Filipa Vale

Pathogen Genome Bioinformatics and Computational Biology

Our lab is focused on genomic studies based on genome sequencing and application of computational and bioinformatics approaches, as well as computation-driven experimental approaches, to comprehend the evolution, epidemiology, virulence, population level genomic variation and phylogeography of pathogens.

Genomics and evolution of H. pylori

The human gastric carcinogen Helicobacter pylori infects half the world’s population. We are interested in describing the worldwide genomic and epigenomic variation of H. pylori to identify molecular determinants of carcinogenicity, virulence, antibiotic resistance and phylogeography.


Prophages and genome dynamics

Bacteriophages (phages) specifically infect and eliminate bacteria. There are about 10E31 phages in the planet, but <1% are estimated to be described. We aim to characterize prophages of gut bacteria and to disclose prophage role in the fitness and pathogenicity of H. pylori.

Phage lysin therapy

Use of a computer driven approach to identify prophages in bacteria and their lytic enzymes, which, in combination with an experimental biotechnological approach aims to produce enzybiotics (phage lysin therapy) against antibiotic resistant bacteria declared by the World Health Organization as a priority to develop novel antibiotics.

Bioinformatics and Computational Biology

Additionally, we aim to develop bioinformatics tools for efficient big data analysis, cooperate and provide services to other in-house and foreign groups.

Muñoz AB, Trespalacios-Rangel AA, Vale FF. An American lineage of Helicobacter pylori prophages found in Colombia. Helicobacter 2021; 26:e12779. DOI: 10.1111/hel.12779.
Muñoz-Ramirez ZY, Pascoe B, Mendez-Tenorio A, Mourkas E, Sandoval-Motta S, Perez-Perez G, Morgan DR, Dominguez RL, Ortiz-Princz D, Cavazza ME, Rocha G, Queiroz DMM, Catalano M, Palma GZ, Goldman CG, Venegas A, Alarcon T, Oleastro M, Vale FF, Goodman KJ, Torres RC, Berthenet E, Hitchings MD, Blaser MJ, Sheppard SK, Thorell K, Torres J. A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas. ISME J 2021; 15:78-92. DOI: 10.1038/s41396-020-00758-0.
Marques AT, Vítor JMB, Santos A, Oleastro M, Vale FF. Trends in Helicobacter pylori resistance to clarithromycin: from phenotypic to genomic approaches. Microb Genom 2020; 6:e000344. DOI: 10.1099/mgen.0.000344.
Yahara K., Lehours P., Vale FF. Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species. Microb Genom 2019; 5:e000282. DOI: 10.1099/mgen.0.000282
F.F. Vale, A. Nunes, M. Oleastro, J.P. Gomes, D.A. Sampaio, R. Rocha, J.M.B. Vítor, L. Engstrand, B. Pascoe, E. Berthenet, S. Sheppard, M.D. Hitchings, F. Mégraud, J. Vadivelu, P. Lehours. Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins. Sci. Rep. 2017; 7:42471. DOI: 10.1038/srep42471.

Filipa Vale

Group Leader


Phone: (+351) 217946463 (Ext. 14265)

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Faculdade de Farmácia da Universidade de Lisboa | Av. Professor Gama Pinto
1649-003 Lisboa | Portugal

Phone | +351 217 946 400
Fax | +351 217 946 470
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