Postdoctoral research associate

Oct 2017 - Current

The Genome Center, University of California - Davis, USA
Supervisor: Professor Harris A. Lewin

My current projects are:

1. Vertebrate chromosome evolution. I am performing the reconstruction of ancestral genomes across the mammal phylogeny taking advantage of the availability of chromosome-level genome assemblies (or near) for most extant mammalian orders. We use these reconstructions to more accurately identify and date chromosomal rearrangements along the mammalian lineage and shed light into the role of chromosomal rearrangements in species divergence and phenotype evolution. As new high-quality genome assemblies are being generated and made available for other vertebrate clades, we plan to use similar methodologies to better understand how chromosomes evolved in the vertebrate lineage.
2. Yeasts’ chromosome evolution. We are using comparative and functional genomics tool to understand the role of chromosomal rearrangements in the lipid production and accumulation mechanisms observed in oleaginous yeast strains. This project comprises both wet-lab and computational stages and it includes DNA/RNA extraction and purification, sequencing, genome assembly and annotation, and subsequent comparative analyses.
3. Evaluation of genome sequences in the context the international consortia DNA Zoo (https://www.dnazoo.org/), Vertebrates Genomes Project (https://vertebrategenomesproject.org/), and Earth Biogenome Project (https://www.earthbiogenome.org/).
4. Identification of species at risk for SARS-CoV-2 infection. We created a ranking system, based on protein sequence similarity to the human receptor for SARS-CoV-2 (ACE2), for the prediction of propensity for ACE2/SARS-CoV-2 binding in vertebrate species.

PhD researcher

Mar 2014 - Sep 2017

Royal Veterinary College, University of London, UK
Supervisor: Dr. Denis Larkin

My project, entitled “Reconstruction and evolutionary analysis of whole genome sequences from fragmented assemblies” comprised three main objectives (A) development of a new methodology to upgrade short read animal genomes from scaffold- to chromosome-level, (B) application of the new methodology to avian genome assemblies, and (C) study avian chromosomal evolution.
The methodology we developed, for upgrading genome assemblies, involves the use of computational and wet-lab techniques. During development, I prepared input data for the reference-assisted chromosome assembly (RACA) algorithm, including performing read mappings and pairwise whole genome alignments. I also, performed wet-lab verification of the RACA-generated predicted chromosome fragments by amplification of putatively chimeric adjacencies through PCR. I designed an avian universal panel of bacterial artificial chromosomes to use as probes in fluorescence in situ hybridization (FISH). I received FISH training at Professor Griffin’s lab (University of Kent, Canterbury, UK) where I performed a fraction of the FISH experiments, used to further verify and assembled the genomes of the pigeon (Columba livia) and the peregrine falcon (Falco peregrinus). This work resulted in one first-author publication (Damas et al., 2017).
The third aim of my project consisted in the study of avian chromosomal evolution. To do that, I reconstructed ancestral chromosome structures along the avian phylogeny, identified and dated evolutionary breakpoint regions, and performed association analyses with diverse genomic features (i.e. GC content, transposable element density). This work resulted in one first-author publication (Damas et al., 2018).

To download my PhD thesis click here (english) .

Research fellow

Oct 2010 - Nov 2013

Institute of Molecular Pathology and Immunology of the University of Porto, Portugal
Supervisor: Dr. Filipe Pereira

My project, titled “The causes and consequences of mitochondrial DNA deletions in animals cells” comprised the study of the causes of mitochondrial (mt) DNA deletions on humans, with special focus of DNA secondary structures (e.g. DNA hairpins), and their association with human disease. To do that, I designed and implemented the mtDNA deletion database MitoBreak, I performed in silico DNA secondary structure predictions and, also, performed DNA modification followed by regular/denaturation polyacrylamide gel electrophoresis to detected DNA secondary structures in vitro. This project resulted in three first-author publications (Damas et al., 2012; Damas et al, 2014a,b).

MSc researcher

Sep 2008 - Oct 2010

Institute of Molecular Pathology and Immunology of the University of Porto, Portugal
Supervisor: Dr. Leonor Gusmao

My project, consisted in the development of an insertion/deletion (InDel) polymorphisms PCR multiplex to facilitate human Y chromosome haplogroup definition. During this project, I identified candidate InDels from publicly available databases which I then tested if were real Y chromosome polymorphisms through PCR and Sanger sequencing. This project resulted in a conference proceedings paper (Damas et al., 2011).

To download my MSc thesis click here (portuguese) .