Sérgio Matos

Position	Researcher
Affiliation	IEETA
Group	Biomedical Informatics and Technologies
Status	Researcher with PhD
Country	Portugal
Students	Jorge Miguel Silva, João Figueira Silva, Rui Antunes
Former PhD students	David Campos, Paulo Gaspar
Former masters students	Show list
Courses
Projects	SOCA - Smart Open Campus
Past projects	EMIF, EU-ADR, IF/01694/2013/CP1162/CT0018, MMIR, NeuroPath, QueryTermExp, SCREEN-DR, 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

• 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
• 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
• Sérgio Matos. Configurable web-services for biomedical document annotation. Journal of Cheminformatics, vol. 10, p. 68, December 2018 [IF 2017: 3.893 (Q1, 16/148)]
• 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)]
• 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)]
• 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)]
• 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)]
• 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)]
• Jorge A. Vanegas, Sérgio Matos, Fabio A. Gonzalez, José Luís Oliveira. An Overview of Biomolecular Event Extraction from Scientific Documents. Computational and Mathematical Methods in Medicine, vol. 2015, no. 571381, August 2015 [IF 2015: 0.887 (Q3, 42/56)]
• David Campos, Sérgio Matos, José Luís Oliveira. A document processing pipeline for annotating chemical entities in scientific documents. Journal of Cheminformatics, vol. 7, no. Suppl. 1, p. S7, January 2015 [IF 2015: 3.949 (Q1, 36/163)] [IF 2017: 3.893 (Q1, 16/148)]
• Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, SV Ramanan, Senthil Nathan, Slavko Žitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A Akhondi, Jan A Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C Lee Giles, Hongfang Liu, Komandur Elayavilli Ravikumar, Andre Lamurias, Francisco M Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usié, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia. The CHEMDNER corpus of chemicals and drugs and its annotation principles. Journal of Cheminformatics, vol. 7, no. Suppl 1, p. S2, January 2015 [IF 2015: 3.949 (Q1, 36/163)] [IF 2017: 3.893 (Q1, 16/148)]
• David Campos, Jóni Lourenço, Sérgio Matos, José Luís Oliveira. Egas: a collaborative and interactive document curation platform. Database, vol. 2014, no. 10.1093, p. 1-12, June 2014 [IF 2014: 3.372 (Q1, 7/57)]
• José Carlos Santos, Sérgio Matos. Analysing Twitter and web queries for flu trend prediction. Theoretical Biology and Medical Modelling, vol. 11, no. Suppl 1, p. S6, May 2014 [IF 2014: 0.950 (Q3, 41/57)]
• Edgar Coelho, Joel Arrais, Sérgio Matos, Carlos Pereira, Nuno Rosa, Maria José Correia, Marlene Barros, José Luís Oliveira. Computational prediction of the human-microbial oral interactome. BMC Systems Biology, vol. 8, p. 24, February 2014 [IF 2014: 2.435 (Q1, 13/57)]
• Víctor M. Prieto, Sérgio Matos, Manuel Álvarez, Fidel Cacheda, José Luís Oliveira. Twitter: A Good Place to Detect Health Conditions. PLoS ONE, vol. 9, no. 1, p. e86191, January 2014 [IF 2014: 3.234 (Q1, 9/57)] [IF 2017: 2.766 (Q1, 15/64)]
• David Campos, Sérgio Matos, José Luís Oliveira. A modular framework for biomedical concept recognition. BMC Bioinformatics, vol. 14, no. 281, September 2013 [IF 2013: 2.672 (Q1, 8/52)]
• ...further results

Other articles in journals

• Micael Pedrosa, Jorge Miguel Silva, João Figueira Silva, Sérgio Matos, Carlos Costa. SCREEN-DR: Collaborative platform for diabetic retinopathy. International Journal of Medical Informatics, January 2019 [IF 2017: 2.957 (Q1, 35/148)]
• 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

• 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

• 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
• 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
• João Figueira Silva, Jorge Miguel Silva, António Guerra, Sérgio Matos, Carlos Costa. Ejection Fraction Classification in Transthoracic Echocardiography Using a Deep Learning Approach. 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS), Karlstad, Sweden, p. 123-128, June 2018
• Carlos Costa, Micael Pedrosa, Jorge Miguel Silva, Sérgio Matos. Research PACS for diabetic retinopathy screening. International Journal of Computer Assisted Radiology and Surgery, Berlin, Germany, vol. 13 (Supp1), p. S32--S33, June 2018
• Rui Antunes, Sérgio Matos. Evaluation of word embedding vector averaging functions for biomedical word sense disambiguation. INForum 2017 - Atas do Nono Simpósio de Informática, Aveiro, p. 25-30, October 2017
• Sérgio Matos. Extracting Chemical-Protein Interactions using Long Short-Term Memory Networks. Proceedings of the VI BioCreative Challenge Evaluation Workshop, Bethesda, MA, USA, p. 151-154, October 2017
• Sérgio Matos, Rui Antunes. Identifying relevant literature for precision medicine using deep neural networks. Proceedings of the BioCreative VI Challenge Evaluation Workshop, Bethesda, MA, USA, p. 99-101, October 2017
• Rui Antunes, Sérgio Matos. Biomedical word sense disambiguation with word embeddings. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, p. 273-279, June 2017
• Sérgio Matos. Improving Document Prioritization for Protein-Protein Interaction Extraction Using Shallow Linguistics and Word Embeddings. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, Porto, p. 43-49, June 2017
• André Santos, Sérgio Matos. Neji: DIY web services for biomedical concept recognition. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, Barcelona, Spain, p. 191-195, April 2017
• André Santos, Sérgio Matos. Neji: Recognition of Chemical and Gene Mentions in Patent Texts. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, Barcelona, Spain, p. 54-60, April 2017
• Rui Antunes, Sérgio Matos. Machine learning with word embeddings applied to biomedical concept disambiguation. Proceedings of the 22nd Portuguese Conference on Pattern Recognition, RecPad 2016, Aveiro, p. 77-78, October 2016
• André Santos, Sérgio Matos, David Campos, José Luís Oliveira. A Curation Pipeline and Web-Services for PDF Documents. Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, Potsdam, Germany, August 2016
• Eriksson Monteiro, Pedro Sernadela, Sérgio Matos, Carlos Costa, José Luís Oliveira. Semantic Knowledge Base Construction from Radiology Reports. Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, Rome, Italy, p. 345-352, February 2016
• Pedro Sernadela, Sérgio Matos, José Luís Oliveira. Ann2RDF: moving annotations to semantic web,. 17th International Conference on Information Integration and Web-based Applications & Services (iiWAS 2015), Brussels, Belgium, December 2015
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Assisted Mining and Curation of Genomic Variants using Egas. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 396-402, September 2015
• Sérgio Matos, José Sequeira, David Campos, José Luís Oliveira. Identification of chemical and gene mentions in patent texts using feature-rich conditional random fields. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 76-81, September 2015
• Sérgio Matos, André Santos, David Campos, José Luís Oliveira. Neji: a BioC compatible framework for biomedical concept recognition. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 17-21, September 2015
• Sérgio Matos, José Sequeira, José Luís Oliveira. BioinformaticsUA: Machine Learning and Rule-Based Recognition of Disorders and Clinical Attributes from Patient Notes. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015), Denver, Colorado (USA), p. 422-426, June 2015
• ...further results