Sérgio Matos

Position	Researcher
Affiliation	IEETA
Group	Biomedical Informatics and Technologies
Status	Researcher with PhD
Country	Portugal
Students	Tiago Almeida
Former PhD students	David Campos, Paulo Gaspar
Former masters students	Show list
Courses
Projects
Past projects	EMIF, EU-ADR, IF/01694/2013/CP1162/CT0018, MMIR, NeuroPath, QueryTermExp, SCREEN-DR, SOCA - Smart Open Campus, World Search
Events	BioCreative VI workshop'2017, BioCreative & Becalm workshop'2017, INForum 2017, ISMB-ECCB'2017, PACBB'2017
Proposals
ORCID	0000-0003-1941-3983
Personal page	http://bioinformatics.ua.pt/?p=570

Publications

Articles in international journals listed in the ISI

• Jorge Miguel Silva, Diogo Pratas, Tânia Caetano, Sérgio Matos. The complexity landscape of viral genomes. GigaScience, vol. 11, August 2022 [IF 2018: 4.688 (Q1, 13/69)]
• Sara Pereira, Olga Fajarda, Sérgio Matos, José Luís Oliveira, Raquel Silva. NAPRT Expression Regulation Mechanisms: Novel Functions Predicted by a Bioinformatics Approach. Genes, vol. 12, no. 12, p. 2022, December 2021 [IF 2018: 3.331 (Q2, 61/174)]
• João Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira. A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases. Journal of Biomedical Informatics, vol. 120, p. 103849, August 2021 [IF 2018: 2.950 (Q2, 33/106)]
• Jorge Miguel Silva, Diogo Pratas, Rui Antunes, Sérgio Matos, Armando J. Pinho. Automatic analysis of artistic paintings using information-based measures. Pattern Recognition, p. 107864, February 2021 [IF 2018: 5.165 (Q1, 10/202)]
• João Figueira Silva, João Almeida, Sérgio Matos. Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach. JMIR Medical Informatics, vol. 8, no. 12, December 2020 [IF 2020: 2.955 (Q3, 17/30)]
• 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, vol. 22, no. 1, January 2020 [IF 2018: 2.419 (Q2, 28/81)]
• Rui Antunes, Sérgio Matos. Extraction of chemical–protein interactions from the literature using neural networks and narrow instance representation. Database, vol. 2019, no. baz095, October 2019 [IF 2018: 3.683 (Q1, 7/59)]
• Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altınel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database, vol. 2019, no. bay147, January 2019 [IF 2018: 3.683 (Q1, 7/59)]
• Sérgio Matos. Configurable web-services for biomedical document annotation. Journal of Cheminformatics, vol. 10, p. 68, December 2018
• Micael Pedrosa, Jorge Miguel Silva, João Figueira Silva, Sérgio Matos, Carlos Costa. SCREEN-DR: Collaborative platform for diabetic retinopathy. International Journal of Medical Informatics, vol. 120, p. 137-146, December 2018 [IF 2018: 2.731 (Q2, 57/155)]
• Richard D Turner, Surinder S Birring, Mathina Darmalingam, Richard L Hooper, Heinke Kunst, Sérgio Matos, Graham H Bothamley. Daily cough frequency in tuberculosis and association with household infection. The International Journal of Tuberculosis and Lung Disease, vol. 22, no. 8, p. 863-870, August 2018
• Sérgio Matos, Rui Antunes. Protein-protein interaction article classification using a convolutional recurrent neural network with pre-trained word embeddings. Journal of Integrative Bioinformatics, vol. 14, no. 4, December 2017
• Rui Antunes, Sérgio Matos. Supervised learning and knowledge-based approaches applied to biomedical word sense disambiguation. Journal of Integrative Bioinformatics, vol. 14, no. 4, December 2017
• Arietta Spinou, Kai K Lee, Aish Sinha, Caroline Elston, Michael R Loebinger, Robert Wilson, Kian Fan Chung, Nadia Yousaf, Ian D Pavord, Sérgio Matos, Rachel Garrod, Surinder S Birring. The Objective Assessment of Cough Frequency in Bronchiectasis. Lung, vol. 195, no. 5, p. 575-585, October 2017
• Carlos Viana Ferreira, António Guerra, João Figueira Silva, Sérgio Matos, Carlos Costa. An Intelligent Cloud Storage Gateway for Medical Imaging. Journal of Medical Systems, vol. 41, no. 9, p. 141, September 2017 [IF 2017: 2.098 (Q2, 46/94)] [IF 2018: 2.415 (Q2, 12/26)]
• Kai K Lee, Sérgio Matos, Katie Ward, Gerrard F Rafferty, John Moxham, David H Evans, Surinder S Birring. Sound: a non-invasive measure of cough intensity. BMJ Open Respiratory Research, vol. 4, no. 1, p. e000178, May 2017
• Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydın, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, and Donald C. Comeau. BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database, vol. 2016, no. baw121, September 2016 [IF 2016: 3.290 (Q1, 8/57)] [IF 2018: 3.683 (Q1, 7/59)]
• Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza K. Irin, Lars J. Jensen, Silvia Jimenez, Toni R. Jue, Ingrid Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole Vasilevsky, Xiaodong Wang, Andrew Chatr-Aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna McEntyre, Sandra Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary Schaeffer, Cathy H. Wu, Lynette Hirschman, and Cecilia N. Arighi. Overview of the interactive task in BioCreative V. Database, vol. 2016, p. baw119, September 2016 [IF 2016: 3.290 (Q1, 8/57)] [IF 2018: 3.683 (Q1, 7/59)]
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database, vol. 2016, June 2016 [IF 2016: 3.290 (Q1, 8/57)] [IF 2018: 3.683 (Q1, 7/59)]
• Carlos Viana Ferreira, Luis Ribeiro, Sérgio Matos, Carlos Costa. Pattern Recognition for Cache Management in Distributed Medical Imaging Environments. International Journal of Computer Assisted Radiology and Surgery, vol. 11, no. 2, p. 327-336, February 2016 [IF 2016: 1.863 (Q2, 97/197)]
• ...further results

Other articles in journals

• Carlos Viana Ferreira, Sérgio Matos, Carlos Costa. Long-term prefetching for cloud medical imaging repositories. Studies in Health Technology and Informatics, vol. 210, p. 1028-1030, May 2015
• David Campos, Quoc-Chinh Bui, Sérgio Matos, José Luís Oliveira. TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. Source Code for Biology and Medicine, vol. 9, no. 1, January 2014
• Sérgio Matos, Hugo Araújo, José Luís Oliveira. Biomedical literature exploration through latent semantics. Advances in Distributed Computing and Artificial Intelligence Journal, vol. 1, no. 5, p. 65-74, August 2013
• Sérgio Matos, José Luís Oliveira. Classification methods for finding articles describing protein-protein interactions in PubMed. Journal of Integrative Bioinformatics, vol. 8, no. 3, p. 178, September 2011

Chapters in books

• João Almeida, João Figueira Silva, Alejandro Pazos, Sérgio Matos, José Luís Oliveira. Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. Biomedical Engineering Systems and Technologies, Xuesong Ye, Filipe Soares, Elisabetta De Maria, Pedro Gómez Vilda, Federico Cabitza, Ana Fred, Hugo Gamboa (Ed.), Springer International Publishing, vol. 1400, p. 521-540, March 2021
• David Campos, Sérgio Matos, José Luís Oliveira. Current methodologies for biomedical Named Entity Recognition. Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Mourad Elloumi and Albert Y. Zomaya (Ed.), Wiley, p. 1390, January 2014
• David Campos, Sérgio Matos, José Luís Oliveira. Biomedical Named Entity Recognition: A Survey of Machine-Learning Tools. Theory and Applications for Advanced Text Mining, Shigeaki Sakurai (Ed.), InTech, p. 175-195, November 2012
• Joel Arrais, Sérgio Matos, José Luís Oliveira. Integração de dados biomédicos. Nano, Bio, Info y Cogno (Convergencia de tecnologias NBIC), Conceptos y aplicaciones, J. Aguiló, A. Figueras, A. Freire, D. de la Iglesia, F. Martín, A. Pazos (Ed.), CYTED, p. 185-224, 2011
• Joel Arrais, Sérgio Matos, José Luís Oliveira. Expansão de termos de pesquisa usando redes de conceitos associadas a genes. Nuevas Fronteras Tecnológicas, Alejandre Pazos (Ed.), CYTED, 2010

Articles in conference proceedings

• Jorge Miguel Silva, Diogo Pratas, Tânia Caetano, Sérgio Matos. Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods. Proceedings of the 10th Iberian Conference on Pattern Recognition and Image Analysis, IbPRIA, Aveiro, Portugal, p. 309-320, May 2022
• Jorge Miguel Silva, Diogo Pratas, Tania Caetano, Sérgio Matos. Archaea Taxonomic Classification. Proceedings of the 27th Portuguese Conference on Pattern Recognition, RecPad 2021, Évora, Portugal, November 2021
• Tiago Almeida, Rui Antunes, João Figueira Silva, João Almeida, Sérgio Matos. Chemical detection and indexing in PubMed full text articles using deep learning and rule-based methods. Proceedings of the BioCreative VII Challenge Evaluation Workshop, Online event, p. 119-123, November 2021
• Rui Antunes, Tiago Almeida, João Figueira Silva, Sérgio Matos. Chemical–protein relation extraction in PubMed abstracts using BERT and neural networks. Proceedings of the BioCreative VII Challenge Evaluation Workshop, Online event, p. 76-79, November 2021
• João Figueira Silva, Tiago Almeida, Rui Antunes, João Almeida, Sérgio Matos. Drug mention recognition in Twitter posts using a deep learning approach. Proceedings of the BioCreative VII Challenge Evaluation Workshop, Online event, p. 210-213, November 2021
• João Figueira Silva, Sérgio Matos. Patient Trajectory Modelling in Longitudinal Data: A Review on Existing Solutions. The 2021 34th IEEE International Symposium on Computer-based Medical Systems (CBMS), Aveiro, Portugal, June 2021
• João Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira. A Recommender System to Help Refining Clinical Research Studies. 31st Medical Informatics Europe conference, Studies in health technology and informatics, May 2021
• Jorge Miguel Silva, Diogo Pratas, Sérgio Matos. Comparison and Evaluation of Information-based Measures in Images. Proceedings of the 26th Portuguese Conference on Pattern Recognition, RecPad 2020, Évora, Portugal, October 2020
• Tiago Almeida, Sérgio Matos. Calling Attention to Passages for Biomedical Question Answering. 42nd European Conference on Information Retrieval, ECIR 2020, Online event, p. 69-77, April 2020
• João Figueira Silva, Rui Antunes, João Almeida, Sérgio Matos. Clinical concept normalization on medical records using word embeddings and heuristics. 30th Medical Informatics Europe conference, MIE 2020, Studies in health technology and informatics, vol. 270, p. 93-97, April 2020
• Alina Trifan, Rui Antunes, Sérgio Matos, José Luís Oliveira. Understanding depression from psycholinguistic patterns in social media texts. 42nd European Conference on Information Retrieval, ECIR 2020, Online event, April 2020
• Rui Antunes, João Figueira Silva, Sérgio Matos. Evaluating semantic textual similarity in clinical sentences using deep learning and sentence embeddings. The 35th ACM/SIGAPP Symposium On Applied Computing, Online event, March 2020
• João Almeida, Sérgio Matos. Rule-based extraction of family history information from clinical notes. The 35th ACM/SIGAPP Symposium On Applied Computing, Online event, p. 670–675, March 2020
• João Almeida, João Figueira Silva, Alejandro Sierra, Sérgio Matos, José Luís Oliveira. Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, vol. 5, p. 254-262, February 2020
• Jorge Miguel Silva, Diogo Pratas, Sérgio Matos. Evaluation of Statistical Complexity in Viral Genome Sequences. 25th Portuguese Conference on Pattern Recognition, RECPAD2019, Porto, Portugal, October 2019
• Rui Antunes, João Figueira Silva, Arnaldo Pereira, Sérgio Matos. Rule-based and machine learning hybrid system for patient cohort selection. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, Prague, Czech Republic, p. 59-67, February 2019
• Micael Pedrosa, Jorge Miguel Silva, Sérgio Matos, Carlos Costa. SCREEN-DR - Software Architecture for the Diabetic Retinopathy Screening. Studies in health technology and informatics, vol. 247, p. 396-400, 2018
• Vitor Pereira, Sérgio Matos, José Luís Oliveira. Automated ICD-9-CM medical coding of diabetic patient's clinical reports. Proceedings of the First International Conference on Data Science, E-learning and Information Systems, Madrid, October 2018
• Pedro Matos, Sérgio Matos. Recognition of genetic mutations in text using deep learning. Proceedings of the First International Conference on Data Science, E-learning and Information Systems, Madrid, October 2018
• Jorge Miguel Silva, António Guerra, João Figueira Silva, Carlos Costa, Sérgio Matos. A Novel 3D-CNN Approach For Ejection Fraction Classification in Transthoracic Echocardiography. International Journal of Computer Assisted Radiology and Surgery, Berlin, Germany, vol. 13 (Supp1), p. S131--S132, June 2018
• ...further results