Research

Instituto Gulbenkian de Ciência

1. Evolutionary cell biology

We study the evolutionary origins of cellular properties and their evolutionary dynamics. We have a special interest in compartmentalization, in other words, the modular nature of cell biology.
We focus our research in:

the origins of compartmentalization in cell biology, with a strong emphasis on the origins and evolution of the endomembrane system
the molecular determinants of shape and movement, with an emphasis on microtubule-derived organelles
the molecular basis of cell differentiation in bacteria

Current projects include:

The study of the origins of intracellular compartments, by cataloguing the evolutionary dynamics of protein repertoires and interactions

The development of data integration environments where protein, interaction and localization information can be intersected with morphological descriptions of organelles and processes. The flagship resources we are developing are:

A data integration platform for microtubule-derived organelles, where organelle morphology is considered in its evolutionary and molecular context.
This is a collaborative project with:
Monica Bettencourt-Dias (IGC, PT)
Juliette Azimzadeth (UCSF, PT)
Keith Gull (Oxford University, UK)
Michel Bornens (Inst. Curie, FR)

The automated reconstruction of repertoires and interactions mediating protein trafficking in organisms with complete genome sequences

The molecular machinery controlling bacterial sporulation, and the molecular determinants of spore morphology.
This is a collaborative project with:
Adriano Henriques (ITQB, PT)

The development of improved orthology detection methods suitable to use in highly divergent and coiled-coil reach repertoires such as those found in protein trafficking and microtubule-derived organelles

2. Translational bioinformatics

Translational bioinformatics is a term that describes the use of bioinformatics methods in translational research, i.e. aimed at solving medical problems (diagnosis, predict prognosis, new therapies, personalized medicine, etc.). To us it is the ultimate test ground of the sometimes very abstract research that we do in computational biology.

Currently, our main research lines are:

Identifying Prognostic markers for triple-negative breast cancer:
Triple negative breast cancer is a subtype of breast cancer with heterogeneous prognosis and response to chemotherapy. We are integrating molecular and epidemiological data to develop a prognostic predictor for this disease.
This is a collaborative project with:
Jose Luis Passos Coelho (IPO, PT)
Anabela Miranda (ROR - IPO, PT)
Manuela Martins (Hosp. São José, PT)
Carlos Caldas (Univ. Cambridge, UK)

Dissecting centrosomal abnormalities in tumor progression:
Numerical and structural centrosomal abnormalities are observed in a variety of cancers. Are they cause or consequence in tumor progression? Do their effects transcend a potential role in causing aneuploidy?
This is a collaborative project with:
Monica Betencourt Dias (IGC, PT)
Paula Chaves (IPO, PT)
David Pellam (Dana Farber Inst., USA)
Max Loda (Dana Farber Inst., USA)

Protein trafficking in cancer:
Protein trafficking is a central process in eukaryotic cells, that has been implicated in a variety of human diseases. The latest one is cancer, and we are dissecting the precise role of the trafficking machinery in breast cancer.
This is a collaboration with:
Miguel C. Seabra (FCM, PT)
Manuela Martins (Hosp. São José, PT)

Drug repositioning:
Drug development pipelines are drying, and few new drugs are entering on the market. There is however some indication that current drugs may have broader uses than currently known. We are exploring bioinformatics and evolutionary approaches to find new antibacterial and anticancer uses of existing drugs.
This is a collaborative project with:
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