Diogo Pratas
From IEETA
| Position | Aux. researcher |  |
|---|---|---|
| Affiliation | IEETA | |
| Group | Information Systems and Processing | |
| Status | Researcher with PhD | |
| Country | Portugal | |
| Students | ||
| 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 | https://pratas.github.io | |
Contents |
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
- Jorge Miguel Silva, Diogo Pratas, Tânia Caetano, Sérgio Matos. The complexity landscape of viral genomes. GigaScience, vol. 11, August 2022 [IF 2018: 4.688 (Q1, 13/69)]
- Weihong Qi, Yi-Wen Lim, Andrea Patrignani, Pascal Schläpfer, Anna Bratus-Neuenschwander, Simon Grüter, Christelle Chanez, Nathalie Rodde, Elisa Prat, Sonia Vautrin, Margaux-Alison Fustier, Diogo Pratas, Ralph Schlapbach, Wilhelm Gruissem. The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. GigaScience, vol. 11, March 2022 [IF 2018: 4.688 (Q1, 13/69)]
- Outi I. Mielonen, Diogo Pratas, Klaus Hedman, Antti Sajantila, Maria F. Perdomo. Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation. Viruses, vol. 14, no. 1, p. 133, January 2022 [IF 2018: 3.811]
- João Monteiro, Diogo Pratas, Arnaldo Videira, Filipe Pereira. Revisiting the Neurospora crassa mitochondrial genome. Letters in Applied Microbiology, August 2021 [IF 2018: 2.858]
- Milton Silva, Diogo Pratas, Armando J. Pinho. AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models. Entropy, vol. 23, no. 5, p. 530, April 2021 [IF 2018: 2.419 (Q2, 28/81)]
- Mari Toppinen, Antti Sajantila, Diogo Pratas, Klaus Hedman, Maria F. Perdomo. The Human Bone Marrow Is Host to the DNAs of Several Viruses. Frontiers in Cellular and Infection Microbiology, vol. 11, p. 329, April 2021 [IF 2018: 3.584 (Q1)]
- Jorge Miguel Silva, Diogo Pratas, Rui Antunes, Sérgio Matos, Armando J. Pinho. Automatic analysis of artistic paintings using information-based measures. Pattern Recognition, p. 107864, February 2021 [IF 2018: 5.165 (Q1, 10/202)]
- João Almeida, Diogo Pratas, José Luís Oliveira. A semi-automatic methodology for analysing distributed and private biobanks. Computers in Biology and Medicine, vol. 130, p. 104180, January 2021 [IF 2018: 2.895]
- Milton Silva, Diogo Pratas, Armando J. Pinho. Efficient DNA sequence compression with neural networks. GigaScience, vol. 9, no. 11, p. giaa119, November 2020 [IF 2020: 6.520 (Q1, 10/71)] [IF 2018: 4.688 (Q1, 13/69)]
- 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 2020: 6.520 (Q1, 10/71)] [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 2020: 6.520 (Q1, 10/71)] [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)]
- ...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
- Jorge Miguel Silva, Diogo Pratas, Tânia Caetano, Sérgio Matos. Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods. Proceedings of the 10th Iberian Conference on Pattern Recognition and Image Analysis, IbPRIA, Aveiro, Portugal, p. 309-320, May 2022
- Jorge Miguel Silva, Diogo Pratas, Tania Caetano, Sérgio Matos. Archaea Taxonomic Classification. Proceedings of the 27th Portuguese Conference on Pattern Recognition, RecPad 2021, Évora, Portugal, November 2021
- Jorge Miguel Silva, Diogo Pratas, Sérgio Matos. Comparison and Evaluation of Information-based Measures in Images. Proceedings of the 26th Portuguese Conference on Pattern Recognition, RecPad 2020, Évora, Portugal, October 2020
- Morteza Hosseini, Diogo Pratas, António Amorim, João Carneiro. Improving the detection of mtDNA rearrangements using a fast and accurate algorithm. XV Encontro Nacional de Biologia Evolutiva, Porto, Portugal, November 2019
- Morteza Hosseini, Diogo Pratas, Armando J. Pinho. Clustering DNA sequences by relative compression. 25th Portuguese Conference on Pattern Recognition, RecPad, Porto, Portugal, October 2019
- Jorge Miguel Silva, Diogo Pratas, Sérgio Matos. Evaluation of Statistical Complexity in Viral Genome Sequences. 25th Portuguese Conference on Pattern Recognition, RECPAD2019, Porto, Portugal, October 2019
- 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
- ...further results
PhD thesis
- Diogo Pratas. Compression and analysis of genomic data. PhD Thesis, Universidade de Aveiro, Aveiro, Portugal, January 2016