INESC-ID   Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa
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  Past Projects  
     
 
-TGV - Techniques for Global Functional Verification of Complex Digital Systems (IE02012)
Arlindo Manuel Limede de Oliveira
From 01-Jun-1999 to 31-Dec-2003
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: Cadence Design Systems (Company) - San Jose, USA
Members: Arlindo Manuel Limede de Oliveira, José Carlos Alves Pereira Monteiro, João Paulo Marques da Silva, José Carlos Campos Costa, Paulo Ferreira Godinho Flores, Lino José Baeta Pinchete
Development of algorithms for verification of digital designs.
     
-Data Mining (II10004)
Arlindo Manuel Limede de Oliveira
From 01-Jan-2002 to 30-Dec-2008
Prime Contractor: INESC-ID (Other)
Financed by: Cadence Design Systems
The objectives of this project are the development of new machine learning and data mining techniques for application in the domains of computer aided design, information retrieval and systems biology.
     
-Análise de cabazes de compras para aquisições on-line (IE02021)
Acronym: PMELink
Arlindo Manuel Limede de Oliveira
From 01-Jan-2004 to 01-Apr-2004
Prime Contractor: INESC-ID (Other)
Financed by: IAPMEI
Partnerships: LINK Consulting (Company) - Lisboa, Portugal, PME Link (Company) - Lisboa, Portugal
Members: Arlindo Manuel Limede de Oliveira, Cláudia Martins Antunes
Application of basket analysis algorithms to the B2B online market.
     
-BioGrid - Parallel Algorithms for Gene Annotation (IE02020) (Project Link)
Acronym: BioGrid
Arlindo Manuel Limede de Oliveira
From 01-Feb-2004 to 30-Jun-2007
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: Instituto Gulbenkian da Ciência (Other) - Oeiras, Portugal
Members: Arlindo Manuel Limede de Oliveira, Ana Teresa Correia de Freitas, José Carlos Alves Pereira Monteiro, Luis Miguel Teixeira D Avila Pinto da Silveira, Paulo Ferreira Godinho Flores, Alexandra Sofia Martins de Carvalho, Alexandre Paulo Lourenço Francisco, Ana Paula Proença Ramalho, Orlando Miguel Cruz da Anunciação, Pedro Tiago Gonçalves Monteiro
The objective of this project is to capitalize on the know-how of the research team on algorithms and complexity to develop an integrated system that uses grid computing to make available the full power of bioinformatics algorithms to a large community of users. In particular, we propose to improve existing approaches for motif identification, both by algorithmic improvements and by making use of the computing power made available by a grid.
     
-DBYeast: A Framework for the development and application of algorithms to the analysis and identification of gene regulatory networks (IE02023) (Project Link)
Acronym: DBYeast
Arlindo Manuel Limede de Oliveira
From 01-Jan-2005 to 31-Dec-2007
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: Center for Biological and Chemical Engineering (CEBQ) - IST (University) - Lisboa, Portugal, Université Claude Bernard (University) - Lyon, France
Members: Arlindo Manuel Limede de Oliveira, Ana Teresa Correia de Freitas, Luis Pedro Fragão Bento Coelho, José Miguel Ranhada Vellez Caldas, Alexandra Sofia Martins de Carvalho, Susana de Almeida Mendes Vinga Martins
The objective of this project is the study of interaction networks and their underlying complexity, focusing on gene regulation networks. Research is centered on unveiling the gene regulatory mechanisms of a simple organism, the yeast (Saccharomyces cerevisiae), extensively used by the scientific community as an experimental platform.
     
-Insights into the complex regulatory networks acting in yeast cells changed with drugs/chemical stresses: genome wide expressions approaches supported by bioinformatics (IE02027)
Acronym: STRESSE
Ana Teresa Correia de Freitas
From 02-Jan-2006 to 31-Dec-2007
Prime Contractor: Instituto Superior Técnico (University) - Lisboa, Portugal
Financed by: FCT
Members: Ana Teresa Correia de Freitas, Arlindo Manuel Limede de Oliveira, Nuno Miguel Dias Mendes, Pedro Tiago Gonçalves Monteiro
The objective of this project is to unravel the mechanisms ensuring the coordinate transcriptional regulation of yeast genes in response to drugs/chemical stress by combining the expertise of two research groups: the Biological Sciences Research Group (BSRG), Instituto Superior Técnico and the Knowledge Discovery and Bioinformatics Group (KDBIO/ALGOS), INESC-ID. The specific biological problems focused include: 1) the reguçatory networks underlying yeast responses to: i) two weak acids of relevance either in the food industry as a preservative (propionic acid) or in agriculture (the herbicide 2,4-dichlorophenoxyacetic acid/2,4-D); and ii) three anti-malarial/anti-arrhythmic drugs (quinine, quinidine and artesunate); and 2) the role of the poorly characterized transcriptional regulator Rim101p in yeast response to propionic acid-induced stress. The results of gene transcription regulation to be examined are essentially those very recently obtained by the BSRG based on microarray analysis. The promoter sequences of genes found to be co-ordinately expressed under a specific stress will be analyzed to discover shared motifs, which may correspond to regulatory elements. Candidate cis-acting elements will be matched against a database of known binding-sites, under construction. This database will be completed, consolidated, explored and made available to the scientific community during the project.



     
-Unveiling Metabolic and Genetic Networks in Living Cells (IE02ID01004)
Acronym: MAGIC
Ana Teresa Correia de Freitas
From 01-Mar-2006 to 31-Dec-2007
Prime Contractor: INESC-ID (Other)
Financed by: INESC-ID
Members: Ana Teresa Correia de Freitas, Susana de Almeida Mendes Vinga Martins
The central goal of this project is the development of methods that will partially automate the study, identification and modelling of mechanisms found in many living organisms that control gene expression. Obtaining effective methods and algorithms to integrate information from a number of different sources in order to derive effective models for genetic and metabolic networks is the first major objective of this project. Making widely available to the scientific community the results obtained in this project, both in terms of designed tools and of new biological results, represents the second major scientific objective of this project.
     
-Dynamical Modeling, Control and Optimization of Metabolic Networks (II10001) (Project Link)
Acronym: DYNAMO
Susana de Almeida Mendes Vinga Martins
From 01-Sep-2007 to 31-Aug-2010
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: Georgia Institute of Technology (University) - Georgia, US, ITQB (Other), University of Texas M.D.Anderson Cancer Center (University) - Houston, USA
Members: Ana Teresa Correia de Freitas, João Manuel Lage de Miranda Lemos, Rodrigo Madrugo Piedade
The first objective of this project is to develop and validate mathematical models and computational tools for the analysis and simulation of the dynamical behavior of complex metabolic networks. The main goal is to produce interpretable models that accurately describe the metabolic system and have prediction and generalization capabilities. A second objective is to create control and optimization strategies to alter the fluxes and concentrations of metabolites, both transiently and at steady-state, by proposing the manipulation of enzymes gene expression. A third objective is the creation of an integrative bioinformatics infrastructure to store the experimental data and to implement and deploy the algorithms developed, thus fostering model interchange between systems. A forth objective is the acquisition of experimental in vivo metabolite concentration time series data, the creation of mutant bacterial strains with desired metabolic behavior and the experimental validation of the models previously proposed.
     
-Models for the Dynamic Behavior of Biological Networks (II10002)
Acronym: DYABLO
Arlindo Manuel Limede de Oliveira
From 30-Dec-2007 to 30-Dec-2010
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: Instituto Superior Técnico (University) - Lisboa, Portugal
Members: Arlindo Manuel Limede de Oliveira, Ana Teresa Correia de Freitas, Pedro Tiago Gonçalves Monteiro
The objectives of this project are the development of new techniques and models for accurate simulation of biochemical networks. Coupled with higher abstraction models, these techniques can be used to study the properties of the state spaces of complex biological systems, using model checking algorithms. Finally, these techniques and models will be applied to actual biological systems, with emphasis on the regulation mechanisms of the FLR1 stress response network of Yeast.
     
-Algorithms for the identification of genetic Regulatory Networks (II10003) (Project Link)
Acronym: ARN
Ana Teresa Correia de Freitas
From 01-Jan-2008 to 31-Dec-2010
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: FFCUL (Other), INRIA Rhône-Alpes (Other) - Grenoble, FRANCE, Institute National de la Recherche Agronomique (Other) -Toulouse, Instituto Superior Técnico (University) - Lisboa, Portugal
Members: Arlindo Manuel Limede de Oliveira, Susana de Almeida Mendes Vinga Martins, João André Nogueira Custódio Carriço, Alexandra Sofia Martins de Carvalho, Nuno Miguel Dias Mendes, Sara Alexandra Cordeiro Madeira
The objectives of this project are:
- The development of new methods and models to search and extract evidence of regulatory mechanisms in biological data and literature. This includes the improvement of the models used to represent complex regulatory signals and small functional RNA motifs and the development of algorithms to explore the cooperative characteristic of all these signals; the development of algorithms for the identification of local patterns in expression data; and the development of text-mining methods for extracting gene regulations from BioLiterature and from gene annotations.
- The design of new algorithms to derive effective models for gene regulatory networks. This includes the development of methods to piece together information from different sources.
The project will use the YEASTRACT platform (www.yeastract.com) as a launching pad for a much more ambitious system.

     
-Characterization and modeling of a specific transcriptional regulatory network required for multidrug resistance in yeast (II10009)
Acronym: FLR1-NET
Arlindo Manuel Limede de Oliveira
From 01-Jan-2008 to 30-Sep-2010
Prime Contractor: Instituto Superior Técnico (University) - Lisboa, Portugal
Financed by: FCT
Partnerships: Instituto Superior Técnico (University) - Lisboa, Portugal
Members: Arlindo Manuel Limede de Oliveira, Ana Teresa Correia de Freitas
The main objectives of this project are to unveil the hierarchy and synergy that lies behind the combined action of the transcription factors involved in yeast response to drugs and other chemical aggressions and to develop computational tools for modeling the dynamic of these transcription regulatory networks.
     
-Data Mining Applied to Credit Systems Software (II10007)
Acronym: VANTYX
Arlindo Manuel Limede de Oliveira
From 01-Jan-2008 to 30-Sep-2008
Prime Contractor: Vantyx (Other)
Financed by: AdI - Agência de Inovação
Partnerships: Vantyx (Other)
Members: Arlindo Manuel Limede de Oliveira, Ana Teresa Correia de Freitas
Deploy data mining technology developed at INESC-ID to improve the ability of Vantyx software to satisfy customer needs.
     
-Genome-wide analysis of short RNAs as modulators in dehydration stress tolerance using tolerant and genetic model systems (II10005)
Acronym: ERA-PG
Ana Teresa Correia de Freitas
From 01-Jan-2008 to 31-Jul-2010
Prime Contractor: IBET (Other)
Financed by: IBET
Partnerships: IBET/ITQB - Instituto de Biologia Experimental e Tecnológica (Other), Universität Bonn / Institut für Zellulare und Molekulare Botanik Zellbiologie der Pflanzen (University), University of East Anglia (University) - Norwich, UK
Members: Ana Teresa Correia de Freitas, Susana de Almeida Mendes Vinga Martins, Nuno Miguel Dias Mendes
Drought stress is a common adverse environmental condition that seriously affects crop productivity worldwide. Due to the complexity of drought as a stress signal and the fact that drought stress is difficult to manipulate, deciphering dehydration tolerance mechanisms is a major challenge.
The objective of this project is to explore potential roles of regulatory small 21-25nt RNAs (sRNAs) in dehydration stress tolerance. We propose to construct libraries of sRNAs from the desiccation tolerant model plant Craterostigma plantagineum, the dehydration tolerant legume Medicago truncatula and the genetic model plant Arabidopsis thaliana at different stages of dehydration. We aim to identify new families of sRNAs using genomics tools and test the expression profile of selected sRNAs. Our results will have important implications for gene regulation under dehydration stress and also contribute significantly to the long-term goal of having a comprehensive profile of sRNAs in plants.

     
-Scanning for candidates genes underlying a pulp yield QTL in Eucalyptus globulus (II10006) (Project Link)
Acronym: Eucalyptus
Ana Teresa Correia de Freitas
From 01-Jan-2008 to 31-Dec-2010
Prime Contractor: IBET (Other)
Financed by: FCT
Partnerships: IBET (Other), Instituto Superior Técnico (University) - Lisboa, Portugal, RAIZ - Instituto de Investigação da Floresta e Papel (Other)
Members: Ana Teresa Correia de Freitas, Susana de Almeida Mendes Vinga Martins, João André Nogueira Custódio Carriço, Mauro Dala Santos
The main objective is to identify and characterize the genomic region that underlies strong effect pulp yield QTL in E. globulus, combining map-based cloning and transcriptomic approaches. Knowledge of the genomic loci responsible for quantitative variation of wood traits of interest (pulp yield), is of major interest in molecular assisted breeding. This will allow identifying genes responsible for that variation, and gathering new knowledge about the molecular mechanisms of gene expression and regulation in wood forming tissues.
     
-Managing the Complexity of the Open Source Infrastructure (II10008) (Project Link)
Acronym: MANCOOSI
Arlindo Manuel Limede de Oliveira
From 01-Feb-2008 to 31-Jan-2011
Prime Contractor: Universite Paris Diderot (University) - Paris, France
Financed by: European Commission
Partnerships: Caixa Mágica Software (Company) -Portugal, Edge-IT (Company) -France, ILOG (Company) -France, Pixart (Company) -Argentina, Tel Aviv University (University) -Israel, Università degli Studi dell'Aquila (University) -Italy, Université Catholique de Louvain (University) -Belgium, Université Nice Sophia Antipolis (University) -France
Members: Arlindo Manuel Limede de Oliveira
The main objective of the Mancoosi project is to develop the scientific knowledge and build the tools necessary to manage the complexity of the open source infrastructure. This infrastructure is one of the essential building blocks of tomorrow’s software architectures: the success of LAMP (Linux, Apache, MySQL, Php) inside as well as outside the data centers is clear evidence of this. Yet, this infrastructure undergoes a fast-paced and distributed evolution that is too often maintained in ad-hoc ways using tools and processes that have clearly attained their limits today. There is a need for new and innovative technology, and this is what Mancoosi will provide.
We explicitly target the difficult problems that arise when one wants to efficiently and safely upgrade a set of software components in complex software infrastructures, like those found in open source software distributions, which are among the most complex software systems known, made of tens of thousands of components that evolve over time without centralized design: this is a challenging endeavor.
We have chosen the Free and Open Source infrastructure as our main target, as it provides today a real-world example of what tomorrow’s complex, quickly changing software systems will look like: the applicability of these models and algorithms goes far beyond Free and Open Source software, and technologies developed in Mancoosi will pave the way to the maintainability of the software systems of the future, especially for systems of systems, even when they are not Free or Open Source.

     
-Fourteenth International Conference on Research in Computational Molecular Biology (II10010) (Project Link)
Acronym: RECOMB 2010
Arlindo Manuel Limede de Oliveira
From 01-Jun-2008 to 06-Aug-2010
Prime Contractor: INESC-ID (Other)
Financed by: Inesc-ID
Partnerships: INESC-ID (Other), Instituto Gulbenkian da Ciência (Other) - Oeiras, Portugal, MIT Computer Science and Artificial Intelligence Laboratory (University) - Cambridge, USA
Members: Ana Teresa Correia de Freitas, Susana de Almeida Mendes Vinga Martins
Conference Organization
     
-Confronting the clinical relevance of biocide induced antibiotic resistance (II10011) (Project Link)
Acronym: BIOHYPO
Ana Teresa Correia de Freitas
From 07-Jun-2009 to 06-Jun-2012
Prime Contractor: Università di Siena (University) - Siena, Italy
Financed by: European Commision (FP7-KBBE-2008-2B-ID
Partnerships: Advanced Analytical Technologies, Inc. (AATI) (Company) - AMES, United States of America, Biolab Española, S.L (Company) - Barcelona, Spain, Centro Nacional de Biotecnologia - CSIC (Other) - Madrid, Spain, Gazi University (University) - Ankara, Turkey, Istituto Superior di Sanitá - ISS (Other) - Roma, Italy, Lysoform (Company) - Glarus, Switzerland, Middle East Technical University - METU (University) - Ankara, Turkey, Quotient Bioresearch Limited (Company) - Cambridgeshire, England, Universitat Bern (University) - Bern, Switzerland, Università degli Studi di Firenze (University), Università di Milano (University) - Milano, Italy, Università di Siena (University) - Siena, Italy
Members: Ana Teresa Correia de Freitas, Arlindo Manuel Limede de Oliveira, Jonas S. Almeida, Sara Alexandra Cordeiro Madeira, Alexandra Sofia Martins de Carvalho, Alexandre Paulo Lourenço Francisco, João André Nogueira Custódio Carriço
Biocides have been in use for hundreds of years for antisepsis, disinfection and preservation. Despite this widespread and ever increasing use most bacterial and fungal species remain susceptible to biocides. The dramatic increase and spread of resistance to antibiotics linked to reports of co- and cross-resistance between antibiotics and biocides raised speculations on potential hazard of biocide use. The overarching question which BIOHYPO is aimed to address is: has the use of biocides contributed to the development and spread of clinically significant antibiotic resistance in human pathogens? Core of BIOHYPO are a high throughput screening approach on collections of thousands of well characterized microorganisms and an interactive web based data analysis platform. Phenotypic screening for reduced susceptibility to biocides, detection of novel resistance genes and mobile elements, and screening for their molecular epidemiology and metagenomics will be accompanied by methodological innovation for testing, risk evaluation and registration of biocides. Altogether BIOHYPO aims to provide solid data and analysis to direct future issuing of guidelines for safe environmental, medical and industrial use of biocides.
     
-Control based on dynamic modeling of HIV-1 infection for therapy design (II10013) (Project Link)
Acronym: HIVCONTROL
Susana de Almeida Mendes Vinga Martins
From 01-Jan-2010 to 01-Dec-2012
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: Faculdade de Medicina da Universidade de Lisboa (University) - Lisbon, Portugal, INESC-ID (Other), Instituto de Sistemas e Robótica (Other) - Lisboa, PORTUGAL
Members: Susana de Almeida Mendes Vinga Martins
Immunology is increasingly recognized as a major field in the area of Biomedicine. Establishing efficient therapeutics for infectious diseases is a major problem of the human society. In particular, this is illustrated by the emergence of the Acquired Immune Deficiency Syndrome (AIDS), which raised new problems and concerns worldwide. Controlling this type of diseases has thus a significant socio-economical impact. Furthermore it also raises challenging problems that only an interdisciplinary approach can tackle. In this respect a systems’ approach is attracting more and more attention in recent years and forms a global framework for this proposal. The aim of this project consists of designing personalized therapy strategies to control HIV-1 infection using model based nonlinear control and estimation techniques.
     
-A comprehensive dissection of pneumococcal-host interactions (II10012) (Project Link)
Acronym: PNEUMOPATH
Susana de Almeida Mendes Vinga Martins
From 01-Mar-2010 to 03-Feb-2012
Prime Contractor: Professor Peter W Andrew, University of Leicester (University) - Leicester, United Kingdom
Financed by: EC-HEALTH-2007-2.3.1-2
Partnerships: CNRS - Université Paul Sabatier (University) - Toulouse, France, deCODE genetics (Other) - Reykjavik, Iceland, INESC-ID (Other), Institut National des Sciences Appliquees (Other) - Toulouse, France, Instituto de Tecnologia Química e Biológica (Other) - Oeiras, Portugal, Intercell AG (Company) - VIenna, Austria, IQTherapeutics BV (Other) - Groningen, Netherlands, Karolinska Institutet (Other) - Stockholm, Sweden, MRC Mouse Genome Unit (Other) - Harwell, United Kingdom, Mucosis BV (Other) - Groningen, Netherlands, Radboud University Nijmegen Medical Centre (University) - Nijmegen, Netherlands, Swedish Institute for Infectious Disease Control (Other) - Stockholm, Sweden, Univeristy of Leicester (University) - Leicester, United Kingdom, Università di Siena (University) - Siena, Italy, University of Groningen (University) -Netherlands, University of Kaiserslautern (University) -Germany
Members: Jonas S. Almeida, Susana de Almeida Mendes Vinga Martins, Mauro Dala Santos, Alexandra Sofia Martins de Carvalho
: Transmission of Streptococcus pneumoniae to a new host can result in clearance, asymptomatic colonisation or progress to invasive disease. To date, study of infection has tended to be a reductionist approach, considering the contribution of each virulence factor or host factor in isolation. Consequently, in searching for targets for antimicrobial therapy or for enhancement of host defence, the contribution of individual factors may be inaccurately estimated. The aim of this project is, through a systems approach to host-pneumococcal interaction, identify the most important and consistently involved host and pneumococcal factors.
     
-A systems biology approach to the role of pneumococcal carbon metabolism in colonization and invasive disease (II10015)
Acronym: PNEUMOSYS
Susana de Almeida Mendes Vinga Martins
From 01-Apr-2010 to 31-Mar-2013
Prime Contractor: ITQB (Other)
Financed by: FCT
Partnerships: INESC-ID (Other), ITQB (Other), Universidade Nova de Lisboa (University) - Lisboa, Portugal, University of Leicester (University) -England
Members: Susana de Almeida Mendes Vinga Martins, Jonas S. Almeida, Nuno Miguel Martins Tenazinha
The ultimate GOAL of this project is to develop a multi-level mathematical model that can predict factors in sugar assimilation essential to thrive in the different host niches. However, a systematic, systems biology approach towards determining the factors governing sugar metabolism is far from trivial. The specific AIMS of this project are to obtain the response of S. pneumoniae to changing carbon sources by a variety of global technologies including metabolomics (Task 2), transcriptomics, and proteomics (Task 3), with the goal of fuelling the mathematical representation (Task 4). To verify the model, deletion mutants of predicted essential factors will be constructed and tested for the ability to colonize and cause invasive disease (pneumonia and bacteraemia) in vivo (Task 5)
     
-Heterogeneous Multi-Core Architecture for Biological Sequence Analysls (II10021) (Project Link)
Acronym: HELIX
Luis Manuel Silveira Russo
From 01-Jan-2011 to 01-Dec-2013
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: INESC-ID (Other)
Members: Luis Manuel Silveira Russo, Arlindo Manuel Limede de Oliveira
This project will adapt an entirely new approach to SPMD parallel [C). To speed up this set of algorithms issues related to bio-informatics, a parallel architecture with multiple processing cores, flexible, programmable and extremely efficient, will be developed and implemented in order to obtain a significant acceleration in
implementation of the kernels computationally intensive that are shared by these applications.

     
-The power of the short - Tools and Algorithms for next Generation Sequencing applications (II10019) (Project Link)
Acronym: TAGS
Ana Teresa Correia de Freitas
From 01-Jan-2011 to 31-Dec-2013
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: INESC-ID (Other), LNCC-Laboratório Nacional de Computação Científica (Other) -Brasil, SIPS GROUP (Other) -Lisbon
Members: Ana Teresa Correia de Freitas, Luis Manuel Silveira Russo, Paulo Gustavo Soares da Fonseca, Francisco Jorge Dias Oliveira Fernandes
This project will address the models and methods thal will be used to effectively re-sequence genomes, taking Into account the
characterislics of the new HT5R technologies. An integrated parallel programmlng framework will be developed In order to
implement lhe algorithms developed in this project.

     
-COST Action BM1006 NEXT GENERATION SEQUENCING DATA ANALYSIS NETWORK (II10020) (Project Link)
Acronym: BM1006
Ana Teresa Correia de Freitas
From 17-Jan-2011 to 01-Mar-2015
Prime Contractor: Dr Erik Bongcam Rudloff Uppsala (Other) -Sweden
Financed by: COST
Partnerships: COST (Other)
Members: Ana Teresa Correia de Freitas, Paulo Gustavo Soares da Fonseca
Next Generation Sequencing (NGS) is a highly parallelised approach for quickly and economically sequencing new genomes, re-sequencing large numbers of known genomes, or for rapidly investigating transcriptomes under different conditions. The massive data volumes being generated by these new technologies require new data handling and storage methods. Hence, the life science community urgently needs new and improved approaches to facilitate NGS data management and analysis. This COST Action unites bioinformaticians, computer scientists and biomedical scientists, harnessing their expertise to bring NGS data management and analysis to new levels of efficiency and integration. Rigorous surveillance of NGS technology and NGS-related software developments
will allow the partners to generate software solutions for future NGS opportunities in a timely manner. The Action will increase the ability of European groups to maximally benefit from NGS technology, and will create a nucleus for world-wide activities to jointly address the upcoming biomedical informatics revolution.

     
-Understanding NEUROdegenerative diseases through CLINical and OMICS data integration (II10018) (Project Link)
Acronym: NEUROCLINOMICS
Sara Alexandra Cordeiro Madeira
From 01-Mar-2011 to 28-Feb-2014
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: Instituto de Medicina Molecular (Other) - Lisboa, Portugal, Katholicke Universiteit Leuven (University) - Leuven, Belgium
Members: Sara Alexandra Cordeiro Madeira, Alexandre Paulo Lourenço Francisco, Pedro Filipe Zeferino Aidos Tomás, Arlindo Manuel Limede de Oliveira, Leonel Augusto Pires Seabra de Sousa, Joana Sofia de Pinho Gonçalves, Orlando Miguel Cruz da Anunciação
Declines in cognitive and motors functions, together with other evidences of neurological degeneration, become increasingly likely as healthy people age. Everyone wilI experience altered brain functions, ones at an earlier age or at a faster rate than others. As such. distinguishing the
motor and cognitive declines of normal aging from those due to pathological processes, such as Alzheimer's disease or Amyotrophic lateral
Sclerosis, and understanding the individualized disease diagnostic and prognostic patterns are ongolng research challenges.
This project is an innovative approach to understanding neurodegenerative diseases through heterogeneous data integration. Asophisticated
knowledge discovery system willl integrate powerful mining algorithms to unravel potentially relevant links between omics and clinical data.
Disease diagnostic and prognostic markers, disease progression rates, and patient profiles will be tackled. Apart from the challenging goal of
studying complex diseases, developing efficient and effective integrative approaches to biomedical data analysis is a research hot topic, not
only due to the highly heterogeneity of data but also to their massive volume.

     
-NetDyn: Understanding real large networks, from structure to dynamics (II10022) (Project Link)
Acronym: NetDyn
Alexandre Paulo Lourenço Francisco
From 01-Jan-2012 to 30-Jun-2014
Prime Contractor: INESC-ID (Other)
Financed by: FCT (PTDC/EIA-EIA/118533/2010)
Partnerships: Instituto de Medicina Molecular (Other) - Lisboa, Portugal, Yahoo Research and University Pompeu Fabra (Other) - Barcelona, Spain
Members: Alexandre Paulo Lourenço Francisco, Arlindo Manuel Limede de Oliveira, Helena Sofia Andrade Nunes Pereira Pinto, Pedro Tiago Gonçalves Monteiro, Sara Alexandra Cordeiro Madeira, Cátia Raquel Jesus Vaz
In recent years, with the explosive growth of real networks and structured data sets, a new class of graphs came to light. This kind of graphs are huge and very sparse in general, with some prevailing characteristics. The structure of such networks is hard to describe in general and, moreover, the structure is only a starting point. When we think about complex networks, we should take into account connectedness both at the level of structure and of behavior. This means that, in addition to tools to analyze network structure, we also need a framework for reasoning about behavior and interaction in network contexts, where a single event may cause subtle cause-effect events. Although it is commonly accepted that structure has influence on behavior, to our knowledge little work has been done on how dynamics influence network structure. On the other hand, since complete observation may not be possible and tinkering with real systems may lead to unexpected disruptions, suitable simulation models and tools are a must. This project comes in this line of research, with the aim of developing new models and tools for the study of large networks structure evolution and processes dynamics.
     
-CAMP - Computational Analysis of MicroRNAs in Plants (II10023)
Acronym: CAMP
Ana Teresa Correia de Freitas
From 01-Mar-2012 to 28-Feb-2015
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: INESC-ID (Other), INRIA (Other), Instituto de Investigação Científica e Tropical (Other) -Portugal
Members: Ana Teresa Correia de Freitas, Paulo Gustavo Soares da Fonseca, Alexandre Paulo Lourenço Francisco, Nuno Miguel Dias Mendes, Manuel Borges Dias dos Reis
The objective of this project is to develop new computational tools for the study of miRNA-mediated gene regulation. The
methods that will be developed will focus on plant genomes, in particular woody plants. The reasons for this are pragmatic. First, the
biogenesis and the binding of miRNA to their targets are different in animal and plants, and therefore the computational methods
need to be specialised for either kingdom. Between the two, the plant miRNA bioinformatics is less developed and hence offers
more research opportunities. Secondly, and crucially, this project intends to complement and to capitalise on the public
investment already made in other projects run by (part of) our team, namely the FCT-funded GeneGLobWq and migroEGO
projects, both dedicated to woody plants, in particular Eucalyptus species that are of great importance for Portugal's economy.

     
-Whole Brain Connectivity Analysis of Ultra-High Field fMRI (II10026)
Acronym: HIFI-MRI
Arlindo Manuel Limede de Oliveira
From 01-Jan-2013 to 30-Jun-2015
Prime Contractor: INESC-ID (Other)
Financed by: FCT
Partnerships: INESC-ID (Other), IST-ID (University) -Portugal
Members: Arlindo Manuel Limede de Oliveira, Alexandre Paulo Lourenço Francisco, Ana Teresa Correia de Freitas, Joana Maria Rosado da Silva Coelho
The three mainobectives of this project are: (1) new fMRI data of whole-brain activity obtained using ultra-high field r-fMRI, and pre-processing of this data in order to make it suitable for complex network analysis; (2) extraction of functional connectivity patterns across the brain and underlying functional network and improved methods and algorithms for the analysis of functional networks, with emphasis on methods for the identification of recurrent patterns and clusters in scale-free complex networks; and (3) increased understanding of the added value of ultra-high field MRI in the analysis of resting state brain functional connectivity, as compared with data obtained using other methods.

     
-Towards a semi-automatic model revision of logical regulatory network (II08019)
Acronym: IFCT
Pedro Tiago Gonçalves Monteiro
From 01-Jan-2015 to 31-Dec-2018
Prime Contractor: IF/01333/2013/CP1 204/CT0001 (Other)
Financed by: FCT
Partnerships: INESC-ID (Other)
Members: Pedro Tiago Gonçalves Monteiro
The foremost question in Systems Biology is how to interpret vast amount of multiscale data, in order to predict and explain the behavior of complex biological systems. The present proposal addresses this question and is subdivided into two main interconnected parts: methods and applications.
A comparative genomics approach will be used among closely related species, for the identification of a comprehensive regulatory network scaffold (top-down). Then starting with homologous regulatory elements we will proceed with the definition of a logical model (bottom-up), complemented with formal verification techniques for model analysis and validation.
Additionally, methods aimed at the full characterization of complex cyclic attractors, which is still an open problem, will be developed using the circuit functionality contexts.
These methods will be applied to the prediction of Multidrug Resistance in yeasts due to its importance on the control of highly opportunistic pathogen on human impaired immune system [20]. Also, using the Segment Polarity cross-regularity module to simulate a 2D grid cross-signaling of cells O will push the limits of current logical regulatory networks.

     
-Deciphering the mechanisms of transcriptional regulation that control antifungal drug resistance in pathogenic yeast Candida glabrata: aiming at the development of improved diagnosis and therapeutic (II08022)
Acronym: CANTROL
Pedro Tiago Gonçalves Monteiro
From 01-Mar-2016 to 28-Feb-2019
Prime Contractor: IST-ID (University) -Portugal
Financed by: FCT
Partnerships: Faculdade de Medecina da Universidade do Porto (University) - Porto, Portugal, Fundação Calouste Gulbenkian (Other) - Lisboa, Portugal, INESC-ID (Other), IST-ID (University) -Portugal
Members: Pedro Tiago Gonçalves Monteiro
Results obtained within this project are expected to shed light into MDR regulation mechanisms in fungal pathogens and their clinical implications. The gathered knowledge is also expected to guide the delineation of strategies to surpass the widespread of multidrug resistance among fungal pathogens with implications in Human Health and Biotechnology.