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2020 – today

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2024
[c34]
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Armando J. Pinho, Diogo Pratas:
Copy models for protein sequence compression. DCC 2024: 342-351
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Diogo Pratas, Armando J. Pinho:
An experimental sorting method for improving metagenomic data encoding. DCC 2024: 578
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Maria J. P. Sousa, Armando J. Pinho, Diogo Pratas:
Asensitive Compression-Based Method for Filtering Targeted FASTQ Sequencing Reads. EUSIPCO 2024: 1561-1565
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Tiago Fonseca, Maria J. P. Sousa, Armando J. Pinho, Diogo Pratas:
A Sorting Tool for Improving FASTA Data Compression Tools. EUSIPCO 2024: 1566-1570
[c30]
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Maria J. P. Sousa, Armando J. Pinho, Diogo Pratas:
Improving the Generation of Viral Consensus Sequences Using Adaptive Models. EUSIPCO 2024: 1691-1695
[i5]
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Diogo Pratas, Armando J. Pinho:
An experimental sorting method for improving metagenomic data encoding. CoRR abs/2401.01786 (2024)
2023
[j16]
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João Carneiro, Rita P. Magalhães, Victor M. de la Oliva Roque, Manuel Simões, Diogo Pratas, Sergio F. Sousa:
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa. J. Comput. Aided Mol. Des. 37(5): 265-278 (2023)
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Diogo Pratas, Armando J. Pinho:
JARVIS2: a data compressor for large genome sequences. DCC 2023: 288-297
[c28]
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Jorge Miguel Silva, Diogo Pratas, Sérgio Matos:
Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications. DoCEIS 2023: 161-174
2022
[c27]
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Jorge Miguel Silva, Diogo Pratas, Tânia Caetano, Sérgio Matos:
Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods. IbPRIA 2022: 309-320
2021
[j15]
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Diogo Pratas, Jorge Miguel Silva:
Persistent minimal sequences of SARS-CoV-2. Bioinform. 36(21): 5129-5132 (2021)
[j14]
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João Rafael Almeida, Diogo Pratas, José Luís Oliveira:
A semi-automatic methodology for analysing distributed and private biobanks. Comput. Biol. Medicine 130: 104180 (2021)
[j13]
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Milton Silva, Diogo Pratas, Armando J. Pinho:
AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models. Entropy 23(5): 530 (2021)
[j12]
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Jorge Miguel Silva, Diogo Pratas, Rui Antunes, Sérgio Matos, Armando J. Pinho:
Automatic analysis of artistic paintings using information-based measures. Pattern Recognit. 114: 107864 (2021)
[i4]
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Jorge Miguel Silva, Diogo Pratas, Rui Antunes, Sérgio Matos, Armando J. Pinho:
Automatic analysis of artistic paintings using information-based measures. CoRR abs/2102.01767 (2021)
2020
[j11]
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Jorge Miguel Silva, Eduardo Pinho, Sérgio Matos, Diogo Pratas:
Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model. Entropy 22(1): 105 (2020)
[j10]
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João Rafael Almeida, Armando J. Pinho, José Luís Oliveira, Olga Fajarda, Diogo Pratas:
GTO: A toolkit to unify pipelines in genomic and proteomic research. SoftwareX 12: 100535 (2020)

2010 – 2019

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2019
[j9]
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Seyed Morteza Hosseini, Diogo Pratas, Armando J. Pinho:
Cryfa: a secure encryption tool for genomic data. Bioinform. 35(1): 146-148 (2019)
[j8]
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Diogo Pratas, Seyed Morteza Hosseini, Jorge Miguel, Armando J. Pinho:
A Reference-Free Lossless Compression Algorithm for DNA Sequences Using a Competitive Prediction of Two Classes of Weighted Models. Entropy 21(11): 1074 (2019)
[c26]
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Morteza Hosseini, Diogo Pratas, Armando J. Pinho:
A Probabilistic Method to Find and Visualize Distinct Regions in Protein Sequences. EUSIPCO 2019: 1-5
[c25]
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Diogo Pratas, Seyed Morteza Hosseini, Armando J. Pinho:
Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes. PACBB 2019: 129-136
[c24]
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Diogo Pratas, Seyed Morteza Hosseini, Armando J. Pinho:
GeCo2: An Optimized Tool for Lossless Compression and Analysis of DNA Sequences. PACBB 2019: 137-145
2018
[j7]
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Diogo Pratas, Raquel M. Silva, Armando J. Pinho:
Comparison of Compression-Based Measures with Application to the Evolution of Primate Genomes. Entropy 20(6): 393 (2018)
[j6]
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João M. Carvalho, Susana Brás, Diogo Pratas, Jacqueline Ferreira, Sandra C. Soares, Armando J. Pinho:
Extended-alphabet finite-context models. Pattern Recognit. Lett. 112: 49-55 (2018)
[c23]
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Armando J. Pinho, Diogo Pratas:
An Application of Data Compression Models to Handwritten Digit Classification. ACIVS 2018: 487-495
[c22]
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Diogo Pratas, Armando J. Pinho:
Metagenomic composition analysis of sedimentary ancient DNA from the Isle of Wight. EUSIPCO 2018: 1177-1181
[c21]
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Diogo Pratas, Seyed Morteza Hosseini, Armando J. Pinho:
Compression of Amino Acid Sequences. PACBB 2018: 105-113
[c20]
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Manuel Gaspar, Diogo Pratas, Armando J. Pinho:
NET-ASAR: A Tool for DNA Sequence Search Based on Data Compression. PACBB 2018: 114-122
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Diogo Pratas, Armando J. Pinho:
A DNA Sequence Corpus for Compression Benchmark. PACBB 2018: 208-215
2017
[c18]
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Diogo Pratas, Seyed Morteza Hosseini, Raquel M. Silva, Armando J. Pinho, Paulo Jorge S. G. Ferreira:
Visualization of Distinct DNA Regions of the Modern Human Relatively to a Neanderthal Genome. IbPRIA 2017: 235-242
[c17]
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Diogo Pratas, Armando J. Pinho:
On the Approximation of the Kolmogorov Complexity for DNA Sequences. IbPRIA 2017: 259-266
[c16]
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Seyed Morteza Hosseini, Diogo Pratas, Armando J. Pinho:
On the Role of Inverted Repeats in DNA Sequence Similarity. PACBB 2017: 228-236
[c15]
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Diogo Pratas, Seyed Morteza Hosseini, Armando J. Pinho:
Substitutional Tolerant Markov Models for Relative Compression of DNA Sequences. PACBB 2017: 265-272
[c14]
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Diogo Pratas, Seyed Morteza Hosseini, Armando J. Pinho:
Cryfa: A Tool to Compact and Encrypt FASTA Files. PACBB 2017: 305-312
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Daniel Figueiredo, Carlos Martín-Vide, Diogo Pratas, Miguel A. Vega-Rodríguez:
Algorithms for Computational Biology - 4th International Conference, AlCoB 2017, Aveiro, Portugal, June 5-6, 2017, Proceedings. Lecture Notes in Computer Science 10252, Springer 2017, ISBN 978-3-319-58162-0 [contents]
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João M. Carvalho, Susana Brás, Diogo Pratas, Jacqueline Ferreira, Sandra C. Soares, Armando J. Pinho:
Extended-Alphabet Finite-Context Models. CoRR abs/1709.07346 (2017)
2016
[b1]
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Diogo Pratas:
Compression and analysis of genomic data. University of Aveiro, Portugal, 2016
[j5]
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Seyed Morteza Hosseini, Diogo Pratas, Armando J. Pinho:
A Survey on Data Compression Methods for Biological Sequences. Inf. 7(4): 56 (2016)
[c13]
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Diogo Pratas, Armando J. Pinho, Paulo Jorge S. G. Ferreira:
Efficient Compression of Genomic Sequences. DCC 2016: 231-240
[c12]
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Armando J. Pinho, Diogo Pratas, Paulo Jorge S. G. Ferreira:
Authorship Attribution Using Relative Compression. DCC 2016: 329-338
2015
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Raquel M. Silva, Diogo Pratas, Luísa Castro, Armando J. Pinho, Paulo Jorge S. G. Ferreira:
Three minimal sequences found in Ebola virus genomes and absent from human DNA. Bioinform. 31(15): 2421-2425 (2015)
2014
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Armando J. Pinho, Diogo Pratas:
MFCompress: a compression tool for FASTA and multi-FASTA data. Bioinform. 30(1): 117-118 (2014)
[c11]
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Armando J. Pinho, Diogo Pratas, Paulo Jorge S. G. Ferreira:
Information Profiles for DNA Pattern Discovery. DCC 2014: 420
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Diogo Pratas, Armando J. Pinho:
A Conditional Compression Distance that Unveils Insights of the Genomic Evolution. DCC 2014: 421
[c9]
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Diogo Pratas, Armando J. Pinho:
Exploring deep Markov models in genomic data compression using sequence pre-analysis. EUSIPCO 2014: 2395-2399
[c8]
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Armando J. Pinho, Diogo Pratas, Paulo Jorge S. G. Ferreira:
A New Compressor for Measuring Distances among Images. ICIAR (1) 2014: 30-37
[i2]
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Diogo Pratas, Armando J. Pinho:
A conditional compression distance that unveils insights of the genomic evolution. CoRR abs/1401.4134 (2014)
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Armando J. Pinho, Diogo Pratas, Paulo Jorge S. G. Ferreira:
Information profiles for DNA pattern discovery. CoRR abs/1401.4725 (2014)
2013
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Sara P. Garcia, João M. O. S. Rodrigues, Sérgio Santos, Diogo Pratas, Vera Afreixo, Carlos A. C. Bastos, Paulo Jorge S. G. Ferreira, Armando J. Pinho:
A Genomic Distance for Assembly Comparison Based on Compressed Maximal Exact Matches. IEEE ACM Trans. Comput. Biol. Bioinform. 10(3): 793-798 (2013)
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Luís M. O. de Matos, Diogo Pratas, Armando J. Pinho:
A Compression Model for DNA Multiple Sequence Alignment Blocks. IEEE Trans. Inf. Theory 59(5): 3189-3198 (2013)
2012
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Diogo Pratas, Armando J. Pinho, Sara P. Garcia:
Computation of the Normalized Compression Distance of DNA Sequences using a Mixture of Finite-context Models. BIOINFORMATICS 2012: 308-311
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Diogo Pratas, Armando J. Pinho:
On the Detection of Unknown Locally Repeating Patterns in Images. ICIAR (1) 2012: 158-165
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Luís M. O. de Matos, Diogo Pratas, Armando J. Pinho:
Compression of Whole Genome Alignments Using a Mixture of Finite-Context Models. ICIAR (1) 2012: 359-366
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Diogo Pratas, Armando J. Pinho, Sara P. Garcia:
Exon: A Web-Based Software Toolkit for DNA Sequence Analysis. PACBB 2012: 217-224
2011
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Armando J. Pinho, Diogo Pratas, Paulo Jorge S. G. Ferreira, Sara P. Garcia:
Symbolic to numerical conversion of DNA sequences using finite-context models. EUSIPCO 2011: 2024-2028
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Diogo Pratas, Armando J. Pinho:
Compressing the Human Genome Using Exclusively Markov Models. PACBB 2011: 213-220
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  - https://dblp.org/rec/conf/usab/PinhoPG11
Armando J. Pinho, Diogo Pratas, Sara P. Garcia:
Complexity Profiles of DNA Sequences Using Finite-Context Models. USAB 2011: 75-82

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