Pedro Barbosa

Pedro Barbosa

Bioinformatics researcher

Localidade
Braga e Região, Portugal
Setor
Biotechnology

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Pedro Barbosa's Overview

Current
  • Researcher at CEB-IBB, Center of Biological Engineering, University of Minho
Education
Connections

194 connections

Pedro Barbosa's Experience

Instituição acadêmica; 1.001-5.000 funcionários; Setor de Higher Education

fevereiro de 2014Presente (8 meses)

Pedro Barbosa's Skills & Expertise

  1. Bioinformatics
  2. NGS
  3. Systems Biology
  4. R
  5. Matlab
  6. Java
  7. Python
  8. Metagenomics
  9. Genetics
  10. Bash
  11. LaTeX
  12. Molecular Evolution
  13. Phylogenetic Analysis
  14. Transcriptomics
  15. DNA microarray
  16. SQL
  17. DNA sequencing
  18. Molecular Biology
  19. PCR
  20. Genetic Engineering
  21. Biotechnology

View All (21) Skills View Fewer Skills

Pedro Barbosa's Education

Universidade do Minho / University of Minho

Master's degree, Bioinformátiva

20112013

Grade: 17/20

Lunds universitet

Six Months abroad under the Erasmus program, Molecular ecology and evolution

20112011

Grade: A

Universidade do Minho / University of Minho

Bachelor's degree, Applied Biology

20082011

Grade: 15/20

Pedro Barbosa's Projects

  • Taxonomic and functional analysis of metagenomes

    • janeiro de 2013 até outubro de 2013
    Membros da equipe: Pedro Barbosa

    Over the years, metagenomics has demonstrated to play an essential role on the study of the microorganisms that live in microbial communities, particularly those who inhabit the human body. Several bioinformatic tools and pipelines have been developed, but usually they only address one question: ”Who is there?” or ”What are they doing?”.

    This work aimed to develop a computational framework to answer the two questions simultaneously, that is, perform a taxonomic and functional analysis of microbial communities. Merlin, a previously developed software designed for the construction of genome-scale metabolic models for single organisms, was extended to deal with metagenomics data. It has an user-friendly and intuitive interface, not requiring command-line knowledge and further libraries dependencies or installation, as many other tools.

    The extended version of Merlin can predict the taxonomic composition of an environmental sample based on the results of homology searches, where the proportions of phyla and genera present are discriminated. Regarding the metabolic analysis, it allows to identify which enzymes are present and calculate their abundance, as well as to find out which metabolic pathways are effectively present.

    The performance of the tool was evaluated with samples from the Human Microbiome Project, particularly from the saliva. In the end, Merlin demonstrated to be a reliable standalone alternative
    to web services for those scientists that have concerns about sharing data.

  • Strategies to assemble and finish the genome sequence of Pseudomonas sp. M1 using NGS methods

    • março de 2012 até julho de 2012
    Membros da equipe: Pedro Barbosa

    Pseudomonas sp. M1 strain owns a potential of biotransform monoterpene compounds which may originate a wide range of products with applications in several areas from biotechnology to medicine. Thus, sequencing its entire genome is crucial for understanding these mechanisms and drive the processes to an industrial level. The genome was sequenced using next-generation sequencing technologies, where one long read dataset from Roche 454 FLX and two short paired-reads from Illumina Genome Analyser IIx were obtained. I aimed in this project assemble the entire genome of this bacteria using different bioinformatic tools and strategies in order to obtain a pipeline for finishing genome sequences from NGS technologies.

  • Colonization patterns of the blue tits Cyanistes caeruleus in the Canary Islands inferred from mitochondrial and nuclear genetic data

    • março de 2011 até julho de 2011
    Membros da equipe: Pedro Barbosa

    This project was made in order to clarify the two different possibilities of colonization pattern in Canary islands proposed in mtDNA (Kvist et al 2005 and Dietzen et al 2008) or if yet another would come through. There were quite different results using cytochrome b gene sequences (Dietzen et al. 2008) and control region data (Kvist et al 2005) and in this study I had the strength of combining cytochrome b and control region sequences from the same individuals, which gave me a wider knowledge about the mitochondrial data.
    I also used four nuclear markers, including intronic sequences. This DNA nuclear data provided complementary data since different genes could evolve in such radically different ways, and that their phylogenetic signals and substitution processes could be very different , making such analysis together with different markers being extremely challenging.

  • Phylogeography of Cetti's Warbler

    • fevereiro de 2011 até março de 2011
    Membros da equipe: Pedro Barbosa, Hugo Pereira

    This project proposed to sequence the mitochondrial ND2 gene of individuals belonging to a Portuguese population of this specie and compare the results with some sequences already published in Genbank from a Russian population of the same specie in an attempt to clarify how many refuges this species had during the last glaciations and the demographics of the populations.

Pedro Barbosa's Languages

  • Portuguese

    (Fluente ou nativo)
  • English

    (Nível intermediário)

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