Publications — Diogo Pratas

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2026

4 publications

Conference Paper

A Machine Learning Method for Authentication of Human Ancient Mitochondrial DNA

Yamunaque D., Pinho A.J., Sajantila A., Pratas D.

Lecture Notes in Computer Science, 15938 LNCS, 59–70 DOI Scopus

Journal Article Open Access

An evaluation of computational methods for reconstruction of human viral DNA genomes

Sousa M.J.P., Toppinen M., Pyöriä L., Hedman K., Sajantila A., Perdomo M.F., Pratas D.

GigaScience, 15, giaf159 DOI Scopus

Conference Paper

ECOmpress: A Web Tool for Boosting Energy Efficiency Through Data Compression

Lei D., Yamunaque D., Pinho A.J., Pratas D.

Lecture Notes in Computer Science, 15938 LNCS, 297–308 DOI Scopus

Journal Article Open Access

FALCON2: compression-based metagenomic classification of ancient viruses

Marques L.L., Pinho A.J., Pratas D.

Bioinformatics, 42(5), btag155 DOI Scopus

2025

3 publications

Conference Paper

AIDetx: A Compression-Based Method for Identification of Machine-Learning Generated Text

Almeida L., Rodrigues P., Magalhaes D., Pinho A.J., Pratas D.

Data Compression Conference Proceedings, 358 DOI Scopus

Conference Paper

Optimization of Data Compression Parameters Using Genetic Algorithms

Pinho A.J., Pratas D.

Data Compression Conference Proceedings, 395 DOI Scopus

Journal Article Open Access

Reactivation of a Transplant Recipient's Inherited Human Herpesvirus 6 and Implications to the Graft

Hannolainen L., Pyöriä L., Pratas D., Lohi J., Skuja S., Rasa-Dzelzkaleja S., Murovska M., Hedman K., Jahnukainen T., Perdomo M.F.

Journal of Infectious Diseases, 231(2), e267–e276 DOI Scopus

2024

9 publications

Conference Paper Open Access

A sensitive compression-based method for filtering targeted FASTQ sequencing reads

Sousa M.J.P., Pinho A.J., Pratas D.

European Signal Processing Conference, 1561–1565 DOI Scopus

Conference Paper Open Access

A sorting tool for improving FASTA data compression tools

Fonseca T., Sousa M.J.P., Pinho A.J., Pratas D.

European Signal Processing Conference, 1566–1570 DOI Scopus

Journal Article Open Access

AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data

Silva J.M., Pinho A.J., Pratas D.

GigaScience, 13, giae086 DOI Scopus

Conference Paper Open Access

An experimental sorting method for improving metagenomic data encoding

Pratas D., Pinho A.J.

Data Compression Conference Proceedings, 578 DOI Scopus

Conference Paper Open Access

Copy models for protein sequence compression

Pinho A.J., Pratas D.

Data Compression Conference Proceedings, 342–351 DOI Scopus

Conference Paper

Improving the generation of viral consensus sequences using adaptive models

Sousa M.J.P., Pinho A.J., Pratas D.

European Signal Processing Conference, 1691–1695 DOI Scopus

Journal Article Open Access

Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome

Pyöriä L., Pratas D., Toppinen M., Simmonds P., Hedman K., Sajantila A., Perdomo M.F.

Nucleic Acids Research, 52(21), 13073–13093 DOI Scopus

Journal Article Open Access

JARVIS3: An efficient encoder for genomic data

Sousa M.J.P., Pinho A.J., Pratas D.

Bioinformatics, 40(12), btae725 DOI Scopus

Journal Article Open Access

Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation

Soares R., Azevedo L., Vasconcelos V., Pratas D., Sousa S.F., Carneiro J.

Journal of Chemical Information and Modeling, 64(24), 9576–9593 DOI Scopus

2023

7 publications

Journal Article Open Access

AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data

Silva J.M., Qi W., Pinho A.J., Pratas D.

GigaScience, 12, giad101 DOI Scopus

Conference Paper Open Access

Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications

Silva J.M., Pratas D., Matos S.

IFIP Advances in Information and Communication Technology, 678, 161–174 DOI Scopus

Journal Article Open Access

Herpesviruses, polyomaviruses, parvoviruses, papillomaviruses, and anelloviruses in vestibular schwannoma

Jauhiainen M.K., Mohanraj U., Lehecka M., Niemelä M., Hirvonen T.P., Pratas D., Perdomo M.F., Söderlund-Venermo M., Mäkitie A.A., Sinkkonen S.T.

Journal of NeuroVirology, 29(2), 226–231 DOI Scopus

Conference Paper

JARVIS2: A data compressor for large genome sequences

Pratas D., Pinho A.J.

Data Compression Conference Proceedings, 2023-March, 288–297 DOI Scopus

Journal Article Open Access

Mapping human pathogens in wastewater using a metatranscriptomic approach

Carneiro J., Pascoal F., Semedo M., Pratas D., Tomasino M.P., Rego A., Carvalho M.D.F., Mucha A.P., Magalhães C.

Environmental Research, 231, 116040 DOI Scopus

Journal Article Open Access

TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa

Carneiro J., Magalhães R.P., de la Oliva Roque V.M., Simões M., Pratas D., Sousa S.F.

Journal of Computer-Aided Molecular Design, 37(5-6), 265–278 DOI Scopus

Journal Article Open Access

Unmasking the tissue-resident eukaryotic DNA virome in humans

Pyöriä L., Pratas D., Toppinen M., Hedman K., Sajantila A., Perdomo M.F.

Nucleic Acids Research, 51(7), 3223–3239 DOI Scopus