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Diogo Pratas was born in Aveiro. He graduated in Information and Communication Technologies at the University of Aveiro, in 2008. During his degree, he participated in the Erasmus program in Computer Engineering at the Pontifical University of Salamanca, Spain. He worked in the private sector from 2008 to 2010 in the areas of Networks and IT security and in the development of Linux systems. In 2016, he obtained his PhD in Informatics at the University of Aveiro with a dissertation on compression and analysis of genomic sequences. He carried out postdoctoral research in Computer Science from 2016 to 2019 at the University of Aveiro. In 2019, he was a Staff Bioinformatician at the University of Helsinki, Finland. Since the end of 2019, he has been an auxiliary researcher at the University of Aveiro in the areas of Informatics, Bioinformatics, and Artificial Intelligence. Since 2022, he has been a visiting researcher at the Department of Virology at the University of Helsinki, Finland. Since 2019, he teaches Algorithmic Information Theory at the Department of Electronics, Telecommunications, and Informatics at the University of Aveiro. He has organized several scientific conferences, workshops, and competitions, including the International Conference on Algorithms for Computational Biology, the Iberian Conference on Pattern Recognition, the Workshop on Genomics for Physicians, and the Portuguese League of Bioinformatics. He actively participates in scientific associations, including the European Society for Clinical Virology (ESCV) and the Portuguese Association for Pattern Recognition (APRP), having served as secretary of the APRP (2018-2020). His main areas of interest and research are Bioinformatics, Computational Biology, and Information Theory. He developed extensive research on automatic pattern recognition to analyze and minimize the content of biological information, having focused, in particular, on the subject of Computational Virology. He has participated as a speaker at various international conferences and scientific meetings and is the author of several publications and articles in the areas of Informatics, Medicine, and Biology.
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Identification

Personal identification

Full name
Diogo Pratas

Citation names

  • Pratas, Diogo

Author identifiers

Ciência ID
5A1C-F0F0-7E62
ORCID iD
0000-0003-1176-552X
Google Scholar ID
HasPwO0AAAAJ
Scopus Author Id
49361962700

Addresses

  • IEETA, Campus Universitário de Santiago, 3810-193, Aveiro, Aveiro, Portugal (Professional)

Websites

  • pratas.github.io (Scholar)

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Upper intermediate (B2) Upper intermediate (B2) Upper intermediate (B2) Upper intermediate (B2) Upper intermediate (B2)
French Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1)
Education
Degree Classification
2011/09/01 - 2016/01/19
Concluded
 Informática (Doutoramento)
Major in Bioinformática
Universidade de Aveiro, Portugal
"Compressão e análise de dados genómicos " (THESIS/DISSERTATION)
2004 - 2008
Concluded
 Técnologias de Informação e Comunicação (Licenciatura)
Universidade de Aveiro, Portugal
Affiliation

Science

Category
Host institution 		Employer
2022/06/01 - Current Visiting Researcher (Research) Helsingin Yliopisto, Finland
2019/08 - Current Auxiliary Researcher (Research) Universidade de Aveiro, Portugal
Universidade de Aveiro, Portugal
2019/03/17 - 2019/07/17 Contracted Researcher (Research) Helsingin Yliopisto, Finland
Helsingin yliopisto Haartman-instituutti, Finland

Other Careers

Category
Host institution 		Employer
2009 - 2010 Consultor de Informática (Categorias e Funções Especificas) IPortalMais, Portugal
2008 - 2008 Técnico de Informática Estagiário (Técnico de informática) Dimension Data UK, United Kingdom

Others

Category
Host institution 		Employer
2016/06/01 - 2019/03 Researcher of the project: “The normalized relative compression distance”. Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2015 - 2018 Researcher Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2012/11/01 - 2016/03/31 Researcher of the project: "RD-CONNECT – An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research" Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2012/10/01 - 2013/12/31 IEETA Integrated member. Subject: Compression and analysis of genomic data Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2011 - 2013 Researcher Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2010/07/01 - 2012/09/30 Researcher of the project: "Analysis of DNA sequences through compression based complexity profiles" Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2009/12/01 - 2010/06/30 Researcher of the project: "Finite-context models for DNA" Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Projects

Contract

Designation Funders
2024 - 2028 The Human Tissue Virome - Comprehensive Impact Analysis #5
Not Applicable
Researcher
Jane ja Aatos Erkon Säätiö
Ongoing
2023 - 2027 Time, Place, and DNA - Ancient host-pathogen genomics in Finland
Not applicable
Researcher
Helsingin Yliopisto, Finland
 Suomen Kulttuurirahasto
Ongoing
2021/01 - 2025/12 Laboratório Associado de Sistemas Inteligentes
168241UID
LA/P/0104/2020
10.54499/LA/P/0104/2020
Universidade Nova de Lisboa Centro de Tecnologias e Sistemas, Portugal

Universidade de Aveiro Centro de Tecnologia Mecânica e Automação, Portugal

Instituto Politécnico do Porto Centro de Investigação em Sistemas Computacionais Embebidos e de Tempo-Real, Portugal

Universidade do Minho, Portugal

Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Centro de Matemática, Portugal

Universidade Nova de Lisboa, Portugal

Universidade do Porto Laboratório de Inteligência Artificial e Ciência de Computadores, Portugal

Universidade de Aveiro, Portugal

Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal

Universidade do Minho Instituto de Polímeros e Compósitos, Portugal

Universidade do Minho Centro ALGORITMI, Portugal

Universidade Nova de Lisboa Unidade de Investigação e Desenvolvimento em Engenharia Mecânica e Industrial, Portugal

Universidade de Coimbra Departamento de Engenharia Civil, Portugal

Instituto Politécnico do Porto Instituto Superior de Engenharia do Porto, Portugal

Universidade de Coimbra, Portugal

Instituto Politécnico do Porto Grupo de Investigação em Engenharia e Computação Inteligente para a Inovação e o Desenvolvimento, Portugal

Instituto Politécnico do Cávado e do Ave, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021 - 2025 Molecular genetic time travel and ancient diseases
Not applicable
Researcher
Helsingin Yliopisto, Finland
 Suomalainen Tiedeakatemia
Ongoing
2023 - 2024 The Human Tissue Virome - Comprehensive Impact Analysis #3
not applicable
Researcher
Helsingin Yliopisto, Finland
 Finska Läkaresällskapet
Ongoing
2023 - 2024 The Human Tissue Virome - Comprehensive Impact Analysis #4
N/A
Researcher
Helsingin Yliopisto, Finland
 Suomen Lääketieteen Säätiö
Ongoing
2021 - 2024 Levänluhta and Käldamäki water burials – will molecules and isotopes solve an Iron Age mystery?
Not applicable
Researcher
Helsingin Yliopisto, Finland
 Koneen Säätiö
Ongoing
2020 - 2024 The Human Tissue Virome - Comprehensive Impact Analysis #2
not applicable
Researcher
Helsingin Yliopisto, Finland
 Medicinska Understödsföreningen Liv och Hälsa rf
Ongoing
2020 - 2024 Levänluhta and Käldamäki water burials – will molecules and isotopes solve an Iron Age mystery?
not applicable
Researcher
Kuvataideakatemia
2019 - 2024 Intelligent Reconstruction and Analysis of Ancient Genomes
CEECINST/00026/2018
Principal investigator
Universidade de Aveiro, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2022 - 2023 Ancient Virus Infections in the Chachapoya Population of South American Mountain Forests
not applicable
Researcher
2021 - 2022 Understanding ancient pathogen genomics – understanding future pandemics
not applicable
Researcher
Societas Scientiarum Fennica
2021 - 2022 Understanding ancient pathogen genomics – understanding future pandemics
not applicable
Researcher
2019 - 2021 The Human Tissue Virome - Comprehensive Impact Analysis #1
not applicable
Researcher
Helsingin Yliopisto, Finland
 Suomen Lääketieteen Säätiö
Concluded
2019/01/01 - 2019/12/31 Institute of Electronics and Informatics Engineering of Aveiro
UID/CEC/00127/2019
Universidade de Aveiro, Portugal

Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016 - 2019 The normalized relative compression distance
PTDC/EEI-SII/6608/2014
Post-doc Fellow
Universidade de Aveiro, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2013 - 2016 RD-CONNECT - An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research
305444
PhD Student Fellow
European Commission
Concluded
2010 - 2013 Analysis of DNA sequences through compression-based complexity profiles
PTDC/EIA-EIA/103099/2008
Research Fellow
Universidade de Aveiro, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2009 - 2010 Finite context models for DNA
PTDC/EIA/72569/2006
Research Fellow
Universidade de Aveiro, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2024/01/01 - 2025/12/31 ILLIANCE energy efficiency
10.54499/LA/P/0104/2020
Ongoing
2024/01/01 - 2025/12/31 OLI PUSH - ILLIANCE energy efficiency
10.54499/LA/P/0104/2020
Ongoing
Outputs

Publications

Book
  1. Figueiredo, D.; Martín-Vide, C.; Pratas, D.; Vega-Rodríguez, M.A.. Algorithms for Computational Biology. Springer. 2017.
    Published
Book chapter
  1. Pinho, A.J.; Pratas, D.; Garcia, S.P.. "Compressing resequencing data with GReEn". In Deep Sequencing Data Analysis,. 2013.
    10.1007/978-1-62703-514-9_2
Conference abstract
  1. Sousa, Maria J. P.; Pratas, Diogo. "A method to reconstruct persistent human viral sequences cooperatively". Paper presented in Research Summit 2024, Aveiro, 2024.
    Published
  2. Sousa, Maria J. P.; Pratas, Diogo. "A method for improving the generation of viral consensus sequences using adaptive models". Paper presented in 6th Statistics on Health Decision Making: Artificial Intelligence, SHDM 2024, Aveiro, 2024.
    Published
  3. Sousa, Maria J. P.; Pratas, Diogo. "A cooperative method to reconstruct persistent human viral sequences". Paper presented in The 20th Portugaliæ Genetica: DNA - Ancient and New, Porto, 2024.
    Published
Conference paper
  1. Sousa, Maria J. P.; Pratas, Diogo. "A method for improving the generation of consensus sequences". Paper presented in 19th Workshop on Informatics Engineering Research, WIER 2024, Porto, 2024.
    Published
  2. Sousa, Maria J. P.; Pratas, Diogo. "A method for accurate reconstruction of persistent human viral sequences". Paper presented in Portuguese Conference on Pattern Recognition, Coimbra, 2023.
    Published
  3. Jorge Miguel Silva; Diogo Pratas; Sérgio Matos. "Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications". Paper presented in Doctoral Conference on Computing, Electrical and Industrial Systems, 2023.
    Published • 10.1007/978-3-031-36007-7_12
  4. Pratas, Diogo; Pinho, Armando J.. "JARVIS2: a data compressor for large genome sequences". Paper presented in Data Compression Conference, 2023.
    10.1109/dcc55655.2023.00037
  5. J. M. Silva; D. Pratas; T. Caetano; S. Matos. "Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods". Paper presented in Pattern Recognition and Image Analysis, IbPRIA 2022, 2022.
    Published • 10.1007/978-3-031-04881-4_25
  6. Sousa, Maria J. P.; Pratas, Diogo. "A survey on computational tools for human viral genomes reconstruction". Paper presented in Portuguese Conference on Pattern Recognition, Leiria, 2022.
    Published
  7. Sousa, Maria J. P.; Rita Ferrolho; Tiago Fonseca; Armando J. Pinho; Pratas, Diogo. "Improving the compression of a complete Telomere-to- Telomere (T2T) human genome sequence". Paper presented in Portuguese Conference on Pattern Recognition, Leiria, 2022.
    Published
  8. Jorge Miguel Ferreira da Silva; Pratas, Diogo; Caetano, Tania; Matos, Sérgio. "Archaea Taxonomic Classification". Paper presented in 27th Portuguese Conference on Pattern Recognition, RecPad 2021, Évora, 2021.
    Published
  9. Jorge Miguel Ferreira da Silva; Pratas, Diogo; Matos, Sérgio. "Comparison and Evaluation of Information-based Measures in Images.". Paper presented in 26th Portuguese Conference on Pattern Recognition, RecPad 2020, Évora, 2020.
    Published
  10. Pratas, D.; Hosseini, M.; Pinho, A.J.. "Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes". Paper presented in International Conference on Practical Applications of Computational Biology & Bioinformatics, 2019.
    10.1007/978-3-030-23873-5_16
  11. Pratas, D.; Hosseini, M.; Pinho, A.J.. "GeCo2: An Optimized Tool for Lossless Compression and Analysis of DNA Sequences". Paper presented in International Conference on Practical Applications of Computational Biology & Bioinformatics, 2019.
    10.1007/978-3-030-23873-5_17
  12. Hosseini, M.; Pratas, D.; Pinho, A.J.. "A probabilistic method to find and visualize distinct regions in protein sequences". 2019.
    10.23919/EUSIPCO.2019.8902695
  13. Pratas, D.; Pinho, A.J.. "A DNA sequence corpus for compression benchmark". Paper presented in International Conference on Practical Applications of Computational Biology & Bioinformatics, 2019.
    10.1007/978-3-319-98702-6_25
  14. Hosseini, Morteza; Pratas, Diogo; Armando J. Pinho. "Clustering DNA sequences by relative compression". Paper presented in 25th Portuguese Conference on Pattern Recognition, RecPad 2019, Porto, 2019.
    Published
  15. Jorge Miguel Ferreira da Silva; Pratas, Diogo; Matos, Sérgio. "Evaluation of Statistical Complexity in Viral Genome Sequences". Paper presented in 25th Portuguese Conference on Pattern Recognition, RecPad 2019, Porto, Porto, 2019.
    Published
  16. Pratas, D.; Hosseini, M.; Pinho, A.J.. "Compression of amino acid sequences". Paper presented in International Conference on Practical Applications of Computational Biology & Bioinformatics, 2018.
    10.1007/978-3-319-98702-6_13
  17. Gaspar, M.; Pratas, D.; Pinho, A.J.. "NET-ASAR: A tool for DNA sequence search based on data compression". Paper presented in NET-ASAR: A tool for DNA sequence search based on data compression, 2018.
    10.1007/978-3-319-98702-6_14
  18. Pratas, D.; Pinho, A.J.. "Metagenomic composition analysis of sedimentary ancient DNA from the Isle of Wight". 2018.
    10.23919/EUSIPCO.2018.8553297
  19. Pinho, A.J.; Pratas, D.. "An Application of Data Compression Models to Handwritten Digit Classification". Paper presented in International Conference on Advanced Concepts for Intelligent Vision Systems, 2018.
    10.1007/978-3-030-01449-0_41
  20. Ana Teixeia; Pratas, Diogo; Armando J. Pinho; Raquel M. Silva. "Evolutionary insights from the comparative analysis of hominid genomes". Paper presented in 24th Portuguese Conference on Pattern Recognition, RecPad 2018, Coimbra, 2018.
    Published
  21. Catarina Figueiredo; Pratas, Diogo; Armando J. Pinho; Raquel M. Silva. "Identification of antifungal targets using alignment-free methods". Paper presented in 24th Portuguese Conference on Pattern Recognition, RecPad 2018, Coimbra, 2018.
    Published
  22. Pratas, D.; Hosseini, M.; Pinho, A.J.. "Substitutional tolerant markov models for relative compression of DNA sequences". Paper presented in International Conference on Practical Applications of Computational Biology, 2017.
    10.1007/978-3-319-60816-7_32
  23. Pratas, D.; Hosseini, M.; Pinho, A.J.. "Cryfa: A tool to compact and encrypt FASTA files". Paper presented in 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017.
    10.1007/978-3-319-60816-7_37
  24. Pratas, D.; Pinho, A.J.. "On the approximation of the Kolmogorov complexity for DNA sequences". Paper presented in Book cover Iberian Conference on Pattern Recognition and Image Analysis, 2017.
    10.1007/978-3-319-58838-4_29
  25. Hosseini, M.; Pratas, D.; Pinho, A.J.. "On the role of inverted repeats in DNA sequence similarity". Paper presented in International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017.
    10.1007/978-3-319-60816-7_28
  26. Pratas, D.; Hosseini, M.; Silva, R.M.; Pinho, A.J.; Ferreira, P.J.S.G.. "Visualization of distinct DNA regions of the modern human relatively to a neanderthal genome". Paper presented in Book cover Iberian Conference on Pattern Recognition and Image Analysis, 2017.
    10.1007/978-3-319-58838-4_26
  27. Pratas, D.; Pinho, A.J.; Ferreira, P.J.S.G.. "Efficient Compression of Genomic Sequences". 2016.
    10.1109/DCC.2016.60
  28. Pinho, A.J.; Pratas, D.; Ferreira, P.J.S.G.. "Authorship Attribution Using Relative Compression". 2016.
    10.1109/DCC.2016.53
  29. Pratas, Diogo; Raquel M. Silva; Armando J. Pinho. "Detection and visualisation of regions of human DNA not present in other primates". Paper presented in 21st Portuguese Conference on Pattern Recognition, RecPad 2015, Faro, 2015.
    Published
  30. Pratas, D.; Pinho, A.J.. "A conditional compression distance that unveils insights of the genomic evolution". 2014.
    10.1109/DCC.2014.58
  31. Pratas, D.; Pinho, A.J.. "Exploring deep Markov models in genomic data compression using sequence pre-analysis". 2014.
  32. Pinho, A.J.; Pratas, D.; Ferreira, P.J.S.G.. "Information profiles for DNA pattern discovery". 2014.
    10.1109/DCC.2014.54
  33. Pinho, A.J.; Pratas, D.; Ferreira, P.J.S.G.. "A new compressor for measuring distances among images". Paper presented in International Conference Image Analysis and Recognition, 2014.
    10.1007/978-3-319-11758-4_4
  34. Pratas, Diogo; Raquel M. Silva; Armando J. Pinho. "Large-scale inversions between human reference assemblies". Paper presented in 20th Portuguese Conference on Pattern Recognition, RecPad 2014, Covilhã, 2014.
    Published
  35. Raquel M. Silva; Castro, Luísa; Pratas, Diogo; Armando J. Pinho. "Towards personalized medicine: ebola virus absent words in the human genome". Paper presented in 20th Portuguese Conference on Pattern Recognition, RecPad 2014, Covilhã, 2014.
    Published
  36. Pratas, Diogo; Armando J. Pinho. "Insights into primates genomic evolution using a compression distance". Paper presented in 19th Portuguese Conference on Pattern Recognition, RecPad 2013, Lisbon, 2013.
    Published
  37. Pratas, D.; Pinho, A.J.; Garcia, S.P.. "Computation of the normalized compression distance of DNA sequences using a mixture of finite-context models". 2012.
  38. Pratas, D.; Pinho, A.J.. "On the detection of unknown locally repeating patterns in images". Paper presented in International Conference Image Analysis and Recognition, 2012.
    10.1007/978-3-642-31295-3_19
  39. Pratas, D.; Pinho, A.J.; Garcia, S.P.. "Exon: A web-based software toolkit for DNA sequence analysis". Paper presented in 6th International Conference on Practical Applications of Computational, 2012.
    10.1007/978-3-642-28839-5_25
  40. Matos, L.M.O.; Pratas, D.; Pinho, A.J.. "Compression of whole genome alignments using a mixture of finite-context models". Paper presented in nternational Conference Image Analysis and Recognition, 2012.
    10.1007/978-3-642-31295-3_42
  41. Pratas, Diogo; Armando J. Pinho. "On the compression of FASTQ quality-scores". Paper presented in 18th Portuguese Conference on Pattern Recognition, RecPad 2012, Coimbra, 2012.
    Published
  42. Pratas, Diogo; Armando J. Pinho. "M6: a method for compressing complete genomes using markov models". Paper presented in 7th Doctoral Symposium in Informatics Engineering, DSIE 2012, Porto, 2012.
    Published
  43. Pratas, D.; Bastos, C.A.C.; Pinho, A.J.; Neves, A.J.R.; Matos, L.M.O.. "DNA synthetic sequences generation using multiple competing Markov models". 2011.
    10.1109/SSP.2011.5967639
  44. Pinho, A.J.; Pratas, D.; Ferreira, P.J.S.G.. "Bacteria DNA sequence compression using a mixture of finite-context models". 2011.
    10.1109/SSP.2011.5967637
  45. Pinho, A.J.; Pratas, D.; Ferreira, P.J.S.G.; Garcia, S.P.. "Symbolic to numerical conversion of DNA sequences using finite-context models". 2011.
  46. Pratas, D.; Pinho, A.J.. "Compressing the human genome using exclusively Markov models". Paper presented in 5th International Conference on Practical Applications of Computational, 2011.
    10.1007/978-3-642-19914-1_29
  47. Pinho, A.J.; Pratas, D.; Garcia, S.P.. "Complexity profiles of DNA sequences using finite-context models". Paper presented in Symposium of the Austrian HCI and Usability Engineering Group, 2011.
    10.1007/978-3-642-25364-5_8
  48. Pratas, Diogo; Sara P. Garcia; Armando J. Pinho. "Analysis of patterns in S. pombe genome through compression-based complexity profiles". Paper presented in 17th Portuguese Conference on Pattern Recognition, RecPad 2011, Porto, 2011.
    Published
  49. Pratas, Diogo; Armando J. Pinho. "Analysis of DNA sequences using finite-context modelling and compression". Paper presented in 16th Portuguese Conf. on Pattern Recognition, RecPad 2010, Vila Real, 2010.
    Published
  50. Pratas, Diogo; Armando J. Pinho; Neves, Antonio J. R.; Carlos A. C. Bastos. "DNA synthetic sequences generated by finite-context models". Paper presented in 16th Portuguese Conf. on Pattern Recognition, RecPad 2010, Vila Real, 2010.
    Published
Conference poster
  1. C013-652B-F437; Sousa, Sérgio F.; Vítor J. Sá; Pratas, Diogo; Carneiro, João. "A Multi-Omics and Primer Database for Virus Identification: Focus on HIV, Ebola, and SARS-CoV-2". Paper presented in XIX International meeting of Portuguese Association for Evolutionary Biology (ENBE), 2024.
  2. Diana Lourenço; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. "Exploring Microalgae-Enzymes for Sustainable Plastic Biodegradation". Paper presented in XIX International meeting of Portuguese Association for Evolutionary Biology (ENBE), 2024.
  3. Sousa, Maria J. P.; Pinho, Armando J.; Pratas, Diogo. "Improving the generation of viral consensus sequences using adaptive models". Paper presented in 32nd European Signal Processing Conference, EUSIPCO 2024, 2024.
  4. Sousa, Maria J. P.; Pinho, Armando J.; Pratas, Diogo. "A sensitive compression-based method for filtering targeted FASTQ sequencing reads". Paper presented in 32nd European Signal Processing Conference, EUSIPCO 2024, 2024.
  5. Fonseca, Tiago; Sousa, Maria J. P.; Armando J Pinho; Pratas, Diogo. "A sorting tool for improving FASTA data compression tools". Paper presented in 32nd European Signal Processing Conference, EUSIPCO 2024, 2024.
  6. 761B-0575-6338 ; 671E-AA3E-3770; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Decoding the Genomic Diversity of Hepatitis E Virus in European Rabbits: A Step Towards Understanding Zoonotic Transmission". Paper presented in "The 20th Portugaliæ Genetica: DNA - Ancient and New" 21-22 March 2024, 2024.
  7. 761B-0575-6338 ; 671E-AA3E-3770; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Evolutionary Insights into Plastic-Degrading Enzymes: A Data-Driven Approach to Bioremediation". Paper presented in "The 20th Portugaliæ Genetica: DNA - Ancient and New" 21-22 March 2024, 2024.
  8. Mariana Fernandes; Clara Cerqueira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. "Exploring the Evolution of PET-Degrading Enzymes: Insights from Sequence Alignment and Phylogenetic Analysis". Paper presented in "The 20th Portugaliæ Genetica: DNA - Ancient and New" 21-22 March 2024, 2024.
  9. Clara Cerqueira; E11D-C109-D995; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Creating a Comprehensive Database of Plastic Degrading Enzymes for Machine Learning Applications". Paper presented in Bioinformatics Open Days XIII Edition 14-16 March 2024, 2024.
  10. Mariana Fernandes; Clara Cerqueira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. "Unifying Information on Plastic Degrading Enzymes Across Different Databases". Paper presented in Bioinformatics Open Days XIII Edition 14-16 March 2024, 2024.
Journal article
  1. Maria J P Sousa; Armando J Pinho; Diogo Pratas; Inanc Birol. "JARVIS3: an efficient encoder for genomic data". Bioinformatics (2024): https://doi.org/10.1093/bioinformatics/btae725.
    10.1093/bioinformatics/btae725
  2. Renato Soares; Luísa Azevedo; Vitor Vasconcelos; D. Pratas; Sérgio F. Sousa; João Carneiro. "Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds". Journal of Chemical Information and Modeling 64 24 (2024): 9576-9593. https://researchportal.helsinki.fi/en/publications/dedb78f5-39c5-49de-8a99-2c56bb3a0d8e.
    10.1021/acs.jcim.4c00995
  3. Jorge Miguel Ferreira da Silva; Armando J Pinho; Diogo Pratas. "AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data". (2024): https://doi.org/10.1093/gigascience/giae086.
    10.1093/gigascience/giae086
  4. Lari Pyöriä; Diogo Pratas; Mari Toppinen; Peter` Simmonds; Klaus Hedman; Antti Sajantila; Maria Perdomo. "Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome". (2024): https://doi.org/10.1093/nar/gkae871.
    10.1093/nar/gkae871
  5. Leo Hannolainen; Lari Pyöriä; D. Pratas; Jouko Lohi; Sandra Skuja; Santa Rasa-Dzelzkaleja; Modra Murovska; et al. "Reactivation of a Transplant Recipient's Inherited Human Herpesvirus 6 and Implications to the Graft". Journal of Infectious Diseases (2024): https://researchportal.helsinki.fi/en/publications/673f742b-dfd9-4443-95c5-04771b0c33ae.
    10.1093/infdis/jiae268
  6. Leo Hannolainen; Lari Pyöriä; D. Pratas; Jouko Lohi; Sandra Skuja; Santa Rasa-Dzelzkaleja; Modra Murovska; et al. "Perinnöllinen herpesvirus elinsiirron kiusana". Duodecim 140 13-14 (2024): https://researchportal.helsinki.fi/en/publications/b5a46b4a-396d-48a1-9981-4b5424aa3d51.
  7. Silva, Jorge M; Qi, Weihong; Pinho, Armando J; Pratas, Diogo. "AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data". GigaScience 12 (2023): http://dx.doi.org/10.1093/gigascience/giad101.
    10.1093/gigascience/giad101
  8. João Carneiro; Francisco Pascoal; Miguel Semedo; Diogo Pratas; Maria Paola Tomasino; Adriana Rego; Carvalho MF; Ana Paula Mucha; Catarina Magalhães. "Mapping human pathogens in wastewater using a metatranscriptomic approach". Environmental Research (2023): 116040-116040. http://dx.doi.org/10.1016/j.envres.2023.116040.
    10.1016/j.envres.2023.116040
  9. João Carneiro; Rita P. Magalhães; Victor M. de la Oliva Roque; Manuel Simões; D. Pratas; Sergio F. Sousa. "TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa". Journal of Computer-Aided Molecular Design (2023): http://dx.doi.org/10.1007/s10822-023-00505-5.
    10.1007/s10822-023-00505-5
  10. Lari Pyöriä; D. Pratas; Mari Toppinen; Klaus Hedman; Antti Sajantila; Maria F. Perdomo. "Elimistömme on lukuisten terveyteemme vaikuttavien virusten koti". Duodecim 139 8 (2023): https://researchportal.helsinki.fi/en/publications/be81265b-11ca-4bdd-832d-11269fc86887.
  11. Lari Pyöriä; D. Pratas; Mari Toppinen; Klaus Hedman; Antti Sajantila; Maria F. Perdomo. "Unmasking the tissue-resident eukaryotic DNA virome in humans". Nucleic Acids Research (2023): http://dx.doi.org/10.1093/nar/gkad199.
    10.1093/nar/gkad199
  12. Maria Jauhiainen; Ushanandini Mohanraj; Martin Lehecka; Mika Niemelä; Timo P. Hirvonen; Diogo Pratas; Maria F. Perdomo; et al. "Herpesviruses, polyomaviruses, parvoviruses, papillomaviruses, and anelloviruses in vestibular schwannoma". Journal of NeuroVirology (2023): http://dx.doi.org/10.1007/s13365-023-01112-8.
    10.1007/s13365-023-01112-8
  13. Weihong Qi; Yi-Wen Lim; Andrea Patrignani; Pascal Schläpfer; Anna Bratus-Neuenschwander; Simon Grüter; Christelle Chanez; et al. Corresponding author: Wilhelm Gruissem. "The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features". GigaScience 11 (2022): http://dx.doi.org/10.1093/gigascience/giac028.
    10.1093/gigascience/giac028
  14. Outi Ilona Mielonen; D. Pratas; Klaus Hedman; Antti Sajantila; Maria Fernanda Perdomo Cruz. "Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation". Viruses (2022): https://www.mdpi.com/1999-4915/14/1/133.
    10.3390/v14010133
  15. Silva, Jorge Miguel; Pratas, Diogo; Caetano, Tânia; Matos, Sérgio. "The complexity landscape of viral genomes". GigaScience 11 (2022): http://dx.doi.org/10.1093/gigascience/giac079.
    10.1093/gigascience/giac079
  16. J Monteiro; Pratas, Diogo; A Videira; F Pereira. Corresponding author: F Pereira. "Revisiting the Neurospora crassa mitochondrial genome". Letters in Applied Microbiology 73 4 (2021): 495-505. http://dx.doi.org/10.1111/lam.13538.
    10.1111/lam.13538
  17. Mari Toppinen; A Sajantila; Pratas, Diogo; K Hedman; MF Perdomo. Corresponding author: MF Perdomo. "The Human Bone Marrow Is Host to the DNAs of Several Viruses". Frontiers in Cellular and Infection Microbiology 11 (2021): http://dx.doi.org/10.3389/fcimb.2021.657245.
    10.3389/fcimb.2021.657245
  18. Milton Silva; D. Pratas; Armando J Pinho. "AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models". Entropy (2021): https://www.mdpi.com/1099-4300/23/5/530.
    10.3390/e23050530
  19. Silva, J.M.; Pratas, D.; Antunes, R.; Matos, S.; Pinho, A.J.. "Automatic analysis of artistic paintings using information-based measures". Pattern Recognition 114 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85100446723&partnerID=MN8TOARS.
    10.1016/j.patcog.2021.107864
  20. Almeida, J.R.; Pratas, D.; Oliveira, J.L.. "A semi-automatic methodology for analysing distributed and private biobanks". Computers in Biology and Medicine 130 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85098456035&partnerID=MN8TOARS.
    10.1016/j.compbiomed.2020.104180
  21. Pratas, Diogo. "Efficient DNA sequence compression with neural networks". GigaScience 9 11 (2020): http://dx.doi.org/10.1093/gigascience/giaa119.
    10.1093/gigascience/giaa119
  22. Pratas, Diogo. "The landscape of persistent human DNA viruses in femoral bone". Forensic Science International: Genetics (2020): http://dx.doi.org/10.1016/j.fsigen.2020.102353.
    10.1016/j.fsigen.2020.102353
  23. Pratas, Diogo. "A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level". GigaScience (2020): http://dx.doi.org/10.1093/gigascience/giaa086.
    10.1093/gigascience/giaa086
  24. Pratas, Diogo. "Persistent minimal sequences of SARS-CoV-2". Bioinformatics (2020): http://dx.doi.org/10.1093/bioinformatics/btaa686.
    10.1093/bioinformatics/btaa686
  25. Pratas, Diogo. "GTO: A toolkit to unify pipelines in genomic and proteomic research". SoftwareX (2020): http://dx.doi.org/10.1016/j.softx.2020.100535.
    10.1016/j.softx.2020.100535
  26. Pratas, Diogo. "Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements". GigaScience (2020): http://dx.doi.org/10.1093/gigascience/giaa048.
    10.1093/gigascience/giaa048
  27. Jorge Miguel Silva; Eduardo Pinho; Sérgio Matos; D. Pratas. "Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model". Entropy (2020): https://www.mdpi.com/1099-4300/22/1/105.
    10.3390/e22010105
  28. D. 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 (2019): https://www.mdpi.com/1099-4300/21/11/1074.
    10.3390/e21111074
  29. Hosseini, M.; Pratas, D.; Pinho, A.J.. "AC: A Compression Tool for Amino Acid Sequences". Interdisciplinary Sciences: Computational Life Sciences 11 1 (2019): 68-76. http://www.scopus.com/inward/record.url?eid=2-s2.0-85062690507&partnerID=MN8TOARS.
    10.1007/s12539-019-00322-1
  30. Hosseini, M.; Pratas, D.; Pinho, A.J.. "Cryfa: A secure encryption tool for genomic data". Bioinformatics 35 1 (2019): 146-148. http://www.scopus.com/inward/record.url?eid=2-s2.0-85058744156&partnerID=MN8TOARS.
    10.1093/bioinformatics/bty645
  31. D. Pratas; Morteza Hosseini; Gonçalo Grilo; Armando J Pinho; Raquel M Silva; Caetano T; João Carneiro; Filipe Pereira. "Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard". Genes (2018): http://www.mdpi.com/2073-4425/9/9/445.
    10.3390/genes9090445
  32. Pratas, Diogo. "Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes". Entropy (2018): http://www.mdpi.com/1099-4300/20/6/393.
    10.3390/e20060393
  33. Carvalho, João M.; Brás, Susana; Pratas, Diogo; Ferreira, Jacqueline; Soares, Sandra C.; Pinho, Armando J.. "Extended-alphabet finite-context models". (2018): http://hdl.handle.net/10773/27612.
    10.1016/j.patrec.2018.05.026
  34. Hosseini, M.; Pratas, D.; Pinho, A.J.. "A survey on data compression methods for biological sequences". Information (Switzerland) 7 4 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-85007393441&partnerID=MN8TOARS.
    10.3390/info7040056
  35. Pratas, D.; Silva, R.M.; Pinho, A.J.; Ferreira, P.J.S.G.. "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports 5 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84929429321&partnerID=MN8TOARS.
    10.1038/srep10203
  36. Matos, L.M.O.; Neves, A.J.R.; Pratas, D.; Pinho, A.J.. "Mafco: A compression tool for MAF files". PLoS ONE 10 3 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84929484087&partnerID=MN8TOARS.
    10.1371/journal.pone.0116082
  37. Silva, R.M.; Pratas, D.; Castro, L.; Pinho, A.J.; Ferreira, P.J.S.G.. "Three minimal sequences found in Ebola virus genomes and absent from human DNA". Bioinformatics 31 15 (2015): 2421-2425. http://www.scopus.com/inward/record.url?eid=2-s2.0-84943639957&partnerID=MN8TOARS.
    10.1093/bioinformatics/btv189
  38. Pratas, D.; Pinho, A.J.; Rodrigues, J.M.. "XS: a FASTQ read simulator.". BMC research notes 7 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84908135542&partnerID=MN8TOARS.
    10.1186/1756-0500-7-40
  39. Pinho, A.J.; Pratas, D.. "Mfcompress: A compression tool for fasta and multi-fasta data". Bioinformatics 30 1 (2014): 117-118. http://www.scopus.com/inward/record.url?eid=2-s2.0-84891355058&partnerID=MN8TOARS.
    10.1093/bioinformatics/btt594
  40. De Matos, L.M.O.; Pratas, D.; Pinho, A.J.. "A compression model for DNA multiple sequence alignment blocks". IEEE Transactions on Information Theory 59 5 (2013): 3189-3198. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876759103&partnerID=MN8TOARS.
    10.1109/TIT.2012.2236605
  41. Garcia, S.P.; Rodrigues, J.M.O.S.; Santos, S.; Pratas, D.; Afreixo, V.; Bastos, C.A.C.; Ferreira, P.J.S.G.; Pinho, A.J.. "A genomic distance for assembly comparison based on compressed maximal exact matches". IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 3 (2013): 793-798. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887940267&partnerID=MN8TOARS.
    10.1109/TCBB.2013.77
  42. Pinho, A.J.; Garcia, S.P.; Pratas, D.; Ferreira, P.J.S.G.. "DNA sequences at a glance". PLoS ONE 8 11 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84896690677&partnerID=MN8TOARS.
    10.1371/journal.pone.0079922
  43. Pinho, A.J.; Pratas, D.; Garcia, S.P.. "GReEn: A tool for efficient compression of genome resequencing data". Nucleic Acids Research 40 4 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84857860662&partnerID=MN8TOARS.
    10.1093/nar/gkr1124
Online resource
  1. Clara Cerqueira; Mariana Fernandes; Joana Rocha; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. Plastizyme: a central Hub for plastic biodegradation research. 2024. https://ml3denzymeoptimization.jc-biotechaiteam.com/.
  2. Margarida Cardeano Pinheiro; Abrantes, Joana; Lopes, Ana M; Pratas, Diogo; Carneiro, João. HEV in European Rabbits Resource Hub. 2024. https://rhev-primers-identification-db.jc-biotechaiteam.com/.
  3. Rafael Primo Vieira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. AptaCom: Bridging aptamer knowledge. 2024. http://jc-biotechaiteam.com/AptaCom.
Preprint
  1. Jorge Miguel Silva; Weihong Qi; Armando J Pinho; D. Pratas. "AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data". 2022. http://dx.doi.org/10.1101/2023.04.17.537157.
    10.1101/2023.04.17.537157
  2. Diogo Pratas; Armando J. Pinho; Raquel M. Silva; João M. O. S. Rodrigues; Morteza Hosseini; Tânia Caetano; Paulo J. S. G. Ferreira. "FALCON-meta: a method to infer metagenomic composition of ancient DNA". 2018. https://doi.org/10.1101/267179.
    10.1101/267179
Thesis / Dissertation
  1. Pratas, Diogo. "Compression and analysis of genomic data". PhD, 2016. http://hdl.handle.net/10773/16286.

Other

Software
  1. Jorge Miguel Silva; Pratas, Diogo. "canvas: Complexity Analysis Viral Sequences". 1.0. Universidade de Aveiro Instituto de Engenharia Electrónica e Telemática de Aveiro. https://github.com/jorgeMFS/canvas. 2022.
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023 - Current Intelligent reconstruction and analysis of viral genome sequences
Supervisor
Universidade de Aveiro, Portugal
2023 - Current Study of the impact of data compression on reducing energy consumption
Supervisor
Universidade de Aveiro, Portugal
2023 - Current Age estimation of ancient DNA samples in archaeology
Supervisor
Universidade de Aveiro, Portugal
2022 - Current Parameter optimization for improving data compession of DNA sequences
Supervisor
Universidade de Aveiro, Portugal
2023 - 2024 Machine Learning-Enhanced Optimization of Plastic-Degrading Enzymes for Sustainable Ocean Cleanup
Supervisor
Universidade do Porto, Portugal
2023 - 2024 Designing Optimal 3D Enzyme Computational Models for Efficient Plastic Degradation
Co-supervisor
Universidade do Porto, Portugal
2023 - 2024 Designing In-Silico Aptamers for Potential Use in Marine Bioremediation
Co-supervisor
Universidade do Porto, Portugal
2023 - 2024 Genomic Diversity and Zoonotic Potential of Hepatitis E Virus in European Rabbits: Implications for Diagnostic and Therapeutic Approaches
Supervisor
Universidade do Porto, Portugal
2022 - 2023 Impact of sorting in DNA sequence compression
Supervisor
Universidade de Aveiro, Portugal
2022 - 2023 Improving a Database of Cyanobacterial Bioactive Compounds that can be used for Therapeutic Approaches in Human Diseases.
Co-supervisor
Universidade do Porto, Portugal
2022 - 2023 Automatic reconstruction of persistent human virus genome
Supervisor
Universidade de Aveiro, Portugal
2019 - 2023 Algorithmic Information Approximations in Data Analysis
Co-supervisor
Universidade de Aveiro, Portugal
2020 - 2021 Reconstruction and classification of unknown DNA sequences
Supervisor
Universidade de Aveiro, Portugal
2020 - 2021 Efficient biosequence compression using neural network
Supervisor
Universidade de Aveiro, Portugal
2016 - 2020 Compression models and tools for omics data
Co-supervisor
Universidade de Aveiro, Portugal
2016 - 2017 Automatic system for approximate and noncontiguous DNA sequences search
Co-supervisor
Universidade de Aveiro, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2022 - Current Liga Portuguesa de Bioinformática (https://lpb.pt) (2022)
Other (Co-organisor)
2021 - 2022 Iberian Conference on Pattern Recognition and Image Analysis (2022/05/04 - 2022/05/06)
Conference (Member of the Organising Committee)
 Universidade de Aveiro, Portugal
2019/03 - 2019/06 Workshop on Genomics for Physicians (2019/04 - 2019/06)
Workshop (Co-organisor)
 Helsingin Yliopisto, Finland
2017 - 2017 International Conference on Algorithms for Computational Biology (2017/06/05 - 2017/06/06)
Conference (Co-organisor)
 Universidade de Aveiro, Portugal
2016 - 2016 Portuguese Conference on Pattern Recognition (2016/10/28 - 2016/10/28)
Conference (Member of the Organising Committee)
 Universidade de Aveiro, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023 Molecular evolution of DNA topoisomerases in animals
(Thesis) Arguer
 Filipa Moreira (PhD)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2022 Development of DNA sequence classifiers based on deep learning
(Thesis) Main arguer
 João Abreu (Master)
Universidade do Minho, Portugal

Association member

Society Organization name Role
2019 - Current European Society for Clinical Virology Membro
2015 - Current Portuguese Association for Pattern Recognition Membro (ex Secretário)
2007 - Current Super Dimension Fortress
2019 - 2020 International Society for Computational Biology Member

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2019 - Current Algorithmic Information Theory (Mestrado) Universidade de Aveiro, Portugal
2013 - 2014 Programming I (Licenciatura) Universidade de Aveiro, Portugal

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2023/06/15 - 2023/06/16 International Review Panel – Future Digital Challenge Concept Phase Review – Green Transition and Digital Transformation
Evaluator
 Science Foundation Ireland, Ireland Science Foundation Ireland
Distinctions

Other distinction

2024 Honor mention at SHDM 2024 – 6th Statistics on Health Decision Making (SHDM)
2018 Award of scientific excellence, Toledo, Spain
2018 Best oral communication: "Metagenomic composition analysis of ancient DNA samples", 18th Portugaliæ Genetica Genetic Diversity in Structure and Regulation, 22 & 23 March 2018, I3S, Porto, Portugal
2015 Best paper at RECPAD 2015, Faro, Portugal
Universidade do Algarve, Portugal
2013 Honor mention at Research Day 2013
Universidade de Aveiro, Portugal
2012 PAAMS'12 Award of scientific excellence, Salamanca, Spain