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  1. A systematic review and benchmarking of modern metagenomic tools for taxonomic classification

    Article • Computers in Biology and Medicine, April 2026, Elsevier

    Dr. Jorge Miguel Silva

  2. HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification

    Article • GigaScience, January 2026, Oxford University Press (OUP)

    Dr. Jorge Miguel Silva

  3. A Hybrid Metagenomic Pipeline for Taxonomic Classification

    Article • November 2025, Springer Science + Business Media

    Dr. Jorge Miguel Silva

  4. VCFX: A Minimalist, Modular Toolkit for Streamlined Variant Analysis

    Article • November 2025, Springer Science + Business Media

    Dr. Jorge Miguel Silva

  5. BioChef: A Client-Side WebAssembly-Based Workflow Builder for Genomic Data Analysis

    Article • October 2025, Springer Science + Business Media

    Dr. Jorge Miguel Silva

  6. How Can We Train AI Models Together Without Sharing Patient Data

    Article • June 2025, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Jorge Miguel Silva

  7. PhenoQC: fast quality checks for clinical phenotype tables in genomic research

    Article • Informatics in Medicine Unlocked, January 2025, Elsevier

    Dr. Jorge Miguel Silva

  8. Phenoqc: An Integrated Toolkit for Quality Control of Phenotypic Data in Genomic Research

    Article • January 2025, Elsevier

    Dr. Jorge Miguel Silva

  9. Phenoqc: An Integrated Toolkit for Quality Control of Phenotypic Data in Genomic Research

    Article • January 2025, Elsevier

    Dr. Jorge Miguel Silva

  10. Using Data Compression to Classify DNA: A Faster, Smarter Way to Identify Organisms

    Article • Artificial Intelligence in Medicine, October 2024, Elsevier

    Dr. Jorge Miguel Silva

  11. A comprehensive study of databases to assess the reliability of metagenomic tools

    Article • August 2024, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Jorge Miguel Silva

  12. HealthDBFinder: a question-answering task for health database discovery

    Article • June 2024, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Jorge Miguel Silva

  13. AltaiR: A Powerful Tool for Analyzing Large-Scale Genome Data Without Alignments

    Article • GigaScience, January 2024, Oxford University Press (OUP)

    Dr. Jorge Miguel Silva

  14. A FAIR Approach to Real-World Health Data Management and Analysis

    Article • June 2023, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Jorge Miguel Silva

  15. SecureFASTA: Ensuring privacy and trust when sharing genomic data

    Article • June 2023, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Jorge Miguel Silva

  16. A Reliable and Secure Method for Sharing Genomic Data

    Article • May 2023, IOS Press

    Dr. Jorge Miguel Silva

  17. AlcoR: A User-Friendly Tool to Identify and Visualize Low-Complexity Regions in Genomic Sequences

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Dr. Jorge Miguel Silva

  18. Classifying and discovering genomic sequences in metagenomic repositories

    Article • Procedia Computer Science, January 2023, Elsevier

    Dr. Jorge Miguel Silva

  19. Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications

    Article • January 2023, Springer Science + Business Media

    Dr. Jorge Miguel Silva

  20. Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach

    Article • January 2023, Springer Science + Business Media

    Dr. Jorge Miguel Silva

  21. AlcoR: A User-Friendly Tool to Identify and Visualize Low-Complexity Regions in Genomic Sequences

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

    Dr. Jorge Miguel Silva

  22. A New Approach to Organizing Genetic Material in Environmental Samples

    Article • August 2022, IOS Press

    Dr. Jorge Miguel Silva, João Rafael Almeida

  23. Using compression to improve taxonomic identification of unknown organisms

    Article • July 2022, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Jorge Miguel Silva, João Rafael Almeida

  24. Studying the Complexity Landscape of Viruses

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

    Dr. Jorge Miguel Silva, Dr. Diogo Pratas

  25. Identifying Archaea using Compression and Genomic Sequences

    Article • January 2022, Springer Science + Business Media

    Dr. Jorge Miguel Silva, Dr. Diogo Pratas

  26. Automating Artistic Painting Analysis with Information-Based Measures

    Article • Pattern Recognition, June 2021, Elsevier

    Dr. Jorge Miguel Silva, Rui Antunes, Dr. Diogo Pratas

  27. 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)

    Dr. Jorge Miguel Silva, Dr. Diogo Pratas

  28. Improving Medical Education and Research with the Dicoogle Framework

    Article • July 2020, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Jorge Miguel Silva

  29. Uncovering patterns in Turing machine tapes

    Article • Entropy, January 2020, MDPI AG

    Dr. Jorge Miguel Silva, Dr. Diogo Pratas

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

    Article • Entropy, November 2019, MDPI AG

    Dr. Jorge Miguel Silva, Dr. Diogo Pratas

  31. Web-based DICOM Validation Service for Improved Medical Imaging Interoperability

    Article • Computer Standards & Interfaces, January 2019, Elsevier

    Dr. Jorge Miguel Silva

  32. Revolutionizing Diabetic Retinopathy Detection with a Collaborative Platform

    Article • International Journal of Medical Informatics, December 2018, Elsevier

    Dr. Jorge Miguel Silva

  33. Automating Heart Function Classification using AI in TTE Exams

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

    Dr. Jorge Miguel Silva

  34. Ensuring Patient Privacy in Neuroimaging Studies: A Facial De-Identification Service

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

    Dr. Jorge Miguel Silva

  35. Secure and Searchable Medical Imaging for Sharing and Research

    Article • Journal of Biomedical Informatics, January 2018, Elsevier

    Dr. Jorge Miguel Silva

  36. Opinionated Framework for Building Reactive Services for Web Development

    Article • January 2018, Scitepress

    Dr. Jorge Miguel Silva

  37. SCREEN-DR

    Article • January 2018, IOS Press

    Dr. Jorge Miguel Silva

  38. Web Validation Service for Ensuring Adherence to the DICOM Standard

    Article • January 2017, IOS Press

    Dr. Jorge Miguel Silva

  39. Soft X-ray resonant magnetic scattering study of magnetization reversal in low dimensional magnetic heterostructures

    Article • Applied Surface Science, October 2007, Elsevier

    Dr. Jorge Miguel Silva

  40. Magnetic domain pinning in an anisotropy-engineered GdTbFe thin film

    Article • Journal of Applied Physics, August 2006, American Institute of Physics

    Dr. Jorge Miguel Silva