All Stories

  1. Revealing persistent childhood viruses in the body and organs of adults

    Article • Nucleic Acids Research, March 2023, Oxford University Press (OUP)

    Dr Lari Pyöriä, Dr. Maria Fernanda Perdomo, Dr. Diogo Pratas

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

    Article • Journal of NeuroVirology, March 2023, Springer Science + Business Media

    Dr. Maria Fernanda Perdomo, Dr. Diogo Pratas

  3. Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation

    Article • Viruses, January 2022, MDPI AG

    Dr. Maria Fernanda Perdomo, Dr. Diogo Pratas

  4. Studying the Complexity Landscape of Viruses

    Article • GigaScience, January 2022, Oxford University Press (OUP)

    Jorge Miguel Silva, Dr. Diogo Pratas

  5. Identifying Archaea using Compression and Genomic Sequences

    Article • January 2022, Springer Science + Business Media

    Jorge Miguel Silva, Dr. Diogo Pratas

  6. The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

    Article • GigaScience, January 2022, Oxford University Press (OUP)

    Dr. Diogo Pratas

  7. Revisiting the Neurospora crassa mitochondrial genome

    Article • Letters in Applied Microbiology, July 2021, Oxford University Press (OUP)

    Dr. Diogo Pratas

  8. Automating Artistic Painting Analysis with Information-Based Measures

    Article • Pattern Recognition, June 2021, Elsevier

    Jorge Miguel Silva, Rui Antunes, Dr. Diogo Pratas

  9. AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models

    Article • Entropy, April 2021, MDPI AG

    Dr. Diogo Pratas

  10. The Human Bone Marrow Is Host to the DNAs of Several Viruses

    Article • Frontiers in Cellular and Infection Microbiology, April 2021, Frontiers

    Dr. Maria Fernanda Perdomo, Dr. Diogo Pratas

  11. A semi-automatic methodology for analysing distributed and private biobanks

    Article • Computers in Biology and Medicine, March 2021, Elsevier

    Dr. Diogo Pratas

  12. Efficient DNA sequence compression with neural networks

    Article • GigaScience, November 2020, Oxford University Press (OUP)

    Dr. Diogo Pratas

  13. The landscape of persistent human DNA viruses in femoral bone

    Article • Forensic Science International Genetics, September 2020, Elsevier

    Dr. Maria Fernanda Perdomo, Dr. Diogo Pratas

  14. A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level

    Article • GigaScience, August 2020, Oxford University Press (OUP)

    Dr. Maria Fernanda Perdomo, Dr Lari Pyöriä, Dr. Diogo Pratas

  15. A new method that shows the presence of short persistent DNA/RNA sequences in SARS-CoV-2

    Article • Bioinformatics, July 2020, Oxford University Press (OUP)

    Jorge Miguel Silva, Dr. Diogo Pratas

  16. GTO: A toolkit to unify pipelines in genomic and proteomic research

    Article • SoftwareX, July 2020, Elsevier

    Dr. Diogo Pratas

  17. Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements

    Article • GigaScience, May 2020, Oxford University Press (OUP)

    Dr. Diogo Pratas

  18. Uncovering patterns in Turing machine tapes

    Article • Entropy, January 2020, MDPI AG

    Jorge Miguel Silva, Dr. Diogo Pratas

  19. Enhancing DNA Sequence Compression with a Novel Weighted Model Method

    Article • Entropy, November 2019, MDPI AG

    Jorge Miguel Silva, Dr. Diogo Pratas

  20. A Probabilistic Method to Find and Visualize Distinct Regions in Protein Sequences

    Article • September 2019, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  21. GeCo2: An Optimized Tool for Lossless Compression and Analysis of DNA Sequences

    Article • June 2019, Springer Science + Business Media

    Dr. Diogo Pratas

  22. Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes

    Article • June 2019, Springer Science + Business Media

    Dr. Diogo Pratas

  23. AC: A Compression Tool for Amino Acid Sequences

    Article • Interdisciplinary Sciences Computational Life Sciences, February 2019, Springer Science + Business Media

    Dr. Diogo Pratas

  24. Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard

    Article • Genes, September 2018, MDPI AG

    Dr. Diogo Pratas

  25. Extended-alphabet finite-context models

    Article • Pattern Recognition Letters, September 2018, Elsevier

    Dr. Diogo Pratas

  26. Metagenomic composition analysis of sedimentary ancient DNA from the Isle of Wight

    Article • September 2018, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  27. A DNA Sequence Corpus for Compression Benchmark

    Article • August 2018, Springer Science + Business Media

    Dr. Diogo Pratas

  28. Compression of Amino Acid Sequences

    Article • August 2018, Springer Science + Business Media

    Dr. Diogo Pratas

  29. NET-ASAR: A Tool for DNA Sequence Search Based on Data Compression

    Article • August 2018, Springer Science + Business Media

    Dr. Diogo Pratas

  30. Cryfa: a secure encryption tool for genomic data

    Article • Bioinformatics, July 2018, Oxford University Press (OUP)

    Dr. Diogo Pratas

  31. Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes

    Article • Entropy, May 2018, MDPI AG

    Dr. Diogo Pratas

  32. An Application of Data Compression Models to Handwritten Digit Classification

    Article • January 2018, Springer Science + Business Media

    Dr. Diogo Pratas

  33. Cryfa: A Tool to Compact and Encrypt FASTA Files

    Article • January 2017, Springer Science + Business Media

    Dr. Diogo Pratas

  34. On the Approximation of the Kolmogorov Complexity for DNA Sequences

    Article • January 2017, Springer Science + Business Media

    Dr. Diogo Pratas

  35. On the Role of Inverted Repeats in DNA Sequence Similarity

    Article • January 2017, Springer Science + Business Media

    Dr. Diogo Pratas

  36. Substitutional Tolerant Markov Models for Relative Compression of DNA Sequences

    Article • January 2017, Springer Science + Business Media

    Dr. Diogo Pratas

  37. Visualization of Distinct DNA Regions of the Modern Human Relatively to a Neanderthal Genome

    Article • January 2017, Springer Science + Business Media

    Dr. Diogo Pratas

  38. A Survey on Data Compression Methods for Biological Sequences

    Article • Information, October 2016, MDPI AG

    Dr. Diogo Pratas

  39. Authorship Attribution Using Relative Compression

    Article • March 2016, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  40. Efficient Compression of Genomic Sequences

    Article • March 2016, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  41. An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

    Article • Scientific Reports, May 2015, Springer Science + Business Media

    Dr. Diogo Pratas

  42. Three minimal sequences found in Ebola virus genomes and absent from human DNA: Fig. 1.

    Article • Bioinformatics, April 2015, Oxford University Press (OUP)

    Dr. Diogo Pratas

  43. MAFCO: A Compression Tool for MAF Files

    Article • PLoS ONE, March 2015, PLOS

    Dr. Diogo Pratas

  44. A Conditional Compression Distance that Unveils Insights of the Genomic Evolution

    Article • March 2014, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  45. Information Profiles for DNA Pattern Discovery

    Article • March 2014, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  46. A New Compressor for Measuring Distances among Images

    Article • January 2014, Springer Science + Business Media

    Dr. Diogo Pratas

  47. XS: a FASTQ read simulator

    Article • BMC Research Notes, January 2014, Springer Science + Business Media

    Dr. Diogo Pratas

  48. DNA Sequences at a Glance

    Article • PLoS ONE, November 2013, PLOS

    Dr. Diogo Pratas

  49. MFCompress: a compression tool for FASTA and multi-FASTA data

    Article • Bioinformatics, October 2013, Oxford University Press (OUP)

    Dr. Diogo Pratas

  50. A Compression Model for DNA Multiple Sequence Alignment Blocks

    Article • IEEE Transactions on Information Theory, May 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  51. A Genomic Distance for Assembly Comparison Based on Compressed Maximal Exact Matches

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, May 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  52. Compressing Resequencing Data with GReEn

    Article • January 2013, Springer Science + Business Media

    Dr. Diogo Pratas

  53. Compression of Whole Genome Alignments Using a Mixture of Finite-Context Models

    Article • January 2012, Springer Science + Business Media

    Dr. Diogo Pratas

  54. Exon: A Web-Based Software Toolkit for DNA Sequence Analysis

    Article • January 2012, Springer Science + Business Media

    Dr. Diogo Pratas

  55. On the Detection of Unknown Locally Repeating Patterns in Images

    Article • January 2012, Springer Science + Business Media

    Dr. Diogo Pratas

  56. GReEn: a tool for efficient compression of genome resequencing data

    Article • Nucleic Acids Research, December 2011, Oxford University Press (OUP)

    Dr. Diogo Pratas

  57. Bacteria DNA sequence compression using a mixture of finite-context models

    Article • June 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  58. DNA synthetic sequences generation using multiple competing Markov models

    Article • June 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Diogo Pratas

  59. Complexity Profiles of DNA Sequences Using Finite-Context Models

    Article • January 2011, Springer Science + Business Media

    Dr. Diogo Pratas

  60. Compressing the Human Genome Using Exclusively Markov Models

    Article • January 2011, Springer Science + Business Media

    Dr. Diogo Pratas