Identification
Personal identification
- Full name
- Pedro Gabriel Dias Ferreira
- Date of birth
- 1978/05/10
- Gender
- Male
Citation names
- Ferreira, Pedro G.
Author identifiers
- 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
Email addresses
- pgferreira@fc.up.pt (Professional)
Addresses
- Rua Campo Alegre 1021/1055, FC6, 4169-007, Porto, Porto, Portugal (Professional)
Websites
- https://scholar.google.com/citations?user=X097-20AAAAJ (Scholar)
- http://orcid.org/0000-0003-3838-8664 (Scholar)
- http://www.researcherid.com/rid/J-6379-2013 (Scholar)
- https://www.scopus.com/authid/detail.uri?authorId=13405242500 (Scholar)
- https://publons.com/researcher/1284228/pedro-g-ferreira/ (Scholar)
Knowledge fields
- Exact Sciences - Computer and Information Sciences - Bioinformatics
- Exact Sciences - Computer and Information Sciences - Computer Sciences
Languages
Language | Speaking | Reading | Writing | Listening | Peer-review |
---|---|---|---|---|---|
Portuguese | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) |
Spanish; Castilian | Advanced (C1) | Advanced (C1) | Advanced (C1) | Advanced (C1) | Advanced (C1) |
English | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) | Proficiency (C2) |
Education
Degree | Classification | |
---|---|---|
2022/10/14
Concluded
|
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." (THESIS/DISSERTATION)
|
|
2007
Concluded
|
Doutoramento em Informática (Doutoramento)
Universidade do Minho Escola de Engenharia, Portugal
"Sequence Pattern Mining in Biochemical Data" (THESIS/DISSERTATION)
|
Unanimidade |
2002
Concluded
|
Licenciatura em Engenharia de Sistemas e Informática (Licenciatura)
Universidade do Minho Escola de Engenharia, Portugal
"Engenharia de Sistemas e Informática" (THESIS/DISSERTATION)
|
16 |
Affiliation
Science
Category Host institution |
Employer | |
---|---|---|
2019/03/01 - Current | Researcher (Research) | Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência, Portugal |
Instituto de Engenharia de Sistemas e Computadores, Portugal | ||
2015/05/01 - Current | Researcher (Research) | Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal |
2015/05/01 - 2019/01/31 | Auxiliary Researcher (Research) | Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal |
2012/11/01 - 2014/06/01 | Postdoc (Research) | Universite de Geneve Faculte de Medecine, Switzerland |
2008/01/01 - 2012/11/01 | Postdoc (Research) | Centre de Regulació Genòmica, Spain |
2003/10/01 - 2007/09/01 | Researcher (Research) | Universidade do Minho Escola de Engenharia, Portugal |
2002/04/01 - 2002/10/01 | Visiting Researcher (Research) | Philips Research, Natuurkunde Laboratorium, IST, Netherlands |
Teaching in Higher Education
Category Host institution |
Employer | |
---|---|---|
2019/02/01 - Current | Assistant Professor (University Teacher) | Universidade do Porto Faculdade de Ciências, Portugal |
Universidade do Porto Faculdade de Ciências, Portugal |
Others
Category Host institution |
Employer | |
---|---|---|
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 |
Projects
Grant
Designation | Funders | |
---|---|---|
2008/01 - 2010/12 | Searching for high level rules in protein folding and unfolding: from amyloid diseases to protein structure prediction | Universidade de Coimbra |
Contract
Designation | Funders | |
---|---|---|
2018/06/01 - Current | Solving the 3D chromatin structure of CDH1 locus to identify disease-associated mechanisms
POCI-01-0145-FEDER-030164
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
|
Fundação para a Ciência e a Tecnologia
Ongoing
|
2018/06/01 - Current | AVC em translação: Biomarcadores para diagnóstico e decisão terapêutica no AVC isquémico
POCI-01-0145-FEDER-031674
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
|
Fundação para a Ciência e a Tecnologia
Ongoing
|
2018/06/01 - Current | NaSA - Neoantigen signature algorithm to predict immunotherapy response
POCI-01-0145-FEDER-032018
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
|
Fundação para a Ciência e a Tecnologia
Ongoing
|
2018/06/01 - Current | Tregs in cancer immune response
POCI-01-0145-FEDER-032462
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
|
Ongoing
|
2018/06 - Current | Tregs in cancer immune response
POCI-01-0145-FEDER-032462
|
N/A |
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 |
2017/06/01 - 2020/05/30 | GenomePT – National Laboratory for Genome Sequencing and Analysis
POCI-01-0145-FEDER-022184
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
|
Ongoing
|
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
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
|
Ongoing
|
2016/02/01 - 2019/07/31 | The yin and yang of somatic mutations in cancer immunosurveillance
PTDC/BIM-MEC/2834/2014
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
|
Ongoing
|
2015/05/01 - 2019/01/31 | Understanding the impact of acquired and germline genetic variants in the complexity of gastric cancer
IF/01127/2014
Principal investigator
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
|
Fundação para a Ciência e a Tecnologia
Concluded
|
Other
Designation | Funders | |
---|---|---|
2016/01/01 - Current | Advancing cancer research: from basic knowledgment to application II
ORTE-01-0145-FEDER-000029
Researcher
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.
.
Principal investigator
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
|
Microsoft Azure
Concluded
|
Outputs
Publications
Book |
|
Conference paper |
|
Journal article |
|
Preprint |
|
Activities
Oral presentation
Presentation title | Event name Host (Event location) |
|
---|---|---|
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, Spain)
|
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, United Kingdom)
|
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, United States)
|
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)
|
Supervision
Thesis Title Role |
Degree Subject (Type) Institution / Organization |
|
---|---|---|
2022 - 2026 | Deepening the understanding of Alzheimer's disease risk and progression: a multimodal approach.
Co-supervisor
|
Bioinformatics (PhD)
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).
Supervisor
|
Bioinformatics (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
|
2021 - 2025 | BioPredictor: a tool to predict the outcome of molecular alterations (SFRH/BD/05763/2020).
Co-supervisor
|
Bioinformatics (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
|
2022 - 2023 | Exploring the Human Phenotype-Gene Network
Supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2022 - 2023 | A multi-caller pipeline to maximize the output of somatic exome sequencing analysis
Co-supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2022 - 2023 | Novos Antídotos para o Veneno da Víbora Terciopelo
Co-supervisor
|
Bioinformática e Biologia Computacional (Master)
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).
Supervisor
|
Bioinformatics (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
|
2019 - 2023 | Towards a Modular and Scalable Privacy-preserving Machine Learning Framework (SFRH/BD/146528/2019).
Co-supervisor
|
Informatics (PhD)
Universidade do Minho, Portugal
|
2021 - 2022 | Understanding the impact of Mycobacterium tuberculosis complex diversity in tuberculosis
Co-supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2021 - 2022 | Modelling and Predicting Acute Ischaemic Stroke Outcomes
Co-supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2021 - 2022 | RISK - New RNA signatures of therapy evasion in Cancer
Co-supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2017 - 2022 | A framework for predicting drug sensitivity and synergy in cancer cells using deep learning
Co-supervisor
|
Informatics (PhD) |
2020 - 2021 | Analysis and comparison tool for multiple variant calling results from germline NGS data with clinical applications
Co-supervisor
|
Bioinformática e Biologia Computacional (Master)
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
Co-supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2020 - 2021 | A model validation pipeline for healthy tissue genome-scale metabolic models.
Co-supervisor
|
Bioinformática (Master)
Universidade do Minho, Portugal
|
2020 - 2021 | Developing deep learning methods to predict phenotypes and clinical outcomes from transcriptomics data
Co-supervisor
|
Bioinformática (Master)
Universidade do Minho, Portugal
|
2017 - 2021 | Study of control of protein abundance using multi-omics data from cancer samples
Supervisor
|
Biomedical / Bioinformatics (PhD)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
|
2019 - 2020 | Evaluating clustering and high- dimensionality reduction techniques for genomics data.
Supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2019 - 2020 | Data analysis of clinical datasets to support laboratory diagnostics using machine learning.
Supervisor
|
Ciência de Dados (Data Science) (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2019 - 2020 | HSA/CD42: a cardiomyocyte precursor biomarker and/or a gateway to cardiomyogenesis.
Co-supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2019 - 2020 | Neoantigen Signature Automatized Pipeline to predict Immunotherapy response
Supervisor
|
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
|
2017 - 2018 | Implementation and comparison of computational pipelines for variant calling in sequencing data
Supervisor
|
Bioinformática (Master)
Universidade do Minho, Portugal
|
2017 - 2018 | Mining cancer genomic data with Probabilistic Logic Programming
Supervisor
|
Bioinformática (PhD)
Universidade do Minho, Portugal
|
2017 - 2018 | Pathogen identification in human cancer cells
Co-supervisor
|
Engenharia Informática e Computação (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
|
2017 - 2018 | Sentiment analysis from medical records
Co-supervisor
|
Engenharia Informática (Master)
Universidade do Minho, Portugal
|
2016 - 2017 | Developing Deep Learning tools for cancer using omics data
Co-supervisor
|
Bioinformática (Master)
Universidade do Minho, Portugal
|
2016 - 2017 | Deep Learning for genomic data analysis
Co-supervisor
|
Engenharia Informática e Computação (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
|
2016 - 2016 | Post-doc fellowship from the José Castillejo program for Spanish young doctors
Supervisor
|
Bioinformatics (Other)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
|
2015 - 2016 | Análise de padrões em dados genómicos multi- plataforma disponíveis pelo TCGA.
Supervisor
|
Bioinformática (Master)
Universidade do Minho, Portugal
|
2015 - 2016 | Identification of pathogens in human cell cancers
Co-supervisor
|
Engenharia Informática e Computação (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
|
2015 - 2016 | Assessing the impact of alternative splicing in thyroid cancer
Co-supervisor
|
Engenharia Informática e Computação (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
|
2014 - 2015 | A Computational platform for assessing the impact of alternative splicing in cancer
Co-supervisor
|
Engenharia Informática e Computação
Universidade do Porto Faculdade de Engenharia, Portugal
|
Conference scientific committee
Conference name | Conference host | |
---|---|---|
2021/04 - Current | 10th International Conference on Data Science, Technology and Applications (DATA 2021) | |
2021/03 - Current | 30th International Joint Conference on Artificial Intelligence | |
2021/03 - Current | 7th-8th International Conference on Algorithms for Computational Biology (AlCoB 2020 & 2021) | |
2021 - Current | 13th International Conference on Knowledge Discovery and Information Retrieval (KDIR 2021) | |
2021 - Current | European Society of Human Genetics (Bioinformatics and Computational methods section; 2016 & 2017 & 2021) | |
2018 - Current | Technical Committee (Data Science) and Reviewer for Inforum (2018) | |
2017 - Current | IEEE International Conference on Data Science and Advanced Analytics (2017) | |
2017 - Current | Technical Committee and Reviewer for International Conference on Computational Chemistry and Biology (2017) | |
2009 - Current | 6th International Meeting Computational Intelligence Methods for Bioinformatics and Biostatistics | |
2017 - 2021 | International Conference on Practical Applications of Computational Biology & Bioinformatics |
Evaluation committee
Activity description Role |
Institution / Organization | Funding entity | |
---|---|---|---|
2022 - 2022 | Reviewer for FCT and Google Initiative for AI in Portugal (CPCA-IAC)
Evaluator
|
Rede Nacional de Computação Avançada, Portugal | |
2021 - 2021 | Call on Advanced Computing Projects (2nd edition)
Evaluator
|
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).
Evaluator
|
||
2013 - 2013 | Post-Doctoral Return programme, for young post-doc researchers returning to France, from the Agence Nationale de Recherche,
France, 2013
Evaluator
|
Agence nationale de la recherche, France |
Journal scientific committee
Journal title (ISSN) | Publisher | |
---|---|---|
2021/01/04 - Current | Knowledge and Information Systems | Springer |
2021 - Current | ACM Transactions on Intelligent Systems and Technology | |
2020 - Current | Cancers | MDPI |
2017/01/01 - Current | PeerJ | PerrJ Publishing |
Distinctions
Award
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
|
Other distinction
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, United States
|
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, United States
|