Work Experience

skills
From October 2017
Postdoctoral Research Associate
UC Davis Genome Center, Davis CA
Supervisor: Prof Harris A Lewin

Field of research: Comparative genomics and cancer genomics

April 2014 - September 2017
Bioinformatics
  • Experience with high performance computing (HPC) cluster usage.
  • Intermediate user of Perl, R and bash.
  • Basic user of Python, html and MySQL.
PhD research degree
Royal Veterinary College, University of London, UK
Supervisor: Dr Denis Larkin

Project title: "Reconstruction and evolutionary analysis of whole genome sequences from fragmented assemblies".

This project comprises 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.
 
  • Developed a novel methodology to upgrade genome assemblies involving the use of computational (reference-assisted assembly algorithm; RACA) and wet-lab techniques (DNA amplification by PCR and fluorescence in situ hybridization (FISH)).
  • Prepared RACA input data, including read mappings with Bowtie2 and genome alignments with LastZ.
  • Performed PCR verification of the predicted chromosome fragments (PCFs) created by RACA.
  • Designed avian universal panel of bacterial artificial chromosomes (BACs) to use as probes in FISH.  
  • Received FISH training at Prof Griffin’s lab (University of Kent, Canterbury) and performed a small fraction of the FISH experiments.
  • Reconstructed ancestral chromosome structures with ANGES and InferCARs software.
  • Performed multispecies genome alignments with progressiveCactus software and synteny blocks definition with maf2synteny tool.


October 2010 - November 2013
Research Fellow
Institute of Molecular Pathology and Immunology of the University of Porto, Portugal
PI: Dr Filipe Pereira

Project title: “The causes and consequences of mitochondrial DNA deletions in animals cells”.

This project 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.
 
  • Designed and implemented the mtDNA deletion database MitoBreak.
  • Performed in silico DNA secondary structure prediction using Unafold package.
  • Performed DNA modification followed by regular/denaturation polyacrylamide gel electrophoresis to detected DNA secondary structures in vitro.
Molecular Biology
  • DNA extraction, amplification and electrophoresis.
  • Fluorescence in situ hybridization.
  • Bacterial cell culture.
September 2009 - October 2010
Research Trainee
Institute of Molecular Pathology and Immunology of the University of Porto, Portugal
Supervisor: Dr Leonor Gusmao

Project title: “Strategies to the development of an InDel PCR multiplex for Y-chromosome haplogroup definition”.

This project comprised the development of an insertion/deletion (InDel) polymorphisms PCR multiplex to facilitate Y chromosome haplogroup definition.
 
  • Performed verification of Y chromosome InDel polymorphisms through PCR and Sanger sequencing.