Diogo Pratas

Position	Aux. researcher
Affiliation	IEETA
Group	Information Systems and Processing
Status	Researcher with PhD
Country	Portugal
Students	Jorge Miguel Silva
Former PhD students	Morteza Hosseini
Former masters students
Courses
Projects
Past projects	DNA-Profiles, FCM-DNA, NRCD, RD-Connect
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

• Mari Toppinen, Diogo Pratas, Elina Väisänen, Maria Söderlund-Venermo, Klaus Hedman, Maria F. Perdomo, Antti Sajantila. The landscape of persistent human DNA viruses in femoral bone. Forensic Science International: Genetics, vol. 48, p. 102353, September 2020 [IF 2018: 4.884 (Q1, 1/17)]
• Diogo Pratas, Mari Toppinen, Lari Pyöriä, Klaus Hedman, Antti Sajantila, Maria F. Perdomo. A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level. GigaScience, vol. 9, no. 8, p. 11, August 2020 [IF 2018: 4.688 (Q1, 13/69)]
• Diogo Pratas, Jorge Miguel Silva. Persistent minimal sequences of SARS-CoV-2. Bioinformatics, vol. btaa686, p. 4, August 2020 [IF 2018: 4.531 (Q1, 4/59)]
• João Almeida, Armando J. Pinho, José Luís Oliveira, Olga Fajarda, Diogo Pratas. GTO: A toolkit to unify pipelines in genomic and proteomic research. SoftwareX, vol. 12, p. 100535, July 2020
• Morteza Hosseini, Diogo Pratas, Burkhard Morgenstern, Armando J. Pinho. Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements. GigaScience, vol. 9, no. 5, May 2020 [IF 2018: 4.688 (Q1, 13/69)]
• Jorge Miguel Silva, Eduardo Pinho, Sérgio Matos, Diogo Pratas. Statistical Complexity Analysis of Turing Machine Tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model. Entropy, vol. 22, no. 1, January 2020 [IF 2018: 2.419 (Q2, 28/81)]
• Diogo Pratas, Morteza Hosseini, Jorge Miguel Silva, Armando J. Pinho. A reference-free lossless compression algorithm for DNA sequences using a competitive prediction of two classes of weighted models. Entropy, vol. 21, p. 1074, November 2019 [IF 2018: 2.419 (Q2, 28/81)]
• Morteza Hosseini, Diogo Pratas, Armando J. Pinho. AC: A Compression Tool for Amino Acid Sequences. Interdisciplinary Sciences: Computational Life Sciences, vol. 11, no. 1, p. 68-76, March 2019 [IF 2018: 1.418 (Q3, 40/59)]
• 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 2018: 2.810 (Q2, 50/134)]
• 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 [IF 2018: 3.331 (Q2, 61/174)]
• Morteza Hosseini, Diogo Pratas, Armando J. Pinho. Cryfa: a secure encryption tool for genomic data. Bioinformatics, p. bty645, July 2018 [IF 2018: 4.531 (Q1, 4/59)]
• 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 2018: 2.419 (Q2, 28/81)]
• Morteza Hosseini, Diogo Pratas, Armando J. Pinho. A Survey on Data Compression Methods for Biological Sequences. Information, vol. 7, no. 4, October 2016
• 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 2018: 4.011 (Q1, 15/69)]
• 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)] [IF 2018: 4.531 (Q1, 4/59)]
• 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 2018: 2.776 (Q2, 24/69)]
• 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)] [IF 2018: 4.531 (Q1, 4/59)]
• 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 2018: 2.776 (Q2, 24/69)]
• 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)]
• ...further results

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

• Morteza Hosseini, Diogo Pratas, Armando J. Pinho. A Probabilistic method to find and visualize distinct regions in protein sequences. Proceedings of the 27th European Signal Processing Conference, EUSIPCO 2019, A Coruña, Spain, September 2019
• Diogo Pratas, Morteza Hosseini, Armando J. Pinho. GeCo2: An Optimized Tool for Lossless Compression and Analysis of DNA Sequences. Proceedings of the 13th International Conference on Practical Applications of Computational Biology & Bioinformatics, Avila, Spain, p. 137-145, June 2019
• Diogo Pratas, Morteza Hosseini, Armando J. Pinho. Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes. Proceedings of the 13th International Conference on Practical Applications of Computational Biology & Bioinformatics, Avila, Spain, p. 129-136, June 2019
• Ana Teixeira, Diogo Pratas, Armando J. Pinho, Raquel Silva. Evolutionary insights from the comparative analysis of hominid genomes. Proceedings of the 24th Portuguese Conference on Pattern Recognition, RecPad2018, Coimbra, October 2018
• Catarina Figueiredo, Diogo Pratas, Armando J. Pinho, Raquel Silva. Identification of antifungal targets using alignment-free methods. Proceedings of the 24th Portuguese Conference on Pattern Recognition, RecPad2018, Coimbra, October 2018
• 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
• ...further results

PhD thesis

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