Scope:
Program for Advanced Medical Education
(Doctoral program for physicians)
Subject:
Graduate course - Computational and high-hroughput methods in Biomedical Research
Dates:
14-18 November
Place:
IGC - Theano Auditorium (below the library), except for monday afternoon (Champalimaud CU)
Faculty:
James Brenton - Cancer Research UK Cambridge Research Institute - UK
Yu-Hui Rogers - J. Craig Venter Institute, USA
Nuno Palma - BIAL, PT
Francois Balloux - Imperial College, UK
Ana Teresa Freitas - INESC-ID/IST - PT
Isabel Gordo - Instituto Gulbenkian de Ciência - PT
Jorge Carneiro - Instituto Gulbenkian de Ciência - PT
Sofia Braga - Instituto Gulbenkian de Ciência - PT
Joana Cardoso - Instituto Gulbenkian de Ciência - PT
Catarina Coreia - Instituto Gulbenkian de Ciência & Inst. Nacional de Saúde Ricardo Jorge - PT
Marie Bonnet - Instituto Gulbenkian de Ciência - PT
Jose Pereira-Leal - Instituto Gulbenkian de Ciência - PT
Schedule:
Monday 14
9:00 - 10:00 - Introduction - J.Pereira-Leal
BREAK
10:30 - 12:30 - TUTORIAL: a primer in bioinformatics
LUNCH
------ monday afternoon sessions @ Champalimaud's CU -----
14:00 - 16:00 - TBA -J.Brenton
16:00 - 16:30 - BREAK
16:30 - 17:00 - Research Project in Computational ... Oncology (Breast) - S. Braga
17:00 - 17:30 - Research project in Computational ... Oncology (Esophagus) - J. Cardoso
------ end ---------
Tuesday 15
9:00 - 10:30 - Evolutionay genomics of pathogenics bacteria - JPLeal
nano BREAK
11:15 - 11:35 - Research Projects in Computational... computational... hum... evolutionary genomics into the direction of personalized medicine, with some immunology mixed in - M. Bonnet.
11:45 - 12:00 nanoBREAK
12:00 - 13:00 - IGC SEMINAR
LUNCH
14:00 - 16:00 - Modeling Chemistry and Biology in Drgu Discovery - NPalma
BREAK
16:30 - 18:30 - Bioinformatics Practical (Your laptops and an internet connection)
Wednesday 16
9:30 - 10:00 - Research Projects in Computational ... Medical Genetics -C. Correia
10:00 - 11:30 - "Isabel: The fitness effects of mutations in bacteria : the good and the bad"- Isabel Gordo
BREAK
free time
LUNCH
14:30 -"Genome dynamics and evolutionary history of the plague, Yersinia pestis" - Francois Balloux
BREAK
16:30 - long JC
Thursday 17
09:30 - 11:00 - "MicroRNAs and Human Disease: which role bioinformactics is playing" - ATFreitas
BREAK
preparation for short JC
LUNCH
14:00 - 16:00 - The dynamics of physiological and pathological autoimmunity - J. Carneiro
BREAK
16:30 - 18:30 - Short JC
Friday 18
9:30 -11:00 - "From Reading to Writing the Code of Life" -YHRogers
BREAK
12:00 - 13:00 - IGC SEMINAR
LUNCH
14:30 - 17:00 - Research projects (no preparation needed).
17:00 - Project celebration
Journal club papers:
Long JC (3 groups of 3 people)
Aim for up to 20 minutes presentation, but remember that you don't have to discuss every single figure, although you may have to delve into the supplementary materials.We want to discuss the logic of the questions and approach, rather than the specific technicalities of each paper.
A - Campillos et al. Drug target identification using side-effect similarity. Science (2008) vol. 321 (5886) pp. 263-6
B - Ashley et al. Clinical assessment incorporating a personal genome. Lancet (2010) vol. 375 (9725) pp. 1525-35
C - Kaddurah-Daouk Ret al (2011) Enteric Microbiome Metabolites Correlate with Response to Simvastatin Treatment. PLoS ONE, 6:e25482.
Short JCs (9 individual presentations)
You will need to identify one paper that is:
i - original (not a review); ii - computational (including genomics); iii - claims to address a biomedical problem of medical relevance
You will have to present the paper in 10 minutes, including a) identify the question, b) the approach, c) the critical experiment, d) the conclusion, e) the medical relevance (or absence of) - time will be strictly enforced
We will vote the best paper based on your presentations, and an awe-inspiring and magnificent prize will be awarded to the best paper (best to be defined on the spot, but although presentation skill will obviously matter, what will be evaluated is the quality and interest of the paper).
I am sure we will have lots of fun on this one!!
Suggestion - journals that you may wish to consider are: Nature, Science, Nature Genetics, PLoS genetics, PLoS Computational Biology, Nature Medicine, PLos Pathogens, PNAS, J. Theoretical Biology, etc.
Good luck!