Diogo Pratas
From IEETA
| Position | Post-doc researcher |  |
|---|---|---|
| Affiliation | IEETA | |
| Group | Information Systems and Processing | |
| Status | Researcher with PhD | |
| Country | Portugal | |
| Students | 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 | |
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
- 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)]
- 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
- 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
- Diogo Pratas, Armando J. Pinho. On the compression of FASTQ quality-scores. Proceedings of the 18th Portuguese Conference on Pattern Recognition, Coimbra, Portugal, October 2012
- Sara Pinto Garcia, João M. O. S. Rodrigues, Diogo Pratas, Armando J. Pinho. Comparing maximal exact repeats in human genome assemblies using a normalized compression distance. 20th Annual International Conference on Intelligent Systems for Molecular Biology, Long Beach, California, USA, July 2012
- ...further results
PhD thesis
- Diogo Pratas. Compression and analysis of genomic data. PhD Thesis, Universidade de Aveiro, Aveiro, Portugal, January 2016