A. Lourenço

发表

Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing

Eugénio C. Ferreira, Luis Mateus Rocha, Miguel Rocha, 2009, IWANN.

Evaluation of Linear Classifiers on Articles Containing Pharmacokinetic Evidence of Drug-Drug Interactions

Lang Li, Luis Mateus Rocha, Anália Lourenço, 2012, Pacific Symposium on Biocomputing.

Overview of the CHEMDNER patents task

Gael Pérez Rodríguez, Martín Pérez Pérez, A. Valencia, 2015 .

Information Retrieval and Text Mining Technologies for Chemistry.

A. Valencia, Martin Krallinger, A. Lourenço, 2017, Chemical reviews.

Stringent response of Escherichia coli: revisiting the bibliome using literature mining

E. Ferreira, I. Rocha, A. Lourenço, 2011, Microbial Informatics and Experimentation.

Using Twitter to Understand the Human Bowel Disease Community: Exploratory Analysis of Key Topics

F. Fdez-Riverola, A. Lourenço, M. Pérez-Pérez, 2019, Journal of medical Internet research.

Reconstruction of the Network of Experimentally Validated AMP-Drug Combinations Against Pseudomonas aeruginosa Infections

Gael Pérez Rodríguez, F. Fdez-Riverola, A. Lourenço, 2016 .

Quorum sensing inhibition in Pseudomonas aeruginosa biofilms: new insights through network mining

A. Lourenço, M. O. Pereira, M. Pérez-Pérez, 2017, Biofouling.

Critical review on biofilm methods

Anália Lourenço, Tom Coenye, Nuno F Azevedo, 2017, Critical reviews in microbiology.

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

Anália Lourenço, Maria Olívia Pereira, Paula Jorge, 2012, Biofouling.

Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces.

Anália Lourenço, Paul Stoodley, Hans-Curt Flemming, 2014, Pathogens and disease.

A harmonised vocabulary for communicating and interchanging Biofilms experimental results

A. Lourenço, M. O. Pereira, N. Azevedo, 2014, Journal of integrative bioinformatics.

IDENTIFICATION AND RESOLUTION ON DATA WAREHOUSING POPULATING PROCESS

A. Lourenço, O. Belo, 2003 .

Probiotics, gut microbiota, and their influence on host health and disease

A. Lourenço, S. Delgado, J. Espín, 2017, Molecular nutrition & food research.

In silico prediction reveals the existence of potential bioactive neuropeptides produced by the human gut microbiota.

F. Fdez-Riverola, A. Lourenço, A. Blanco-Míguez, 2019, Food research international.

Tackling probiotic and gut microbiota functionality through proteomics.

A. Lourenço, L. Ruiz, A. Blanco-Míguez, 2016, Journal of proteomics.

Exploring anti-quorum sensing and anti-virulence based strategies to fight Candida albicans infections: an in silico approach

A. Lourenço, M. Pérez-Pérez, P. Jorge, 2018, FEMS yeast research.

A network perspective on antimicrobial peptide combination therapies: the potential of colistin, polymyxin B and nisin.

A. Lourenço, M. O. Pereira, M. Pérez-Pérez, 2017, International journal of antimicrobial agents.

Searching for new strategies against biofilm infections: Colistin-AMP combinations against Pseudomonas aeruginosa and Staphylococcus aureus single- and double-species biofilms

A. Lourenço, M. O. Pereira, W. Kamysz, 2017, PloS one.

A new approach to bacterial colony morphotyping by matrix-assisted laser desorption ionization time of flight-based mass spectrometry.

J. D. Nunes-Miranda, M. Reboiro-Jato, J. Capelo, 2013, Talanta.

Metabolic network reconstruction of the pathogen Enterococcus faecalis

E. Ferreira, I. Rocha, A. Lourenço, 2009 .

Faculty Opinions recommendation of BioBERT: a pre-trained biomedical language representation model for biomedical text mining.

A. Lourenço, 2022, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

Original Text mining for the biocuration workflow

Thomas C. Wiegers, Cathy H. Wu, Karen G. Dowell, 2012 .

From amino acid sequence to bioactivity: The biomedical potential of antitumor peptides

F. Fdez-Riverola, A. Lourenço, A. Blanco-Míguez, 2016, Protein science : a publication of the Protein Society.

Computational resources and strategies to construct single-molecule metabolic models of microbial cells

Anália Lourenço, Gonçalo Monteiro, Nuno F. Azevedo, 2016, Briefings Bioinform..

Polymicrobial Ventilator-Associated Pneumonia: Fighting In Vitro Candida albicans-Pseudomonas aeruginosa Biofilms with Antifungal-Antibacterial Combination Therapy

A. Lourenço, M. O. Pereira, M. Henriques, 2017, PloS one.

Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties

Anália Lourenço, Maria Olívia Pereira, Nadine Castelhano Santos, 2015, Briefings Bioinform..

HaemoKBS: A knowledge-based system for real-time, continuous categorisation of adverse reactions in blood recipients

Anália Lourenço, Florentino Fernández Riverola, Augusto Ramoa, 2021, Neurocomputing.

Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective

F. Fdez-Riverola, A. Lourenço, L. Ruiz, 2020, Microorganisms.

In Silico Screening of the Human Gut Metaproteome Identifies Th17-Promoting Peptides Encrypted in Proteins of Commensal Bacteria

F. Fdez-Riverola, A. Lourenço, A. Blanco-Míguez, 2017, Front. Microbiol..

The Evolving Role of Information Technology in Haemovigilance Systems

Florentino Fdez-Riverola, Anália Lourenço, Augusto Ramoa, 2018, Journal of healthcare engineering.

Data Quality in Biofilm High-Throughput Routine Analysis: Intralaboratory Protocol Adaptation and Experiment Reproducibility.

A. Lourenço, M. O. Pereira, P. Jorge, 2015, Journal of AOAC International.

Extraction of Pharmacokinetic Evidence of Drug–Drug Interactions from the Literature

Heng-Yi Wu, Lang Li, Luis Mateus Rocha, 2014, PloS one.

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota

Anália Lourenço, Florentino Fernández Riverola, Aitor Blanco-Míguez, 2019, Briefings Bioinform..

Heteroresistance to colistin in Klebsiella pneumoniae is triggered by small colony variants sub-populations within biofilms.

A. Lourenço, M. O. Pereira, A. Sousa, 2016, Pathogens and disease.

Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae

Anália Lourenço, Nuno F Azevedo, Beatriz T Magalhães, 2019, Briefings Bioinform..

@Note: A workbench for Biomedical Text Mining

Eugénio C. Ferreira, Miguel Rocha, Anália Lourenço, 2009, J. Biomed. Informatics.

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota

Anália Lourenço, Florentino Fernández Riverola, Aitor Blanco-Míguez, 2017, Database J. Biol. Databases Curation.

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

Alfonso Valencia, Diana de la Iglesia, Juergen Haas, 2017, bioRxiv.

Influence of the region of origin on the mycobiota of grapes with emphasis on Aspergillus and Penicillium species.

A. Lourenço, A. Venâncio, R. Serra, 2006, Mycological research.

Computational prediction of the bioactivity potential of proteomes based on expert knowledge

Anália Lourenço, Florentino Fernández Riverola, Aitor Blanco-Míguez, 2019, J. Biomed. Informatics.

FISHji: New ImageJ macros for the quantification of fluorescence in epifluorescence images

Anália Lourenço, Nuno F. Azevedo, Pedro Madureira, 2016 .

Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets

Anália Lourenço, Florentino Fernández Riverola, Markus Göker, 2016, PLoS Comput. Biol..

Attenuating the Effect of Data Abnormalities on Data Warehouses

Anália Lourenço, Orlando Belo, A. Lourenço, 2004, ICEIS.

Evaluation of chemical and gene/protein entity recognition systems at BioCreative V.5: the CEMP and GPRO patents tracks

Alfonso Valencia, Martín Pérez-Pérez, Anália Lourenço, 2017 .

Mining the sociome for Health Informatics: Analysis of therapeutic lifestyle adherence of diabetic patients in Twitter

Martín Pérez-Pérez, Anália Lourenço, Florentino Fernández Riverola, 2020, Future Gener. Comput. Syst..

Semantic annotation of biological concepts interplaying microbial cellular responses

Rui Pereira, Miguel Rocha, Eugénio C. Ferreira, 2011, BMC Bioinformatics.

Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature

Luis Mateus Rocha, Michael D. Conover, Andrew Wong, 2011, BMC Bioinformatics.

The extracellular proteins of Lactobacillus acidophilus DSM 20079T display anti-inflammatory effect in both in piglets, healthy human donors and Crohn’s Disease patients

F. Fdez-Riverola, A. Lourenço, A. Blanco-Míguez, 2020 .

Web scraping technologies in an API world

Anália Lourenço, Florentino Fernández Riverola, Daniel Glez-Peña, 2014, Briefings Bioinform..

Text mining for the biocuration workflow

K. Bretonnel Cohen, Alfonso Valencia, Thomas C. Wiegers, 2012, Database J. Biol. Databases Curation.

An ontology-based approach to systems biology literature retrieval and processing

Miguel Rocha, Eugénio C. Ferreira, José João Almeida, 2007 .

Online visibility of software-related web sites: The case of biomedical text mining tools

Martín Pérez-Pérez, Anália Lourenço, Florentino Fernández Riverola, 2019, Inf. Process. Manag..

In silico and functional analyses of immunomodulatory peptides encrypted in the human gut metaproteome

F. Fdez-Riverola, A. Lourenço, A. Blanco-Míguez, 2020 .

Understanding the social evolution of the Java community in Stack Overflow: A 10-year study of developer interactions

Anália Lourenço, Florentino Fernández Riverola, Roi Pérez-López, 2020, Future Gener. Comput. Syst..

Overview of the BioCreative VI chemical-protein interaction Track

Anália Lourenço, Martin Krallinger, Obdulia Rabal, 2017 .

Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework

Daniel Glez-Peña, Florentino Fdez-Riverola, Nuno F Azevedo, 2015, BioMed research international.

Stroke risk factors classification modelling

Anália Lourenço, Orlando Belo, Ana Cristina Braga, 2002 .

An harmonised vocabulary for communicating and interchanging Biofilms experimental results

Anália Lourenço, Ana Margarida Sousa, Maria Olívia Pereira, 2014, J. Integr. Bioinform..

Targeted depletion of pks+ bacteria from a fecal microbiota using specific antibodies

J. Cubiella, F. Fdez-Riverola, A. Lourenço, 2023, mSystems.

Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of Pseudomonas aeruginosa and Candida albicans

Martín Pérez-Pérez, Anália Lourenço, Florentino Fdez-Riverola, 2018, Biofouling.

Single Molecule Simulation of Diffusion and Enzyme Kinetics.

Martín Pérez-Pérez, Anália Lourenço, Nuno F Azevedo, 2016, The journal of physical chemistry. B.

High performance computing for three-dimensional agent-based molecular models.

G Pérez-Rodríguez, M Pérez-Pérez, F Fdez-Riverola, 2016, Journal of molecular graphics & modelling.

MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies

Anália Lourenço, Ana Margarida Sousa, Maria Olívia Pereira, 2015, J. Biomed. Informatics.

A framework to extract biomedical knowledge from gluten-related tweets: The case of dietary concerns in digital era

Martín Pérez-Pérez, Anália Lourenço, Gilberto Igrejas, 2021, Artif. Intell. Medicine.

Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli

Martín Pérez-Pérez, Anália Lourenço, Florentino Fernández Riverola, 2019, Comput. Biol. Medicine.

Bringing Named Entity Recognition on Drupal Content Management System

Anália Lourenço, José Ferrnandes, A. Lourenço, 2014, PACBB.

Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow

Martín Pérez-Pérez, Anália Lourenço, Florentino Fernández Riverola, 2016, Database J. Biol. Databases Curation.

BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines

Anália Lourenço, Florentino Fernández Riverola, Alberto G. Jácome, 2016, Comput. Methods Programs Biomed..

A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature

Hagit Shatkay, Luis Mateus Rocha, Anália Lourenço, 2011, BMC Bioinform..

Testing extensive use of NER tools in article classification and a statistical approach for method interaction extraction in the protein-protein interaction literature

Andrew K. C. Wong, Hagit Shatkay, Luis Mateus Rocha, 2010 .

A framework for the development of Biomedical Text Mining software tools

Eugénio C. Ferreira, Miguel Rocha, Anália Lourenço, 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

A Novel Search Engine Supporting Specific Drug Queries and Literature Management

Anália Lourenço, Florentino Fernández Riverola, Alberto G. Jácome, 2015, PACBB.

A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways

E. Ferreira, I. Rocha, J. P. Pinto, 2011, J. Integr. Bioinform..

Interpreting the Regulatory Interplay in E. coli Metabolic Pathways

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2011, PACBB.

A framework for the integrated analysis of metabolic and regulatory networks

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

DEWE: A novel tool for executing differential expression RNA-Seq workflows in biomedical research

Anália Lourenço, Florentino Fernández Riverola, Hugo López-Fernández, 2019, Comput. Biol. Medicine.

BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results

Anália Lourenço, Florentino Fdez-Riverola, Aitor Blanco-Míguez, 2018, PloS one.

In silico Approach for Unveiling the Glycoside Hydrolase Activities in Faecalibacterium prausnitzii Through a Systematic and Integrative Large-Scale Analysis

F. Fdez-Riverola, A. Lourenço, A. Margolles, 2019, Front. Microbiol..

Catching web crawlers in the act

Anália Lourenço, Orlando Belo, A. Lourenço, 2006, ICWE '06.

Challenges in integrating Escherichia coli molecular biology data

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2011, Briefings Bioinform..

Marky: A tool supporting annotation consistency in multi-user and iterative document annotation projects

Martín Pérez-Pérez, Anália Lourenço, Florentino Fernández Riverola, 2015, Comput. Methods Programs Biomed..

Uncovering mechanisms underlying the Escherichia coli stringent response : application of text mining approaches to identify meaningful relations in text documents

E. Ferreira, I. Rocha, Miguel Rocha, 2009 .

BiofOmics: A Web Platform for the Systematic and Standardized Collection of High-Throughput Biofilm Data

Anália Lourenço, Andreia Ferreira, Maria Olivia Pereira, 2012, PloS one.

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota

F. F. Riverola, A. Lourenço, A. Blanco-Míguez, 2019, Briefings Bioinform..

P4P: a peptidome-based strain-level genome comparison web tool

Anália Lourenço, Florentino Fernández Riverola, Aitor Blanco-Míguez, 2017, Nucleic Acids Res..

A peptidome-based phylogeny pipeline reveals differential peptides at the strain level within Bifidobacterium animalis subsp. lactis.

Anália Lourenço, Florentino Fdez-Riverola, Aitor Blanco-Míguez, 2016, Food microbiology.

Boosting biomedical document classification through the use of domain entity recognizers and semantic ontologies for document representation: The case of gluten bibliome

F. F. Riverola, G. Igrejas, A. Lourenço, 2021, Neurocomputing.

Computational Resources and Strategies to Construct Single-Molecule Models of FISH.

Beatriz T. Magalhães, A. Lourenço, N. Azevedo, 2021, Methods in molecular biology.

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

A. Lourenço, M. O. Pereira, P. Jorge, 2012, Biofouling.

An harmonised vocabulary for communicating and interchanging Biofilms experimental results

A. Lourenço, A. Sousa, Maria Olívia Pereira, 2014, J. Integr. Bioinform..

Enabling systematic, harmonised and large-scale biofilms data computation: The Biofilms Experiment Workbench

Anália Lourenço, Florentino Fernández Riverola, Daniel Glez-Peña, 2015, Comput. Methods Programs Biomed..

Antimicrobial combination therapies : a network perspective

A. Lourenço, M. O. Pereira, P. Jorge, 2014 .

Networking the Way towards Antimicrobial Combination Therapies

Anália Lourenço, Maria Olívia Pereira, Paula Jorge, 2014, PACBB.

The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts

Alfonso Valencia, Martín Pérez-Pérez, Anália Lourenço, 2017, IberEval@SEPLN.

Mining the sociome for Health Informatics: Analysis of therapeutic lifestyle adherence of diabetic patients in Twitter

Gael Pérez Rodríguez, F. F. Riverola, A. Lourenço, 2020, Future Gener. Comput. Syst..

Combining syntactic and ontological knowledge to extract biologically relevant relations from scientific papers

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2009 .

A tool for the automatic and manual annotation of biomedical documents

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2008, SMBM 2008.