Diogo Pratas

Position	Post-doc researcher
Affiliation	IEETA
Group	Information Systems and Processing
Status	Researcher with PhD
Country	Portugal
Students	Jorge Miguel Silva, Morteza Hosseini
Former PhD students
Former masters students
Courses
Projects	NRCD, RD-Connect
Past projects	DNA-Profiles, FCM-DNA
Events	IbPRIA'2017, Microbial Genomics & Metagenomics
Proposals
ORCID	0000-0003-1176-552X
Personal page	http://sweet.ua.pt/pratas

Publications

Books

• Daniel Figueiredo, Carlos Martín-Vide, Diogo Pratas, Miguel A. Vega-Rodríguez. Algorithms for Computational Biology. Springer International Publishing, June 2017

Articles in international journals listed in the ISI

• João M. Carvalho, Susana Brás, Diogo Pratas, Jacqueline Ferreira, Sandra C. Soares, Armando J. Pinho. Extended-Alphabet Finite-Context Models. Pattern Recognition Letters, no. 112, p. 49-55, September 2018 [IF 2016: 1.995 (Q2, 58/133)]
• Diogo Pratas, Morteza Hosseini, Gonçalo Grilo, Armando J. Pinho, Raquel Silva, Tânia Caetano, João Carneiro, Filipe Pereira. Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard. Genes, vol. 9, no. 9, p. 445, September 2018
• Morteza Hosseini, Diogo Pratas, Armando J. Pinho. Cryfa: a secure encryption tool for genomic data. Bioinformatics, p. bty645, July 2018
• Diogo Pratas, Raquel Silva, Armando J. Pinho. Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes. Entropy, vol. 20, no. 6, p. 393, May 2018 [IF 2016: 1.821 (Q2, 26/79)]
• Diogo Pratas, Raquel Silva, Armando J. Pinho, Paulo J S G Ferreira. An alignment-free method to find and visualise rearrangements between pairs of DNA sequences. Scientific Reports, vol. 5, p. 10203, May 2015 [IF 2015: 5.228 (Q1, 7/63)] [IF 2016: 4.259 (Q1, 10/64)]
• Raquel Silva, Diogo Pratas, Luísa Castro, Armando J. Pinho, Paulo J S G Ferreira. Three minimal sequences found in Ebola virus genomes and absent from human DNA. Bioinformatics, vol. 31, no. 15, p. 2421-2425, April 2015 [IF 2015: 5.766 (Q1, 3/56)]
• Luís Matos, António J. R. Neves, Diogo Pratas, Armando J. Pinho. MAFCO: A compression tool for MAF files. PLoS ONE, vol. 10, no. 3, p. e0116082, March 2015 [IF 2015: 3.057 (Q1, 11/63)] [IF 2016: 2.806 (Q1, 15/64)]
• Armando J. Pinho, Diogo Pratas. MFCompress: a compression tool for FASTA and multi-FASTA data. Bioinformatics, vol. 30, no. 1, p. 117-118, January 2014 [IF 2014: 4.981 (Q1, 3/57)]
• Diogo Pratas, Armando J. Pinho, João M. O. S. Rodrigues. XS: a FASTQ read simulator. BMC Research Notes, vol. 7, no. 40, January 2014
• Armando J. Pinho, Sara Pinto Garcia, Diogo Pratas, Paulo J S G Ferreira. DNA sequences at a glance. PLoS ONE, vol. 8, no. 11, p. e79922, November 2013 [IF 2013: 3.534 (Q1, 8/55)] [IF 2016: 2.806 (Q1, 15/64)]
• Luís Matos, Diogo Pratas, Armando J. Pinho. A compression model for DNA multiple sequence alignment blocks. IEEE Transactions on Information Theory, vol. 59, no. 5, p. 3189-3198, May 2013 [IF 2013: 2.650 (Q1, 14/135)]
• 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)]
• Armando J. Pinho, Diogo Pratas, Sara Pinto Garcia. GReEn: a tool for efficient compression of genome resequencing data. Nucleic Acids Research, vol. 40, no. 4, p. e27, February 2012 [IF 2012: 8.278 (Q1, 27/290)]

Other articles in journals

• Morteza Hosseini, Diogo Pratas, Armando J. Pinho. A Survey on Data Compression Methods for Biological Sequences. Information, vol. 7, no. 4, October 2016

Chapters in books

• Armando J. Pinho, Diogo Pratas, Sara Pinto Garcia. Compressing resequencing data with GReEn. Deep Sequencing Data Analysis, Noam Shomron (Ed.), Humana Press, vol. 1038 (Methods in Molecular Biology), p. 27-37, July 2013

Articles in conference proceedings

• Armando J. Pinho, Diogo Pratas. An Application of Data Compression Models to Handwritten Digit Classification. International Conference on Advanced Concepts for Intelligent Vision Systems. Springer, Cham., p. 487-495, September 2018
• Diogo Pratas, Armando J. Pinho. Metagenomic composition analysis of sedimentary ancient DNA from the Isle of Wight. 26th edition of the European Signal Processing Conference, EUSIPCO 2018, Rome, Italy, September 2018
• Diogo Pratas, Armando J. Pinho. A DNA sequence corpus for compression benchmark. PACBB 2018 - 12th International Conference on Practical Applications of Computational Biology & Bioinformatics, Toledo, Spain, June 2018
• Diogo Pratas, Morteza Hosseini, Armando J. Pinho. Compression of amino acid sequences. PACBB 2018 - 12th International Conference on Practical Applications of Computational Biology & Bioinformatics, Toledo, Spain, June 2018
• Manuel Gaspar, Diogo Pratas, Armando J. Pinho. NET-ASAR: a tool for DNA sequence search based on data compression. PACBB 2018 - 12th International Conference on Practical Applications of Computational Biology & Bioinformatics, Toledo, Spain, June 2018
• Diogo Pratas, Morteza Hosseini, Armando J. Pinho. Cryfa: a tool to compact and encrypt FASTA files. PACBB 2017 - 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, Portugal, vol. AISC 616, p. 305-312, June 2017
• Diogo Pratas, Armando J. Pinho. On the approximation of the Kolmogorov complexity for DNA sequences. IbPRIA 2017 - 8th Iberian Conference on Pattern Recognition and Image Analysis, Faro, Portugal, vol. LNCS 10255, p. 259-266, June 2017
• Morteza Hosseini, Diogo Pratas, Armando J. Pinho. On the role of inverted repeats in DNA sequence similarity. PACBB 2017 - 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, Portugal, vol. AISC 616, p. 228-236, June 2017
• Diogo Pratas, Morteza Hosseini, Armando J. Pinho. Substitutional tolerant Markov models for relative compression of DNA sequences. PACBB 2017 - 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, Portugal, vol. AISC 616, p. 265-272, June 2017
• Diogo Pratas, Morteza Hosseini, Raquel Silva, Armando J. Pinho, Paulo J S G Ferreira. Visualization of distinct DNA regions of the modern human relatively to a Neanderthal genome. IbPRIA 2017 - 8th Iberian Conference on Pattern Recognition and Image Analysis, Faro, Portugal, vol. LNCS 10255, p. 235-242, June 2017
• Armando J. Pinho, Diogo Pratas, Paulo J S G Ferreira. Authorship attribution using relative compression. Proc. of the Data Compression Conference, DCC-2016, Snowbird, UT, p. 329-338, March 2016
• Diogo Pratas, Armando J. Pinho, Paulo J S G Ferreira. Efficient compression of genomic sequences. Proc. of the Data Compression Conference, DCC-2016, Snowbird, UT, p. 231-240, March 2016
• Diogo Pratas, Raquel Silva, Armando J. Pinho, Paulo J S G Ferreira. Detection and visualisation of regions of human DNA not present in other primates. Proceedings of the 21st Portuguese Conference on Pattern Recognition, RecPad 2015, Faro, Portugal, October 2015
• Armando J. Pinho, Diogo Pratas, Paulo J S G Ferreira. A new compressor for measuring distances among images. Proc. of the International Conference on Image Analysis and Recognition, ICIAR-2014, Vilamoura, Portugal, vol. LNCS 8814, p. 30-37, October 2014
• Diogo Pratas, Raquel Silva, Armando J. Pinho. Large-scale inversions between human reference assemblies. Proceedings of the 20th Portuguese Conference on Pattern Recognition, RecPad 2014, Covilhã, Portugal, October 2014
• Raquel Silva, Luísa Castro, Diogo Pratas, Armando J. Pinho. Towards personalized medicine: ebola virus absent words in the human genome. Proceedings of the 20th Portuguese Conference on Pattern Recognition, RecPad 2014, Covilhã, Portugal, October 2014
• Diogo Pratas, Armando J. Pinho. Exploring deep Markov models in genomic data compression using sequence pre-analysis. Proc. of the 22nd European Signal Processing Conference, EUSIPCO-2014, Lisbon, Portugal, September 2014
• Diogo Pratas, Armando J. Pinho. A conditional compression distance that unveils insights of the genomic evolution. Proc. of the Data Compression Conference, DCC-2014, Snowbird, UT, p. 421, March 2014
• Armando J. Pinho, Diogo Pratas, Paulo J S G Ferreira. Information profiles for DNA pattern discovery. Proc. of the Data Compression Conference, DCC-2014, Snowbird, UT, p. 420, March 2014
• Diogo Pratas, Armando J. Pinho. Insights into primates genomic evolution using a compression distance. Proc. RecPad 2013, Lisbon, November 2013
• ...further results

PhD thesis

• Diogo Pratas. Compression and analysis of genomic data. PhD Thesis, Universidade de Aveiro, Aveiro, Portugal, January 2016