Vera Afreixo

Position	Aux. professor
Affiliation	DMat / University of Aveiro
Group	Information Systems and Processing
Status	Researcher with PhD
Country	Portugal
Students
Former PhD students
Former masters students	Show list
Courses
Projects
Past projects	DNA symmetry, DNA-Profiles, NeuroPath
Events
Proposals
ORCID	0000-0003-1051-8084
Personal page

Publications

Articles in international journals listed in the ISI

• Ana H. M. P. Tavares, Jakob Raymaekers, Peter J. Rousseeuw, Raquel Silva, Carlos A C Bastos, Armando J. Pinho, Paula Brito, Vera Afreixo. Comparing reverse complementary genomic words based on their distance distributions and frequencies. Interdisciplinary Sciences: Computational Life Sciences, vol. 10, no. 1, p. 1-11, March 2018
• Ana H. M. P. Tavares, Armando J. Pinho, Raquel Silva, João M. O. S. Rodrigues, Carlos A C Bastos, Paulo J S G Ferreira, Vera Afreixo. DNA word analysis based on the distribution of the distances between symmetric words. Scientific Reports, vol. 7, no. 728, April 2017
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos, Ana H.M.P. Tavares, Raquel Silva. Exceptional symmetry by genomic word. Interdisciplinary Sciences: Computational Life Sciences, vol. 9, no. 1, p. 14-23, March 2017
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos, Raquel Silva. The exceptional genomic word symmetry along DNA sequences. BMC Bioinformatics, vol. 17, no. 59, p. 1-10, February 2016 [IF 2016: 2.448 (Q1, 10/57)]
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos. Analysis of single-strand exceptional word symmetry in the human genome: new measures. Biostatistics, vol. 16, no. 2, p. 209-221, April 2015 [IF 2015: 2.109 (Q1, 13/123)]
• Vera Afreixo, Carlos A C Bastos, Sara Pinto Garcia, João M. O. S. Rodrigues, Armando J. Pinho, Paulo J S G Ferreira. The breakdown of word symmetry in the human genome. Journal of Theoretical Biology, vol. 335, p. 153-159, October 2013 [IF 2013: 2.303 (Q1, 10/52)]
• Sara Pinto Garcia, João M. O. S. Rodrigues, Sérgio Santos, Diogo Pratas, Vera Afreixo, Carlos A C Bastos, Paulo J S G Ferreira, Armando J. Pinho. A genomic distance for assembly comparison based on compressed maximal exact matches. IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 3, p. 793-798, May 2013 [IF 2013: 1.536 (Q1, 24/119)]
• Vera Afreixo, Carlos A C Bastos, Armando J. Pinho, Sara Pinto Garcia, Paulo J S G Ferreira. Genome analysis with distance to the nearest dissimilar nucleotide. Journal of Theoretical Biology, vol. 275, no. 1, p. 52-58, April 2011 [IF 2011: 2.208 (Q1, 11/47)]
• Adelaide Freitas, Vera Afreixo, Miguel Pinheiro, José Luís Oliveira, Gabriela Moura, Manuel A.S. Santos. Improving the Performance of the Iterative Signature Algorithm for the Identification of Relevant Patterns. Statistical Analysis and Data Mining, vol. 4, no. 1, p. 71-83, February 2011
• Vera Afreixo, Carlos A C Bastos, Armando J. Pinho, Sara Pinto Garcia, Paulo J S G Ferreira. Genome analysis with inter-nucleotide distances. Bioinformatics, vol. 25, no. 23, p. 3064-3070, December 2009 [IF 2009: 4.926 (Q1, 2/29)] [IF 2017: 5.481 (Q1, 3/59)]
• Miguel Pinheiro, Vera Afreixo, Gabriela Moura, Adelaide Freitas, Manuel A. S. Santos, José Luís Oliveira. Statistical, computational and visualization methodologies to unveil gene primary structure features. Methods of Information in Medicine, vol. 45, no. 2, p. 163–168, 2006 [IF 2006: 1.684, 1.684]
• Armando J. Pinho, António J. R. Neves, Vera Afreixo, Carlos A C Bastos, Paulo J S G Ferreira. A three-state model for DNA protein-coding regions. IEEE Transactions on Biomedical Engineering, vol. 53, no. 11, p. 2148-2155, November 2006 [IF 2006: 2.302]
• Gabriela Moura, Miguel Pinheiro, R. Silva, I. Miranda, Vera Afreixo, G. Dias, Adelaide Freitas, José Luís Oliveira, Manuel A. S. Santos. Comparative context analysis of codon pairs on an ORFeome scale. Genome Biology, vol. 6, no. 3, 2005 [IF 2005: 9.712]
• Vera Afreixo, Paulo J S G Ferreira, Dorabella Santos. Fourier Analysis of Symbolic Data: A Brief review. Digital Signal Processing, vol. 14, no. 6, p. 523-530, November 2004 [IF 2004: 0.676]
• Vera Afreixo, Paulo J S G Ferreira, Dorabella Santos. Spectrum and symbol distribution of nucleotide sequences. Physical Review E, vol. 70, no. 3, p. 031910, September 2004 [IF 2004: 2.352]

Other articles in journals

• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos. Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. Journal of Integrative Bioinformatics, vol. 11, no. 3, p. 250, October 2014
• Carlos A C Bastos, Vera Afreixo, Sara Pinto Garcia, Armando J. Pinho. Inter-STOP symbol distances for the identification of coding regions. Journal of Integrative Bioinformatics, vol. 10, no. 3, p. 230, November 2013
• Vera Afreixo, Sara Pinto Garcia, João M. O. S. Rodrigues. The breakdown of symmetry in word pairs in 1,092 human genomes. Jurnal Teknologi, vol. 63, no. 3, p. 1-8, August 2013
• Carlos A C Bastos, Vera Afreixo, Armando J. Pinho, Sara Pinto Garcia, João M. O. S. Rodrigues, Paulo J S G Ferreira. Inter-dinucleotide distances in the human genome: an analysis of the whole-genome and protein-coding distributions. Journal of Integrative Bioinformatics, vol. 8, no. 3, September 2011

Articles in conference proceedings

• Carlos A C Bastos, Vera Afreixo, João M. O. S. Rodrigues, Armando J. Pinho. An analysis of symmetric words in human DNA: adjacent vs non-adjacent word distances. PACBB 2018 - 12th International Conference on Practical Applications of Computational Biology & Bioinformatics, Toledo, Spain, June 2018
• Ana H. M. P. Tavares, Jakob Raymaekers, Peter J. Rousseeuw, Raquel Silva, Carlos A C Bastos, Armando J. Pinho, Paula Brito, Vera Afreixo. Dissimilar symmetric word pairs in the human genome. PACBB 2017 - 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, Portugal, vol. AISC 616, p. 248-256, June 2017
• Vera Enes, João M. O. S. Rodrigues, Vera Afreixo. Single nucleotide variation context in human genome. Proceedings of RecPad 2016, Aveiro, Portugal, p. 105--107, October 2016
• Ana H.M.P. Tavares, João M. O. S. Rodrigues, Carlos A C Bastos, Armando J. Pinho, Paulo J S G Ferreira, Paula Brito, Vera Afreixo. Detection of exceptional genomic words: a comparison between species. Proceedings of COMPSTAT 2016 (22nd International Conference on Computational Statistics), Oviedo, Spain, p. 255--266, August 2016
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos, Raquel Silva. Exceptional symmetry profile: a genomic word analysis. International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB), Sevilla, Spain, vol. 477 (in Springer series Advances in Intelligent Systems and Computing), p. 151--159, June 2016
• Vera Afreixo, Carlos A C Bastos, João M. O. S. Rodrigues, Raquel Silva. Identification of DNA CpG Islands Using Inter-dinucleotide Distances. Optimization in the Natural Sciences. 30th Euro Mini-Conference, EmC-ONS 2014. Aveiro, Portugal, February 5–9, 2014. Revised Selected Papers. (Series: Communications in Computer and Information Science), Springer International Publishing, Switzerland, vol. 499, p. 162-172, 2015
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos. Exploring the exceptional genomic word symmetry among regions (Poster). 2015 annual workshop on Statistical Methods for Post Genomic Data (SMPGD), Munich, Germany, February 2015
• Ana Helena Tavares, Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos. The Symmetry of Oligonucleotide Distance Distributions in the Human Genome. ICPRAM 2015 - 4th International Conference on Pattern Recognition Applications and Methods, Lisbon, vol. 2, p. 256-263, January 2015
• Vera Afreixo, João M. O. S. Rodrigues, Carlos A C Bastos. Exceptional Single Strand DNA Word Symmetry: Universal Law?. 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014), Salamanca, Spain, vol. Advances in Inteligent Systems and Computing 294, p. 137-143, June 2014
• Vera Afreixo, João Antunes, Carlos A C Bastos. Identification of DNA CpG islands using inter-dinucleotide distances. EURO Mini conference on Optimization in Natural Sciences 2014, Aveiro, Portugal, vol. (Abstract), February 2014
• Vera Afreixo, Carlos A C Bastos. Testando, estatisticamente, a segunda lei de Chargaff. Livro de atas do XX Congresso Anual da Sociedade Portuguesa de Estatística, p. 15, 2013
• Vera Afreixo, João M. O. S. Rodrigues, Sara Pinto Garcia. Analysis of word symmetries in human genomes using next-generation sequencing data. 7th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB), Salamanca, Spain, vol. Advances in Intelligent Systems and Computing, 222, p. 7-13, May 2013
• Carlos A C Bastos, Vera Afreixo, Sara Pinto Garcia, Armando J. Pinho. Segmentation of DNA into coding and Noncoding region based on inter-STOP symbols distances. Advances in Intelligent Systems and Computing, Proc. of the 7th Int. Conf. on Practical Applications of Computational Biology & Bioinformatics, PACBB 2013, Salamanca, Spain, vol. 222, p. 23-28, May 2013
• Sónia Gouveia, Vera Afreixo, Manuel Scotto, Paulo J S G Ferreira. Exploring the correlation structure of inter-nucleotide DNA distances. 5th International Conference of the ERCIM WG on Computing & Statistics (ERCIM 2012), Oviedo, Spain, December 2012
• Sérgio Santos, João M. O. S. Rodrigues, Vera Afreixo, Sara Pinto Garcia. Word count variation in 1,092 human genomes. (Poster). Proceedings of the 18th Portuguese Conference on Pattern Recognition (RECPAD), Coimbra, Portugal, October 2012
• Carlos A C Bastos, Vera Afreixo, Armando J. Pinho, Sara Pinto Garcia, João M. O. S. Rodrigues, Paulo J S G Ferreira. Distances between dinucleotides in the human genome. Advances in Intelligent and Soft Computing, Proc. of the 5th Int. Conf. on Practical Applications of Computational Biology & Bioinformatics, PACBB 2011, Salamanca, Spain, vol. 93, p. 205-211, April 2011
• Armando J. Pinho, Sara Pinto Garcia, Paulo J S G Ferreira, Vera Afreixo, Carlos A C Bastos, António J. R. Neves, João M. O. S. Rodrigues. Exploring homology using the concept of three-state entropy vector. Pattern Recognition in Bioinformatics, 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, vol. LNBI 6282, p. 161-170, September 2010
• Vera Afreixo, Carlos A C Bastos, Armando J. Pinho, Sara Pinto Garcia, Paulo J S G Ferreira. DNA inter-nucleotide distances. Challenges in Bioinformatics, JB-2009, Lisbon, Portugal, p. 1, November 2009
• Paulo J S G Ferreira, António J. R. Neves, Vera Afreixo, Armando J. Pinho. Exploring three-base periodicity for DNA compression and modeling. Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2006, Toulouse, France, vol. 5, p. 877-880, May 2006

PhD thesis

• Vera Afreixo. Sinais simbólicos e aplicações em genómica. PhD Thesis, Universidade de Aveiro, Portugal, October 2008