Programme for Advanced Medical Education

Transcription

1 Programme for Advanced Medical Education 3rd Edition Faculty and Courses 1

2 PFMA 2010/ Courses Date Course Place Organizer October 1 Opening Lecture - Erna Möller IGC Leonor Parreira Seminar - Cecilia Náucler October 2-15 Gene Expression IMM João Ferreira October Structural Biology IGC José Leal October Cell cycle & Disease IGC Mónica Bettencourt-Dias November 1-5 Statistics FM-UP A. Teixeira Pinto November 8-12 Computational Biology IGC José Leal November Epidemiology IGC Isabel Silva November Genetics IGC C. Penha Gonçalves January 3-7 Pathogens & Hosts IGC Adriano Henriques January Cancer IPATIMUP Raquel Seruca January Neurocognitive Disorders IMM Tiago Outeiro/Rui Costa January Regenerative Medicine IMM Domingos Henrique January 31-February 4 Inflammation FCM-UNL Miguel Seabra February 7-11 Inflammation IMM Luis Graça February Scientific Integrity IMM João Lobo Antunes February Evolution & Medicine IGC Thiago Carvalho February Preparing for research IMM/IGC M. Trindade/Sheila Dias IGC -, Oeiras IMM - Instituto de Medicina Molecular, Lisboa FM-UP - Faculdade de Medicina, Universidade do Porto FCM-UNL - Faculdade de Ciências Médicas, Universidade Nova de Lisboa IPATIMUP - Instituto de Patologia e Imunologia Molecular, Porto 2

3 Faculty from International Institutions Patrick Varga-Weisz Paul Martin Ana Teresa Maia James Brenton Carla Martins Isabel Santos Silva Pablo Perel Frank Dudbridge Andrew Jackson Buzz Baum Tim Williams Sheik Tamir Rashid Robert Clarke Taane Clark Susana Campino Thomas Dan Otto Peter Jackson Ramana Madupu Yu-Hui Rogers Ted Weinert Jaroslaw Harezlak Roland Liblau Jamal Tazi Valerie McCormack Christian Muchardt Ivo Gomperts Boneca Patrick Aloy Guillermo Montoya Nuria Lpopez-Bigas Christine Mummery Ellen Nollen Geir Bjorkoy Fran Borovecki Alain Le Moine Babraham Institute, Cambridge, UK Bristol Univ, UK Cancer Research UK Cambridge Research Institute - UK Cancer Research UK Cambridge Research Institute - UK Cancer Research, UK London School of Hygiene & Tropical Medicine, UK London School of Hygiene & Tropical Medicine, UK London School of Hygiene & Tropical Medicine, UK MRC, Edinburgh, UK UCL, London, UK Imperial College, London, UK Univ. Cambridge, UK University of Manchester, UK Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK Genentech, California, USA J. Craig Venter Institute, USA J. Craig Venter Institute, USA Univ Arizona, USA Univ Indiana, USA INSERM, Tolouse, France Institut de Génètique Molèculaire, Montpellier, France International Agency for Research on Cancer, Lyon, France Institut Pasteur, Paris, France Institut Pasteur, Paris, France Institute for Biomedical Research, Barcelona, Spain CNIO, Madrid, Spain University Pompeu Fabra, Spain (courtesy of GTPB) Leiden Univ, Netherlands UMCG, Groningen, Netherlands University of Tromsø, Norway Zagreb Universtiy, Croatia Brussels, Belgium Faculty from National Institutions Albino Jorge Oliveira Maia Alekos Athanasiadis António Coutinho Carlos Penha Gonçalves Florence Janody 3

4 Isabel Gordo Isabel Marques Jorge Carneiro José Pereira-Leal Lars Jansen Lounes Chikhi Luisa Henriques Miguel Godinho Ferreira Miguel Soares Mónica Bettencourt-Dias Rui Martinho Sheila Vidal Sofia Braga Thiago Carvalho Vitor Barbosa Carlos Ribeiro Fundação Champalimaud Megan Carey Fundação Champalimaud Michael Orger Fundação Champalimaud Rui Costa Fundação Champalimaud Domingos Henrique Instituto de Medicina Molecular Francisco Enguita Instituto de Medicina Molecular J. E. Fonseca Instituto de Medicina Molecular Joana Cardoso Instituto de Medicina Molecular Joana Marques Instituto de Medicina Molecular João Eurico Fonseca Instituto de Medicina Molecular João Ferreira Instituto de Medicina Molecular João Lobo Antunes Instituto de Medicina Molecular Joaquim Ferreira Instituto de Medicina Molecular Luis F. Moita Instituto de Medicina Molecular Luis Graça Instituto de Medicina Molecular Margarida Trindade Instituto de Medicina Molecular Pedro Simas Instituto de Medicina Molecular Tiago Outeiro Instituto de Medicina Molecular Ana Pego INEB, Universidade do Porto Maria José Oliveira INEB, Universidade do Porto Ana Teresa Freitas INESC, Universidade Técnica de Lisboa Celso Reis IPATIMUP, Universidade do Porto Fátima Carneiro IPATIMUP, Universidade do Porto Fernando Schmitt IPATIMUP, Universidade do Porto Gabriela Almeida IPATIMUP, Universidade do Porto Hugo Osório IPATIMUP, Universidade do Porto Joana Paredes IPATIMUP, Universidade do Porto Jorge Lima IPATIMUP, Universidade do Porto Leonor David IPATIMUP, Universidade do Porto M. Sobrinho Simões IPATIMUP, Universidade do Porto 4

5 Paula Soares IPATIMUP, Universidade do Porto Raquel Almeida IPATIMUP, Universidade do Porto Raquel Seruca IPATIMUP, Universidade do Porto Valdemar Máximo IPATIMUP, Universidade do Porto Cláudia Lobato IST, Universidade Técnica de Lisboa Manuel Prieto IST, Universidade Técnica de Lisboa Adriano Henriques ITQB, Universidade Nova de Lisboa Claudio Gomes ITQB, Universidade Nova de Lisboa Karina B. Xavier ITQB, Universidade Nova de Lisboa Luís Jaime Mota ITQB, Universidade Nova de Lisboa A. Sousa Guerreiro CEDOC, Universidade Nova de Lisboa Ana Gomes CEDOC, Universidade Nova de Lisboa José Delgado Alves CEDOC, Universidade Nova de Lisboa Miguel Seabra CEDOC, Universidade Nova de Lisboa A. Vaz Carneiro FM-Universidade de Lisboa Margarida Gama Carvalho FC-Universidade de Lisboa Carlos Farinha FC-Universidade de Lisboa Ana Cristina Rego CNC, FM-Universidade de Coimbra Jorge Pacheco Dep Física, Universidade do Minho Victor Gil H. Fernando da Fonseca M. Miguel Rosa H. Santa Maria Manuel Abecassis IPO-Lisboa Sergio Dias IPO-Lisboa Pedro Marques da Silva C. Hospitalar Lisboa Centro 5

6 1. GENE EXPRESSION, October, 1-15, 2010 Organized by João Ferreira, IMM/FML, Lisbon Aims: To learn the basics of gene expression and how gene expression is studied. To be initiated in the skills of: scientific reasoning; translating questions into experiments; identifying a good question and turn it into a research proposal To learn how to read and present a scientific article To see the research done at the IMM Method: Overview lectures by invited speakers and Faculty; seminars and tutorials; visits to labs and talking with scientists in their environment; presentations of research articles; research proposals. FACULTY João Ferreira - IMM / FML Luis F. Moita IMM / FML Margarida G Carvalho FML/FCUL Carlos Farinha - FCUL Francisco Enguita IMM / FML Joana Cardoso - IMM Jamal Tazi - Institut de Génètique Molèculaire, Montpellier Patrick Varga-Weisz, Babraham Institute, Cambridge Christian Muchardt Institut Pasteur, Paris Schedule: 1 st October (Fri) Morning: Introduction to the Programme (IGC, Oeiras). 12:00 Erna Moller (Karolinska Institutet, Stockholm). Translational medical research what is it really about? Cecilia Naucler (Karolinska Institutet, Stockholm) (seminar ans discussion) 2 nd October (Sat) Morning and afternoon: seminar sessions by João Ferreira (IMM, Lisbon). 6

7 Topics: Introduction to the gene expression module. A primer on gene expression. How gene expression is studied. Transcription in eukaryotes, basal and regulated. Relevance of the chromatin template. After genes are transcribed what happens to their messages. How gene messages are interpreted by the cell and how they influence cell functioning. 4th October (Mon) Morning: seminar sessions by João Ferreira (IMM, Lisbon) Noon: attendance of IMM seminar Lunch at IMM with an IMM group leader Afternoon: visit to IMM labs; preparation of selected articles for presentation 5 th October (Tue) Morning: Discussions related to presentation of selected articles Lunch at IMM Afternoon: Presentation of selected articles by the students 6 th October (Wed) Morning: Free discussions and thinking about a project theme Lunch at IMM with an IMM group leader Afternoon: Presentation of selected articles by the students 7 th October (Thu) Morning: Scientific reasoning; the process of raising and maturing a scientific question. Session with two group leaders. Lunch with an IMM group leader/staff scientist Afternoon: Gene expression overview and sum-up, João Ferreira (IMM, Lisbon) Preparation of articles for presentation 8 th October (Fri) Morning: Margarida Gama Carvalho (Faculty of Medicine and BioFig - Faculty of Sciences, Lisbon). Splicing and how gene expression is coordinated (tutorial). Noon: Seminar (IGC or IMM) Lunch (IGC or IMM) with Margarida Carvalho Afternoon: presentation of selected articles by the PFMA students. 11 th October (Mon) Morning: Carlos Farinha (Faculty of Sciences, Lisbon). Protein folding and modification (tutorial) 7

8 Lunch at IMM with Carlos Farinha Afternoon: Presentation of selected articles by the PFMA students 12 th October (Tue) Morning: 09:30-12:00 Francisco Enguita and Luis Moita (IMM/FML, Lisbon), Regulation of gene expression by RNAs (tutorials). Noon: students attend the Monday IMM seminar Lunch at IMM with F. Enguita and L. Moita Afternoon: 14:30-17:00 Francisco Enguita (IMM/FML, Lisbon), micrornas and their targets in silico analysis (practical); Joana Cardoso (IMM, Lisbon), Large-scale approaches to the study of gene expression (tutorial) Preparation of articles for presentation 13 th October (Wed) Morning: 09:30-12:00 Jamal Tazi (Institut de Génétique Moléculaire, Montpellier), Splicing and disease (tutorial) Lunch at IMM with Jamal Tazi Afternoon: 14:30-16:30 Presentation of selected articles by the PFMA students Students discuss with Jamal Tazi their ideas for research proposals Preparation of articles for presentation 14 th October (Thu) Morning: 09:30-12:00 Patrick Varga-Weisz (Babraham Institute, Cambridge). Chromatin states and gene expression (tutorial) Lunch at IMM with Patrick Varga-Weisz Afternoon: 14:30-16:30 Presentation and discussion of selected articles Students discuss with P. Varga-Weisz their ideas for research proposals Preparation of individual research proposals 15 th October (Fri) Morning: 09:00-11:30 Presentation research proposals by the PFMA students Noon: Christian Muchardt (Institut Pasteur, Paris), Keynote lecture (Role of Chromatin in Gene Expression; title may be altered) Lunch at IMM with Christian Muchardt Afternoon: 15:00-16:00 Presentation of research proposals by the PFMA students 8

9 Concluding remarks and legacy of the module, João Ferreira Night: Farewell dinner in a Lisbon restaurant e.mail addresses: 1. Jamal Tazi: [email protected] 2. Patrick Varga-Weisz: [email protected] 3. Chriatian Muchardt: [email protected] 2. Structural Biology, October, 18-22, 2010 Organized by José Pereira-Leal, IGC Faculty: Guillermo Montoya, CNIO, Spain Francisco Enguita, IMM Claudio Gomes, ITQB Nuno Palma, BIAL, PT Alekos Athanasiadis, IGC Maria Luisa Rodrigues, IGC Bruno Victor, ITQB Jose Pereira-Leal, IGC Schedule: Monday 10:30-12:30 - Protein Structure - Francisco Enguita 14:00-15:30 - Protein evolution - Jose Pereira-Leal 16:00 - tba Tuesday 09:30-10:30 - RNA Structure - Francisco Enguita 10:30-11:30 - Tools and databases - Jose Pereira-Leal 9

10 12:00-13:00 - IGC seminar 14:00-17:00 - Visualisation Practical Wednesday 09:30-10:15 - Basic principles of protein Folding and structure - Claudio Gomes 10:30-11:00 - Protein Folding in the Cell - Claudio Gomes 11:15-12:00 - Diseases of protein folding: Protein misfolding, aggregation and amyloids - Claudio Gomes 12:15-13:00 - Research Seminar: highlights from the lab - Claudio Gomes 14:30-17:30 - JOURNAL CLUB (with JPL, FE, AA) Thursday 10:00-12:00 - On the recognition of foreign nucleic acids by innate immunity - Alekos Athanasiadis 14:00-16:00 - Methods to study protein structures - Guillermo Montoya 17:00-18:30 - Meeting with António Coutinho Friday 10:00-12:00 - Homing endonucleases: from basics to therapeutic applications - Guillermo Montoya 12:00-13:00 - IGC seminar 14:00-16:00 - in-silico strategies in drug design - Nuno Palma 16:00-17:00 - PROJECT 17:00 - Beer in the rain Journal club papers: (30 min presentation + discussion per group) Dunkle, J.A., Xiong, L., Mankin, A.S. and Cate, J.H. Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyltransferase center explain spectra of drug action. Proc Natl Acad Sci U S A. Yamasaki, M., Li, W., Johnson, D.J. and Huntington, J.A. (2008) Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization. Nature, 455, Lee et al. Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. Cancer Research (2010) vol. 70 (12) pp Cígler et al. From nonpeptide toward noncarbon protease inhibitors: metallacarboranes as specific and potent inhibitors of HIV protease. Proc Natl Acad Sci USA (2005) vol. 102 (43) pp

11 3. Cell Cycle, Cytoskeleton & Disease, October, 25-29, 2010 Organized by Mónica Bettencourt-Dias, IGC Mon 25 Oct Cytoskeleton: tubulin & actin 09:30 10:00 Introduction to Course by Monica Bettencourt Dias (IGC). 10:00 11:30 Buzz Baum (UCL)- Tubulin & Actin cytoskeleton. 12:00 13:00 Buzz Baum Seminar -Cell shape through the cell cycle. 13:00 14:30 Lunch with Buzz Baum and Florence Janody. 14:30 15:30 Florence Janody (IGC)-Flies, actin and cancer. 15:30 17:30 Project challenge-monica Bettencourt Dias & Buzz Baum & Florence Janody No Preparation Needed. 17:30 18:00 Papers & guidelines for journal clubs- divide in 4 teams: 2 author teams; 2 reviewer teams. Tue 26 Oct Mitosis 09:30 11:30 Mitosis- Helder Maiato (IBMC). 12:00 13:00 Institute Internal Seminar. 13:00 14:30 Lunch with Lars Jansen, Helder Maiato & Rui Martinho :30 Lars Jansen- Centromeres and Epigenetics. 15:30 16:30 Rui Martinho - Flies in Medical Research Journal Club preparation. Wed 27 Oct Cell Cycle Basis & Checkpoints 09: Ted Weinert- Checkpoints, a Brief History and What s "New" Discuss papers in small groups (3 or 4 per group, 3 groups). (Preparation needed) 12:00 13:00 Ted Weinert s seminar- Repeats, Dicentrics and Genome Instability: Lessons from Yeast. 13:00 14:30 Lunch with Ted Weinert & Miguel Godinho & Vitor Barbosa. 14:30-17:00 Ted Weinert- Paper Presenting & Speed Dating. 11

12 (Preparation needed). 17:15 18:00 Vitor Barbosa Meiotic Checkpoints in Metazoans. 18:00 18:45 Miguel Godinho - Chromatin & Telomeres. Thu 28 Oct Cytoskeleton: Centrosomes and Human diseases 09:30 10:30 MonicaBDias- Centrosomes & Cell Cycle. 10:45 11:45 Andrew Jackson- centrosomes and human disease. 12:00 13:00 Andrew Jackson seminar -Cellular Pathways determining brain size. 13:00 14:30 Lunch with Andrew Jackson & Monica. 14:30-16:00 Journal Club Preparation Journal Club 2-Andrew & Monica & more discussion with Andrew (Preparation needed) :00 Carla Martins- Signalling and cancer. 19:30 21:30 PUT IN DIARY! Course Dinner in Solar do Marques sponsored by City Council. Fri 29 Oct Cell Cycle & Protein Degradation & Cilia Diseases 09:30 11:45 Peter Jackson - Cell Cycle in Cancer 45 minutes; Cilia and Human Disease 45 minutes; Biotech: What we do, how it differs from Academia, and how it fits in to the big picture. 45 minutes 12:00 13:00 Peter Jackson seminar -How The Cell Smells: Organizing Signaling within Primary Cilia 13:00 14:30 Lunch with Peter Jackson 14:30 15:30 Journal Club 3-Peter Jackson (Preparation needed) 15:30 18:00 Check Things in Labs - students divided in groups and see experimental approaches in different IGC groups Lars Jansen; Victor Barbosa; Miguel Godinho & Monica B Dias Journal Club Papers & Activities Monday: Project proposals. No preparation needed. Three groups of 3 or 4 each discuss a scientific observation, define a hypothesis, identify experiments and propose a project. 12

13 Observations: 1-Gastric tumors have in common that all express very high levels of the isoforms 1 and 2 of Tropomyosin 5. However, it is not known whether increased levels of those isoforms have any role in tumoral development. Tropomyosins are a family of closely related proteins present in muscle and nonmuscle cells. In striated muscle, tropomyosin mediates the interactions between the troponin complex and actin so as to regulate muscle contraction. The role of tropomyosin in smooth muscle and nonmuscle tissues is not clear. 2-Patients with Wiskott-Aldrich syndrome develop eczema, thrombocytopenia and immunodeficiency. Patients lack the WASP protein, which favors nucleation of branched actin filaments. However, it is not known whether this syndrome is a direct consequence of deficient actin organization in haematopoetic cells. 3-Cell division is coordinated with adhesion. It is not known whether a cell dividing into two daughter cells outside of its normal microenvironment may encounter problems (implications for cancer metastasis). Wednesday: Session 1AM Checkpoints, a Brief History and Whats "New"; I will present a <1 hr perspective in 5 brief parts": 1. earliest ideas: phage, caffeine, rad9; 2. Checkpoints are general...and relevant: spindle checkpoint, ATMp53; 3. Current View and Cool Facts: DNA damage/replication checkpoints; 4. Digression: Bars and Arrows Considered; 5. What's "new": Affect on Replication Forks Session 2AM Discuss papers in small groups (3 or 4 per group, 3 groups) Each group of 3 or 4 will have read and "digested" the paper(s) in their group. During this session 2, each group meets and discusses amongst themselves what the paper meant, and then how to present key elements to their fellow students who have NOT read the paper. During each presentation, first someone from the group summarizes, on the board, the key question and ideas and findings. Then, a few key figures are presented, to give the listeners a feeling for the types of data behind the ideas and models. This is a lesson in how to understand your paper, and then how to make it sound simple to others. 1. Davoli, Denchi, de Lange Persistent. Telomere Damage Induces Bypass of Mitosis and Tetraploid. Cell 141, Ana Sadio; Jorge Ruivo; Patrícia Costa Reis 2. a. Gorgoulis, et al. Activation of the DNA damage checkpoint and genome instability in human precancerous lesions. Nature 434, b. Bartova, Bartek et al. DNA damage response as a anti-cancer barrier in early human tumorigenesis. Nature 434, Joaquim Alves da Silva; Ricardo Rodrigues Pinto; Ana Rita Matos; Dulce Alfaiate 3. Nicklas, B. How Cells Get the Right Chromosomes Science 275, Luís Rocha Lopes, Assunção Tuna, Eva Serrão Session 3 PM. Each subgroup will present their paper to the rest of the group. 20 minutes each. Session 4PM. Speed dating. Papers: Each person will have found a paper in the literature that they think is just very cool. 13

14 It can be on anything...the bigger the picture and the cooler the story, the better. They will have read it, of course, and have two pieces of paper; One is a model of what the paper says, and the second is key data from that paper. The topics can be literally on anything, from signaling systems to genome sequence of human diseases to details of a biological process. In this hour, we will pair off, and each person explains their story to the other person in ~8 min or so (<10 min). Every 20 minutes, we switch partners and do it again, x 3. Thursday Journal club- Authors vs. Referees One paper presented by one group and reviewed by another group. Group Presenting- Luís Rocha Lopes; Assunção Tuna; Eva Serrão Group Refereeing- Ana Sadio; Jorge Ruivo; Paper- Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Bilgüvar K, Oztürk AK, Louvi A, Kwan KY, Choi M, Tatli B, Yalnizoğlu D, Tüysüz B, Cağlayan AO, Gökben S, Kaymakçalan H, Barak T, Bakircioğlu M, Yasuno K, Ho W, Sanders S, Zhu Y, Yilmaz S, Dinçer A, Johnson MH, Bronen RA, Koçer N, Per H, Mane S, Pamir MN, Yalçinkaya C, Kumandaş S, Topçu M, Ozmen M, Sestan N, Lifton RP, State MW, Günel M. Nature Sep 9;467(7312): Epub 2010 Aug 22. Friday Journal club: One paper presented by one group and reviewed by another group. Group Presenting- Patrícia Costa Reis; Joaquim Alves da Silva; Ricardo Rodrigues Pinto Group Refereeing- Ana Rita Matos; Dulce Alfaiate Paper- A core complex of BBS proteins cooperates with the GTPase Rab8 to promote ciliary membrane biogenesis.nachury MV, Loktev AV, Zhang Q, Westlake CJ, Peränen J, Merdes A, Slusarski DC, Scheller RH, Bazan JF, Sheffield VC, Jackson PK. Cell Jun 15;129(6): Suggested General Books Pollard, T.D. and Earnshaw, W.C. (2007) Cell Biology. Second Edition. W.B. Saunders, New York, NY. David Morgan. The Cell Cycle. Principles of Control. Oxford University Press. Alberts et al, Molecular Biology of the Cell, Garland Science External Faculty Buzz Baum- 14

15 Ted Weinert- Helder Maiato- IBMC (Porto, Portugal) Carla Martins- Andrew Jackson- Peter Jackson- Genentech, Californiahttp:// rsrchonc/cellreg/jackson/profile.html Internal (IGC) faculty: Monica Bettencourt Dias- Centrosomes & Cell Cycle-IGChttp://sites.igc.gulbenkian.pt/ccr/ Miguel Godinho Ferreira- Telomeres and Genome Stability Florence Janody-Actin Cytoskeleton & Cancer- IGChttp:// Lars Jansen- Centromeres & Epigenetics- IGChttp:// Rui Martinho- Early Fly Development- IGChttp:// Vitor Barbosa- Meiosis & Development- IGChttp:// 4. Statistics, November, 1-5, 2010 Organized by Armando Teixeira Pinto, Faculdade de Medicina-Universidade do Porto; Instructor: Armando Teixeira-Pinto Classes: 6 hours daily for 1 week (mixed theoretical and lab sessions) Grading: Final exam (16 out of 20 points) Assignments (4 out 20 points) Jaroslaw Harezlak Univ Indiana, USA OBJECTIVES: In this course we will be studying basic methods of descriptive and inferential statistics commonly used in health research. No previous knowledge of statistics is required. There will be a strong emphasis on the application of these methods to real data problems. Classes will be supported by the statistical software SPSS and students will be using individual computers during the course. After each session, there will be a mandatory assignment due the day after. At the end of the course, students should be able to recognize situations where the statistical methods covered in the course can be applied; understand and verify their assumptions; interpret the results; and be able to critique the statistical section and results in medical literature. COURSE TOPICS: 1. Data: types of data; data entry; data management. (1h+1h) 15

16 2. Descriptive statistics: Frequency tables, summary measures (location and dispersion); data presentation (tables and graphs). (1:30h+1h) 3. Normal distribution and other theoretical distributions. (1h) 4. Distribution of sample statistics and confidence intervals: Central limit theorem and the distribution of the sample mean, standard error of the mean, confidence intervals for the mean, confidence intervals for proportions. (2h+1h) 5. Hypothesis testing: parametric tests (t test, One-Way ANOVA); non-parametric tests - Mann-Whintey, Kruskal-Wallis, Wilcoxon and qui-square tests. (4h+3h) 6. Statistical power and sample size calculation. (1h) 7. Diagnostic Tests (extra topic): Bayes theorem, sensitivity, specificity, likelihood ratio, false positives, false positives, ROC curves. (2h+1h) 8. Correlation and simple linear regression: Pearson and Spearman correlation coefficients, the linear model assumptions, interpretation of the regression parameters, inference on the parameters estimates, model checking. (2:30h+1h) 9. Basics of multiple linear regression: interpretation of the regression parameters model building. (2h+1h) 10.Introduction to logistic regression: the logit link, interpretation of the regression parameters. (2h+1h) 11.Introduction to Survival Analysis (extra topic): survival tables, Kaplan-Meyer estimator, log rank test. (2h+1h) Bibliography: (required) Pagano, Marcello; Gauvreau, Kimberlee. Princípios de bioestatística. São Paulo: Pioneira Thomson Learning, p. Swinscow,T D V. Statistics at Square One (available at ( 5. Computational Biology, November, 8-12, 2010 Organized by José Pereira-Leal, IGC Faculty Patrick Aloy - Institute for Biomedical Research - ES James Brenton - Cancer Research UK Cambridge Research Institute - UK 16

17 Sofia Braga - - PT Ana Teresa Maia - Cancer Research UK Cambridge Research Institute - UK Isabel Gordo - - PT Jorge Carneiro - - PT Ana Teresa Freitas - INESC-ID - PT Ramana Madupu - J. Craig Venter Institute, USA Yu-Hui Rogers - J. Craig Venter Institute, USA Jose Pereira-Leal - - PT Schedule: Monday 9:30-10:30 - Introduction - J.Pereira-Leal 11:00-13:00 - tba - P. Aloy 14:00-15:00 - tba - N. Lopez-Bigas 15:00-16:00 - Evolutionary genomics of pathogenic bacteria - J.Pereira-Leal 16:30-17:30 - Evolutionary vell biology of microtubule-derived organelles- J. Pereira-Leal Tuesday 9:00-10:00 - A PhD project in Computational Oncology - Sofia Braga 10:00-12:00 - tba - A.T. Maia 14:00-16:00 - tba - J. Brenton Wednesday 10:00-12:00 - tba - I.Gordo 16:00-18:00 - Journal Club Thursday 9:30-11:00 - Information systems for human disease - A.T. Freitas 11:30-13:30 - tba - J. Carneiro 15:00-16:00. Journal Club 16:00-18:00 - Your favorite disease... in silico; in omics Friday 9:00-10:20 - tba - YH Rogers 17

18 10:30-12:00 - tba - R. Madupu 12:00 - IGC seminar 14:00-17:00 - PhD thesis discussion in evolutionary cell biology (Zita Santos) 17:00 - Seminar Wallace Marshal 19:00 - Dinner 6. Epidemiology, November, 15-19, 2010 Organized by Isabel Santos Silva, London School of Hygiene & Tropical Medicine Date / Time Session title Lecturer Monday, 15 th Nov Introduction to the course: general aims and programme ISS/VM Epidemiology: the scientific foundation of Public Health ISS Break Exposure and outcome measurement VM Lunch Overview of study designs ISS Practical 1: Study designs VM Break Grant application exercise 1: Defining a question VM/ISS Tuesday, 16 th Nov Measures of occurrence and measures of association VM Break Intervention studies ISS Cohort studies ISS Lunch Analyses of Intervention and Cohort studies VM Practical 2: Cohort studies VM 18

19 Break Grant application exercise 2: Literature review ISS/VM Wednesday,17 th Nov Case-control studies VM Analysis of case-control studies VM Break Practical 3: Case-control studies VM Lunch Interpretation of epidemiological data I: Random errors, bias ISS Interpretation of epidemiological data II: Confounding, causality ISS Break Grant application exercise 2: Choice of study design ISS/VM Thursday,18 th Nov Systematic reviews & meta-analysis I PP Break Systematic reviews & meta-analysis II PP Lunch Systematic reviews & meta-analysis - III PP Break Grant application exercise 3: Finalising outline protocol Deadline for submission of outline protocol ISS/VM /PP Friday,19 th Nov Introduction to molecular and genetic epidemiology ISS Break Mendelian randomisation and causation ISS Grant application exercise 4: Finalising oral presentations VM/ISS Lunch Grant application exercise 5: Oral presentations & Feedback VM/ISS 19

20 Break Course evaluation 7. Genetics, November, 22 24, 2010 Organized by Carlos Penha Gonçalves, IGC Monday, 22 November Genetics, genomic variation and technologies. Introduction to genetic epidemiology Genetic epidemiology, linkage disequilibrium and genome-wide association studies (GWAS) Practical: Power calculations; linkage disequilibrium (Haploview); GWAS in a case control setting point Practical: GWAS (plink) Lecture: Fine-scale mapping Feed-back from participants Tuesday, 23 November Lecture:Family-based analysis, heritability and association Practical: Association analysis using affected offspring - parental trios GWAS for trios (plink) Lecture: Emerging areas in genetic epidemiology. Gene environment interactions, Mendelian randomization; Multiple testing and risk prediction Gene-environment interactions (plink) Feed-back from participants Wednesday, 24 November Lecture: Bioinformatics of next sequencing technologies Practical: Bioinformatics: analysis of sequence data (genomics) Practical: Bioinformatics: analysis of sequence data (RNA-seq) Practical: Bioinformatics: data access and web tools Feed-back from participants Thursday, 25 November Lecture: Population genetics I 20

21 Lecture: Population genetics II Practical: genotyping project: study case Lecture: animal models of complex traits Feed-back from participants Friday, 25 November Journal Club Journal Club General Discussion Faculty: Taane Clark (UK) Susana Campino (Hinxton, UK) Lounes Chicki (IGC) Frank Dudbridge (UK) Thomas Dan Otto (UK) Isabel Marques (IGC) Carlos Penha-Gonçalves (IGC) 8. Pathogens & Hosts, January, 3-7, 2011 Organized by Adriano O. Henriques, ITQB, UN-UL Course topics and lecturers (IGC) Seminars (To be held during the morning, starting at 9am) Seminar Lecturer Topics Date sessions 1 AOH The new bacterial cell biology; cell shape plasticity and the evading of the host innate immunity; sporeformers, probiosis and pathogenesis. 3/1 2 KX Quorum sensing: its role in bacteria-host interactions. 4/1 21

22 3 LJM Mechanisms involved in epithelial cell invasion by enteric pathogens; induction of intestinal inflammation by virulence proteins of enteric pathogens. 4 PS Viral pathogenesis: herpesvirus/b-lymphocyte interactions 5 IGB The biology of Helicobacter pylori; the role of peptidoglycan in host-microbe interactions. 5/1 6/1 7/1 Presentation and discussion of articles in the afternoon; exact schedule to be arranged with the speakers. AH Dr. Adriano Henriques, Microbial Development Group, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa; Phone: (+351) ; [email protected]. KX Dr. Karina B. Xavier, Bacterial Signalling Group, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa and ; Phone: (+351) ; [email protected], [email protected]. LJM Dr. Luís Jaime Mota, Infection Biology Group, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa; Phone: (+351) , [email protected]. PS Dr. Pedro Simas, Viral Pathogenesis, Immunology and Infectious Diseases, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa; Phone: (+351) ; [email protected]. IGB Dr. Ivo Gomperts Boneca, Biology & genetics of the bacterial cell-wall, Department of Microbiology, INSTITUT PASTEUR; Phone: (+33) ; [email protected]. 9. Oncobiology, January, 10-14, 2011 Organized by Raquel Seruca, IPATIMUP, Porto The structure of the module: In this module (10-14 January) students have lectures and work in research projects in the afternoon. The aims of the module: The Oncobiology module will have sessions to discuss biological/molecular mechanisms of cancer development and progression. All sessions will be based on the discussion of clinical cases followed by open discussions with the students about the underlying aetiological factors and the biological pathways underlying pathological lesions. All sessions will have a common structure that should follow (if possible) this scheme, in order to discuss the hallmarks (biological properties) of cancer. 22

23 1- Presentation of clinical cases (sporadic and hereditary) 2- Pathological aspects of the tumours 3- Aetiology and molecular basis of the disease Teachers: Senior Researchers and Professors at IPATIMUP and postdoc Students. In 2011 we will have the collaboration of Maria José Oliveira (INEB) Doctor Robert Clarke (University of Manchester, UK), Geir Bjorkoy (University of Tromsø, Norway), Arsénio Fialho (IBB-IST), and Sergio Dias (IPO-Lisboa) in the scientific program of the module. 10 January Morning: Documents and structure of the module (R Seruca) Introduction to oncobiology (M Sobrinho-Simões) Meeting with the PIs of the projects Afternoon: Cancer proliferation, apoptosis and metabolism Coordination: Paula Soares Participants: Valdemar Máximo, Jorge Lima projects 11 January Morning: Cell and tissue differentiation Coordination: Leonor David Participants: Raquel Almeida, Celso Reis, Hugo Osório Afternoon: projects 12 January Morning: Cell invasion and metastization Coordination: Raquel Seruca Participants: Fátima Carneiro, Fernando Schmitt, Sérgio Dias Afternoon: projects 23

24 13 January Morning: Microenvironment, EMT and cancer stem cells Coordination: Joana Paredes Participants: Maria Oliveira, Gabriela Almeida, Robert Clarke Afternoon: projects 14 January Morning: Cancer therapeutic tools Coordination: Raquel Seruca Participants: José Carlos Machado, Geir Bjorkoy and Arsénio Fialho Afternoon: Presentation of the projects and general discussion. 10. Neurodegenerative and Psychiatric Disorders, January, 17-21, 2011 Organized by Rui Costa (Fundação Champalimaud) and Tiago Fleming Outeiro(IMM) Monday 17th 9.00 Introduction (Tiago Outeiro, Rui Costa) 9.30 Protein folding: a tale from the beginning (Tiago Outeiro) Mitochondria and Neurodegeneration (Ana Cristina Rego) Mitochondrial dysfuntion in Huntington s disease (Ana Cristina Rego) Tuesday 18th 9.00 Parkinson s Disease as a human disease model to practice clinical neuropharmacology (Joaquim Ferreira) Genomic approaches for the study of HD Fran Borovecki Wednesday 19th 9.30 C. elegans as a model to study neurodegenerative disorders Ellen Nollen Understanding circuit disability in Parkinson s Disease and Compulsion (Rui Costa) 24

25 17.00 Lisbon Area Neuroscience Meeting Thursday 20th 9.30 Senescence in zebrafish models (Miguel Godinho Ferreira) Eating and obesity (Albino Jorge Oliveira Maia and Carlos Ribeiro) Friday 21st 9.30 Cerebellar Function (Megan Carey) Zebrafish to study Neural Function (Megan Carey) Fictive grant presentations and discussion Faculty: Tiago Outeiro, IMM Rui Costa, Fundação Champalimaud Ana Cristina Rego Joaquim Ferreira, Hospital de Santa Maria Fran Borovecki Ellen Nollen Miguel Godinho Ferreira Albino Jorge Oliveira Maia Carlos Ribeiro Megan Carey 11. Regenerative Medicine. From Biology to the Clinic, January, 24-28, 2011 Organized by Domingos Henrique, FML/IMM AIMS: To present and discuss the most recent developments in the area of stem cell biology, from the generation of embryonic stem cells to the isolation and characterization of various adult stem cells. In addition, various approaches to stem cell-based therapies will be discussed, with a critical evaluation of the field and future perspectives. 25

26 FACULTY Domingos Henrique, FML/IMM Sheik Tamir Rashid, Cambridge, UK Manuel Abecassis, IPO Lisbon Jorge Pacheco, Physiscs Dept., Braga University Ana Pego, INEB Porto Joaquim Cabral, IST Lisbon Claudia Lobato, IST Lisbon Paul Martin, Bristol University, UK Christine Mummery, Leiden University, Netherlands This Course will include Seminars by the invited speakers, followed by general discussion of the topics, and some Journal Club discussions, led by the students. Sessions will start at 9 or 10am and finish by 6pm. Monday MORNING Domingos Henrique (Introduction to Stemness) AFTERNOON Tamir Rashid (Cambridge UK) Tuesday Tamir Rashid Journal Club Wednesday Thursday Friday Manuel Abecassis (IPO Lisboa) Jorge Pacheco (Univ. Braga) Cláudia Lobato/Joaquim Cabral (IST) Paul Martin Wound Healing Christine Mummery Stem Cells and Heart Regeneration Ana Paula Pego (INEB Porto) WEBSITES FOR SPEAKERS: (Ludovic Vallier s Lab, where Tamir is working)- see also

27 mcellsportal.com/featured-labs/dr-christine-mummerys-lab.html 12. Inflammation and immune mediated inflammatory diseases, January 31 March 4, 2011 Organized by Luis Graça, IM; Monday, January Introduction to course, Luis Graca (IMM) Inflammation, Lecture to students, Miguel P. Soares (IGC) Research Seminar: Regulation and Privilege in Therapeutic Tolerance, Roland Liblau (INSERM, Toulouse) Discussion on neuro-inflammation paper presentation, Roland Liblau and Luis Graca. Tuesday, February Transplantation, Lecture to students, Alain Le Moine (Brussels) Research Seminar: Neonatal tolerance under breastfeeding influence, Alain Le Moine Discussion on transplantation, Alain Le Moine and Luis Graca. Wednesday, February Immune tolerance in pathology and therapy, Lecture to students, Luis Graca Journal Club, student presentations of selected papers and discussion, Luis Graca and Alain Le Moine. Thursday, February Inflammatory joint disease, Lecture to students, João E. Fonseca IMM weekly immunology seminar Journal Club, student presentations of selected papers and discussion, João E. Fonseca and Luis Graca. Friday, February 4 Free to prepare the following week s Inflammation module. 27

28 13. Chronic Inflammation and Immunomodulation, February, 7 11, 2011 Organized by Miguel Seabra, Faculdade de Ciências Médicas, Universidade Nova de Lisboa Attendees: Gulbenkian Programme for Advanced Medical Education 10 InterUniversity Programme in Ageing 4 PhD Programme of Medical School (FCM) 18 Given the number of students, the course will comprise plenary sessions for all participants (noted as (P)) and small group teaching (divided in 2 groups) Staff: Faculty Miguel Seabra, CEDOC (course director) (MS) Tim Williams, Imperial College London (TW) Antonio Coutinho, IGC (AC) Antonio Sousa Guerreiro, CEDOC (ASG) Miguel Soares, IGC (MSo) José Delgado Alves, CEDOC (JDA) Adriano Oliveira Henriques, ITQB (AOH) Luís Graça, IMM (LG) Pedro Marques da Silva, CHLC (PMS) Victor Gil (HFF, EPE)(VG) Ana Gomes (CEDOC) (AG) Other staff from CEDOC MONDAY, 7th FEBRUARY BIOQ Introduction to the course (MS) Inflammation, GI tract and gut microbiota BIOQ. (AOH) Coffee Break BIOQ. Journal Club Preparation Lunch 28

29 BIOQ. Journal Club Presentations (Students) BIOQ Microbiota and Energetic Metabolism (PMS) Coffee Break BIOQ : Microbiota and Metabolic Endotoxemic (ASG) BIOQ Microbiota Modulation by Nutraceutics and Non-Alcoholic Steatohepatitis (ASG) TUESDAY, 8th FEBRUARY Inflammation in Vascular Disease; Mechanisms, Models, Open Questions BIOQ. Introduction (JDA) BIOQ. Vascular Disease and Chronic Inflammation (JDA) Coffee Break BIOQ. Hot topics in Cardiovascular Disease (VG) BIOQ. Pleiotropism in Cardiovascular Diseases Therapeutics (PMS) Lunch BIOQ. Group A: Clinical Investigation in Vascular Disease (JDA) PIBQ. Group B: Clinical Investigation in Vascular Disease (JDA) Coffee Break BIOQ. Group A:Basic Investigation in Vascular Disease (AG) PIBQ. Group B:Basic Investigation in Vascular Disease (AG) BIOQ. Final Commentaries (JDA) WEDNESDAY, 9th FEBRUARY Inflammation and infection Group A: BIOQ. Redefining Immunity: Damage Control and Tolerance to Infection (MSo) Coffee Break BIOQ. IGC Inflammation Lab (MSo) Group B: Free Morning Lunch Group B: 29

30 BIOQ. Redefining Immunity: Damage Control and Tolerance to Infection (MSo) Coffee Break BIOQ. IGC Inflammation Lab (MSo) Group A: Free Afternoon THURSDAY, 10th FEBRUARY Allergy and Asthma BIOQ. Chemical mediators of inflammation Basic Mechanisms (TW) Coffee Break BIOQ. Chemoatraction of Leukocytes/Chemokines (TW) Lunch ANF.2 Seminar: The Discovery of Eotaxin (TW) BIOQ. Induction of Immune Tolerance (LG) Coffee Break BIOQ. Inflammation in Asthma (TW) FRIDAY, 11th FEBRUARY Develop an idea for research in this area; workshops with student presentations Open questions in the field; Future Directions (All Staff) Group A: BIOQ. Students Final Project Presentations Coffee Break BIOQ. Students Final Project Presentations Group B: PIBQ Students Final Project Presentations Coffee Break PIBQ. Students Final Project Presentations Lunch Group A: BIOQ. Students Final Project Presentations 30

31 Coffee Break BIOQ. Students Final Project Presentations Group B: PIBQ Students Final Project Presentations Coffee Break PIBQ. Students Final Project Presentations ANF.2 Final Session: The Future of Inflammation Research: Questions and Answers (AC) 14. Scientific Integrity and Ethics, February, 17 18, 2011 Organized by João Lobo Antunes, IMM/Faculdade de Medicina de Lisboa Faculty: João Lobo Antunes Mário Miguel Rosa, HSM Comissão de Ética Joana Marques, IMM António Vaz Carneiro, FM-UL Thursday 17 Februray J. Lobo Antunes - Scientific Integrity An introduction Discussion M. Miguel Rosa - Human Experimentation Discussion Joana Marques Animal Experimentation Discussion António Vaz Carneiro Evidence in Medicine Facts and Fallacies Discussion Friday 18 February Case discussions 31

32 Evolution and Medicine, February, 21 23, 2011 Organized by Thiago Carvalho, IGC Speakers: Thiago Carvalho, IGC Miguel Godinho, IGC Monday Feb 21 9:30-12:30 Evolution, Disease and Medicine: First Principles Journal club paper assignments Tuesday Feb 22 9:30-12:00 Attack of the clones: Evolutionary Biology and Cancer Therapy Wednesday Feb 23 9:30-12:00 Evolution of Chronic Disease 14:00-16:00 Journal Club I: Evolution of Aging 16:00-18:00 Journal Club II: Human Evolution, Population Structure and Drug Development Note: Monday and Tuesday afternoon are reserved for preparation of journal club presentations. 16. Preparing for Research, February, 24 25, 2011 Organized by Margarida Trindade, IMM and Sheila Vidal, IGC Organizers and Speakers: Sheila Vidal, Head of Research Funding Affairs, IGC Margarida Trindade, Science Funding Manager, IMM Invited speakers: Manuel Prieto, Associate Professor, IST João Eurico da Fonseca, Group Leader, IMM PROGRAMME 24 February 2011, Thursday 9h30 10h00 Welcome and introduction to the course I) The grant environment 32

33 10h00 11h30 Introduction to the grant environment: type of grants and funding agencies International and the European funding sources relative weight of different players National funding sources - FCT, other public and private 11h30 12h00 Break II) MD researcher s funding survival kit 12h00-13h00 Finding research funding from a medical doctor s perspective (João E. Fonseca) 13h00-14h30 Lunch III) Principles of evaluation 14h30-15h00 Review process and learning from criticism 15h00-16h00 Viewing a proposal from the reviewer perspective (Manuel Prieto) 16h00-16h30 Break 16h30-17h30 Practical Exercise - Evaluation Reports IV) Where to look for funding 17h30-18h00 Where to look for funding opportunities: Internet, officers, public sessions, specific tools available at our institutions 18h00-19h00 Practical exercise - Where to look for funding 25 February 2011, Friday V) Self assessment 9h30-10h30 Indicators of scientific productivity (ISI Web of Knowledge) CVs for grant applications: comparison with classical MD CVs 10h30-11h30 Practical exercise - ISI Web of Knowledge 11h30-12h00 Break 12h00-12h30 Wrap up from previous day s exercise 12h30 14h00 Lunch VI) Grant Writing 14h00 14h30 Grant proposal structure: fellowship vs. project grants 14h30 15h00 Practical exercise - Examples of application forms 15h00 16h00 Principles of scientific grant writing, writing tips and common pitfalls 33

34 16h00 16h30 Break 16h30 18h00 Practical exercise - Grant writing and evaluating 34