Scope:
Program for Advanced Medical Education
(Doctoral program for physicians)
Subject:
Graduate course - Computational and high-hroughput methods in Biomedical Research
Dates:
8-12 November
Place:
IGC - Theano Auditorium (below the library)
Faculty:
Patrick Aloy - Institute for Biomedical Research - ES
Nuria Lopez-Bigas - University Pompeu Fabra - ES (courtesy of GTPB)
James Brenton - Cancer Research UK Cambridge Research Institute - UK
Sofia Braga - Instituto Gulbenkian de Ciência - PT
Ana Teresa Maia - Cancer Research UK Cambridge Research Institute - UK
Isabel Gordo - Instituto Gulbenkian de Ciência - PT
Jorge Carneiro - Instituto Gulbenkian de Ciência - PT
Ana Teresa Freitas - INESC-ID/IST - PT
Ramana Madupu - J. Craig Venter Institute, USA
Yu-Hui Rogers - J. Craig Venter Institute, USA
Jose Pereira-Leal - Instituto Gulbenkian de Ciência - PT
Schedule:
Monday
9:00 - 10:00 - Introduction - J.Pereira-Leal
BREAK
10:30 - 12:30 - A network medicine approach to complex diseases- P. Aloy
BREAK - lunch with Patrick
14:00 - 15:00 - Integration of genomics data for the study of cancer - N. Lopez-Bigas
15:00 - 16:30 - Evolutionary genomics of pathogenic bacteria - J.Pereira-Leal
BREAK
17:00 - 18:00 - Evolutionary cell biology of microtubule-derived organelles (and cancer and infertility and ciliopathies and etc.)- J. Pereira-Leal
Tuesday
9:00 - 10:00 - A PhD project in Computational Oncology - Sofia Braga
10:00 - 12:00 - Transcriptional regulation in breast cancer predisposition - A.T. Maia
BREAK - lunch with Ana Teresa Maia
14:00 - 16:00 - tba - J. Brenton
BREAK
16:15 - 17:30 - meet António coutinho
Wednesday
9:00 - 10:00 - JC-A
10:00 -12:00 - Understanding genetic diversity in pathogen populations - I.Gordo
BREAK - lunch with I. Gordo
13:30 - 14:30 - JC-B
14:30 - 15:30 - JC-C
Thursday
09:30 - 11:00 - Improving diagnosis and prognosis of Hypertrophic Cardiomyopathy - A.T. Freitas
11:30 - 13:00 - Short JCs
BREAK
14:30 - 16:00 - Your favorite disease... in silico; in omics
BREAK
16:30 - 18:30 - The dynamics of physiological and pathological autoimmunity - J. Carneiro
Friday
9:00 -10:20 - JCVI Research Overview and Application of Next Generation Sequencing technologies at JCVI - YH Rogers
MICRO BREAK
10:30 - 12:00 - Human Microbiome Studies –Linking Microbiome to Health and Disease - R. Madupu
12:00 - IGC seminar
BREAK - lunch with R. Madupu & YH Rogers
14:00 - 17:00 - PhD thesis discussion in evolutionary cell biology (Zita Santos) - Ionians
17:00 - Seminar Wallace Marshal (UCSF) - Ionians
19:00 - DINNER (to be confirmed)
Journal club papers:
Long JC (3 groups of 4 people)
Aim for up to 30 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 - Mueller et al. Predicting extubation outcome in preterm newborns: a comparison of neural networks with clinical expertise and statistical modeling. Pediatr Res (2004) vol. 56 (1) pp. 11-8
Short JCs (6 groups, 2 people each)
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!