Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (PACBB, 2014)

Identifying interactions between chemical entities in biomedical text. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (J. Integr. Bioinform., 2014)

Annotating biomedical ontology terms in electronic health records using crowd-sourcing. - Andre Lamurias; Vasco Pedro; Luka A. Clarke; Francisco M. Couto (ICBO, 2015)

IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions. - Andre Lamurias; Luka A. Clarke; Francisco M. Couto (ECML/PKDD (3), 2015)

The CHEMDNER corpus of chemicals and drugs and its annotation principles. - 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; et al. (J. Cheminformatics, 2015)

Improving chemical entity recognition through h-index based semantic similarity. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (J. Cheminformatics, 2015)

Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision. - Andre Lamurias; Miguel J. Rodrigues; Luka A. Clarke; Francisco M. Couto (BioNLP (Shared Task), 2016)

ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt. - Márcia Barros; Andre Lamurias; Gonçalo Figueiró; Marta Antunes; Joana Teixeira; Alexandre Pinheiro; Francisco M. Couto (SemEval@NAACL-HLT, 2016)

WS4A: a Biomedical Question and Answering System based on public Web Services and Ontologies. - Miguel J. Rodrigues; Miguel Falé; Andre Lamurias; Francisco M. Couto (CoRR, 2016)

ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events. - Andre Lamurias; Diana F. Sousa; Sofia Pereira; Luka A. Clarke; Francisco M. Couto (SemEval@ACL, 2017)

MER: a shell script and annotation server for minimal named entity recognition and linking. - Francisco M. Couto; Andre Lamurias (J. Cheminformatics, 2018)

LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition. - Andre Lamurias; Francisco M. Couto (BioNLP@ACL, 2019)

A Silver Standard Corpus of Human Phenotype-Gene Relations. - Diana F. Sousa; Andre Lamurias; Francisco M. Couto (NAACL-HLT (1), 2019)

PPR-SSM: personalized PageRank and semantic similarity measures for entity linking. - Andre Lamurias; Pedro Ruas; Francisco M. Couto (BMC Bioinform., 2019)

Using Neural Networks for Relation Extraction from Biomedical Literature. - Diana F. Sousa; Andre Lamurias; Francisco M. Couto (CoRR, 2019)

Semantic Similarity Definition. - Francisco M. Couto; Andre Lamurias (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Text Mining for Bioinformatics Using Biomedical Literature. - Andre Lamurias; Francisco M. Couto (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. - Andre Lamurias; Diana F. Sousa; Luka A. Clarke; Francisco M. Couto (BMC Bioinform., 2019)

An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. - Jiayuan He 002; Dat Quoc Nguyen; Saber A. Akhondi; Christian Druckenbrodt; Camilo Thorne; Ralph Hoessel; Zubair Afzal; Zenan Zhai; Biaoyan Fang; Hiyori Yoshikawa; Ameer Albahem; Jingqi Wang; et al. (CLEF (Working Notes), 2020)

Extreme Multi-Label Classification applied to the Biomedical and Multilingual Panorama. - André Neves; André Lamúrias; Francisco M. Couto (CLEF (Working Notes), 2020)

LasigeBioTM Team at CLEF2020 ChEMU Evaluation Lab: Named Entity Recognition and Event extraction from chemical reactions described in patents using BioBERT NER and RE. - Pedro Ruas; Andre Lamurias; Francisco M. Couto (CLEF (Working Notes), 2020)

Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama. - André Neves; André Lamúrias; Francisco M. Couto (SIIRH@ECIR, 2020)

Towards a Multilingual Corpus for Named Entity Linking Evaluation in the Clinical Domain. - Pedro Ruas; André Lamúrias; Francisco M. Couto (SIIRH@ECIR, 2020)

COVID-19: A Semantic-Based Pipeline for Recommending Biomedical Entities. - Márcia Barros; Andre Lamurias; Diana F. Sousa; Pedro Ruas; Francisco M. Couto (NLP4COVID@EMNLP, 2020)

Priberam Labs at the NTCIR-15 SHINRA2020-ML: Classification Task. - Rúben Cardoso; Afonso Mendes; Andre Lamurias (NTCIR, 2020)

Generating Biomedical Question Answering Corpora From Q&A Forums. - Andre Lamurias; Diana F. Sousa; Francisco M. Couto (IEEE Access, 2020)

A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing. - Diana F. Sousa; Andre Lamurias; Francisco M. Couto (Database J. Biol. Databases Curation, 2020)

Generating Scientific Question Answering Corpora from Q&A forums. - Andre Lamurias; Diana F. Sousa; Francisco M. Couto (CoRR, 2020)

Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature. - Pedro Ruas; Andre Lamurias; Francisco M. Couto (J. Cheminformatics, 2020)

Using Neural Networks for Relation Extraction from Biomedical Literature. - Diana F. Sousa; Andre Lamurias; Francisco M. Couto (Artificial Neural Networks, 3rd Edition, 2021)

Information Retrieval Using Machine Learning for Biomarker Curation in the Exposome-Explorer. - Andre Lamurias; Sofia Jesus; Vanessa Neveu; Reza M. Salek; Francisco M. Couto (Frontiers Res. Metrics Anal., 2021)

Metagenomic binning with assembly graph embeddings. - Andre Lamurias; Mantas Sereika; Mads Albertsen; Katja Hose; Thomas Dyhre Nielsen (Bioinform., 2022)

Graph Neural Networks for Microbial Genome Recovery. - Andre Lamurias; Alessandro Tibo; Katja Hose; Mads Albertsen; Thomas Dyhre Nielsen (CoRR, 2022)

Metagenomic Binning using Connectivity-constrained Variational Autoencoders. - Andre Lamurias; Alessandro Tibo; Katja Hose; Mads Albertsen; Thomas Dyhre Nielsen (ICML, 2023)

BinChill: A Metagenomic Binning Ensemble Method. - Oliver S. Bak; Marcus D. Jensen; Frederik M. Trudslev; Andreas Windfeld; Andre Lamurias (IEEE Access, 2023)

Multilingual bi-encoder models for biomedical entity linking. - Zekeriya Anil Guven; Andre Lamurias (Expert Syst. J. Knowl. Eng., 2023)

DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology. - Muhammad Asif 009; Hugo F. M. C. Martiniano; Andre Lamurias; Samina Kausar; Francisco M. Couto (BMC Bioinform., 2023)

Team NOVA LINCS @ BIOASQ12 MultiCardioNER Track: Entity Recognition with Additional Entity Types. - Rodrigo Gonçalves; André Lamúrias (CLEF (Working Notes), 2024)