Masters thesis (Tiago Almeida)

Tiago Almeida, “Neural Information Retrieval for Biomedical Question-Answering”
July 2019

PhD Defense (Eduardo Pinho)

Eduardo Miguel Coutinho Gomes de Pinho, “Multimodal Information Retrieval in Medical Imaging Repositories”
July 2019

PhD Defense (Fernanda Correia)

Fernanda Brito Correia, “Prediction And Analysis Of Biological Networks Structure And Dynamics”
April 2019

PhD Defense (Luis Bastião)

Luis Bastião Silva, “A federated architecture for biomedical data integration”
Universidade de Aveiro, DETI/IEETA

PhD Defense (Carlos Ferreira)

Carlos Ferreira, “Handling Data Access Latency in Distributed Medical Imaging Environments”
Universidade de Aveiro, DETI/IEETA

Date: 2015.04.10, 10.00 AM
Anfiteatro, Reitoria, Universiade de Aveiro


PhD Defense (Paulo Gaspar)

Paulo Gaspar, “Computational methods for gene characterization and genome knowledge extraction”
Universidade de Aveiro, DETI/IEETA

ACE’14 Workshop on “Designing Systems for Health and Entertainment: what are we missing?”

Systems that aggregate health and entertainment goals are proliferating, but little is known about the way to design and evaluate these systems and how to manage the different (if nor opposite) needs of these two main areas. This workshop will promote the discussion of issues surrounding these areas, enabling a better understanding of the how’s and why’s of designing systems for health and entertainment, as well as the identification of new avenues of research in the field.
Therefore we invite designers, researchers and practitioners to participate in an exciting full-day workshop where they are invited to share their personal views and research on the intersection of technology, health and entertainment.

More information at

SMBM 2014

The 6th International Symposium on Semantic Mining in Biomedicine (SMBM)
6th-7th October, 2014 will be held at the University of Aveiro, Portugal.

SMBM aims to bring together researchers from text and data mining in biomedicine, medical, bio- and chemoinformatics, and researchers from biomedical ontology design and engineering. SMBM 2014 is the follow-up event to SMBM 2012 (University of Zürich, Switzerland) SMBM 2010 (EBI, U.K.), SMBM 2008 (University of Turku, Finland), SMBM 2006 (University of Jena, Germany), and SMBM 2005 (EBI, U.K.).

More information at

PhD Defense (Luis Ribeiro)

Luis Ribeiro, “Platform for on-demand exchange of medical imaging communities”
Universidade de Aveiro, DETI/IEETA

PhD Defense (David Campos)

David Campos, “Term expansion methodologies in biomedical information retrieval”
Universidade de Aveiro, DETI/IEETA

iOS Development Seminar (Rui Pedro Lopes)

A 6-hour iOS Development Seminar will be held by Rui Pedro Lopes, Professor at Polytechnic Institute of Brangança, on the 29th July 2013, at Department of Electronics, Telecommunications and Informatics (DETI), Aveiro.

This Seminar will cover the following main topics: Objective-C, Storyboards, Core Data, Master-Detail User Interface

Universidade de Aveiro, DETI, Room 102, 10h

On Multicriteria Pairwise Sequence Alignment: Algorithms and Applications

Talk from Luís Paquete, Anf. IEETA

The multiobjective formulation of the pairwise sequence alignment problem is introduced, where a vector score function takes into account the substitution score and indels or gaps separately. Two solution methods are introduced: a multiobjective dynamic programming that extends classical algorithms for this problem and an epsilon-constraint algorithm that solves a series of constrained sequence alignment problems. A state pruning technique based on the concept of bound sets is also presented. Finally, its application to phylogenetic tree construction is

Universidade de Aveiro, Anf. IEETA, 14h30

PhD Defense (Pedro Lopes)

Pedro Lopes, “Service Composition in Biomedical Applications”
Universidade de Aveiro, DETI/IEETA

Talk (Kim Sneppen)

Dr. Kim Sneppen from the Niels Bohr Institute, Copenhagen-DK, will give the give the inaugural Lecture of our Systems Biology seminars series entitled Simplified Models of Biological Networks, on the 28th of September.

Universidade de Aveiro, Anf. Ambiente, 14h

PhD Defense (Nuno Rosa)

Nuno Rosa, “From the Salivar Proteome to Oralome”
Universidade Católica Portuguesa, Viseu

International School on SWAT4LS 2012 (May 2nd – 5th, Aveiro)

International School on Semantic Web Applications and Technologies for the Life Sciences 2012
May 2nd – 5th, 2012
Located at the University of Aveiro,
Aveiro, Portugal

More information online at

Talk (Helena Deus)

Helena Deus, “Linked Data and Semantic Web Technologies for improving discovery in the Life Sciences”

We live in a world of data. This is also true for the Life Sciences, where the introduction of omics technologies such as genome sequencing has led to the industrialization of data production beyond a craft-based cottage industry and into a deluge of biological information. Nevertheless, the apparently simple task of collecting and keeping pace with the latest information about a gene of interest is still thwarted by the need for biological researchers to become experts at database-surfing and literature mining.

Linked Data is a set of principles devised for creating a Web of Data where a new generation of Web applications can discover and link relevant pieces of information based on its properties rather than its location in a database. Linked data is also at the root of a movement towards building a knowledge continuum in the Life Sciences and by doing so, has the potential to be a foundation for a platform that will support 21st century Biology.

In this talk, I will present some of the scenarios where Linked Data has been successfully applied in accelerating scientific discovery and translation of Life Sciences knowledge into Health Care and what challenges are still to be addressed.

Helena Deus Bio at

III Workshop Ibero-NBIC – 2011


Hotel Moliceiro, Aveiro, Portugal
October 10-11, 2011

Day 1: Monday, 10

9h00 – 9h30: Opening and Welcome
Boas Vindas
José Luís Oliveira, DETI/IEETA, Universidade de Aveiro, Portugal
Acto de apertura del III Workshop Internacional Redes Ibero-NBIC y NanoRoadmap
Alejandro Pazos & Julián Dorado, Universidade da Coruña, España

9h30 – 11h15:
Vacunología inversa aplicada en malaria
Raúl Isea, IDEA, Fundación de Estudios Avanzados, Venezuela
Bioinformatics, research and applications
Sergio Guíñez Molinos, UCBSM, Universidad de Talca, Chile
Tecnologías NBIC y Nanotoxicidad: Gestión del conocimiento asociado al uso de nanopartículas en medicina
Diana de la Iglesia, GIB, Universidad Politécnica de Madrid, España
Tecnologías de la Información y el Conocimiento en Salud. Un Sistema Basado en Ontologías para el Apoyo a la Toma de Decisión en UCIs
Ana Freire, Universidade de Coruña, España

11h15 – 11h30: Coffee Break

11h30 – 13h00:
Integration of heterogeneous biomedical names taggers
David Campos, DETI/IEETA, Universidade de Aveiro, Portugal
Collecting and Enriching Human Variome Datasets
Pedro Lopes, DETI/IEETA, Universidade de Aveiro, Portugal
Doctoral Program in Nanosciences and Nanotechnology of the University of Aveiro
Tito Trindade, DQ, Universidade de Aveiro, Portugal

13h00 – 14h30: Lunch

14h30 – 16h00:
Integración de la información molecular en un Sistema de Informacion en Salud
Segunda etapa: estándares y control de calidad.
Carlos Otero, HIBA, Buenos Aires, Argentina
Connecting different levels of biological information. From atoms to people
Guillermo López, ISCIII – Instituto de Salud Carlos II, Madrid, España
Posibles aportes de una empresa de Educación Médica Continua a una red de investigación en Salud
Antonio López, EVIMED, Uruguay

16h00 – 16h30: Coffee Break

16h30 – 18h00:
Internal Meeting / Reunión Interna de la Red

Day 2: Tuesday, 11

Visit to Instituto Ibérico de Nanotecnologia (Braga)

Talk (Daniel Sobral)

Daniel Sobral, “Ensembl Regulation”

Ensembl is a world reference for vertebrate genome annotation, providing high quality annotation for more than 50 species. Particularly challenging is the annotation of non-coding functional regions of the genome. Ensembl Regulation aims at making Ensembl
a reference for the annotation of genomic features with a potential role in the transcriptional regulation of gene expression. Combining publicly available data from large projects like ENCODE and The Epigenomics Roadmap, we group overlapping areas of open chromatin and transcription factor binding to build a “best-guess” set of regulatory features, in a cell-aware manner. Finally, we also include histone-modification and polymerase data to generate cell-specific classifications for the regulatory regions. Taking advantage of the role of the EBI as part of the ENCODE data analysis group, we aim at bringing Ensembl to the forefront of the annotation of the regulatory genome.

PhD Defense (Daniel Polónia)

Daniel Polónia, “An electronic market for teleradiology services”