FALCON2: compression-based metagenomic classification of ancient viruses

Bioinformatics

2026 | journal-article

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

GigaScience

2026 | journal-article

A Machine Learning Method for Authentication of Human Ancient Mitochondrial DNA

2026 | book-chapter

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

2026 | book-chapter

Automated Annotation of Plant Gene Regions Using Supervised Machine Learning

2025 | preprint

Metagenomic classification of ancient viruses

2025 | preprint

Optimizing Genomic Data Compression with Genetic Algorithms

2025 | preprint

Accurate Reconstruction of Persistent Human Viral Sequences

International Virus Bioinformatics Meeting 2025 (ViBioM)

2025 | conference-abstract

Plastic Biodegradation by Microalgae: Molecular Prediction

Encontro de Investigação Jovem da U.Porto – IJUP 2025

2025 | conference-poster

ViruScopeDB: a comprehensive multi-omics database for highly infectious viruses

Encontro de Investigação Jovem da U.Porto – IJUP 2025

2025 | conference-poster

Comprehensive multi-omics database for highly infectious viruses: a focus on HIV, Ebola and SARS-CoV-2

Bioinformatics Open Days 2025

2025 | conference-poster

Introducing AptaCom - A centralized aptamer database

Bioinformatic Open Days 2025

2025 | conference-poster

PLASTIC BIODEGRADATION BY MICROALGAE: DATABASE DEVELOPMENT AND SEQUENCE RETRIEVAL

Bioinformatics Open Days 2025

2025 | conference-poster

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

Journal of Infectious Diseases

2025 | journal-article

Comparative evaluation of computational methods for reconstruction of human viral genomes

2025 | preprint

AIDetx

2025 Data Compression Conference, Dcc

2025 | conference-paper

Decoding the Past: Explainable Machine Learning Models for Dating Historical Texts

2025 | preprint

Optimization of data compression parameters using genetic algorithms

2025 Data Compression Conference, Dcc

2025 | conference-paper

A Multi-Omics and Primer Database for Virus Identification: Focus on HIV, Ebola, and SARS-CoV-2

XIX International meeting of Portuguese Association for Evolutionary Biology (ENBE)

2024 | conference-poster

Exploring Microalgae-Enzymes for Sustainable Plastic Biodegradation

XIX International meeting of Portuguese Association for Evolutionary Biology (ENBE)

2024 | conference-poster

JARVIS3: an efficient encoder for genomic data

Bioinformatics

2024 | journal-article

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

Nucleic Acids Research

2024 | journal-article

Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds

Journal of Chemical Information and Modeling

2024 | journal-article

AptaCom: Bridging aptamer knowledge

2024 | online-resource

HEV in European Rabbits Resource Hub

2024 | online-resource

Plastizyme: a central Hub for plastic biodegradation research

2024 | online-resource

A method to reconstruct persistent human viral sequences cooperatively

Research Summit 2024

2024 | conference-abstract

A method for improving the generation of viral consensus sequences using adaptive models

6th Statistics on Health Decision Making: Artificial Intelligence, SHDM 2024

2024 | conference-abstract

A method for improving the generation of consensus sequences

19th Workshop on Informatics Engineering Research, WIER 2024

2024 | conference-paper

A cooperative method to reconstruct persistent human viral sequences

The 20th Portugaliæ Genetica: DNA - Ancient and New

2024 | conference-abstract

Decoding the Genomic Diversity of Hepatitis E Virus in European Rabbits: A Step Towards Understanding Zoonotic Transmission

"The 20th Portugaliæ Genetica: DNA - Ancient and New" 21-22 March 2024

2024 | conference-poster

Evolutionary Insights into Plastic-Degrading Enzymes: A Data-Driven Approach to Bioremediation

"The 20th Portugaliæ Genetica: DNA - Ancient and New" 21-22 March 2024

2024 | conference-poster

Exploring the Evolution of PET-Degrading Enzymes: Insights from Sequence Alignment and Phylogenetic Analysis

"The 20th Portugaliæ Genetica: DNA - Ancient and New" 21-22 March 2024

2024 | conference-poster

Creating a Comprehensive Database of Plastic Degrading Enzymes for Machine Learning Applications

Bioinformatics Open Days XIII Edition 14-16 March 2024

2024 | conference-poster

Unifying Information on Plastic Degrading Enzymes Across Different Databases

Bioinformatics Open Days XIII Edition 14-16 March 2024

2024 | conference-poster

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

GigaScience

2024 | journal-article

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

32nd European Signal Processing Conference, EUSIPCO 2024

2024 | conference-paper

A sorting tool for improving FASTA data compression tools

32nd European Signal Processing Conference, EUSIPCO 2024

2024 | conference-paper

An experimental sorting method for improving metagenomic data encoding

2024 Data Compression Conference (DCC)

2024 | conference-paper

Copy models for protein sequence compression

2024 Data Compression Conference (DCC)

2024 | conference-paper

Improving the generation of viral consensus sequences using adaptive models

32nd European Signal Processing Conference, EUSIPCO 2024

2024 | conference-paper

Perinnöllinen herpesvirus elinsiirron kiusana

Duodecim

2024 | journal-article

Mapping human pathogens in wastewater using a metatranscriptomic approach

Environmental Research

2023 | journal-article

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

Journal of Computer-Aided Molecular Design

2023 | journal-article

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

2023 | preprint

Elimistömme on lukuisten terveyteemme vaikuttavien virusten koti

Duodecim

2023 | journal-article

Unmasking the tissue-resident eukaryotic DNA virome in humans

Nucleic Acids Research

2023 | journal-article

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

Journal of NeuroVirology

2023 | journal-article

JARVIS2: a data compressor for large genome sequences

Proceedings - DCC 2023

2023 | conference-paper

Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications

2023 | book-chapter

The complexity landscape of viral genomes

GigaScience

2022 | journal-article

Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods

Pattern Recognition and Image Analysis

2022 | conference-paper

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

GigaScience

2022 | journal-article

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

Viruses

2022 | journal-article

canvas: Complexity Analysis Viral Sequences

2022 | software

Revisiting the Neurospora crassa mitochondrial genome

Letters in Applied Microbiology

2021 | journal-article

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

Frontiers in Cellular and Infection Microbiology

2021 | journal-article

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

Entropy

2021 | journal-article

A semi-automatic methodology for analysing distributed and private biobanks

Computers in Biology and Medicine

2021 | journal-article

Archaea Taxonomic Classification

27th Portuguese Conference on Pattern Recognition, RecPad 2021

2021 | conference-paper

Automatic analysis of artistic paintings using information-based measures

Pattern Recognition

2021 | journal-article

Efficient DNA sequence compression with neural networks

GigaScience

2020 | journal-article

The landscape of persistent human DNA viruses in femoral bone

Forensic Science International: Genetics

2020 | journal-article

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

GigaScience

2020 | journal-article

Persistent minimal sequences of SARS-CoV-2

Bioinformatics

2020 | journal-article

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

SoftwareX

2020 | journal-article

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

GigaScience

2020 | journal-article

Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model

Entropy

2020 | journal-article

Comparison and Evaluation of Information-based Measures in Images.

26th Portuguese Conference on Pattern Recognition, RecPad 2020

2020 | conference-paper

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

Advances in Intelligent Systems and Computing

2020 | book

Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes

Advances in Intelligent Systems and Computing

2020 | book

A Reference-Free Lossless Compression Algorithm for DNA Sequences Using a Competitive Prediction of Two Classes of Weighted Models

Entropy

2019 | journal-article

A DNA sequence corpus for compression benchmark

Advances in Intelligent Systems and Computing

2019 | book

A probabilistic method to find and visualize distinct regions in protein sequences

European Signal Processing Conference

2019 | conference-paper

AC: A Compression Tool for Amino Acid Sequences

Interdisciplinary Sciences: Computational Life Sciences

2019 | journal-article

Compression of amino acid sequences

Advances in Intelligent Systems and Computing

2019 | book

Cryfa: A secure encryption tool for genomic data

Bioinformatics

2019 | journal-article

NET-ASAR: A tool for DNA sequence search based on data compression

Advances in Intelligent Systems and Computing

2019 | book

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

Genes

2018 | journal-article

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

Entropy

2018 | journal-article

FALCON-meta: a method to infer metagenomic composition of ancient DNA

2018 | preprint

An Application of Data Compression Models to Handwritten Digit Classification

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2018 | book

Extended-alphabet finite-context models

2018 | journal-article

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

European Signal Processing Conference

2018 | conference-paper

Cryfa: A tool to compact and encrypt FASTA files

Advances in Intelligent Systems and Computing

2017 | book

On the approximation of the Kolmogorov complexity for DNA sequences

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2017 | book

On the role of inverted repeats in DNA sequence similarity

Advances in Intelligent Systems and Computing

2017 | book

Preface

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2017 | book

Substitutional tolerant markov models for relative compression of DNA sequences

Advances in Intelligent Systems and Computing

2017 | book

Visualization of distinct DNA regions of the modern human relatively to a neanderthal genome

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2017 | book

A survey on data compression methods for biological sequences

Information (Switzerland)

2016 | journal-article

Authorship Attribution Using Relative Compression

Data Compression Conference Proceedings

2016 | conference-paper

Compression and analysis of genomic data

2016 | dissertation-thesis

Efficient Compression of Genomic Sequences

Data Compression Conference Proceedings

2016 | conference-paper

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

Scientific Reports

2015 | journal-article

Detection and visualisation of regions of human DNA not present in other primates

21st Portuguese Conference on Pattern Recognition, RecPad 2015

2015 | conference-paper

Mafco: A compression tool for MAF files

PLoS ONE

2015 | journal-article

Three minimal sequences found in Ebola virus genomes and absent from human DNA

Bioinformatics

2015 | journal-article

A conditional compression distance that unveils insights of the genomic evolution

Data Compression Conference Proceedings

2014 | conference-paper

A new compressor for measuring distances among images

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2014 | book

Exploring deep Markov models in genomic data compression using sequence pre-analysis

European Signal Processing Conference

2014 | conference-paper

Information profiles for DNA pattern discovery

Data Compression Conference Proceedings

2014 | conference-paper

Mfcompress: A compression tool for fasta and multi-fasta data

Bioinformatics

2014 | journal-article

XS: A FASTQ read simulator

BMC Research Notes

2014 | journal-article

A compression model for DNA multiple sequence alignment blocks

IEEE Transactions on Information Theory

2013 | journal-article

A genomic distance for assembly comparison based on compressed maximal exact matches

IEEE/ACM Transactions on Computational Biology and Bioinformatics

2013 | journal-article

Compressing resequencing data with GReEn

Methods in Molecular Biology

2013 | book

DNA sequences at a glance

PLoS ONE

2013 | journal-article

Insights into primates genomic evolution using a compression distance

19th Portuguese Conference on Pattern Recognition, RecPad 2013

2013 | conference-paper

Compression of whole genome alignments using a mixture of finite-context models

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2012 | book

Computation of the normalized compression distance of DNA sequences using a mixture of finite-context models

BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms

2012 | conference-paper

Exon: A web-based software toolkit for DNA sequence analysis

Advances in Intelligent and Soft Computing

2012 | book

GReEn: A tool for efficient compression of genome resequencing data

Nucleic Acids Research

2012 | journal-article

M6: a method for compressing complete genomes using markov models

7th Doctoral Symposium in Informatics Engineering, DSIE 2012

2012 | conference-paper

On the compression of FASTQ quality-scores

18th Portuguese Conference on Pattern Recognition, RecPad 2012

2012 | conference-paper

On the detection of unknown locally repeating patterns in images

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2012 | book

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

IEEE Workshop on Statistical Signal Processing Proceedings

2011 | conference-paper

Complexity profiles of DNA sequences using finite-context models

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2011 | book

Compressing the human genome using exclusively Markov models

Advances in Intelligent and Soft Computing

2011 | book

DNA synthetic sequences generation using multiple competing Markov models

IEEE Workshop on Statistical Signal Processing Proceedings

2011 | conference-paper

Symbolic to numerical conversion of DNA sequences using finite-context models

European Signal Processing Conference

2011 | conference-paper