Courses that we taught/will teach
Course - Computational Biology and Medicine
Gulbenkian Advanced Training program for Medical Doctors
30/11 - 4/12
Faculty
José Pereira-Leal (Instituto Gulbenkian de Ciência - PT)
James Brenton (University of Cambridge - UK)
Jorge Carneiro (Instituto Gulbenkian de Ciência - PT)
Isabel Gordo (Instituto Gulbenkian de Ciência - PT)
Alfonso Valência (Centro Nacional de Investigaciones Oncologicas - ES)
Jonas Almeida (M.D. Anderson - USA)
Karen Nelson (The Craig Venter Institute - USA)
Patrícia figueiredo (Instituto Superior Técnico - PT)
Monday (30/11)
09:30 - 11:00 - Introduction to Computational Biology, Bioinformatics, etc. (JPL)
11:00 - 11:30 - BREAK
11:30 - 12:30 - Introduction to Computational Biology, Bioinformatics, etc. (JPL)
12:30 - 14:00 - LUNCH
14:00 - 15:30 - How does ovarian carcinoma develop drug resistance? (JB)
15:30 - 16:00 - BREAK
16:00 - 17:30 - JC1
Tuesday (1/12)
09:30 - 11:00 - Drug (re-)targeting (JPL)
11:00 - 11:30 - BREAK
11:30 - 13:00 - JC2
13:00 - 14:30 - LUNCH
14:30 - 16:00 - Do we really understand autoimmune diseases? (JC)
16:00 - 16:30 - BREAK
16:30 - 18:00 - JC3
Wednesday (2/12)
10:00 - 11:00 - Models of pathogen genetic diversity (IG)
11:00 - 11:30 - BREAK
11:30 - 12:30 - Models of pathogen genetic diversity (IG)
12:30 - 14:00 - LUNCH
14:00 - 15:30 - TBA (AV)
15:30 - 16:00 - BREAK
16:00 - 17:30 - JC4
Thursday (3/12)
10:00 - 11:00 - Genomics and Metagenomics (KN)
11:00 - 11:30 - BREAK
11:30 - 12:30 - Genomics and Metagenomics (KN)
12:30 - 14:00 - LUNCH
14:00 - 15:30 - Integrative Bioinformatics: data, analyse thyself! (JA)
15:30 - 16:00 - BREAK
16:00 - 17:30 - What can brain images tell us about the brain? (PF)
Friday (4/12)
morning is free (12-13 - IGC seminar)
14:00 - 15:30 - Project 1
15:30 - 16:00 - BREAK
16:00 - 17:30 - Project 2
JC papers
JC1
Shah et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) vol. 461 (7265) pp. 809-13
JC2
Campillos et al. Drug target identification using side-effect similarity. Science (2008) vol. 321 (5886) pp. 263-6
JC3
Zhong et al. Edgetic perturbation models of human inherited disorders. Molecular Systems Biology (2009) vol. 5 (1) pp.
JC4
Lazebnik. Can a biologist fix a radio?--Or, what I learned while studying apoptosis. Cancer Cell (2002) vol. 2 (3) pp. 179-82
Background Reading
-
Chin L, Gray JW. (2008) Translating insights from the cancer genome into clinical practice. Nature. 452(7187):553-63.
- Mathew JP, et al (2007) From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol. 2007 Feb 23;3(2):e12.
Workshop - Medical Bioinformatics
PhD Program in Computational Biology
TBA
Course - Protein Interaction networks
PhD Program in Computational Biology
March 23-27
Monday
9:00 - 9:30 - Introduction - José Pereira-Leal (Instituto Gulbenkian de Ciência, Portugal)
9:30 - 12:30 - Experimental approaches to study protein-protein interactions - Adriano Henriques (Instituto de Tecnologia Química e Biológica, Portugal)
14:00 - Structural systems biology: modelling protein interactions and complexes" Patrick Aloy (Instituto for Research in Biomedicine, Spain)
16:00 - 17:30- Journal Club 1 & 2
Alber et al., 2007
Yildirim et al., 2007
Tuesday
9:15 - 10:15 - Models of network evolution- José Pereira-Leal (Instituto Gulbenkian de Ciência, Portugal)
10:30 - 12:00 - Protein interactions - André Valente (Biocant, Portugal)
14:30 - 15:30 - Journal Club 3
Lin et al., 2009
15:30 - 16:30 - Journal Club 4
Yu et al., 2008
Wednesday
9:30 - 11:00 - Modularity in protein networks - José Pereira-Leal (Instituto Gulbenkian de Ciência, Portugal)
11:30 - 13:00 - Identifying functional modules in networks - Yoan Dieckmann (PDBC, Portugal) & José Pereira-Leal (Instituto Gulbenkian de Ciência, Portugal)
14:30 - 15:30 - Journal club 5
Dutkowski and Tiuryn, 2007
15:30 - 16:30 - Journal club 6
Tamames et al., 2007
Thursday
9:30 - 11:00 - Prediction of protein-protein interactions - José Pereira-Leal (Instituto Gulbenkian de Ciência, Portugal)
11:30-12:30 - JC - 7
Park et al., 2009
14:00 - 15:00 - JC-8
Chen et al., 2009
15:00 - 16:00 - JC-9
Pujana et al., 2007
16:00 - 17:00 - JC 10
Taylor et al., 2009
Friday
10:00-13:00 - Project discussion
group 1 - outline a (computational!) PhD project involving dynamic modeling of protein interaction networks
group 2 - outline a (computational!) PhD project involving domain-domain interactions in protein interaction networks
group 3 - outline a (computational!) PhD project involving protein interaction networks and the pathogen Coxiella burnetii
group 4 - outline a (computational!) PhD project involving the protein interaction network underlying centriolar function and structure
JC papers
Alber, F., et al. (2007), 'Determining the architectures of macromolecular assemblies', Nature, 450 (7170), 683-94.
Chen, J., B. J. Aronow, and A. G. Jegga (2009), 'Disease candidate gene identification and prioritization using protein interaction networks', BMC Bioinformatics, 10 (1), 73.
Dutkowski, J. and J. Tiuryn (2007), 'Identification of functional modules from conserved ancestral protein-protein interactions', Bioinformatics, 23 (13), i149-58.
Lin, W. H., W. C. Liu, and M. J. Hwang (2009), 'Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks', BMC systems biology, 3 (1), 32.
Park, S. H., et al. (2009), 'Prediction of protein-protein interaction types using association rule based classification', BMC Bioinformatics, 10 (1), 36.
Pujana, M. A., et al. (2007), 'Network modeling links breast cancer susceptibility and centrosome dysfunction', Nat Genet, 39 (11), 1338-49.
Tamames, J., A. Moya, and A. Valencia (2007), 'Modular organization in the reductive evolution of protein-protein interaction networks', Genome Biol, 8 (5), R94.
Taylor, I. W., et al. (2009), 'Dynamic modularity in protein interaction networks predicts breast cancer outcome', Nat Biotechnol, 27 (2), 199-204.
Yildirim, M. A., et al. (2007), 'Drug-target network', Nat Biotechnol, 25 (10), 1119-26.
Yu, H., et al. (2008), 'High-quality binary protein interaction map of the yeast interactome network', Science, 322 (5898), 104-10.
Course - Computational Biology
Gulbenkian Advanced Training program for Medical Doctors
November 20,21, 23,24
Thursday
9:30 - Jose Pereira-Leal (Instituto Gulbenkian de Ciência)
"Introduction: Data sets and data types" (Instituto Gulbenkian de Ciência)
11:00 - José Pereira-Leal
"From evolutionary analysis to drug targets and mechanisms of disease"
13:00 - LUNCH
14:00 . James Brenton (Cambridge Research Institute, UK)
"How should we model the development of clinical drug resistance for genomic analysis?"
16:00 - BREAK
16:30 - Journal Club I
"Parsons et al (2008) An integrated genomic analysis of human glioblastoma multiforme Science 321: 1807-12"
Friday
9:00 -Nuria-Lopez-Bigas (Universitat Pompeu Fabra, Spain)
"Integrating genomics data for the study of cancer"
10:30 - Practical session
13:30 - LUNCH
15:00 - David Balding (Dept Epidemiology and Public Health, Imperial College, UK)
"Statistical approaches to identifying genetic factors in complex diseases"
Monday
10:00 - Journal Club II
"Pujana et al (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction" Nat. Genetics 39:1338-49
11:30 - Dietrich Rebholz (European Bioinformatics Institute, UK)
"From literature facts to biomedical knowledge"
13:30 - LUNCH
15:00 - Jorge Carneiro (Instituto Gulbenkian de Ciencia, PT)
"A systems approach to autoimmunity in health and disease"
16:30 - Journal Club III
Ho et al (1995) Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection Nature 373(6510):123-6
(check this)
17:30 - Project proposal I
Tuesday
10:00 - Karen Nelson (Craig Venter Institute, USA)
"The use of metagenomic approaches to study the human body"
12:30 - LUNCH
14:00 - José Pereira-Leal (Instituto Gulbenkian de Ciência)
"From network biology to disease networks"
16:00 - Journal Club IV
Manichanh, C et al (2008) A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library Nuc. Ac. Res. 36(16): 5180-88
17:00 - Project proposal
Background Reading
-
Swanton C, Szallasi Z, Brenton JD, Downward J. Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer. Breast Cancer Res. 2008 Oct 31;10(5):214.
Ahmed AA, Mills AD, Ibrahim AE, Temple J, Blenkiron C, Vias M, Massie CE, Iyer NG, McGeoch A, Crawford R, Nicke B, Downward J, Swanton C, Bell SD, Earl HM, Laskey RA, Caldas C, Brenton JD. The extracellular matrix protein TGFBI induces microtubule stabilization and sensitizes ovarian cancers to paclitaxel. Cancer Cell. 2007 Dec;12(6):514-27.
Chin L, Gray JW. (2008) Translating insights from the cancer genome into clinical practice. Nature. 452(7187):553-63.
- Mathew JP, et al (2007) From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol. 2007 Feb 23;3(2):e12.
- Gill SR et al (2006) Metagenomic analysis of the human distal gut microbiome Science. 312(5778):1355-9
- Li M et al (2008) Symbiotic gut microbes modulate human metabolic phenotypes Proc. Natl. Acad. Sci. USA 105(6): 2117-22
- McCarthy et al (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges Nat. Rev. Gen 9:356
- Balding (2006) A tutorial on statistical methods for population association studies Nat. Rev. Gen. 7:781
- Carneiro et al (2007) When three is not a crowd: a Crossregulation Model of the dynamics and repertoire selection of regulatory CD4+ T cells Immunological Reviews 216: 48–68
- Leon et al (2004) Inverse correlation between the incidences of autoimmune disease and infection predicted by a model of T cell mediated tolerance. Journal of Autoimmunity 22 (2004) 31–42
Course - Evolution
Gulbenkian PhD Program in multidisciplinary life sciences
(org. Henrique Teotónio)
Nov. 8
Lectures (morning)
- Proteins, homology, mutations
- Genomes, proteomes, protein spaces, networks
Journal Club (afternoon)
- Marques et al (2008) Functional diversification of duplicate genes through subcellular adaptation of encoded proteins Genome Biol. 2008;9(3):R54.
- Peisajovich et al (2006) Evolution of new protein topologies through multistep gene rearrangements. Nat Genet. 2006 Feb;38(2):168-74
- Tokuriki et al (2008) How protein stability and new functions trade off. PLoS computational biology 4(2):e1000002
- Chothia, C & Lesk, AM (1986) The relationship between the divergence of sequence and structure in proteins EMBO J. 5: 823-26 (nor PDF but you can find it in the library - make sure you return the journal back to where you found it!!!)
Background reading
soon...
Lectures - Why Computational Biology
Gulbenkian PhD Program in multidisciplinary life sciences
October 4th
Workshop - Evocell
PhD Program in Computational Biology
Lecture - Modularity in Cell Biology
Masters in Evo-Devo - Faculty of Sciences, University of Lisbon
Course - Protein-Protein Interaction Networks
PhD Program in Computational Biology
date
Lectures - Homology and functional inference
PhD Program - ITQB
