Curriculum vitae

Experience

Full Stack Web Developer

ESEB2013 (2012-2013)

I was the sole web developer and built everything from the ground up. I'm still the current maintainer.

Node.js Express.js Bootstrap MongoDB Redis CoffeeScript Jade Stylus

Geeklist (2013-2013)

I was a team member, responsible for the LinkedIn integration

Node.js

CoBiG² (2013-2013)

I built the new website in Angular.js using many APIs (mostly as an experiment and for learning) but I'm not the current maintainer. I open sourced the code.

Node.js Angular.js Bootstrap LinkedIn API Mendeley API Dropbox API Facebook API Github API

Bioinformatician

Queen Mary University of London (2013-2016)

I'm a PhD Student under the supervision of Yannick Wurm and doing research in population genomics. I'm also contributing for a Crowdsourcing Web App for Gene Annotation, built with Ruby, PostgreSQL and Angular.js

Computational Biology & Population Genomics Group (CoBiG²) (2009-2013)

I've analysed Next-generation sequencing data and also performed sysadmin tasks.

Python

Papers

Published

Vieira B, Sebastiana M, Lino-Neto T, Monteiro F, Figueiredo A, Sousa L, Pais M, Paulo O. (2014) Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling. PLOS One, 9:5. doi: 10.1371/journal.pone.0098376

Talhinhas P, Azinheira H, Vieira B, Loureiro A, Tavares S, Batista D, Morin E, Petitot A, Paulo O, Poulain , Silva C, Duplessis S, Silva M, Fernandez D. (2014) Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection. Frontiers in Plant Science, 5:88. doi: 10.3389/fpls.2014.00088

Bradnam K, Fass J, Alexandrov A, et al. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2:10. doi: 10.1186/2047-217X-2-10

Submitted

Pina-Martins F, Vieira B, Seabra S, Batista D, Paulo O. () 4Pipe4 – A 454 data analysis pipeline specialized for SNP detection.

In conference proceedings

Talhinhas P, Azinheira H, Loureiro A, Batista D, Vieira B, Pina-Martins F, Tisserant E, Petitot A, Paulo O, Duplessis S, Silva M, Fernandez D. (2010) Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix. In proceedings at the 23rd International Conference on Coffee Science from the Association for Science and Information on Coffee (ASIC)

Talks

Pairwise Sequentially Markovian Coalescent ModelSlide: http://bmpvieira.com/labjolly14aLocation: Evolution Lab Jolly, SBCS, Queen Mary, University of London, London, United Kingdom

{"title":"Pairwise Sequentially Markovian Coalescent Model","date":"2014-03-25T00:00:00.000Z","slides":"http://bmpvieira.com/labjolly14a","location":{"name":"Evolution Lab Jolly, SBCS, Queen Mary, University of London, London, United Kingdom","url":"http://sbcs.qmul.ac.uk"},"authors":[{"firstname":"Bruno","lastname":"Vieira"}]}

Docker for reproducible scienceSlide: http://doi.org/10.6084/m9.figshare.1000809Location: Collaborations Workshop 2014, Software Sustainability Institute, University of Oxford, Oxford, United Kingdom

{"title":"Docker for reproducible science","date":2014,"slides":"http://doi.org/10.6084/m9.figshare.1000809","location":{"name":"Collaborations Workshop 2014, Software Sustainability Institute, University of Oxford, Oxford, United Kingdom","url":"http://software.ac.uk/cw14"},"authors":[{"firstname":"Bruno","lastname":"Vieira"}]}

Crowdsourcing Genome AnnotationSlide: Location: Citizen Cyberscience Summit 2014, University College London (UCL), London, United Kingdom

{"title":"Crowdsourcing Genome Annotation","date":2014,"doi":"http://doi.org/10.6084/m9.figshare.1000810","location":{"name":"Citizen Cyberscience Summit 2014, University College London (UCL), London, United Kingdom","url":"http://cybersciencesummit.org"},"authors":[{"firstname":"Bruno","lastname":"Vieira"}]}

Making the best of your 454 dataset using the 4Pipe4 analysis pipeline – from an unknown genome to a detailed SNPs analysis: A case study with a Quercus suber dataset.Slide: Location: XIV Congress of the European Society for Evolutionary Biology (ESEB 2013). Faculty of Sciences of the University of Lisbon (FCUL), Lisbon, Portugal

{"title":"Making the best of your 454 dataset using the 4Pipe4 analysis pipeline – from an unknown genome to a detailed SNPs analysis: A case study with a Quercus suber dataset.","date":2013,"url":"http://eseb2013.com/delegates/fpina-martins#981","location":{"name":"XIV Congress of the European Society for Evolutionary Biology (ESEB 2013). Faculty of Sciences of the University of Lisbon (FCUL), Lisbon, Portugal","url":"http://eseb2013.com"},"authors":[{"firstname":"Francisco","lastname":"Pina-Martins"},{"firstname":"Bruno Miguel","lastname":"Vieira"},{"firstname":"Sofia G","lastname":"Seabra"},{"firstname":"Dora","lastname":"Batista"},{"firstname":"Octávio Salgueiro","lastname":"Paulo"}]}

Analysis of software for the NGS technology: The Survival Guide.Slide: Location: 24th European Conference on Operational Research. Faculty of Sciences of the University of Lisbon (FCUL), Lisbon, Portugal

{"title":"Analysis of software for the NGS technology: The Survival Guide.","date":2010,"url":"http://www.euro2010lisbon.org","location":{"name":"24th European Conference on Operational Research. Faculty of Sciences of the University of Lisbon (FCUL), Lisbon, Portugal","url":"http://fc.ul.pt"},"authors":[{"firstname":"Bruno Miguel","lastname":"Vieira"},{"firstname":"Francisco","lastname":"Pina-Martins"},{"firstname":"Sofia G","lastname":"Seabra"},{"firstname":"Octávio Salgueiro","lastname":"Paulo"}]}