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José Luis Oliveira
Universidade de Aveiro, DETI / IEETA
3810-193 Aveiro, Portugal
jlo@ua.pt
(+351) 234 370 500
Author Archives: Rui Lebre
GTO
About
GTO is a toolkit for genomics and proteomics, namely for FASTQ, FASTA and SEQ formats, with many complementary tools. The toolkit is for Unix-based systems, built for ultra-fast computations. GTO supports pipes for easy integration with the sub-programs belonging to GTO as well as external tools. GTO works as LEGOs, since it allows the […]
Posted in Genomics, Software
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NETDIAMOND Platform
The NETDIAMOND Platform is a web-based system designed to record patient information in clinical studies, focused on a cohort of HFpEF patients. The system was designed to easily create a data schema based on groups of clinical data. For each group, the different institutions involved can read/edit the data of their patients. In the end, […]
Posted in Biomedical informatics, Featured, Software
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Masters thesis (Tiago Almeida)
Tiago Almeida, “Neural Information Retrieval for Biomedical Question-Answering”July 2019
Posted in Events, Front-Page News, News
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PhD Defense (Eduardo Pinho)
Eduardo Miguel Coutinho Gomes de Pinho, “Multimodal Information Retrieval in Medical Imaging Repositories”July 2019
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D4 – Deep Drug Discovery and Deployment
Funding entity: FCT Period: 2018-2021
Funding entity: FCT
Period: 2018-2021
D4 proposes the use of state-of-the-art Deep Learning methods to tackle the challenges identified in each of the initial stages of the drug discovery pipeline. The main contribution of this project is the creation of an improved computational pipeline that uses Deep Learning architectures to support the drug […]
Posted in On-Going Projects, Projects
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EHDEN – European Health Data & Evidence Network
Funding entity: H2020/IMI-JU Period: 2018-2023
Funding entity: H2020/IMI-JU
Period: 2018-2023
Presently, Europe is generating unprecedented amounts of patient-level information contained in Electronic Health Record (EHR) systems and other types of health databases. This includes structured data in the form of diagnoses, medication, laboratory test results, etc., and unstructured data in clinical narratives, all of which likely contain invaluable […]
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PhD Defense (Fernanda Correia)
Fernanda Brito Correia, “Prediction And Analysis Of Biological Networks Structure And Dynamics”April 2019
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Masters thesis defense (João Almeida)
João Rafael Almeida, “Software solution for clinical protocol management”
18 Jul, 18.00h
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18th Portugaliæ Genetica 2018 – Best Poster Award
The work entitled “eQTL analysis of the NAPRT locus” won the Best Poster Award at the 18th Portugaliæ Genetica – Genetic Diversity in Structure and Regulation, that was held on 22-23rd of March 2018 in Porto. The work was carried out by PhD. student Sara Duarte-Pereira, researcher Sérgio Matos, Professors José Luís Oliveira and Raquel […]
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18th Portugaliæ Genetica 2018 – Best Oral Presentation Award
Diogo Pratas was granted Best Oral Presentation Award at the 18th Portugaliæ Genetica – Genetic Diversity in Structure and Regulation, held on 22-23rd of March 2018 in Porto. The work presented is entitled “Metagenomic composition analysis of ancient DNA samples”.
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DICOM Validator
The DICOM validator is a web-based solution for evaluation the compliance of PACS applications with the DICOM standard. It features the “as-a-service” business model, which allows users to immediately reach their goals without the extensive setup efforts required by similar solutions. The DICOM Validator is also a community-driven initiative, where users all around the world […]
Posted in Biomedical informatics, Featured, Software
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SOCA – Smart Open Campus
Funding entity: Centro 2020
Period: 2017-2020
The sensing of the person in physical context enables personalized and predictive responses, and is a major step towards a smarter and safer environment. The main objective of SOCA is to create an open innovation ecosystem where data is gathered from multiple sources, processed, integrated, and made available for applications and users, and that is able to create a service sphere able […]
Posted in On-Going Projects, Projects
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SCALEUS
SCALEUS is a data migration tool that can be used on top of traditional systems to enable semantic web features. This user-friendly tool help users easily create new semantic web applications from scratch. Targeted at the biomedical domain, this web-based platform offers, in a single package, a high-perfomance database, data integration algorithms and optimized text […]
Posted in Featured, Knowledge management, Software
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Ann2RDF
Ann2RDF is an interoperable semantic layer that unifies text-mining results originated from different tools, information extracted by curators, and baseline data already available in reference knowledge bases, enabling a proper exploration using semantic web technologies. This result in a more suitable transition process, in which desired annotations are enriched with the possibility to be shared, […]
Posted in Featured, Software, Text mining
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I2X
I2X is a reactive and event-driven framework that simplifies and automates real-time data integration and interoperability. This platform streamlines the creation of customizable integration tasks connecting heterogeneous data sources with any kind of services. Integration is poll-based, with intelligent agents monitoring data sources, or push-based, where the platform waits for data submission by external resources. I2X delivers data […]
Posted in Featured, Knowledge management, Software
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TASKA
Task management systems are crucial tools in modern organizations, by simplifying the coordination of teams and their work. Those tools were developed mainly for task scheduling, assignment, follow-up, and accountability. On the other hand, scientific workflow systems also appeared to help putting together a set of computational processes through the pipeline of inputs and outputs […]
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MONTRA
MONTRA is a rapid-application development framework designed to facilitate the integration and discovery of heterogeneous objects which may be characterized by distinct data structures. Initially designed as a framework which allows biomedical researchers to easily set up dynamic workspaces, where they can publish and share sensitive information about their data entities, MONTRA is suitable for […]
Posted in Biomedical informatics, Featured, Software
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NETDIAMOND – New Targets in Diastolic Heart Failure: from Comorbidities to Personalized Medicine
Funding entity:P2020/PAC
Period: 2016-2019
Heart failure (HF) is a highly prevalent syndrome of impaired cardiac function that constitutes the main cause of hospitalization and disability amongst the elderly, a leading cause of mortality, morbidity and resource consumption. HF with preserved ejection fraction (HFpEF) is characterized by preserved ejection, impaired cardiac filling, lung congestion and effort intolerance, accounting […]
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Multimodal Information Retrieval in Medical Imaging Repositories
Funding entity:FCT
Period: 2016-2019
Digital medical imaging systems are, nowadays, essential tools in clinical practice, both in decision supporting and in treatment management. The main objective of this project is to investigate new solutions for extracting, merging and searching over multimodal data, including text (DICOM metadata and diagnosis reports) and image information. Relevance feedback will be also […]
Posted in Past Projects, Projects, Uncategorized
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SCREEN-DR – Image Analysis and Machine Learning Platform for Innovation in Diabetic Retinopathy Screening
Funding entity:FCT (CMU-Portugal)
Period: 2016-2019
Diabetic Retinopathy (DR) is a leading cause of blindness in the industrialized world that can be avoided with early treatment, demanding an earlier diagnosis in a stage where the treatment is still possible and effective. DR evolves silently without any visual symptoms, during the early stages of the disease.
Under this context, the […]
Posted in Past Projects, Projects
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