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I am a full professor in the Computer Science and Engineering department (CSE) at Instituto Superior Técnico (IST), conducting scientific research in combinatorial algorithms, machine learning, and computational biology. Within the department, I coordinate the scientific area of programming methodology and technology. Additionally, I serve as the Chairwoman of the School Assembly at IST, an advisory body with 60 representatives. During my 33-year career at IST, I spent the first two decades as a professor in the Department of Electrical and Computer Engineering, conducting research in microelectronics and magneto-optics. During this time, I contributed to the development of the Quickchips project, enabling the establishment of Portugal's first clean room for integrated circuit manufacturing at the Institute of Systems and Computer Engineering (INESC). In 2010, I completed my habilitation exams in computational biology. This project marked the start of my research career at INESC around 36 years ago. After earning my Ph.D. in Electrical and Computer Engineering, I shifted to bioinformatics and computational biology. Over 22 years in this field, I co-founded the Knowledge Discovery and Bioinformatics (KDBIO) research group in 2002. Leading a team of 10 Ph.D. professors and around 25 master's, doctoral, and post-doc students from 2009 to 2014, we became Portugal's largest computational biology research group. In 2011, after a decade in genomics algorithm development, I ventured into technology transfer, founding HeartGenetics, Genetics and Biotechnology SA, a genetic and digital health startup. Serving as CEO for a decade, the company, co-founded in 2013, grew to 30 employees and expanded operations across the EU and Latin America. In 2020, Italian laboratory TOMALAB acquired HeartGenetics after securing over €8 million in funding, marking TOMALAB's first internationalization step. In these years, I pursued advanced training in management and entrepreneurship at the Católica Business School of Lisbon. Between 2012 and 2016, I was a member of the scientific council at IST and served on the Executive Board at the CSE Department. On the European level, I represented Portugal as a Board member (2010-2016) at the European Research Infrastructure for life data, ELIXIR, and served as Vice-chair of the Board in 2017. Currently, I am the Head of Node for ELIXIR Portugal, overseeing the country's participation in the EU’s Genomic Data Infrastructure project valued at €40 million. As a researcher at INESC-ID, I lead the Life and Health Technology thematic line, which brings together 9 research groups and over 50 researchers. In 2023, I became the coordinator for Lisbon in the new European Digital Innovation Hub ATTRACT, focusing on Artificial Intelligence and High-Performance Computing. I have authored and co-authored more than 120 papers in international journals and conferences in the areas of computational biology, bioinformatics, computer aided design and magneto-optics. I have participated in a number of programs and scientific committees of international conferences and I am a permanent reviewer of the main journals in the Computational Biology field, like Nucleic Acid Research, Bioinformatics Oxford journal, PlosOne and BMC Bioinformatics. In March 2023, I received the career award from the Order of Engineers of the Madeira region, for my contributions to the development of technologies in the field of digital health and preventive medicine. In my career I received 8 awards. In my professional activities, I have interacted with over 195 collaborators in co-authoring scientific papers. Currently, my main research focus is in the area of federated learning in healthcare and genomics medicine, where I am developing a collaboration with the Technical University of Science and Technology of Macau and with the National Cancer Center at NIH in Washington DC (where I am currently on sabbatical leave).
Identification

Personal identification

Full name
Ana Teresa Correia de Freitas

Citation names

  • Freitas, Ana Teresa
  • Freitas, Ana T.

Author identifiers

Ciência ID
A419-C626-64E5
ORCID iD
0000-0002-2997-5990

Email addresses

  • atf@inesc-id.pt (Professional)

Websites

Knowledge fields

  • Engineering and Technology - Electrotechnical Engineering, Electronics and Informatics
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Advanced (C1) Advanced (C1) Intermediate (B1) Advanced (C1)
Spanish; Castilian Intermediate (B1) Intermediate (B1) Beginner (A1) Intermediate (B1)
Italian Intermediate (B1) Upper intermediate (B2) Beginner (A1) Upper intermediate (B2) Intermediate (B1)
Education
Degree Classification
2012/09/01 - 2013/03/30
Concluded
Advanced Management Program on Innovation and Entrepreneurship (Diploma de especialização)
Major in Gestão e empreendedorismo
Universidade Católica Portuguesa Faculdade de Economia e Gestão, Portugal
Aprovada
2010/10/17
Concluded
Biologia Computacional (Título de Agregado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Alignment of Biological Sequences" (THESIS/DISSERTATION)
Approved
2002/11/27
Concluded
Engenharia Electrotécnica e de Computadores (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
Approved
1994
Concluded
Engenharia Electrotécnica e de Computadores (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
Very Good
1990
Concluded
Engenharia Eletrotécnica e de Computadores (Mestrado integrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
15 (on 20 point scale)
Affiliation

Science

Category
Host institution
Employer
1990/09/01 - Current Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Teaching in Higher Education

Category
Host institution
Employer
2013 - 2016 Associate Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
2010 - 2013 Associate Professor (University Teacher) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2009/09/01 - 2010/07/30 Visiting Professor (University Teacher) Universidade da Madeira, Portugal
2008/08/15 - 2009/08/14 Visiting Professor (University Teacher) École normale supérieure de Lyon Département des sciences de la Terre, France
2007 - 2009 Assistant Professor (University Teacher) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Positions / Appointments

Category
Host institution
Employer
2023/04/01 - Current Head of Node ELIXIR Portugal - The European Infrastructure for Life Data Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/01/01 - Current Coordinator of the Scientific Area of Methodology and Programming Technologies of the Department of Computer Engineering Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09/01 - Current Coordinator of the "Life and health thecnology" research line at INESC-ID Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2021/01/01 - Current Chairwoman of TECNICO School Assembly Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - 2018 Conselho científico/técnico-científico ou orgão correspondente Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2018 Coordenação ou direção de centro de investigação, departamento ou equivalente Universidade de Lisboa, Portugal
2015 - 2016 Conselho científico/técnico-científico ou orgão correspondente Universidade de Lisboa Instituto Superior Técnico, Portugal

Others

Category
Host institution
Employer
2015/11/15 - Current Full Professor at the Department of Computer Science and Engineering of Instituto Superior Técnico (IST), University of Lisbon (http://www.ist.utl.pt). Field: Algorithms and programming. Universidade de Lisboa Instituto Superior Técnico, Portugal
2013/04/01 - 2022/07/14 CEO HeartGenetics Genetics and Biotechnology SA, Portugal
2017/01/01 - 2017/12/31 Vice-chair of ESFRI ELIXIR (http://www.elixir-europe.org/). European Bioinformatics Institute, United Kingdom
2016/01/01 - 2017/12/31 Coordinator of the disciplinary field of Programming Methodology and Technology from the Department of Computer Science and Engineering of Instituto Superior Técnico Universidade de Lisboa Instituto Superior Técnico, Portugal
2014/09/01 - 2017/12/31 Board member of ELIXIR (http://www.elixir-europe.org/), representing Portugal. ELIXIR unites Europe’s leading life science organisations. Fundação para a Ciência e a Tecnologia, Portugal
2014/01/01 - 2017/12/31 Member of the Health Network Council from Universidade de Lisboa, representing the Instituo Superior Técnico Universidade de Lisboa, Portugal
2014/01/01 - 2016/12/31 Member of Scientific Council of the Biomedical Engineering course at Instituto Superior Técnico Universidade de Lisboa Instituto Superior Técnico, Portugal
2013/01/01 - 2016/12/31 Member of the Scientific Council of Instituto Superior Técnico Universidade de Lisboa Instituto Superior Técnico, Portugal
2013/01/01 - 2016/12/31 Member of the Executive Committee of the Computer Science Department at Instituto Superior Técnico. Universidade de Lisboa Instituto Superior Técnico, Portugal
2010/10/12 - 2015/11/15 Associate Professor (with Habilitation) at the Department of Computer Science and Engineering of Instituto Superior Técnico (IST), University of Lisbon (http://www.ist.utl.pt). Field: Algorithms and p Universidade de Lisboa Instituto Superior Técnico, Portugal
2009/01/01 - 2015/01/01 Head of the Knowledge Discovery and Bioinformatics group (KDBIO) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2002/11/22 - 2010/10/11 Auxiliar Professor at the Department of Electronic Engeneering and Computers Universidade de Lisboa Instituto Superior Técnico, Portugal
2009/09/07 - 2010/07/30 Auxiliar Professor at the Informatics Department Universidade da Madeira, Portugal
2008/08/15 - 2009/07/31 Invited Researcher Université Claude Bernard Lyon 1, France
2007/01/01 - 2008/12/31 Senior researcher of the Knowledge Discovery and Bioinformatics group (KDBIO) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
1990/10/01 - 2002/11/22 Assistant professor at Department of Electronic Engeneering and Computers Universidade de Lisboa Instituto Superior Técnico, Portugal
Projects

Grant

Designation Funders
2008/09/01 - 2009/06/30 DATA INTEGRATION IN SYSTEMS BIOLOGY
SFRH/BSAB/790/2008
Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2023/07/01 - Current Digital Innovation Hub for ArTificial InTelligence and High- PeRformAnce CompuTing @ Portugal
Principal investigator
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
Ongoing
2022/11/01 - Current European Genomic Data Infrastructure (GDI)
Researcher
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
Horizon 2020
Ongoing
2022/09/01 - Current Precise and Efficient Learning using Attention Mechanisms (PRELUNA)
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - 2025/12/31 Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa
LA/P/0078/2020
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - 2023/12/31 OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon
951970
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
European Commission
Concluded
2015/03/01 - 2021/04/01 Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa
UID/CEC/50021/2019
SFRH/BPD/110695/2015
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2020/03/01 - 2021/02/28 DPCx - DeepPathCOVIDx
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2020/07 - 2021/02 Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 infection severity
613401452/388
Fundação Calouste Gulbenkian, Portugal
Concluded
2013/07/01 - 2016/07/03 Tratamento de Dados em Larga-escala em Ambientes Nuvem
EXCL/EEI-ESS/0257/2012
Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Fundacao de Computacao Cientifica Nacional, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2013 - 2015 CAMP: Computational Analysis of MicroRNAs in Plants
PTDC/EIA-EIA/122534/2010
Principal investigator
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2014/01/01 - 2014/11/30 HIFI-MRI: Análise de Conectividade Funcional no Cérebro usando fMRI por Campos de Elevada Intensidade
PTDC/EEI-ELC/3246/2012
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010 - 2013 TAGS : THE POWER OF THE SHORT - TOOLS AND ALGORITHMS FOR NEXT GENERATION SEQUENCING APPLICATIONS.
PTDC/EIA-EIA/112283/2009
Principal investigator
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2010 - 2013 NEXT GENERATION SEQUENCING DATA ANALYSIS NETWORK
COST Action BM1006
Researcher
Concluded
2009 - 2013 MICROEGO - DID YOU ASK FOR SOMETHING SMALL? THE MICRORNAS POWER IN A EUCALYPTUS TENSION WORLD!
PTDC/AGR-GPL/098179/2008
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2011/01/01 - 2012/12/31 Projecto Estratégico - LA 21 - 2011-2012
PEst-OE/EEI/LA0021/2011
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2009 - 2012 Pneumopath, A comprehensive dissection of pneumococcal-host interactions
FP7- HEALTH-2007-2.3.1-2
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2009 - 2012 Biohypo, Tackle the clinical relevance of biocide induced antibiotic resistance
FP7- KBBE-2008-2B"Proposal No 227258
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2008/01/01 - 2010/12/31 Dyablo: Modelos para o Comportamento Dinâmico de Redes Biológicas
PTDC/EIA/71587/2006
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2007/05/01 - 2010/04/30 Genome-wide Analysis of Short RNAs as Modulators in Dehydration Stress Tolerance Using Yolerant and Genetic Model Systems
ERA-PG/0001/2006
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2008 - 2010 GenEglobwq - Scanning for candidate genes underlying a pulp yield QTL in Eucalyptus globulus
PTDC/AGR-GPL/66564/2006
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2007 - 2010 Dyablo - Models for the Dynamic Behavior of Biological Network
PDCT/EIA/71587/2006
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2007 - 2010 ERA-PG - GENOME-WIDE ANALYSIS OF SHORT RNAS AS MODULATORS IN DEHYDRATION STRESS TOLERANCE USING TOLERANT AND GENETIC MODEL SYSTEM
ERAPGFP/06.030A
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2007 - 2010 ARN - ALGORITHMS FOR THE IDENTIFICATION OF GENE REGULATORY NETWORKS
PTDC/EIA/67722/2006
Principal investigator
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2006/01/02 - 2008/01/01 Elucidação das complexas redes de regulação que actuam na levedura sujeita a drogas/stresse químico: abordagens de expressão genómica e de bioinformática
PDCT/BIO/56838/2004
Universidade de Lisboa Instituto Superior Técnico, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2005/01/01 - 2007/12/31 DBYeast: Infraestruturas e algoritmos para análise e identificação de redes de regulação genética
POSC/EIA/57398/2004
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2005 - 2007 MAGIC - Unveiling Metabolic and Genetic Networks in Living Cells
Internal Research and Development Project INESC-ID
Principal investigator
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2004 - 2007 DBYeast - Infrastructures and Algorithms for Analysis and Identification of Gene Regulatory Networks
POSI/EIA/57398/2004
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2004 - 2007 Insights Into the Complex Regulatory Networks Acting in Yeast Cells Changed with Drugs/Chemical Stresses: Genome Wide Expressions Approaches Supported by Bioinformatics
POCTI/BIO/56838/2004
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2002 - 2007 BioGrid - Parallel Algorithms for Gene Annotation
POSI/SRI/47778/2002
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2001 - 2004 COOLCHIPS: An Environment for the Design and Analysis of Power Efficient Systems
POCTI/ESE/33705/2000
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
1997 - 2001 Techniques for the Design of Low Power Circuits
PRAXIS XXI 2/2.1/TIT/1563/95
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
1990 - 1995 QuickChips - A System Supporting ASIC Design and Providing Rapid Turnaround Prototyping
ESPRIT Project 6043
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded

Other

Designation Funders
2022/07/27 - 2024/01/31 Magalhães
contract
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2007 - 2010 DynaMo - Dynamical modeling, control and optimization of metabolic networks
PTDC/EEA-ACR/69530/2006
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2004 - 2007 PI-Vert - Mathematical and Algorithmical Aspects of Biochemical and Evolutionary Network
ACI Nouvelles Interfaces des Mathématiques
Researcher
Université Claude Bernard Lyon 1, France
Concluded
Outputs

Publications

Book
  1. Machado, C.M.; Couto, F.M.; Fernandes, A.R.; Santos, S.; Freitas, A.T.. Toward a translational medicine approach for hypertrophic cardiomyopathy. 2012.
    10.1007/978-3-642-32395-9_12
  2. Freitas, A.T.; Navarro, A.. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface. 2012.
    10.1007/978-3-642-28062-7
  3. Pais, H.C.; McMillan, K.L.; Sentovich, E.M.; Freitas, A.T.; Oliveira, A.L.. Improved model checking techniques for state space analysis of gene regulatory networks. 2009.
    10.4018/978-1-60566-685-3.ch016
  4. Francisco, A.P.; Oliveira, A.L.; Freitas, A.T.. Identification of transcription factor binding sites in promoter regions by modularity analysis of the motif co-occurrence graph. 2008.
    10.1007/978-3-540-79450-9_21
  5. Monteiro, PT; Ropers, D; Mateescu, R; Freitas, AT; de Jong, H; Ghallab, M; Spyropoulos, CD; Fakotakis, N; Avouris, N. Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks. 2008.
  6. Carvalho, A.M.; Freitas, A.T.; Oliveira, A.L.; Sagot, M.-F.. Efficient extraction of structured motifs using box-links. 2004.
    10.1007/978-3-540-30213-1_37
Book chapter
  1. André Salgado; Francisco Fernandes; Ana Teresa Freitas. "CSA-MEM: Enhancing Circular DNA Multiple Alignment Through Text Indexing Algorithms". 2023.
    10.1007/978-981-99-7074-2_41
  2. Freitas, Ana Teresa. "Data-Driven Approaches in Healthcare: Challenges and Emerging Trends". In Multidisciplinary Perspectives on Artificial Intelligence and the Law, 65-80. Springer International Publishing, 2023.
    10.1007/978-3-031-41264-6_4
Conference paper
  1. Coimbra, M.E.; Fernandes, F.; Russo, L.M.S.; Freitas, A.T.. "Parallel efficient aligner of pyrosequencing reads". 2013.
    10.1145/2488551.2488593
  2. Dias, P.J.; Costa, C.P.; Sá-Correia, I.; Teixeira, M.C.; Monteiro, P.T.; Oliveira, A.L.; Freitas, A.T.. "Using systems biology approaches to study a multidrug resistance network". 2011.
    10.1109/ENBENG.2011.6026073
  3. Calçada, D.; Vinga, S.; Freitas, A.T.; Oliveira, A.L.. "Quantitative modeling the Saccharomyces cerevisiae FLR1 regulatory network using an S-system formalism". 2011.
    10.1109/HISB.2011.62
  4. Francisco, A.P.; Schbath, S.; Freitas, A.T.; Oliveira, A.L.. "Using graph modularity analysis to identify transcription factor binding sites". 2010.
    10.1109/BIBMW.2010.5703767
  5. Machado, C.M.; Couto, F.; Fernandes, A.R.; Santos, S.; Cardim, N.; Freitas, A.T.. "Semantic characterization of hypertrophic cardiomyopathy disease". 2010.
    10.1109/BIBMW.2010.5703841
  6. Monteiro, P.T.; Freitas, A.T.; Ropers, D.; Mateescu, R.; De Jong, H.. "Modeling and formal verification of biological regulatory networks: An integrative approach". 2010.
    10.1109/BIBMW.2010.5703920
  7. Carvalho, A.M.; Freitas, A.T.; Oliveira, A.L.; Sagot, M.-F.. "A highly scalable algorithm for the extraction of cis-regulatory regions". 2005.
  8. Carvalho, A.M.; Oliveira, A.L.; Freitas, A.T.; Sagot, M.-F.. "A parallel algorithm for the extraction of structured motifs". 2004.
  9. Freitas, A.T.; Oliveira, A.L.. "Implicit resolution of the Chapman-Kolmogorov equations for sequential circuits: An application in power estimation". 2003.
    10.1109/DATE.2003.1253699
  10. Freitas, A.T.; Oliveira, A.L.. "Circuit partitioning techniques for power estimation using the full set of input correlations". 2001.
  11. Freitas, Ana Teresa; Oliveira, Arlindo; Monteiro, José. "Exact Power Estimation Using Word Level Transition Probabilities". Paper presented in Ninth International Workshop on Power and Timing Modeling, Optimization and Simulation, PATMOS 1999, Kos, 1999.
    Published
Journal article
  1. Freitas, Ana Teresa; Calhau, Conceição; Antunes, Gonçalo; Araújo, Beatriz; Bandeira, Matilde; Barreira, Sofia; Bazenga, Filipa; et al. "Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 disease severity". Scientific Reports 11 1 (2021): http://dx.doi.org/10.1038/s41598-021-99952-z.
    10.1038/s41598-021-99952-z
  2. Miguel Monteiro; Ana Catarina Fonseca; Ana Teresa Freitas; Teresa Pinho e Melo; Alexandre P. Francisco; Jose M. Ferro; Arlindo L. Oliveira. "Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients". IEEE/ACM Transactions on Computational Biology and Bioinformatics 15 6 (2018): 1953-1959. https://doi.org/10.1109/TCBB.2018.2811471.
    10.1109/TCBB.2018.2811471
  3. Alaine B. Guerra; Jorge S. Oliveira; Rita C.B. Silva-Portela; Wydemberg Araújo; Aline C. Carlos; Ana Tereza R. Vasconcelos; Ana Teresa Freitas; et al. "Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation". Environmental Pollution 235 (2018): 869-880. https://doi.org/10.1016/j.envpol.2018.01.014.
    10.1016/j.envpol.2018.01.014
  4. Machado, Catia M.; Rebholz-Schuhmann, Dietrich; Freitas, Anat; Couto, Francisco M.. "The semantic web in translational medicine: current applications and future directions". Briefings in Bioinformatics 16 1 (2015): 89-103. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000348188400009&KeyUID=WOS:000348188400009.
    10.1093/bib/bbt079
  5. Oliveira, Jorge S.; Araujo, Wydemberg; Lopes Sales, Ana Isabela; Brito Guerra, Alaine de; Silva Araujo, Sinara Carla da; de Vasconcelos, Ana Tereza Ribeiro; Agnez-Lima, Lucymara F.; Freitas, Ana Teresa. "BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies". Database : the journal of biological databases and curation 2015 (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:25833955&KeyUID=MEDLINE:25833955.
    10.1093/database/bav033
  6. Fernandes, F.; Freitas, A.T.. "SlaMEM: Efficient retrieval of maximal exact matches using a sampled LCP array". Bioinformatics 30 4 (2014): 464-471. http://www.scopus.com/inward/record.url?eid=2-s2.0-84894518038&partnerID=MN8TOARS.
    10.1093/bioinformatics/btt706
  7. Teixeira, M.C.; Monteiro, P.T.; Guerreiro, J.F.; Gonçalves, J.P.; Mira, N.P.; Dos Santos, S.C.; Cabrito, T.R.; et al. "The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae". Nucleic Acids Research 42 D1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84891806965&partnerID=MN8TOARS.
    10.1093/nar/gkt1015
  8. Coelho, J. R.; Gaspar, I. M.; Silva, A. M.; Freitas, A. T.. "A MACHINE LEARNING APPROACH FOR THE IDENTIFICATION OF RISK FACTORS FOR CARDIOVASCULAR DISEASE". Cardiology 126 (2013): 272-272. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000326437200266&KeyUID=WOS:000326437200266.
  9. Machado, Catia M.; Freitas, Ana T.; Couto, Francisco M.. "Enrichment analysis applied to disease prognosis". Journal of Biomedical Semantics 4 (2013): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000343706100002&KeyUID=WOS:000343706100002.
    10.1186/2041-1480-4-21
  10. Santos, S.; Marques, V.; Nunes, A. C.; Freitas, A. T.; Gouveia, M. R.; Antunes, M.; Carreira, I. M.; et al. "Novel insights in hypertrophic cardiomyopathy (HCM) evaluation: mirs as biomarkers of HCM cardiac remodeling". European Journal of Heart Failure 12 (2013): S30-S30. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000332489100098&KeyUID=WOS:000332489100098.
  11. Coelho, J.R.; Carriço, J.A.; Knight, D.; Martínez, J.-L.; Morrissey, I.; Oggioni, M.R.; Freitas, A.T.. "The Use of Machine Learning Methodologies to Analyse Antibiotic and Biocide Susceptibility in Staphylococcus aureus". PLoS ONE 8 2 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84874218295&partnerID=MN8TOARS.
    10.1371/journal.pone.0055582
  12. Furi, L.; Ciusa, M.L.; Knight, D.; Di Lorenzo, V.; Tocci, N.; Cirasol, D.; Aragones, L.; et al. "Evaluation of reduced susceptibility to quaternary ammonium compounds and bisbiguanides in clinical isolates and laboratory-generated mutants of staphylococcus aureus". Antimicrobial Agents and Chemotherapy 57 8 (2013): 3488-3497. http://www.scopus.com/inward/record.url?eid=2-s2.0-84880261721&partnerID=MN8TOARS.
    10.1128/AAC.00498-13
  13. Da Fonseca, P.G.; Paiva, J.A.; Almeida, L.G.; Vasconcelos, A.T.; Freitas, A.T.. "Empirical assessment of sequencing errors for high throughput pyrosequencing data". BMC Research Notes 6 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84872462642&partnerID=MN8TOARS.
    10.1186/1756-0500-6-25
  14. Ciusa, M.L.; Furi, L.; Knight, D.; Decorosi, F.; Fondi, M.; Raggi, C.; Coelho, J.R.; et al. "A novel resistance mechanism to triclosan that suggests horizontal gene transfer and demonstrates a potential selective pressure for reduced biocide susceptibility in clinical strains of Staphylococcus aureus". International Journal of Antimicrobial Agents 40 3 (2012): 210-220. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864624743&partnerID=MN8TOARS.
    10.1016/j.ijantimicag.2012.04.021
  15. Mendes, N.D.; Heyne, S.; Freitas, A.T.; Sagot, M.-F.; Backofen, R.. "Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches". Bioinformatics 28 23 (2012): 3034-3041. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870441808&partnerID=MN8TOARS.
    10.1093/bioinformatics/bts574
  16. Paiva, Jorge AP; Rodrigues, José Carlos; Fevereiro, Pedro; Neves, Lucinda; Araújo, Clara; Marques, Cristina; Freitas, Ana Teresa; Bergès, Hélène; Grima-Pettenati, Jacqueline. "Building up resources and knowledge to unravel transcriptomics dynamics underlying Eucalyptus globulusxylogenesis". BMC Proceedings 5 S7 (2011): http://dx.doi.org/10.1186/1753-6561-5-s7-o52.
    Published • 10.1186/1753-6561-5-s7-o52
  17. Abdulrehman, D.; Monteiro, P.T.; Teixeira, M.C.; Mira, N.P.; Lourenço, A.B.; Dos Santos, S.C.; Cabrito, T.R.; et al. "YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface". Nucleic Acids Research 39 SUPPL. 1 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-78651272522&partnerID=MN8TOARS.
    10.1093/nar/gkq964
  18. CalÇada, D.; Vinga, S.; Freitas, A.T.; Oliveira, A.L.. "Quantitative modeling of the saccharomyces cerevisiae FLR1 regulatory network using an s-system formalism". Journal of Bioinformatics and Computational Biology 9 5 (2011): 613-630. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053654755&partnerID=MN8TOARS.
    10.1142/S0219720011005690
  19. Monteiro, P.T.; Dias, P.J.; Ropers, D.; Oliveira, A.L.; Sá-Correia, I.; Teixeira, M.C.; Freitas, A.T.. "Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae". IET Systems Biology 5 5 (2011): 308-316. http://www.scopus.com/inward/record.url?eid=2-s2.0-80054711652&partnerID=MN8TOARS.
    10.1049/iet-syb.2011.0001
  20. Fernandes, F.; da Fonseca, P.G.S.; Russo, L.M.S.; Oliveira, A.L.; Freitas, A.T.. "Efficient alignment of pyrosequencing reads for re-sequencing applications". BMC Bioinformatics 12 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79958812542&partnerID=MN8TOARS.
    10.1186/1471-2105-12-163
  21. Calcada, Dulce; Vinga, Susana; Freitas, Ana T.; Oliveira, Arlindo L.. "QUANTITATIVE MODELING OF THE SACCHAROMYCES CEREVISIAE FLR1 REGULATORY NETWORK USING AN S-SYSTEM FORMALISM". Journal of Bioinformatics and Computational Biology 9 5 (2011): 613-630. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000297095900003&KeyUID=WOS:000297095900003.
    10.1142/s0219720011005690
  22. Paiva, J.A.P.; Prat, E.; Vautrin, S.; Santos, M.D.; San-Clemente, H.; Brommonschenkel, S.; Fonseca, P.G.S.; et al. "Advancing Eucalyptus genomics: Identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries". BMC Genomics 12 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79952202673&partnerID=MN8TOARS.
    10.1186/1471-2164-12-137
  23. Teixeira, M.C.; Dias, P.J.; Monteiro, P.T.; Sala, A.; Oliveira, A.L.; Freitas, A.T.; Sá-Correia, I.. "Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches". Molecular BioSystems 6 12 (2010): 2471-2481. http://www.scopus.com/inward/record.url?eid=2-s2.0-78149432402&partnerID=MN8TOARS.
    10.1039/c004881j
  24. Mendes, N.D.; Freitas, A.T.; Vasconcelos, A.T.; Sagot, M.-F.. "Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi". BMC Genomics 11 1 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77957127423&partnerID=MN8TOARS.
    10.1186/1471-2164-11-529
  25. Monteiro, P.T.; Dumas, E.; Besson, B.; Mateescu, R.; Page, M.; Freitas, A.T.; De Jong, H.. "A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks". BMC Bioinformatics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-75649131791&partnerID=MN8TOARS.
    10.1186/1471-2105-10-450
  26. Fernandes, F.; Freitas, A.T.; Almeida, J.S.; Vinga, S.. "Entropic profiler - Detection of conservation in genomes using information theory". BMC Research Notes 2 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-77049089315&partnerID=MN8TOARS.
    10.1186/1756-0500-2-72
  27. Fernandes, F.; Pereira, L.; Freitas, A.T.. "CSA: An efficient algorithm to improve circular DNA multiple alignment". BMC Bioinformatics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68949145849&partnerID=MN8TOARS.
    10.1186/1471-2105-10-230
  28. Mendes, ND; Freitas, AT; Sagot, MF. "Current tools for the identification of miRNA genes and their targets". Nucleic Acids Research 37 8 (2009): 2419-2433. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000265953000010&KeyUID=WOS:000265953000010.
    10.1093/nar/gkp145
  29. Monteiro, P.T.; Mendes, N.D.; Teixeira, M.C.; D'orey, S.; Tenreiro, S.; Mira, N.P.; Pais, H.; et al. "YEASTRACT-DISCOVERER: New tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae". Nucleic Acids Research 36 SUPPL. 1 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-38549135468&partnerID=MN8TOARS.
    10.1093/nar/gkm976
  30. Monteiro, P.T.; Ropers, D.; Mateescu, R.; Freitas, A.T.; de Jong, H.. "Temporal logic patterns for querying dynamic models of cellular interaction networks". Bioinformatics 24 16 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-49549083532&partnerID=MN8TOARS.
    10.1093/bioinformatics/btn275
  31. Casimiro, A.C.; Vinga, S.; Freitas, A.T.; Oliveira, A.L.. "An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance". BMC Bioinformatics 9 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-41449103756&partnerID=MN8TOARS.
    10.1186/1471-2105-9-89
  32. CARVALHO, AM; FREITAS, AT; OLIVEIRA, AL; et al.. "An efficient algorithm for the identification of structured motifs in DNA promoter sequences". IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 3 2 (2006): 126-140. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000237260400003&KeyUID=WOS:000237260400003.
  33. TEIXEIRA, MC; MONTEIRO, P; JAIN, P; et al.. "The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae". NUCLEIC ACIDS RESEARCH 34 (2006): D446-D451. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000239307700098&KeyUID=WOS:000239307700098.
    10.1093/nar/gkj013
  34. Mendes, N.D.; Casimiro, A.C.; Santos, P.M.; Sá-Correia, I.; Oliveira, A.L.; Freitas, A.T.. "MUSA: A parameter free algorithm for the identification of biologically significant motifs". Bioinformatics 22 24 (2006): 2996-3002. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845359995&partnerID=MN8TOARS.
    10.1093/bioinformatics/btl537
  35. Carvalho, A.M.; Freitas, A.T.; Oliveira, A.L.; Sagot, M.-F.. "An efficient algorithm for the identification of structured motifs in DNA promoter sequences". IEEE/ACM Transactions on Computational Biology and Bioinformatics 3 2 (2006): 126-139. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646730147&partnerID=MN8TOARS.
    10.1109/TCBB.2006.16
  36. CARVALHO, AM; FREITAS, AT; OLIVEIRA, AL; et al.. "Efficient extraction of structured motifs using box-links". STRING PROCESSING AND INFORMATION RETRIEVAL, PROCEEDINGS 3246 (2004): 267-268. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000224377200037&KeyUID=WOS:000224377200037.
  37. FREITAS, AT; OLIVEIRA, AL. "Implicit resolution of the Chapman-Kolmogorov equations for sequential circuits: An application in power estimation". DESIGN, AUTOMATION AND TEST IN EUROPE CONFERENCE AND EXHIBITION, PROCEEDINGS (2003): 1199-1199. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000182683800122&KeyUID=WOS:000182683800122.
  38. FREITAS, AT; OLIVEIRA, AL. "Circuit partitioning techniques for power estimation using the full set of input correlations". ICECS 2001: 8TH IEEE INTERNATIONAL CONFERENCE ON ELECTRONICS, CIRCUITS AND SYSTEMS, VOLS I-III, CONFERENCE PROCEEDINGS (2001): 1642-1642. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000176019100217&KeyUID=WOS:000176019100217.
  39. MELO, LV; RODRIGUES, LM; SOUSA, AT; et al.. "GMR multilayer patterned structures". MAGNETIC ULTRATHIN FILMS, MULTILAYERS AND SURFACES 384 (1995): 553-553. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:A1995BE33K00048&KeyUID=WOS:A1995BE33K00048.
  40. LEAL, JL; RODRIGUES, LM; SOUSA, AT; et al.. "NARROW TRACKWIDTH TBCO-BIASED MAGNETORESISTIVE SPIN-VALVE SENSORS". JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS 140 (1995): 2215-2216. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:A1995QM73000364&KeyUID=WOS:A1995QM73000364.
  41. FREITAS, PP; LEAL, JL; MELO, LV; et al.. "SPIN-VALVE SENSORS EXCHANGE-BIASED BY ULTRATHIN TBCO FILMS". APPLIED PHYSICS LETTERS 65 4 (1994): 493-495. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:A1994NY41400038&KeyUID=WOS:A1994NY41400038.
  42. LEAL, JL; OLIVEIRA, NJ; RODRIGUES, LM; et al.. "UNSHIELDED SPIN-VALVE SENSORS EXCHANGE-BIASED BY THIN TBCO LAYERS". IEEE TRANSACTIONS ON MAGNETICS 30 6 (1994): 3831-3833. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:A1994PU42900012&KeyUID=WOS:A1994PU42900012.
  43. Coelho, J.C.U.; Brenner, A.S.; Freitas, A.T.; Campos, A.C.L.; Wiederkehr, J.C.. "Progressive preoperative pneumoperitoneum in the repair of large abdominal hernias". European Journal of Surgery, Acta Chirurgica 159 6-7 (1993): 339-341. http://www.scopus.com/inward/record.url?eid=2-s2.0-0027164841&partnerID=MN8TOARS.

Other

Other output
  1. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. 2018. Luis Pedro Coelho; Renato Alves; Paulo Monteiro; Jaime Huerta-Cepas; Ana Teresa Freitas; Peer Bork. https://doi.org/10.1101/367755.
    10.1101/367755
Activities

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2024/02/01 - Current Enhancing Colorectal Cancer Risk Prediction: Integrating Microbiome Data and Clinical Information with Advanced Machine Learning Pipelines
Supervisor
Doutoramento em engenharia informática e de computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2013 - Current Design and Implementation of a Domain Specific Language for Next Generation Sequencing
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/11/01 - 2024/05/31 Deep Learning on Chaos Game Representation for Resistome
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/10/01 - 2024/05/31 Enhancing Antibiotic Resistance Binning in Microbiome Data Analysis through Machine Learning Algorithms
Supervisor
Ciências de Engenharia - Engenharia Biológica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/10/01 - 2024/05/31 Clinical Application of Polygenic Risk Scores: the case of type 2 diabetes
Supervisor
Bioengenharia em Medicina Regenerativa e de Precisão (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09/01 - 2023/11/13 CSA-MEM: Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico Campus Taguspark, Portugal
2022/01/01 - 2023/07/14 Automatizing cancer genetic testing reporting using deep-learning techniques
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/09/01 - 2022/06/01 Development of a visual solution for genetic data analysis communication
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/11/01 - 2018/09/28 A New Value Proposition For A Genetic Test Of Hereditary Thrombophilia
Supervisor
Ciências de Engenharia - Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/11/01 - 2018/09/28 Analysis of a genetic test in the context of arterial hypertension
Supervisor
Ciências de Engenharia - Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2014/01/02 - 2018/04/03 Identification and characterization of new genes involved in the degradation of hydrocarbons and production of surfactants using computational methods, PhD Thesis, Universidade Federal do Rio Grande do Norte - Brasil, Apr 2018 (Advisor)
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2014/05/01 - 2015/06/01 Computational prediction of microRNAs in plant genomes
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2010/09/01 - 2014/11/09 Towards a mathematical model of risk assessment of biocide induced antibiotic resistance", Technical University of Lisbon, Work in progress, 2010 - 2014.
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2009/09/01 - 2014/11/02 Knowledge representation for data integration and exploration in translational medicine
Co-supervisor
Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2009/09/02 - 2013/12/03 Efficient algorithms to align DNA sequences
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012/05/01 - 2013/11/01 Metagenomic Assembler
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012/09/01 - 2013/10/01 A web-based data management system for linked data
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2013/03/01 - 2013/09/01 Host-pathogen interaction upon infection with Listeria using NGS techniques
Supervisor
2011/06/01 - 2013/05/01 Algoritmos Eficientes para Identificar Micro RNAs em Plantas
Supervisor
Ciências de Engenharia - Engenharia Biológica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2008/09/01 - 2011/03/03 Efficient algorithms for the identification of miRNA motifs in DNA sequences
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2009/09/01 - 2010/10/01 A system for automated genome annotation
Supervisor
Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2008/09/01 - 2010/05/01 Towards an integrative approach for the modeling and formal verication of biological regulatory networks
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Event organisation

Event name
Type of event (Role)
Institution / Organization
2023/06/01 - 2023/11/30 2nd Microbiome Summit https://biodata.pt/microbiome (2023/10/26 - 2023/10/27)
Conference (President of the Organising Committee)
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Evaluation committee

Activity description
Role
Institution / Organization Funding entity
2024/02/01 - 2025/02/01 Member of the evaluation board of the Belgium ELIXIR Node - Research Foundation-Flanders (FWO)
Evaluator
Distinctions

Award

2021 Award GHP – Global Health & Pharma
2020 Prémio HINTT | Maturidade Digital

Other distinction

2023 Prémio Carreira atribuído pela Ordem dos Engenheiros
Ordem dos Engenheiros, Portugal
2016 EU eHealth Competition 2016 (Amsterdam) selected as 1 of the 16 finalists, (http://www.ehealthcompetition.eu).
2016 EIT GoGlobal DigiHealth EU Program 2016 at Stanford GSV Labs in Silicon Valley (http://gsvlabs.com/portfolio-item/stanford/), selected as 1 of the 8 finalists (https://eithealth.eu/go-global-with-your-digital-health-start-up/).
2016 Health 2.0 2016 US Conference (Silicon Valley, US), selected as 1 of the 10 finalists.
2015 World Health Summit 2015 (Berlin), selected as 1 of the 10 finalists
2013 Everis Foundation Entrepreneurship Award 2013
2007 Prize Sartorius for Innovation in Biotechnology, at Micro-Biotec 2007, for the work that lead to the Yeastract information system and the article YEASTRACT-DISCOVERER
2001 Best paper award
1990 Scholarship