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I am a Computer Scientist with a background in Systems and Informatics Engineering (1997-2002, University of Minho) and a PhD in Artificial Intelligence (2003-2007, University of Minho) and Habilitation in Computer Science (2022, University of Porto). My work is focused in the ACM areas of Applied computing, namely bioinformatics, computational biology, genomics and health informatics and in the area of Computing Methodologies, namely machine learning, data mining and artificial intelligence. During my PhD training, I had two pivotal professional experiences. Early on, I worked as a scientist in the Information Technology department at Philips Research Laboratories in Eindhoven, where I contributed to innovative projects. Later, I collaborated as a researcher on two projects with PT Inovação, the leading Portuguese telecom company, further expanding my industry expertise. Additionally, a key publication from my PhD work earned me a prestigious grant award from the IEEE Computational Intelligence Society. From 2008 to 2012, I was a Postdoctoral Fellow at the Bioinformatics and Genomics Laboratory, Center for Genomic Regulation (CRG), Barcelona. In November 2012, I moved to a second Postdoctoral period at the University of Geneva, where I have worked on computational advancements for personalized health. In August 2014, I joined the start-up company Coimbra Genomics, where I have worked in the design and development of clinical decision support systems for personalized medicine. In 2015, I was awarded a Starting Grant from the FCT Investigator Programme to recruit outstanding researchers and joined Ipatimup/i3S as an independent researcher (2015-2019). My main research focus was in the development of information systems to interpret personal genomics data for clinical diagnosis and precision medicine. During this period, I was also an Invited Assistant Professor at Department of Informatics at University of Minho (2015-2018). I am currently an Assistant Professor with Habilitation and Tenure at Department of Computer Science, Faculty of Sciences from University of Porto and a Senior Researcher at the Artificial Intelligence and Decision Support Group at INESCTEC. I am the Director of the BSc in Bioinformatics, Sub-Director of the BSc in Artificial Intelligence and Data Science and Sub-Director of the MSc in Bioinformatics and Computational Biology (M:BBC). From 2021-2023 I was the Director of M:BBC. I am involved in the successful supervision of 1 post-doc fellow, 4 PhDs, 28 Master students and 4 Research Fellows and the ongoing supervision of 5 PhD students and 3 Master students. I published several papers in high-profile journals, including: Nature, Science, Nature Communications, Scientific Reports and PNAS and in top ranking specialized journals in Computational Biology, such as: Bioinformatics, PLOS Computational Biology, Genome Biology, Genome Research or Cell Genomics, or in Computer Science journal as: IEEE Access, BMC Bioinformatics or Machine Learning. I am an author of 2 books and more than 40 papers in Q1 journals, with an h-index of 35 and summing more than 33 000 citations. I have participated in several major international consortia: ENCODE (The Encyclopedia of DNA Elements), GTEx (Genotype-Tissue Expression), GEUVADIS (Genetic European Variation in Health and Disease) or the ICGC-CLL (International Cancer Genome Consortium-Chronic Lymphocytic Leukemia). I have extensive editorial activity, serving as an associate editor for four journals and reviewer for several high-profile journals. I have served as an expert evaluator for several institutions and highly competitive funding programmes, including the European Commission (EC), the Portuguese Foundation for Science and Technology (FCT), the National Network for Advanced Computing (RNCA-FCCN) or Agency for Evaluation and Accreditation of Higher Education (A3ES).
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Identificação

Identificação pessoal

Nome completo
Pedro Gabriel Dias Ferreira
Data de nascimento
1978/05/10
Género
Masculino

Nomes de citação

  • Ferreira, Pedro G.

Identificadores de autor

Ciência ID
6E1E-0D58-A2D6
ORCID iD
0000-0003-3838-8664
Google Scholar ID
https://scholar.google.com/citations?user=X097-20AAAAJ
Researcher Id
J-6379-2013
Scopus Author Id
13405242500

Endereços de correio eletrónico

  • pedrogabrieldf@gmail.com (Profissional)
  • pgferreira@fc.up.pt (Profissional)
  • pedro.g.ferreira@inesctec.pt (Profissional)

Moradas

  • Rua Campo Alegre 1021/1055, FC6, 4169-007, Porto, Porto, Portugal (Profissional)

Websites

Domínios de atuação

  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática
  • Ciências Exatas - Ciências da Computação e da Informação - Ciências da Computação

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2)
Espanhol; Castelhano Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Inglês Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2)
Formação
Grau Classificação
2022/10/14
Concluído
 Ciência de Computadores (Título de Agregado)
Universidade do Porto Faculdade de Ciências, Portugal
"Agregado no ramo de conhecimento de Ciência de Computadores. / Habilitation in Computer Science." (TESE/DISSERTAÇÃO)
 Unanimidade
2007
Concluído
 Doutoramento em Informática (Doutoramento)
Universidade do Minho Escola de Engenharia, Portugal
"Sequence Pattern Mining in Biochemical Data" (TESE/DISSERTAÇÃO)
 Unanimidade
2002
Concluído
 Licenciatura em Engenharia de Sistemas e Informática (Licenciatura)
Universidade do Minho Escola de Engenharia, Portugal
"Engenharia de Sistemas e Informática" (TESE/DISSERTAÇÃO)
 16
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2020/03/01 - Atual Investigador (Investigação) Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência, Portugal
Instituto de Engenharia de Sistemas e Computadores, Portugal
2015/05/01 - Atual Investigador (Investigação) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2015/05/01 - 2019/01/31 Investigador Auxiliar (carreira) (Investigação) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2012/11/01 - 2014/06/01 Pós-doutorado (Investigação) Universite de Geneve Faculte de Medecine, Suiça
2008/01/01 - 2012/11/01 Pós-doutorado (Investigação) Centre de Regulació Genòmica, Espanha
2003/10/01 - 2007/09/01 Investigador (Investigação) Universidade do Minho Escola de Engenharia, Portugal
2002/04/01 - 2002/10/01 Investigador visitante (Investigação) Philips Research, Natuurkunde Laboratorium, IST, Países Baixos

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2019/02/01 - Atual Professor Auxiliar (Docente Universitário) Universidade do Porto Faculdade de Ciências, Portugal
Universidade do Porto Faculdade de Ciências, Portugal

Outros

Categoria Profissional
Instituição de acolhimento 		Empregador
2014/08/01 - 2015/04/01 Senior Bioinformatics Specialist Coimbra Genomics SA, Portugal
2003/01/01 - 2003/09/01 Software Engineer Escripóvoa Software House Lda, Portugal
2001/06/01 - 2001/08/01 Software Programmer Avel Electrónica Lda, Portugal
Projetos

Bolsa

Designação Financiadores
2008/01 - 2010/12 Searching for high level rules in protein folding and unfolding: from amyloid diseases to protein structure prediction
Provided by PTCRIS: 72838
 Universidade de Coimbra

Projeto

Designação Financiadores
2018/06/01 - Atual Solving the 3D chromatin structure of CDH1 locus to identify disease-associated mechanisms
POCI-01-0145-FEDER-030164
Investigador
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2018/06/01 - Atual AVC em translação: Biomarcadores para diagnóstico e decisão terapêutica no AVC isquémico
POCI-01-0145-FEDER-031674
Investigador
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2018/06/01 - Atual NaSA - Neoantigen signature algorithm to predict immunotherapy response
POCI-01-0145-FEDER-032018
Investigador
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2018/06/01 - Atual Tregs in cancer immune response
POCI-01-0145-FEDER-032462
Investigador
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Em curso
2018/06 - Atual Tregs in cancer immune response
POCI-01-0145-FEDER-032462
 N/A
2023/03/01 - 2026/02/28 A multimodal approach for deepening the understanding of Alzheimer's disease
2022.04734.PTDC
DOI: 10.54499/2022.04734.PTDC
Universidad de Valladolid, Espanha

Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2021/01/01 - 2025/12/31 INESC TEC - Instituto de Engenharia de Sistemas e Computadores, Tecnologia e Ciência (INESC TEC)
LA/P/0063/2020
10.54499/LA/P/0063/2020
168195UID
Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2020/01/01 - 2024/12/31 Institute for Research and Innovation in Health
UIDB/04293/2020
10.54499/UIDB/04293/2020
LA/P/0070/2020
10.54499/LA/P/0070/2020
UIDP/04293/2020
10.54499/UIDP/04293/2020
UID/BIM/04293/2019
Instituto Nacional de Engenharia Biomédica, Portugal

Instituto de Astrofísica e Ciências do Espaço, Portugal

Universidade do Porto, Portugal

Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal

Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal

Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2023/01/01 - 2024/06/30 Deconstructing the Cell Communication Routes of mutant KRAS Colorectal Liver to Lung Metastasis: improving patient survival
2022.05346.PTDC
10.54499/2022.05346.PTDC
Instituto Português de Oncologia de Coimbra Francisco Gentil EPE, Portugal

Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2021/03/29 - 2024/03/28 Estimativas de risco ao longo da vida e modificadores genéticos em Cancro Gástrico Difuso Hereditário
10.54499/PTDC/BTM-TEC/6706/2020
PTDC/BTM-TEC/6706/2020
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2018/07/01 - 2022/06/30 Stroke in translation: Biomarkers for diagnosis and management of acute ischemic stroke
PTDC/MEC-NEU/31674/2017
Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal

Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal

Centro Hospitalar Universitário de Santo António, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2018/07/26 - 2021/07/25 Algoritmo preditivo de resposta à imunoterapia baseado na expressão neoantigénica
PTDC/MEC-ONC/32018/2017
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2018/07/01 - 2021/06/30 Definição da estrutura 3D da cromatina no locus CDH1 para identificar mecanismos associados à doença
PTDC/BTM-TEC/30164/2017
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2020/01 - 2020/07 Transcriptomics-based prediction of human phenotypes using scalable and secure machine learning approaches
CPCA/A2/2640/2020
 CPCA/A2/2640/2020
Concluído
2017/06/01 - 2020/05/30 GenomePT – National Laboratory for Genome Sequencing and Analysis
POCI-01-0145-FEDER-022184
Investigador
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Em curso
2017/01/01 - 2020/01/01 Training in Extracellular vesicles: for benefit in Health & Disease
H2020-MSCA-ITN-2016/H2020-MSCA-ITN-2016, Grant nº 722148
Investigador
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Em curso
2018/09/01 - 2019/09/30 O papel dos Tregs na resposta imune ao cancro
PTDC/MED-PAT/32462/2017
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2016/02/01 - 2019/07/31 The yin and yang of somatic mutations in cancer immunosurveillance
PTDC/BIM-MEC/2834/2014
Investigador
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Em curso
2015/05/01 - 2019/01/31 Understanding the impact of acquired and germline genetic variants in the complexity of gastric cancer
IF/01127/2014
Investigador responsável
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2008/01/01 - 2010/12/31 Procura de regras de alto nível em dobragem e desdobragem de proteínas: das doenças amiloidogénicas à previsão da estrutura proteica
PTDC/BIA-PRO/72838/2006
Universidade do Minho, Portugal

Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
Fundação para a Ciência e a Tecnologia
Concluído

Outro

Designação Financiadores
2016/01/01 - Atual Advancing cancer research: from basic knowledgment to application II
ORTE-01-0145-FEDER-000029
Investigador
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2017/05/01 - 2018/04/30 Understanding gender differential susceptibility to cancer through large-scale data analysis with correlation networks and deep neural networks.
.
Investigador responsável
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Microsoft Azure
Concluído
Produções

Publicações

Artigo em conferência
  1. Cláudia Brito; Pedro Ferreira; Bernardo Portela; Rui Oliveira; João Paulo. "SOTERIA: Preserving Privacy in Distributed Machine Learning". 2023.
    10.1145/3555776.3578591
  2. Ferreira, P.G.; Azevedo, P.J.. "Evaluating protein motif significance measures: A case study on prosite patterns". 2007.
    10.1109/CIDM.2007.368869
  3. Librelotto, G.R.; Machado, H.T.; Martins, M.; Ferreira, P.G.D.; Ramalho, J.C.; Henriques, P.R.. "Topic maps applied to PubMed". 2007.
  4. Ferreira, P.G.; Silva, C.G.; Brito, R.M.M.; Azevedo, P.J.. "A closer look on protein unfolding simulations through hierarchical clustering". 2007.
Artigo em revista
  1. Sousa, Bruno; Bessa, Maria; de Mendonça, Filipa L; Ferreira, Pedro G; Moreira, Alexandra; Pereira-Castro, Isabel. "APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data". Bioinformatics 40 11 (2024): https://doi.org/10.1093/bioinformatics/btae689.
    10.1093/bioinformatics/btae689
  2. Ribeiro, Rogério; Moraes, Athos; Moreno, Marta; Ferreira, Pedro G.. "Integration of multi-modal datasets to estimate human aging". Machine Learning 113 10 (2024): 7293-7317. https://doi.org/10.1007/s10994-024-06588-x.
    10.1007/s10994-024-06588-x
  3. Delora Baptista; Shihua Zhang; Pedro G. Ferreira; Miguel Rocha. "A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer". PLOS Computational Biology (2023): https://doi.org/10.1371/journal.pcbi.1010200.
    10.1371/journal.pcbi.1010200
  4. García-Pérez, Raquel; Ramirez, Jose Miguel; Ripoll-Cladellas, Aida; Chazarra-Gil, Ruben; Oliveros, Winona; Soldatkina, Oleksandra; Bosio, Mattia; et al. "The landscape of expression and alternative splicing variation across human traits". Cell Genomics 3 1 (2023): 100244. https://doi.org/10.1016/j.xgen.2022.100244.
    10.1016/j.xgen.2022.100244
  5. Cláudia V. Brito; Pedro G. Ferreira; Bernardo L. Portela; Rui C. Oliveira; João T. Paulo. "Privacy-Preserving Machine Learning on Apache Spark". IEEE Access (2023): https://doi.org/10.1109/ACCESS.2023.3332222.
    10.1109/ACCESS.2023.3332222
  6. Moreno, Marta; Vilaça, Ricardo; Ferreira, Pedro G.. "Scalable transcriptomics analysis with Dask: applications in data science and machine learning". BMC Bioinformatics 23 1 (2022): http://dx.doi.org/10.1186/s12859-022-05065-3.
    10.1186/s12859-022-05065-3
  7. Marta Moreno; Abel Sousa; Marta Melé; Rui Oliveira; Ferreira, Pedro G.. "Predicting Gastric Cancer Molecular Subtypes from Gene Expression Data". Proceedings 54 1 (2020): 59-59. http://dx.doi.org/10.3390/proceedings2020054059.
    Publicado • 10.3390/proceedings2020054059
  8. Ferreira, Pedro G.. "The GTEx Consortium atlas of genetic regulatory effects across human tissues.". Science (New York, N.Y.) (2020): https://europepmc.org/articles/PMC7737656.
    10.1126/science.aaz1776
  9. Ferreira, Pedro G.. "Gender Differential Transcriptome in Gastric and Thyroid Cancers.". Frontiers in genetics (2020): https://europepmc.org/articles/PMC7406663.
    10.3389/fgene.2020.00808
  10. Baptista, Delora; Ferreira, Pedro G; Rocha, Miguel. "Deep learning for drug response prediction in cancer". Briefings in Bioinformatics (2020): http://dx.doi.org/10.1093/bib/bbz171.
    10.1093/bib/bbz171
  11. Ferreira, Pedro G.. "Integrated Analysis of Structural Variation and RNA Expression of FGFR2 and Its Splicing Modulator ESRP1 Highlight the ESRP1amp-FGFR2norm-FGFR2-IIIchigh Axis in Diffuse Gastric Cancer.". Cancers (2019): https://europepmc.org/articles/PMC7017189.
    10.3390/cancers12010070
  12. Pedro G. Ferreira; Manuel Muñoz-Aguirre; Ferran Reverter; Caio P. Sá Godinho; Abel Sousa; Alicia Amadoz; Reza Sodaei; et al. "The effects of death and post-mortem cold ischemia on human tissue transcriptomes". Nature Communications 9 1 (2018): https://doi.org/10.1038/s41467-017-02772-x.
    10.1038/s41467-017-02772-x
  13. Aguet, F.; Brown, A.A.; Castel, S.E.; Davis, J.R.; He, Y.; Jo, B.; Mohammadi, P.; et al. "Genetic effects on gene expression across human tissues". Nature 550 7675 (2017): 204-213. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031313737&partnerID=MN8TOARS.
    10.1038/nature24277
  14. Tukiainen, T.; Villani, A.-C.; Yen, A.; Rivas, M.A.; Marshall, J.L.; Satija, R.; Aguirre, M.; et al. "Landscape of X chromosome inactivation across human tissues". Nature 550 7675 (2017): 244-248. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031299871&partnerID=MN8TOARS.
    10.1038/nature24265
  15. Tan, M.H.; Li, Q.; Shanmugam, R.; Piskol, R.; Kohler, J.; Young, A.N.; Liu, K.I.; et al. "Dynamic landscape and regulation of RNA editing in mammals". Nature 550 7675 (2017): 249-254. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031298074&partnerID=MN8TOARS.
    10.1038/nature24041
  16. Bryois, J.; Buil, A.; Ferreira, P.G.; Panousis, N.I.; Brown, A.A.; Viñuela, A.; Planchon, A.; et al. "Time-dependent genetic effects on gene expression implicate aging processes". Genome Research 27 4 (2017): 545-552. http://www.scopus.com/inward/record.url?eid=2-s2.0-85017531409&partnerID=MN8TOARS.
    10.1101/gr.207688.116
  17. Li, X.; Kim, Y.; Tsang, E.K.; Davis, J.R.; Damani, F.N.; Chiang, C.; Hess, G.T.; et al. "The impact of rare variation on gene expression across tissues". Nature 550 7675 (2017): 239-243. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031302505&partnerID=MN8TOARS.
    10.1038/nature24267
  18. Cummings, B.B.; Marshall, J.L.; Tukiainen, T.; Lek, M.; Donkervoort, S.; Foley, A.R.; Bolduc, V.; et al. "Improving genetic diagnosis in Mendelian disease with transcriptome sequencing". Science Translational Medicine 9 386 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85018570855&partnerID=MN8TOARS.
    10.1126/scitranslmed.aal5209
  19. Alves-Rodrigues, I.; Ferreira, P.G.; Moldón, A.; Vivancos, A.P.; Hidalgo, E.; Guigó, R.; Ayté, J.. "Spatiotemporal Control of Forkhead Binding to DNA Regulates the Meiotic Gene Expression Program". Cell Reports 14 4 (2016): 885-895. http://www.scopus.com/inward/record.url?eid=2-s2.0-84958123507&partnerID=MN8TOARS.
    10.1016/j.celrep.2015.12.074
  20. Ferreira, P.G.; Oti, M.; Barann, M.; Wieland, T.; Ezquina, S.; Friedländer, M.R.; Rivas, M.A.; et al. "Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing". Scientific Reports 6 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84987596952&partnerID=MN8TOARS.
    10.1038/srep32406
  21. Arous, C.; Ferreira, P.G.; Dermitzakis, E.T.; Halban, P.A.. "Short term exposure of beta cells to low concentrations of interleukin-1ß improves insulin secretion through focal adhesion and actin remodeling and regulation of gene expression". Journal of Biological Chemistry 290 10 (2015): 6653-6669. http://www.scopus.com/inward/record.url?eid=2-s2.0-84925004057&partnerID=MN8TOARS.
    10.1074/jbc.M114.611111
  22. Arous, C.; Ferreira, P.G.; Dermitzakis, E.T.; Halban, P.A.. "Erratum: Short term exposure of beta cells to low concentrations of interleukin-1ß improves insulin secretion through focal adhesion and actin remodeling and regulation of gene expression (Journal of Biological Chemistr (2015) 290 (6653-6669))". Journal of Biological Chemistry 290 23 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84930660827&partnerID=MN8TOARS.
    10.1074/jbc.A114.611111
  23. Bassaganyas, L.; Beà, S.; Escaramís, G.; Tornador, C.; Salaverria, I.; Zapata, L.; Drechsel, O.; et al. "Corrigendum: Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis". Leukemia 29 3 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84924408200&partnerID=MN8TOARS.
    10.1038/leu.2014.309
  24. Melé, M.; Ferreira, P.G.; Reverter, F.; DeLuca, D.S.; Monlong, J.; Sammeth, M.; Young, T.R.; et al. "The human transcriptome across tissues and individuals". Science 348 6235 (2015): 660-665. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929015296&partnerID=MN8TOARS.
    10.1126/science.aaa0355
  25. Patalano, S.; Vlasova, A.; Wyatt, C.; Ewels, P.; Camara, F.; Ferreira, P.G.; Asher, C.L.; et al. "Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies". Proceedings of the National Academy of Sciences of the United States of America 112 45 (2015): 13970-13975. http://www.scopus.com/inward/record.url?eid=2-s2.0-84946763289&partnerID=MN8TOARS.
    10.1073/pnas.1515937112
  26. Rivas, M.A.; Pirinen, M.; Conrad, D.F.; Lek, M.; Tsang, E.K.; Karczewski, K.J.; Maller, J.B.; et al. "Effect of predicted protein-truncating genetic variants on the human transcriptome". Science 348 6235 (2015): 666-669. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929015299&partnerID=MN8TOARS.
    10.1126/science.1261877
  27. Ardlie, K.G.; DeLuca, D.S.; Segrè, A.V.; Sullivan, T.J.; Young, T.R.; Gelfand, E.T.; Trowbridge, C.A.; et al. "The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans". Science 348 6235 (2015): 648-660. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929001104&partnerID=MN8TOARS.
    10.1126/science.1262110
  28. Borel, C.; Ferreira, P.G.; Santoni, F.; Delaneau, O.; Fort, A.; Popadin, K.Y.; Garieri, M.; et al. "Biased allelic expression in human primary fibroblast single cells". American Journal of Human Genetics 96 1 (2015): 70-80. http://www.scopus.com/inward/record.url?eid=2-s2.0-84920733410&partnerID=MN8TOARS.
    10.1016/j.ajhg.2014.12.001
  29. Greger, L.; Su, J.; Rung, J.; Ferreira, P.G.; Lappalainen, T.; Dermitzakis, E.T.; Brazma, A.. "Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants". PLoS ONE 9 8 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84940247886&partnerID=MN8TOARS.
    10.1371/journal.pone.0104567
  30. Ferreira, P.G.; Jares, P.; Rico, D.; Gómez-López, G.; Martínez-Trillos, A.; Villamor, N.; Ecker, S.; et al. "Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia". Genome Research 24 2 (2014): 212-226. http://www.scopus.com/inward/record.url?eid=2-s2.0-84893699492&partnerID=MN8TOARS.
    10.1101/gr.152132.112
  31. Ongen, H.; Andersen, C.L.; Bramsen, J.B.; Oster, B.; Rasmussen, M.H.; Ferreira, P.G.; Sandoval, J.; et al. "Putative cis-regulatory drivers in colorectal cancer". Nature 512 1 (2014): 87-90. http://www.scopus.com/inward/record.url?eid=2-s2.0-84905581513&partnerID=MN8TOARS.
    10.1038/nature13602
  32. Monlong, J.; Calvo, M.; Ferreira, P.G.; Guigó, R.. "Identification of genetic variants associated with alternative splicing using sQTLseekeR". Nature Communications 5 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84907346176&partnerID=MN8TOARS.
    10.1038/ncomms5698
  33. Ferreira, P.G.; Dermitzakis, E.T.. "Immune response is a personal matter". eLife 2013 2 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84880642705&partnerID=MN8TOARS.
    10.7554/eLife.00899
  34. Ferreira, P.G.; Patalano, S.; Chauhan, R.; Ffrench-Constant, R.; Gabaldón, T.; Guigó, R.; Sumner, S.. "Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes". Genome Biology 14 2 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84874214846&partnerID=MN8TOARS.
    10.1186/gb-2013-14-2-r20
  35. Lappalainen, T.; Sammeth, M.; Friedländer, M.R.; 'T Hoen, P.A.C.; Monlong, J.; Rivas, M.A.; Gonzàlez-Porta, M.; et al. "Transcriptome and genome sequencing uncovers functional variation in humans". Nature 501 7468 (2013): 506-511. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885645853&partnerID=MN8TOARS.
    10.1038/nature12531
  36. Bava, F.-A.; Eliscovich, C.; Ferreira, P.G.; Miñana, B.; Ben-Dov, C.; Guigó, R.; Valcácel, J.; Méndez, R.. "CPEB1 coordinates alternative 3'-UTR formation with translational regulation". Nature 495 7439 (2013): 121-125. http://www.scopus.com/inward/record.url?eid=2-s2.0-84874732911&partnerID=MN8TOARS.
    10.1038/nature11901
  37. Bassaganyas, L.; Beà, S.; Escaramís, G.; Tornador, C.; Salaverria, I.; Zapata, L.; Drechsel, O.; et al. "Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis". Leukemia 27 12 (2013): 2376-2379. http://www.scopus.com/inward/record.url?eid=2-s2.0-84890437212&partnerID=MN8TOARS.
    10.1038/leu.2013.127
  38. Plass, M.; Codony-Servat, C.; Ferreira, P.G.; Vilardell, J.; Eyras, E.. "RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae". RNA 18 6 (2012): 1103-1115. http://www.scopus.com/inward/record.url?eid=2-s2.0-84861390545&partnerID=MN8TOARS.
    10.1261/rna.030767.111
  39. Dunham, I.; Kundaje, A.; Aldred, S.F.; Collins, P.J.; Davis, C.A.; Doyle, F.; Epstein, C.B.; et al. "An integrated encyclopedia of DNA elements in the human genome". Nature 489 7414 (2012): 57-74. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865790047&partnerID=MN8TOARS.
    10.1038/nature11247
  40. Djebali, S.; Davis, C.A.; Merkel, A.; Dobin, A.; Lassmann, T.; Mortazavi, A.; Tanzer, A.; et al. "Landscape of transcription in human cells". Nature 489 7414 (2012): 101-108. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865757142&partnerID=MN8TOARS.
    10.1038/nature11233
  41. Vieira, J.; Ferreira, P.G.; Aguiar, B.; Fonseca, N.A.; Vieira, C.P.. "Evolutionary patterns at the RNase based gametophytic self - Incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus)". BMC Evolutionary Biology 10 1 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77953954949&partnerID=MN8TOARS.
    10.1186/1471-2148-10-200
  42. Novoa, I.; Gallego, J.; Ferreira, P.G.; Mendez, R.. "Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control". Nature Cell Biology 12 5 (2010): 447-456. http://www.scopus.com/inward/record.url?eid=2-s2.0-77951978351&partnerID=MN8TOARS.
    10.1038/ncb2046
  43. Ferreira, P.G.; Azevedo, P.J.. "Evaluating deterministic motif significance measures in protein databases". Algorithms for Molecular Biology 2 1 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-44449158817&partnerID=MN8TOARS.
    10.1186/1748-7188-2-16
Capítulo de livro
  1. Athos Moraes; Marta Moreno; Rogério Ribeiro; Pedro G. Ferreira. "Predicting Age from Human Lung Tissue Through Multi-modal Data Integration". 2023.
    10.1007/978-3-031-45275-8_43
Livro
  1. Ferreira, Pedro G.. Bioinformatics Algorithms Design and Implementation in Python. Elsevier. 2018.
    Publicado
  2. Ferreira, Pedro G.. Análise e exploração de dados com o R. FCA Editora. 2017.
    Publicado
  3. Alves, R.; Ferreira, P.; Ribeiro, J.; Belo, O.. Detecting abnormal patterns in call graphs based on the aggregation of relevant vertex measures. 2012.
    10.1007/978-3-642-31488-9_8
  4. Silva, C.G.; Ferreira, P.G.; Azevedo, P.J.; Brito, R.M.M.. Using data mining techniques to probe the role of hydrophobic residues in protein folding and unfolding simulations. 2009.
    10.4018/978-1-60566-816-1.ch012
  5. Ferreira, P.G.; Azevedo, P.J.. Deterministic pattern mining on genetic sequences. 2009.
    10.4018/978-1-60566-766-9.ch013
  6. Ferreira, P.G.; Silva, C.G.; Azevedo, P.J.; Brito, R.M.M.. Spatial clustering of molecular dynamics trajectories in protein unfolding simulations. 2009.
    10.1007/978-3-642-02504-4_14
  7. Ferreira, P.G.; Azevedo, P.J.. Deterministic motif mining in protein databases. 2007.
    10.4018/978-1-59904-645-7.ch006
  8. Ferreira, P.G.; Azevedo, P.J.; Silva, C.G.; Brito, R.M.M.. Mining approximate motifs in time series. 2006.
  9. Ferreira, P.; Alves, R.; Belo, O.; Cortesão, L.. Establishing fraud detection patterns based on signatures. 2006.
    10.1007/11790853_41
  10. Ferreira, P.G.; Azevedo, P.J.. Protein sequence pattern mining with constraints. 2005.
    10.1007/11564126_14
  11. Ferreira, P.G.; Azevedo, P.J.. Protein sequence classification through relevant sequence mining and bayes classifiers. 2005.
    10.1007/11595014_24
  12. Alves, R.; Belo, O.; Cavalcanti, F.; Ferreira, P.. Clickstreams, the basis to establish user navigation patterns on web sites. 2004.
Poster em conferência
  1. Pinto, Roberto; Fernandes, Pedro Alexandrino; Maria J. Ramos; Ferreira, Pedro G.. "New antidotes for the Bothrops asper venom: a study of PLA2 protein". Trabalho apresentado em 8th Portuguese Young Chemists Meeting (8th PYCheM), 2023.
  2. Kumar, Darmit M.; Pereira, Luisa; Ribeiro, Pedro; Ferreira, Pedro G.. Autor correspondente: Kumar, Darmit M.. "Phenotype Gene Expression Network". 2023.
Pré-impressão
  1. Jose Miguel Ramirez; Rogério Ribeiro; Oleksandra Soldatkina; Athos Moraes; Raquel García-Pérez; Pedro G. Ferreira; Marta Melé. "Cigarrete smoking drives accelerated aging across human tissues". 2024. https://www.biorxiv.org/content/10.1101/2024.03.14.585016v2.abstract.
    10.1101/2024.03.14.585016
  2. Cláudia V. Brito; Ferreira, Pedro G.; João Paulo. Autor correspondente: Ferreira, Pedro G.. "A Distributed Computing Solution for Privacy-Preserving Genome-Wide Association Studies". 2024.
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2023/04 Invited talk at University of Bern, Faculty of Medicine. Patterns of transcriptomic variation across multiple dimensions in health and disease. Bern, April 2023.
University of Bern (Bern, Suiça)
2023/03 Patterns of transcriptomic variation across multiple dimensions in health and disease Invited talk at Roche Headquarters
Roche (Basel, Suiça)
2022/10 Characterizing gene expression patterns across multiple dimensions in health and disease. Invited talk at University of Zurich.
Bodenmiller Lab (Zurich, Suiça)
2022/10 Invited talk at University of Zurich. Characterizing gene expression patterns across multiple dimensions in health and disease. Zurich, October 2022.
University of Zurich (Zurich, Suiça)
2022/09 Characterizing gene expression patterns across multiple dimensions in health and disease. Invited talk at University of Utrecth
Department of Computer Science, University of Utrecth (Utrecth, Países Baixos)
2022/09 Invited talk at University of Utrecth. Characterizing gene expression patterns across multiple dimensions in health and disease. Utrecht, September 2022
University of Utrecth (Utrecht, Países Baixos)
2022/07 Unsupervised Machine Learning for Gene Expression Analysis. EUGLOH Summer School on Biomedical Data Processing and Artificial Intelligence.
Szeged University (Szeged (online), Hungria)
2021/11 Characterizing gene expression patterns across multiple dimensions in health and disease Invited talk at KULeuven.
KULeuven (Leuven (online, Bélgica)
2021/10 Characterizing gene expression patterns across multiple dimensions in health and disease Invited talk at Technical University of Munich and Helmholtz Zentrum München.
Technical University of Munich and Helmholtz Zentrum München. (Munich (online), Alemanha)
2020/09 Applications of Machine Learning in Cancer Research: a review Invited talk at Cancer Biology: From Basic to Translational Research Workshop
Liga Portuguesa Contra o Cancro (Lisboa (online), Portugal)
2020/06 Unsupervised Machine Learning for Gene Expression Analysis Invited talk at EUGLOH Summer School on Biomedical Data Processing and Global Aspects of COVID-19.
University of Szeged (Szeged (online), Hungria)
2019/11 The effects of death and post-mortem cold ischemia on human tissue transcriptomes. 23ª Reunião Anual / 23rd Annual Meeting da Sociedade Portuguesa de Genética Humana: SPGH
Sociedade Portuguesa de Genética Humana (Coimbra, Portugal)
2018/05 Data Science na era da revolução dos dados / Data Science in the era of data revolution Invited talk at Supercomputing and Data Science Workshop.
(Braga)
2018/05 Large-scale data analysis for the characterization of human gene expression patterns across hundreds of individuals and dozens of tissues Invited Open Class at Universidade Nova de Lisboa
Universidade Nova de Lisboa (Lisboa, Portugal)
2018/03 Characterization of human gene expression patterns across hundreds of individuals and dozens of tissues Invited talk at Barcelona Supercomputing Center
Alfonso Valencia (Barcelona, Espanha)
2017/09/15 Bioinformatics and Computational Biology: a personal perspective. Invited talk at University of Minho at 10th anniversary of the masters in Bioinformatics.
Miguel Rocha
2017/06 The human postmortem transcriptome across 36 tissues Invited talk at ICVS - Life and Health Sciences Research Institute
Rui Reis (Braga, Portugal)
2017/05 The life of genes after death: The human postmortem transcriptome across 36 tissues. Seminar Series at i3s.
(porto, Portugal)
2017/03 Large-scale data analysis for the characterization of human gene expression patterns across hundreds of individuals and dozens of tissues Invited talk at Department of Informatics at Instituto Superior Técnico
Ana Teresa Freitas (Lisboa, Portugal)
2016/07 Patterns of gene expression variation in human populations across tissues and individuals Invited talk at The Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute (EMBL-EBI)
Richard Durbin (Cambridge, Reino Unido)
2016/06 Patterns of gene expression variation in human populations across tissues and individuals: methods behind the scenes Invited talk at the 2nd Porto Meeting in Mathematics and Biology
Paulo Aguiar (Porto, Portugal)
2016/05 Poster presentation at the 29th Annual Meeting on The Biology of Genomes. Poster presentation at the 29th Annual Meeting on The Biology of Genomes.
(Cold Spring Harbor, Estados Unidos)
2016/04 Patterns of gene expression variation in human populations across tissues and individuals Invited talk at 7th Symposium on Bioengineering organized by NEB-FEUP/ICBAS, FEUP
Students of Bioengineering Association (porto, Portugal)
2016/03 Patterns of gene expression variation in human populations across tissues and individuals Invited talk at 17th Meeting Portugaliae Genetica.
(porto, Portugal)

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
2023/09 - Atual Caption Generation for Histological Images
Orientador de Athos Mekana Moraes
 Masters in Bioinformatics and Computational Biology (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2023/09 - 2027/08 Decision support based on artificial intelligence for managing and optimising electricity networks. Funding: AI4REALNET.
Orientador
 Doctoral Program in Computer Science (PD:CC).
Universidade do Porto Faculdade de Ciências, Portugal
2022 - 2026 Deepening the understanding of Alzheimer's disease risk and progression: a multimodal approach.
Coorientador de Miguel Ângelo Pontes Rebelo
 Bioinformatics (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2025/06 BioPredictor: a tool to predict the outcome of molecular alterations (SFRH/BD/05763/2020).
Coorientador de Marta Ferreira
 Bioinformatics (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2025 Integration of multi-modal genomics datasets with expert data: a patient centered approach to improve diagnosis and prognosis (2021.07092.BD).
Orientador de Rogério Ribeiro
 Bioinformatics (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2023/09 - 2024/07 Evaluating Data Fusion Methods for Integrative Analysis of Multi-Omics Data in Cancer.
Orientador
 Masters in Computational Biology. (Mestrado)
Universidade de Coimbra, Portugal
2023/09 - 2024/06 Comparative evaluation of cell type deconvolution methods in human disease tissues
Orientador de Guilherme Vale Puga
 Masters in Bioinformatics and Computational Biology (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2022 - 2023 Exploring the Human Phenotype-Gene Network
Orientador de Darmit Manish Kumar
 Tese de Mestrado em Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2022 - 2023 A multi-caller pipeline to maximize the output of somatic exome sequencing analysis
Coorientador de Inês Sofia Pinheiro Marques
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2022 - 2023 Novos Antídotos para o Veneno da Víbora Terciopelo
Coorientador de Roberto Miguel Pais Pinto
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2023 Transcriptomics-based prediction of human phenotypes using scalable and secure machine learning approaches (SFRH/BD/145707/2019).
Orientador
 Bioinformatics (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2023 Towards a Modular and Scalable Privacy-preserving Machine Learning Framework (SFRH/BD/146528/2019).
Coorientador de Cláudia Vanessa Brito
 Informatics (Doutoramento)
Universidade do Minho, Portugal
2021/09/01 - 2022/12 When pathways cross other pathways, that themselves, have met other pathways: crabs responses to cocktails of contaminants
Coorientador de Sara Sousa Moreira
 Tese de Mestrado em Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2022 Understanding the impact of Mycobacterium tuberculosis complex diversity in tuberculosis
Coorientador de Ana Raquel Maceiras de Oliveira
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2022 Modelling and Predicting Acute Ischaemic Stroke Outcomes
Coorientador de Tiago Santos
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2022 RISK - New RNA signatures of therapy evasion in Cancer
Coorientador de Ana Filipa Lopes de Mendonça
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2017 - 2022 A framework for predicting drug sensitivity and synergy in cancer cells using deep learning
Coorientador
 Informatics (Doutoramento)
2020 - 2021 Analysis and comparison tool for multiple variant calling results from germline NGS data with clinical applications
Coorientador de Francisco Manuel Oliveira de Almeida
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2020 - 2021 NRfinder: A pipeline for the characterization of the number and type of nuclear receptors in a genomic sequence
Coorientador de Marcos António Pereira Domingues
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2020 - 2021 A model validation pipeline for healthy tissue genome-scale metabolic models.
Coorientador de Maria Adília Monteiro
 Bioinformática (Mestrado)
Universidade do Minho, Portugal
2020 - 2021 Developing deep learning methods to predict phenotypes and clinical outcomes from transcriptomics data
Coorientador de Maria Fernanda Vieira
 Bioinformática (Mestrado)
Universidade do Minho, Portugal
2017 - 2021 Study of control of protein abundance using multi-omics data from cancer samples
Orientador de Abel Sousa
 Biomedical / Bioinformatics (Doutoramento)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2019 - 2020 Evaluating clustering and high- dimensionality reduction techniques for genomics data.
Orientador de Sara Carolina Martins Ribeiro
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2020 Data analysis of clinical datasets to support laboratory diagnostics using machine learning.
Orientador
 Ciência de Dados (Data Science) (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2020 HSA/CD42: a cardiomyocyte precursor biomarker and/or a gateway to cardiomyogenesis.
Coorientador
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2020 Neoantigen Signature Automatized Pipeline to predict Immunotherapy response
Orientador
 Bioinformática e Biologia Computacional (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2017 - 2018 Implementation and comparison of computational pipelines for variant calling in sequencing data
Orientador
 Bioinformática (Mestrado)
Universidade do Minho, Portugal
2017 - 2018 Mining cancer genomic data with Probabilistic Logic Programming
Orientador
 Bioinformática (Doutoramento)
Universidade do Minho, Portugal
2017 - 2018 Pathogen identification in human cancer cells
Coorientador de Nélson Rafael Soares Dias da Silva Martins
 Engenharia Informática e Computação (Mestrado)
Universidade do Porto Faculdade de Engenharia, Portugal
2017 - 2018 Sentiment analysis from medical records
Coorientador de João Miguel Lopes
 Engenharia Informática (Mestrado)
Universidade do Minho, Portugal
2016 - 2017 Developing Deep Learning tools for cancer using omics data
Coorientador
 Bioinformática (Mestrado)
Universidade do Minho, Portugal
2016 - 2017 Deep Learning for genomic data analysis
Coorientador
 Engenharia Informática e Computação (Mestrado)
Universidade do Porto Faculdade de Engenharia, Portugal
2016 - 2016 Post-doc fellowship from the José Castillejo program for Spanish young doctors
Orientador
 Bioinformatics (Outra)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2015 - 2016 Análise de padrões em dados genómicos multi- plataforma disponíveis pelo TCGA.
Orientador
 Bioinformática (Mestrado)
Universidade do Minho, Portugal
2015 - 2016 Identification of pathogens in human cell cancers
Coorientador
 Engenharia Informática e Computação (Mestrado)
Universidade do Porto Faculdade de Engenharia, Portugal
2015 - 2016 Assessing the impact of alternative splicing in thyroid cancer
Coorientador
 Engenharia Informática e Computação (Mestrado)
Universidade do Porto Faculdade de Engenharia, Portugal
2014 - 2015 A Computational platform for assessing the impact of alternative splicing in cancer
Coorientador
 Engenharia Informática e Computação
Universidade do Porto Faculdade de Engenharia, Portugal

Júri de grau académico

Tema
Tipo de participação 		Nome do candidato (Tipo de grau)
Instituição / Organização
2024/12 Leveraging Deep Learning Models for Studying RNA Splicing in Health and Disease
Arguente
 Pedro Santos Barbosa (Doutoramento)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2024/11 Deep Learning-based Channel Estimation for the 5G+ Physical Layer
Arguente
 Fábio Daniel Lopes Coutinho (Doutoramento)
Universidade de Aveiro, Portugal
2024/06 Toward the explainability of drug-target interactions: end-to-end deep learning architectures for binding affinity prediction
Arguente
 Nelson Rodrigo Carvalho Monteiro (Doutoramento)
Universidade de Coimbra, Portugal
2023/07/27 A deep learning framework towards the multidimensional topography of carcinogenesis to guide prevention and therapy Provas de Planeamento de Tese no Programa Doutoral em Informática (PDINF)
Arguente principal
 Ana Marta Fernandes Tavares Sequeira (Doutoramento)
Universidade do Minho, Portugal
2023/07/26 Biomedical Information Extraction in Domain-Specific Texts Doctoral Program in Informatics Engineering - PhD Thesis Proposal Defense
Arguente
 André João da Silva Silveira Gonçalves (Outro)
Universidade do Porto Faculdade de Engenharia, Portugal
2022/12 Computational Biology for Modeling Oncological Omics Data: the way towards personalized medicine
Arguente principal
 Ana Carolina Peixoto (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/05 Machine Learning Models for Predicting Disease-related Biological Interactions
Arguente
 Iván Marcelo Carrera Izurieta (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2021/11/26 Defence of the test to assess the work carried out during the PhD Probationary Year
Arguente
 Pedro Miguel da Silva Ferreira (Doutoramento)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2018/12/13 Metabolic modeling based algorithms for drug discovery in cancer DISCUSSION EXAM FOR THE COURSE UNIT - THESIS PLANNING IN BIOMEDICAL ENGINEERING, PART OF THE DOCTORAL PROGRAMME IN BIOMEDICAL ENGINEERING
Arguente principal
 Jorge Miguel Lourenço Ferreira (Doutoramento)
Universidade do Minho, Portugal
2018/12 Alternative mechanisms of gene regulation during hematopoiesis
Arguente principal
 Sebastian Ullrich (Doutoramento)
Universitat Pompeu Fabra, Espanha
2016/07 Integrating Knowledge from Data and Literature for Building Transcriptional Regulatory Networks
Arguente
 Rafael Teodósio Pereira (Doutoramento)
Universidade do Minho, Portugal

Arbitragem científica em conferência

Nome da conferência Local da conferência
2017 - Atual IEEE International Conference on Data Science and Advanced Analytics (2017)
2017 - Atual Technical Committee and Reviewer for International Conference on Computational Chemistry and Biology (2017)
2016 - Atual European Society of Human Genetics (Bioinformatics and Computational methods section; 2016 & 2017 & 2021)
2009 - Atual 6th International Meeting Computational Intelligence Methods for Bioinformatics and Biostatistics
2025/05 - 2025/05 European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases
2025/03 - 2025/03 28th Pacific-Asia Conference on Knowledge Discovery and Data Mining
2024/07 - 2024/07 27th International Conference on Discovery Science
2021 - 2021/06 13th International Conference on Knowledge Discovery and Information Retrieval (KDIR 2021)
2021/04 - 2021/04 10th International Conference on Data Science, Technology and Applications (DATA 2021)
2021/03 - 2021/03 30th International Joint Conference on Artificial Intelligence
2021/03 - 2021/03 7th-8th International Conference on Algorithms for Computational Biology (AlCoB 2020 & 2021)
2017 - 2021 International Conference on Practical Applications of Computational Biology & Bioinformatics
2018 - 2018 Technical Committee (Data Science) and Reviewer for Inforum (2018)

Arbitragem científica em revista

Nome da revista (ISSN) Editora
2022/05/01 - Atual ACM Transactions on Intelligent Systems and Technology ACM
2021/01/04 - Atual Knowledge and Information Systems Springer
2020 - Atual Cancers MDPI
2017/01/01 - Atual PeerJ PerrJ Publishing

Comissão de avaliação

Descrição da atividade
Tipo de assessoria 		Instituição / Organização Entidade financiadora
2025/03 - 2025/06 Evaluator for the Portuguese Agency for Evaluation and Accreditation of Higher Education (A3ES) for the renewal process of the Degree in Bioinformatics from University of Macao.
Avaliador
2024/12 - 2025/02 Expert Evaluator for Doctoral Networks (DN) from European Commission. Horizon MSCA DN 2024. Evaluator of 6 proposals: Individual Phase (4.2 days); Consensus Phase (3 days); Cross-reading and panel meeting (2 days). European Commission Marie Sklodowska-Curie Actions, Bélgica European Commission Marie Sklodowska-Curie Actions
2024/09 - 2024/09 Expert Evaluator for CCDR-NORTE.
Avaliador
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
2024/07 - 2024/07 Project Monitoring Expert Evaluator for Research Executive Agency / European Commission. Expert panel reviewing project CGI-Clinics (101057509), 10 M€. https://www.cgiclinics.eu/ First periodic report. Duties: reading and analysing the background information; participating in the expert briefing; participating in evaluation meetings and hearing; drafting and submitting the evaluation report for the evaluated proposal (3 days). July 2024.
Avaliador
 European Commission Directorate-General for Research and Innovation, Bélgica
2024/03 - 2024/03 Project Monitoring Expert Evaluator for Research Executive Agency / European Commission. Expert panel reviewing project TAXINOMISIS (755320), 6 M€. https://taxinomisis-project.eu/ Fourth and final periodic report. Duties: reading and analysing the background information; participating in the expert briefing; participating in evaluation meetings and hearing; drafting and submitting the evaluation report for the evaluated proposal. Rapporteur for final report (4.5 days).
Avaliador
 European Commission Directorate-General for Research and Innovation, Bélgica
2023/09 - 2023/11 Reviewer for Advanced Computing Project Competition: Artificial Intelligence in the Cloud from FCT and Google Initiative for AI in Portugal (CPCA-IAC). 2023
Avaliador
 Rede Nacional de Computação Avançada, Portugal Fundação para a Ciência e a Tecnologia
2023/09 - 2023/09 Project monitoring Evaluator for Research Executive Agency / European Commission. Expert panel reviewer. Duties: reading and analysing the background information; participating in the expert briefing; participating in evaluation meeting and hearing; drafting and submitting the evaluation report for the evaluated proposal (3 full days). September 2023.
Avaliador
 European Research Executive Agency, Bélgica European Research Executive Agency
2023/05 - 2023/06 Expert Evaluator for Research and Innovation Actions (RIA) from European Commission. Horizon Europe Work programme (2023-24) - Cluster 1. Evaluator of 6 proposals on the Health and Disease Program: Individual Phase (0.7 days per project); Consensus Phase (5 full working days); Cross-reading and panel meeting (2 full days). May to June 2023.
Avaliador
 Horizon 2020, Bélgica European Commission
2022/06 - 2022/06 Evaluator for the Portuguese Agency for Evaluation and Accreditation of Higher Education (A3ES) for the renewal process of the Master in Bioinformatics and Computational Biology from University of Lisboa. ACEF/1415/0417627.
Avaliador
2022 - 2022 Reviewer for FCT and Google Initiative for AI in Portugal (CPCA-IAC)
Avaliador
 Rede Nacional de Computação Avançada, Portugal Fundação para a Ciência e a Tecnologia
2022 - 2022 Reviewer for the Portuguese Agency for Evaluation and Accreditation of Higher Education (A3ES) for the renewal process of the Master Course.
Avaliador
2021/05 - 2021/06 Reviewer for Advanced Computing Project Competition (2nd edition). Rede Nacional de Computação Avançada, Portugal Fundação para a Ciência e a Tecnologia
2021 - 2021 Call on Advanced Computing Projects (2nd edition)
Avaliador
 Rede Nacional de Computação Avançada, Portugal
2020/05 - 2020/06 Reviewer for the Portuguese Agency for Evaluation and Accreditation of Higher Education of three proposals on Master Courses submitted by Portuguese Universities (2020).
Avaliador
2020 - 2020 Reviewer for the Portuguese Agency for Evaluation and Accreditation of Higher Education (A3ES) for the admission of New Cycle of Studies - 3 Masters proposals.
Avaliador
2013 - 2013 Post-Doctoral Return programme, for young post-doc researchers returning to France, from the Agence Nationale de Recherche, France, 2013
Avaliador
 Agence nationale de la recherche, França

Consultoria / Parecer

Descrição da atividade Instituição / Organização
2021 - 2021 Chairman of the Work Group Robotics and Artificial Intelligence. The WG Robotics and AI bring together senior research staff from each of the 5 INESC organisations and is chaired by Pedro Gabriel Ferreira (INESC TEC) and vice-chaired by João Ferreira (INESC INOV).

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2019/02 - 2025/06 I have taught in 2 Universities (U.Porto and U.Minho) in a diversity of courses including 7 at BSc level, 10 at MSc (7 at U.Porto and 3 at U.Minho) and 2 at PhD, in more than 59 semester editions. I was involved in the conception of 5 new curricular units, 3 at BSc level, 1 at MSc level and 1 at PhD level. See the summary of my contributions at FCUP in Table 3. I have represented FCUP lecturing at different international PhD Summer Schools including the EUGLOH Summer School on Biomedical Data Processing and Artificial Intelligence. Computer Science (Outros) Universidade do Porto Faculdade de Ciências, Portugal
2019/02 - 2025/06 In 2019, I proposed a curricular unit on machine learning for the MAP-i Ph.D. programme. Among the courses available in the program, this has been the most selected course (on average 12 students) since the first year. I was the course coordinator for the first two years. - Fundamentals and Applications of Machine Learning at Doctoral Program in Computer Science – MAPi. - Lecturer, Theoretical-Practical classes: (2021-2022 in Aveiro, 2022-2023 in Braga, 2023-2024 in Porto). - Coordinator and Lecturer, Theoretical-Practical classes: (2019-2020 Computer Science (Doutoramento) Universidade do Porto Faculdade de Ciências, Portugal
2020/07 - 2022/07 - EUGLOH Summer School on Biomedical Data Processing and Artificial Intelligence. Unsupervised Machine Learning for Gene Expression Analysis. Szeged, Hungary. July 2022. Selected Lecturer from University of Porto (4 hours). - EUGLOH Summer School on Biomedical Data Processing and Global Aspects of COVID-19. Unsupervised Machine Learning for Gene Expression Analysis. Szeged, Hungary (Online). July 2020. Selected Lecturer from University of Porto (4 hours). Data Science (Postgraduate Certificate) Universidade do Porto Faculdade de Ciências, Portugal
2019/12/13 - 2019/12/13 Introduction to programming in R Clustering of gene expression data with R. Bioinformatics Autumn Course (Outros) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2019/05 - 2019/05 Biomedical data mining in R, University of Minho. May 2019. 25 participants. Lecturer (with Miguel Rocha) of a 3-day workshop (24h). https://www.ceb.uminho.pt/Events/Details/4243 Biomedical data mining with R (Outros) Universidade do Minho, Portugal
2017/06/26 - 2017/06/28 Introduction to Biological Data Analysis with R at i3s. 24 participants. Organizer and lecturer (with Miguel Rocha) of a 3-day workshop (24h). https://training.i3s.up.pt/course/index.php?categoryid=43 This course is designed for those with interest in data analysis and data exploration, in particular for biological data. It provides an introduction to the R system. R is a language and environment for statistical computing and graphics. The course discuss different approaches to summarize and visualize datasets, perform statistical tests (Outros) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2017/04/06 - 2017/04/06 This course will occur as part of the program of the Marie Sklodowska Curie Innovative Training Network (MSCA-ITN) TRAIN-EV. This course focuses on employing Open-source bioinformatics software, tools and resources – including web-based programs, databases and common-line programs – to access and analyse the extraordinary volume of data available and to answer relevant biological questions. (Outros) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal

Outro júri / avaliação

Descrição da atividade Instituição / Organização
2023/07 - 2023/07 International selection for the Executive Director of the Portuguese national network Biodata.pt. Ranking, Interview and Selection (2,5 working days). BioData.pt, Portugal
2021/01 - 2021/01 International selection for doctorate hiring at IBMC/i3S - Institutional Call to Scientific Employment Stimulus. Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2018/09 - 2018/09 Research fellowship BSc level at Ipatimup, ref: BI-L FCT-CADGE Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2018 - 2018 International selection for doctorate hiring at Ipatimup/i3S Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2017/09 - 2017/09 Selection process for a Bioinformatics specialist, at Ipatimup for GenomePT. Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2016/06 - 2016/06 Research fellowship MSc level at Ipatimup, NORTE-01-0145-FEDER-000029. Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2016/05 - 2016/05 Research fellowship MSc level at Ipatimup, BI-M FCT-CADGE. Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Distinções

Prémio

2019 Best Paper Award
2016 Best work (on other tumors category) on the Symposium of the Portuguese Society of Oncology
2015 Basic Research Award 2015
2015 2nd place on EU SME eHealth Competition (Part of the team at Coimbra Genomics that developed award-winning system ELSIE©)
2002 Prémio de Mérito Escolar
Universidade do Minho, Portugal
2002 Bolsa de estudo por Mérito Escolar
2001 Prémio de Mérito Escolar
Universidade do Minho, Portugal
2000 Prémio de Mérito Escolar
Universidade do Minho, Portugal
2000 2º lugar ”O Comércio Tradicional no trilho do Comércio Electrónico”
1999 Prémio de Mérito Escolar
Universidade do Minho, Portugal

Outra distinção

2020 5 Highly cited papers according to Web of Science
2020 1 Paper in Hot papers in field according to Web of Science
2020 3 Recommended papers for special significance in the field
2019 Paper among top-50 most accessed papers in Nature Comminations
2017 Azure for Research Award: Data Science
Microsoft Research, Estados Unidos
2015 FCT Investigator Starting Grant 2014 [IF/01127/2014]
Fundação para a Ciência e a Tecnologia, Portugal
2014 F1000Prime (recommended by the F1000Prime Faculty as being of special significance)
2007 Bolsa de apresentação em conferência
IEEE Computational Intelligence Society, Estados Unidos