Cloud Thinking

Funding entity: QREN MaisCentro
Period: Feb.2013 – Dec.2014

The projects’ ambition is the creation of a new set of solutions based in novel ICT technologies, developing a concept that encompasses the synergistic usage of cloud computing, with large database access and information retrieval, associated with advanced methods for reasoning and data mining (and with the basic scalable algorithms to support the dimensions of the data sets targeted).

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NeuroPath – New Strategies Applied to Neuropathological Disorders

Funding entity: QREN MaisCentro
Period: Feb.2013 – Jun.2015

Neurodegenerative disorders are a major health concern worldwide, Portugal being no exception. With this project the University of Aveiro proposes extend existing research in the field of neurodegenerative diseases through the creation of a consortium of 5 research units from UA (CBC, QOPNA, I3N, IEETA, CICECO). The projects main goal is to offer novel therapeutic strategies to tackle the complex array of existing neuropathologies. By building a multidisciplinary research team that combines experts in molecular neuropathologies, proteomics, metabolomics, bioinformatics, neuronal networks, organic synthesis and drug design from the UA we will be able to attack the problem on many fronts. Upon successful completion of this project, new therapeutic approaches will have been developed which will contribute to the improvement of life quality for neurodegenerative patients, having a high society impact considering the 10 million new patients reported every year.

EU-ADR – Early Detection of Adverse Drug Events by Integrative Mining of Clinical Records and Biomedical Knowledge

Funding entity: FP7-ICT (STREP)

The overall objective of this project is the design, development and validation of a computerized system that exploits data from electronic healthcare records and biomedical databases for the early detection of adverse drug reactions.

An eHealth Successful Project

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Developing new tools for studying mRNA mistranslation

Funding entity: FCT (PTDC/BIA-BCM/72251/2006)
Period: 2008-2011

Implementation of a Nacional Facility for DNA Microarrays: Phase II

Funding entity: FCT (PTDC/BIA-BCM/64745/2006)
Period: 2009-2011

New statistical methodologies for analysis DNA microarrays data

Funding entity: FCT (PTDC/MAT/72974/2006)
Period: 2006-2008

DNA Microarray technology is one of the most promising new technologies for global gene expression analysis. This technology is sophisticated, very expensive, highly interdisciplinary and produces vast amounts of data whose management and analysis pose significant challenges. This project aims to study new bi-clustering approaches that can help to obtain relevant information from gene expression microarrays.

mRNA mistranslation in yeast

Funding entity: HFSP Research Grant
Period: 2005-2008

The very few quantitative mRNA mistranslation studies carried out to date indicate that the average decoding error ranges from 10-4 to 10-5 errors per codon decoded. However, no systematic study has yet been carried out to rank mRNA sequences according to
decoding error and no methodology has yet been developed to identify genes that are prone to decoding error.

In this project, software tools for data visualization and mathematical methodologies for identification of general rules governing  RNA translation, and tools for mapping mRNA regions of high decoding error and for identifying putative gene expression regulatory sequences present in mRNAs, will be developed.

INFOBIOMED – Structuring European Biomedical Informatics to Support Individualised Healthcare

Funding entity: IST FP6 (IST2002-507585) – NoE (Network of Excelence)
Period: 2003-2006

There is a great potential for synergy between medical informatics and bioinformatics with a view on continuity and individualisation of healthcare, so that the benefits of the human genome sequence can reach the population. A collaborative effort between those two disciplines is needed to bridge the current gap between them. Biomedical Informatics (BMI) is an emerging discipline that aims at bringing these two worlds together to foster the development of novel diagnostic and therapeutic methodologies and strategies.

The INFOBIOMED network aims at setting a durable structure for the described collaborative approach at an European level, mobilising the critical mass and the resources necessary for enabling the collaborative approach that supports the consolidation of BMI as a crucial scientific discipline for future healthcare.

An eHealth Successful Project

INFOGENMED – A virtual laboratory for accessing and integrating genetic and medical information for health applications

Funding entity: IST FP5 (IST2001-39013)
Period: 2002-2004

UA/IEETA was the Project Coordinator

One goal currently challenging bio – and clinical informatics is to develop robust computational methods and tools to model, store, retrieve and analyse information at multiple levels of complexity, i.e., from molecule to organism. For example, the unification of heterogeneous databases under one virtual system is an important step towards developing such robust computational models. The latter is the objective of the INFOGENMED project which aims at building a virtual laboratory for accessing and integrating genetic and medical information for health applications. Once built, the system allows practitioners, biologists, chemists and other experts to navigate through local and remote biomedical databases.

INFOGENMED started in September 2002, (http://www.infogenmed.net), and the functionalities already built in the system allow for: (1) defining clinical pathways to guide the user in the navigation of multiple sources over the Internet; (2) identifying and characterizing the most relevant databases to support the molecular medicine practice for selected rare genetic diseases; (3) designing the integration methods, based on virtual databases, mediators and semantic vocabulary servers.

Developing new Bioinformatics tools for genome analysis

Funding entity: POCTI-32030/2001
Period: 2002-2005

Biologists have been wondering for many years how organisms evolved highly accurate information maintenance, transfer and decoding machineries. In particular, how the astonishing translational decoding rate of 20 codons per second is achieved with an average error of 10-4 to 10-5 per codon decoded, and how does the ribosome maintain the reading frame. The tools to answer these questions are not yet available but the row DNA sequencing data is. To shed new light into this important question, we have developed a software package that simulates ribosome scanning and reading during mRNA translation. The software screens fully or partially sequenced genomes and determines the arrangement of any particular codon in relation to the others by simultaneously fixing P-site codons and “memorizing” E and A-site codons during each translocation cycle. In doing so, it builds a genome wide codon context map that allows for identification of potential error prone mRNA sequences and gene expression regulatory points.

In this project, the various tools already developed will be integrated into a single software package to allow for automated search, downloading and editing of row DNA sequence data. Software tools for data display and new mathematical methodologies for identification of general rules governing mRNA translation will be developed. New tools for mapping mRNA regions of high decoding error and putative gene expression regulatory sequences present in the mRNAs, will also be developed. Finally, a database and an Internet Home Page will be built for making the data available to the scientific community. These in silico studies will be complemented with in vivo experiments. For this, a multidisciplinary team including two computing engineers, two mathematicians, one physicist, one biochemist and one molecular biologist has been assembled. To our knowledge this is the first Portuguese multidisciplinary team set up for functional genomics and the only one actively engaged on the development of software tools and mathematical models for genome analysis. It is expected that this project will provide important new insight on the role of the translational machinery on genome evolution.

Functional Proteomics in Candida albicans: Developing an Integrated Database for the Management of Proteomics projects

Funding entity: POCTI-32942/99
Period: 2001-2004

Candida albicans is an important human pathogen which exists as a commensal in at least 50% of the human population. It accounts for more than 60% of all fungal infections and is now the fourth most common form of septicaemia in Western hospitals with an associated mobidity between 30 and 50%. It is also a major cause for concern in HIV-infected populations where 84% of the patients develop oropharyngeal C.albicans colonisation and 55% develop clinical thrush. C. albicans pathogenesis is dependent upon a wide range of virulence factors, namely a myriad of morphogenesis associated factors, represents a major challenge to the elucidation of C. albicans pathogenesis at the molecular level through classic molecular and biochemical methodologies. The diploid nature of C. albicans, its alternative genetic code and its recalcitrance to genetic analysis, add extra difficulties to its study and to the development of new antifungals. However, the advent of new genetics and molecular technologies which allow for genome wide analysis is promising to alter the present situation.

This project aims at integrating classical genetics and biochemical approaches with newly developed, proteomics and bioinformatics methodologies to uncover new virulence factors associated to morphogenesis.

Software tools are been developed for management of biological data extracted from protein 2D-maps, for helping planning and following up experimental protocols and for data storing. Additionally, mathematical algorithms are also been developed for creating theoretical protein 2D-maps for comparative proteomics studies.

Query term expansion methodologies for improved biomedical literature retrieval

Funding entity: FCT PTDC/EIA-CCO/100541/2008
Period: 2010-2013

The objective of this project is to develop a query expansion and document ranking method specially aimed at obtaining, from the MEDLINE database, a ranked list of publications that are most significant to a set of genes.

DICOM Services Over Peer-To-Peer Networks

Funding entity: FCT PTDC/EIA-EIA/104428/2008
Period: 2010-2013

The overall goal is to instantiate a new network connectivity concept for medical imaging data and services at inter-institutional level. This will turn large volumes of clinical information and analytical tools, actually “locked” in clinical units, into shared repositories and high-quality collaborative environments for medical applications, education and research.

GEN2PHEN – Genotype-To-Phenotype Databases: A Holistic Solution

Funding entity: FP7-Health (IP)

The GEN2PHEN project has the overall ambition of unifying human and model organism genetic variation databases, and doing this in such a way that the resulting holistic view of G2P data can be blended with all other biomedical database domains via one or more central genome browsers.

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