work will also be taken into account.


Day 1 - 31st October 2011
9.00 - Introduction to the course (Isabel M Carreira e Joana B Melo)
9.15 – Genomics and Cytogenomics (Isabel M Carreira)
10.45– “Metabonomics in Health and Disease”, Iola Duarte
11.45 –"Monitoring gene expression regulation at the genome
scale: lessons from stressed yeast", Laura Carreto

14.30 – Articles presentation (2)
16.30 – mini-test

Day 2 – 2nd November 2011
9.00 – 15.30 - Practical Day/Hands on with resolution of clinical cases using cytogenomics/genomics tools (Joana B Melo)
    (Lunch break from 12.30-14.00)
15.30 – Discussion of results
16.30 – Brain storming over a “Cheese and Wine”!

Day 3 – 3rd November 2011
9.00 - Pharmacogenomics (Carlos Fontes Ribeiro)
10.00- Bioinformatic tools for “omics” (José Pereira Leal, Miguel Castelo-Branco)
11.30 - Articles presentation (2)

14.30- mini-test
15.00 - Examples of data integration in nutrigenomics studies (Jildau Bouwman)

Day 4 –4th November 2011
9.00 - Development of bioinformatics tools for nutrigenomics studies (Jildau Bouwman)
10.30 – Articles presentation (2)

14.00 - mini-test
15.00 –Open seminar: Personalized health; studies and methods (Jildau Bouwman)

Distribuição dos estudantes por Grupos de trabalho

Artigos a discutir:
Grupo A – Apresentação dia 31/10, 2ªfeira
Rocha et al., 2011, Metabolic Signatures of Lung Cancer in Biofluids: NMR-Based Metabonomics of Blood Plasma. J. Proteome Res. 10, 4314–4324.

Grupo B – Apresentação dia 31/10, 2ªfeira
Huiling et al., 2005, The role of microRNA genes in papillary thyroid carcinoma, PNAS, 102: 19075–19080.

Grupo C – Apresentação dia 3/11, 5ªfeira
Neill et al., 2011, Recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH. Genome Res. 21: 535-544.

Grupo D - Apresentação dia 3/11, 5ªfeira
Zabala-Fernández et al., 2010, A Pharmacogenetics Study of TPMT and ITPA Genes Detects a Relationship with Side Effects and Clinical Responsein Patients with Inflammatory Bowel Disease Receiving Azathioprine. +J Gastrointestin Liver Dis, 3: 247-253.

Grupo E – Apresentação dia 4/11, 6ªfeira
Bakker et al., 2010, An antiinflammatory dietary mix modulates inflammation and oxidative and metabolic stress in overweight men: a nutrigenomics approach. Am J Clin Nutr; 91:1044–59

Grupo F - (terá de apresentar dois artigos): Apresentação dia 4/11, 6ªfeira
van Ommen et al., 2009, Challenging homeostasis to define biomarkers for nutrition related health, Mol. Nutr. Food Res. 53, 795 – 804.
van Ommen et al., 2010, The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research. Genes Nutr 5, 285–296.

Grupos para o dia prático no Laboratório de Citogenética e Genómica na FMUC
Grupo I – A,B
Grupo II – C;D
Grupo III – E,F

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