Course Organizers (2008-2009)

3 - CELL CYCLE, CYTOSKELETON & DISEASE

3-7 November 08

Organizer: Mónica Bettencourt-Dias, IGC
Aims:

To learn the basis of cell cycle and tubulin cytoskeleton

To see good examples of basic research & the use of model organisms and how they relate to human disease

To see examples of translational research in these fields

To be able to read basic biology papers and referee them

To be able to think of exciting questions in these fields and to propose research projects to tackle them

To see the IGC and research done at IGC
Faculty

Phong Tran	University of Philadelphia
Karim Labib	Paterson Institute for Cancer Research
Helder Maiato	IBMC (Porto, Portugal)
Erich Nigg	Max Planck Institute, Martinsried
Florence Janody	IGC
Miguel Godinho	IGC
Monica Bettencourt Dias	IGC
Alvaro Tavares	IGC
Lars Jensen	IGC
Tim Mitchison	Harvard Medical School
Martin Eilers	Philipps-Universität, Marburg

Monday 3

9.30-10.00	Organization of the course (papers the week before)
10.00 -11.30	The Cytoskeleton & Human Disease (basics on actin and tubulin and a little bit of research)	Phong Tran
12.00-12.30	SNAPSHOT of my research on actin & cancer	Florence Janody
12.30-13.00	guidelines- onwards- prepare Journal clubs
14.30	Prepare Journal clubs- 2 groups present, 2 groups criticize, 2 papers related to cytoskeleton and 2 papers related to chromosomes
16.30 –17.30	Basis of Cell Cycle	Alvaro Tavares

Tuesday 4

9.30-10.30	Journal club on cytoskeleton
11.00-12.00	DNA replication & Human Disease	Karim Labib
12.00-13.00	IGC Seminar	IGC Seminar
14.30-15.30		Karim´s seminar
16-17.30	Chromosomes & chromosome maintenance	Miguel Godinho

Wednesday 5

9.30-10.30	Journal Club on chromosomes
11.00-12.00	Signalling and cancer
12.00-13.00	Seminar
14.30-16.00	Centrosomes & Cancer	M.Bettencourt-Dias & Paula Chaves
16.30-17.30	Prepare projects for next day- 3 projects- with help and discussion from IGC students- projects on chromosomes, centrosomes & cytoskeleton

Thursday 6

9.30-11.00	Project Presentation and discussion
11.30-13.00	Mitosis	Helder Maiato
14.30-15.30	about research in cell cycle and cancer	Tim Mitchison
16-17.00	IGC Seminar	Tim Mitchison

Friday 7

9.30-10.15	SNAPSHOT of my research on Epigenetics and Centromeres	Lars Jensen
10.30-11.15	SNAPSHOT- Model organisms in drug discovery	Rui Martinho
11.15- 12.00	Big discussion with students on cell cycle & cancer
12.00-13.00	Centrosomes and cancer, research-talk	Erich Nigg
Afternoon: Divide in 2 groups: 3 hrs- discussion with students, their projects, etc Live imaging at microscope (fly embryos), plus observing fixed cells under the microscope Scoring some flies Passaging some cells; treating them with Taxol, fixing and staining for alpha tubulin, actin and DNA Yeasts

Beer and dinner


4 - GENETICS

10-14 November 2008

Organizer: Dan Holmberg, University of Umea

Aims - Not yet provided

Faculty

Dan Holmberg	Univ. Ümea
Richard Rosenqvist	Univ. Upssala
Arn van den Maagdenberg	Univ. Leiden
Sofia Oliveira	IGC
Carlos Penha-Gonçalves	IGC

Nov 10	Introduction to disease genetics, mapping of monogenic and  complex diseases	C. P- Goncalves D Holmberg
Nov 11	Cancer genetics	Richard Rosenqvist
	Animal models	D Holmberg, C. P-Goncalves
	IGC Seminar	IGC Seminar
Nov 12	Neurogenetics	Arn van den Maagdenberg
	"Journal club"
Nov 13	Genetics of cardiovascular disease	Sofia Oliveira
	Genetics of infectious diseases	not yet named
Nov 14	Overview of statistics in genetics	not yet named
	IGC Seminar	IGC Seminar

5 - RNAi: FROM MOLECULAR MECHANISM TO THERAPEUTICS

17-19 November 2008

Organizer: Luis Moita, IMM
Since RNA interference (RNAi) was discovered to work in mammalian cells, this genetic manipulation technique has been hailed as a revolutionary new approach to basic biological research and drug development and discovery. RNAi is expected to provide critical insights into the mechanisms underlying human disease and accelerating development of treatments for cancer, AIDS and a host of other disorders. In addition, numerous proof-of-concept studies in animal models of human disease demonstrate the broad potential application of RNAi therapeutics.

In this three-day course, we will discuss the biology of RNAi and its usefulness both in discovery and therapeutics. We will transmit the experience of our team in gene function discovery using RNAi and will complement it with that of several international experts in basic and applied science working in this area.

Faculty

Luis F. Moita	IMM
João Gonçalves	IMM
Jonathan Ewbank	Centre d'Immunologie de Marseille-Luminy, Marseille
Richard Colvin	Harvard Medical School, Boston
Judy Lieberman	Harvard Medical School, Boston

Monday, 17^th

9.30	Welcome and course organization	Luis F. Moita
10.00 -11.00	Introduction and molecular mechanisms of RNAi	Luis F. Moita
11.30 -12.30	Model Organisms, Part I: C. elegans	Jonathan Ewbank
14.30 -15.30	Model Organisms, Part II: D. melanogaster and A. gambiae
16.00 -16.30	RNAi in vertetebrates: Introduction	Luis F. Moita
16.30 -17.30	How to perform a screen: focus on an arrayed screen	RicharColvin

Tuesday, 18^th

9.30 – 10.30	How to perform a screen: focus on a pooled screen	João Gonçalves
10.30 – 11.30	RNAi based dissection of Immune responses	Luis F. Moita
12.00 – 13.00	Seminar - RNAi screen reveals that lysosomal exocytosis is required for leukocyte chemotaxis	Richard Colvin
14.30 – 17.30	Students will divide in two groups. Each one will identify a biological problem and will design a strategy to dissect and or correct it using RNAi. In the following day, in the afternoon session, one group presents while the other discusses the project proposed

Wednesday, 19^th

9.30 – 11.30	Use of RNAi for therapy	Judy Lieberman
12.00 – 13.00	IMM Seminar	Judy Lieberman
14.30 – 16.30	presentations and discussion
17.00 – 17.30	Concluding remarks

Dinner

6 - COMPUTATIONAL BIOLOGY

20-25 November

Organizer: José Leal, IGC
High throughput technologies are revolutionizing biomedical research. Instead of investigating single genes, proteins or metabolites we are now able to probe the entire transcriptomes, proteomes, metabolomes, etc. This data deluge requires that we rely more and more on computers and quantitative methods to interpret and derive biological knowledge from this information. Such high throughput methods are increasingly impacting our understanding of human disease, opening up new diagnostic and therapeutic avenues. Above all, it asks from the clinician and researcher alike to be able to interpret a whole new quality of information. In this one-week course we will discuss the concepts underlying analysis of high throughput data, focusing on their use in clinical research and in medical practice.
Faculty

José Leal	IGC
Lopez Bigas	Univ. Pompeu Fabra
Fiona Brinkman	Univ Simon Fraser
Dietrich Rebholz Schumann	EMBL European Bioinformatics Institute, Cambrigde
James Brent	Cancer Research UK, Cambridge
David Balding	Imperial College, London
Karen Nelson	The J. Craig Venter Institute, Maryland

7 - BIOSTATISTICS & EPIDEMIOLOGY

26 November-9 December

Organizer: Gabriela Gomes, IGC
I - Introduction to Biostatistics

26 November-3 December 2008

Instructor: Armando Teixeira-Pinto ([e-mail])

Classes: 6 hours daily for 1 week (mixed theoretical and lab sessions)

Grading: Final exam (16 out of 20 points)

Assignments (4 out of 20 points)

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.

Faculty:

Armando Pinto FM-UP

Course topics:

1. Data (1h+1h)	types of data; data entry; data management.
2. Descriptive statistics (1:30h+1h)	frequency tables, summary measures (location and dispersion); data presentation (tables and graphs)
3. Normal distribution and other theoretical distributions. (1h)
4. Distribution of sample statistics and confidence intervals (2h+1h)	central limit theorem and the distribution of the sample mean, standard error of the mean, confidence intervals for the mean, confidence intervals for proportions.
Hypothesis testing (4h+3h)	parametric tests (t test, One-Way ANOVA); non-parametric tests - Mann-Whintey, Kruskal-Wallis, Wilcoxon and qui-square tests.
6. Statistical power and sample size calculation. (1h)
7. Diagnostic Tests (extra topic). (2h+1h)	Bayes theorem, sensitivity, specificity, likelihood ratio, false positives, false positives, ROC curves
8. Correlation and simple linear regression (2:30h+1h)	Pearson and Spearman correlatio coefficients, the linear model assumptions, interpretation of the regression parameters, inference on the parameters estimates, model checking.
9. Basics of multiple linear regression: (2h+1h)	interpretation of the regression parameters model building
10.Introduction to logistic regression (2h+1h)	the logit link, interpretation of the regression parameters.
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, 2004. 506p.

Swinscow,T D V. Statistics at Square One available at: http://www.gulunap.unina.it/docu/Nutricam_statistics.pdf)

II - Introduction to Epidemiology

4-12 December 2008

Faculty

Armando Pinto	FMUP
Gabriela Gomes	IGC
Laura Rodrigues	London School Hygiene &Tropical Medicine
Sérgio Cunha	ISC/UFBa
Corine Merle	London School Hygiene &Tropical Medicine
John Edmunds	London School Hygiene &Tropical Medicine
Maurício Barreto	Univ. Baía

Objectives: Introduction to the main concepts, measurement and research strategies used in epidemiology.

Thursday, 4 December:

Morning: What is Epidemiology? Definitions, History and Uses (Lecture/discussion) – MB/LR

Afternoon: Infectious Diseases Epidemiology (Lecture/practice) – LR/MB
Friday, 5 December:

Morning: Measures of Frequency (Lecture/ practice) – MB/LR

IGC Seminar

Afternoon: Measures of Association (Lecture/ practice) – LR/MB

Saturday, 6 December:

Morning: Study Design: Overview and Randomized Controlled Trials (Lecture/practice) – MB/LR

Afternoon: Study Design: Observational Studies – Prevalence, Case-Control, Cohort (Lecture/practice) – LR/MB
Monday, 8 December:

Morning: Confounding (Lecture/practice) – SC/CM

Afternoon: Bias (Lecture/practice) – SC/CM
Tuesday, 9 December:

Morning: Validity (Lecture/practice) – SC/CM

IGC Seminar

Afternoon: Association and Causality (Lecture/practice) – SC/CM

Wednesday, 10 December:

Morning: Reading, interpretation and criticism of epidemiological papers – SC/CM

Afternoon: Reading, interpretation and criticism of epidemiological papers – SC/CM
Thursday, 11 December:

Morning: Mathematical Models in Infectious Diseases Epidemiology – GG

Afternoon: Models of Pathogen Evolution. Models of Contact Behaviour – GG/JE
Friday, 12 December:

Morning: Health Economics – JE

IGC Seminar

Afternoon: Problem solving – GG/JE