Filipe Pereira

Researcher | PhD in Genetics | MBA | Founder @ IDENTIFICA

Research topics

Molecular diagnostics and species identification

Our aim is to develop reliable and cost-effective methods for broad spectrum biological identification that are appropriate for use in suboptimal samples and are amenable to different high-throughput genotyping platforms. We also develop molecular kits to be used for characterization of domestic breeds and fraud detection in processed food products.

Non-B DNA conformations, genomic rearrangements and disease

Our main objective is to understand how such high-order DNA and RNA structures are formed in vitro and what is their role in genome organization, instability and evolution. We mainly focus on two models systems: mitochondrial and viral genomes. In particular, animal mtDNA and RNA viruses have in common a high mutation rate, short genomes, large number of available sequences and frequent genomic rearrangements.

Genetic analysis of animal domestication

Our aim is to decipher the origin and subsequent movements of animal pastoralism in different world regions, with emphasis on Southern Europe and Northern Africa. We use data from mitochondrial DNA (mtDNA), Y chromosome and insertionally polymorphic endogenous retroviruses (ERVs) for the investigation of biodiversity, and the characterization of animal genetic resources.

Selected Publications

Carneiro J, Pereira F
EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment
PLOS Neglected Tropical Diseases. 2016. 10(7): e0004757. DOI: 10.1371/journal.pntd.0004757

Damas J, Carneiro J, Amorim A, Pereira F.
MitoBreak: The mitochondrial DNA breakpoints database.
Nucleic Acids Research. 2014. 42 (D1): D1261-D1268 doi:10.1093/nar/gkt982

Damas J, Samuels DC, Carneiro J, Amorim A, Pereira F.
Mitochondrial DNA rearrangements in health and disease – a comprehensive study.
Human mutation. 2014. 35(1):1-14. doi: 10.1002/humu.22452

Damas J, Carneiro J, Gonçalves J, Stewart JB, Samuels DC, Amorim A, Pereira F.
Mitochondrial DNA deletions are associated with non-B DNA conformations.
Nucleic Acids Research. 2012. 40 (16): 7606-7621.

Pereira F, Carneiro J, Matthiesen R, van Asch B, Pinto N, Gusmão L, Amorim A.
Identification of species by multiplex analysis of variable-length sequences.
Nucleic Acids Research. 2010. 38 (22): e203.

Chessa B, Pereira F, Arnaud F, Amorim A, […], Bruford MW, Kantanen J, Spencer TE and Palmarini M.
Revealing the history of sheep domestication using retrovirus integrations.
Science. 2009. 324:532-536.

Pereira F, Soares P, Carneiro J, Pereira L, Richards M, Samuels DC, Amorim A.
Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region.
Molecular Biology and Evolution. 2008. 25:2759–2770.

Top databases

Commercial applications

SPInDel kit

SPInDel kit

AIM-Indel Kit

AIM-Indel Kit

TRANSGENIC SALMON DETECTION KIT

TRANSGENIC SALMON DETECTION KIT

CANINE GENETIC IDENTIFICATION

CANINE GENETIC IDENTIFICATION

Meat species testing

Meat species testing