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RICARDO JORGE FONSECA TAVARES GODINHO PAIS. Completed the Doutoramento in Systems Biology in 2018/12/14 by Universidade Nova de Lisboa, Mestrado in Medical Biochemistry in 2011/07/28 by Universidade de Lisboa Faculdade de Ciências and Licenciatura in Bioquímica in 2008/09/18 by Universidade de Lisboa Faculdade de Ciências. Is Researcher in Egas Moniz Cooperativa de Ensino Superior CRL. Published 18 articles in journals. Has 4 section(s) of books. Participates and/or participated as PhD Student Fellow in 1 project(s), Research Fellow in 1 project(s) and Researcher in 1 project(s). Works in the area(s) of Exact Sciences with emphasis on Computer and Information Sciences with emphasis on Bioinformatics and Natural sciences with emphasis on Biological Sciences with emphasis on Biochemistry. In his curriculum Ciência Vitae the most frequent terms in the context of scientific, technological and artistic-cultural output are: Data analysis ; Machine learning; Pattern recognition; Predictive Modelling; Biomarker detection ; Proteomics; Transcriptomics; Mathematical modelling; Mass spectrometry ; Simulation of biochemical systems; Oxidative Stress; Cancer biology; UV-Vis Spectrometry; Logical modelling; EMT; Metastasis; .
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Identificação

Identificação pessoal

Nome completo
RICARDO JORGE FONSECA TAVARES GODINHO PAIS

Nomes de citação

  • Pais, Ricardo J.
  • Ricardo Jorge Pais
  • R. Pais

Identificadores de autor

Ciência ID
0B19-5971-FCE5
ORCID iD
0000-0001-5489-8790

Endereços de correio eletrónico

  • rjpais@bioenhancersystems.com (Profissional)

Websites

Domínios de atuação

  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática
  • Ciências Naturais - Ciências Biológicas - Bioquímica

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português (Idioma materno)
Inglês Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C1)
Formação
Grau Classificação
2019/10/01 - 2019/10/23
Concluído
 TensorFlow: Machine Learning & Deep Learning with Python (Outros)
Udemy Inc, Estados Unidos
2013/01/01 - 2018/12/14
Concluído
 Systems Biology (Doutoramento)
Especialização em Biology
Universidade Nova de Lisboa, Portugal
"How cells initiate Epithelial-to-Mesenchymal Transition? A computational modelling of cellular and supra-cellular networks to unravel the control of EMT" (TESE/DISSERTAÇÃO)
 unanimously approved
2018/05/06 - 2018/06/01
Concluído
 Data Science A/Z (Outros)
Udemy Inc, Estados Unidos
2018/03/05 - 2018/03/09
Concluído
 Advanced Biostatistics for Bioinformatics using R (Outros)
Gulbenkian Training Program in Bioinformatics , Portugal
2017/10/06 - 2017/10/10
Concluído
 Analysis of Differential Expression with RNAseq (Outros)
Gulbenkian Training Program in Bioinformatics , Portugal
2016/05/05 - 2016/05/10
Concluído
 Proteomics Data Analysis (Outros)
Gulbenkian Training Program in Bioinformatics , Portugal
2015/04/19 - 2015/04/24
Concluído
 Bioinformatics using Python for Biomedical Researchers (Outros)
Gulbenkian Training Program in Bioinformatics , Portugal
2010/09/01 - 2011/07/28
Concluído
 Medical Biochemistry (Mestrado)
Especialização em Biochemistry
Universidade de Lisboa Faculdade de Ciências, Portugal
"Biochemical systems analysis of the reactive oxygen species: A study on the origin of oxidative stress in evolution" (TESE/DISSERTAÇÃO)
 17
2003/09/01 - 2008/09/18
Concluído
 Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Cloning and overexpression 3Cys and 4 Cys iron and copper substituted rubredoxins" (TESE/DISSERTAÇÃO)
 14
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2020/02/01 - Atual Investigador (Investigação) Egas Moniz Cooperativa de Ensino Superior CRL, Portugal
2013/01/01 - 2018/12/01 Investigador (Investigação) Instituto Gulbenkian de Ciência, Portugal
2011/05/01 - 2013/01/01 Investigador (Investigação) Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2009/02/01 - 2011/03/01 Investigador (Investigação) Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
Universidade de Lisboa Faculdade de Ciências, Portugal

Outros

Categoria Profissional
Instituição de acolhimento 		Empregador
2018/01/01 - 2020/02/01 Data Scientist & Bioinformatician MAP Sciences Ltd, Reino Unido
Projetos

Bolsa

Designação Financiadores
2013/01/01 - 2017/09/30 How cells initiate Epithelial-to-Mesenchymal Transition?A computational modelling of cellular and supra-cellular networks to unravel the control of EMT
SFRH/BD/52175/2013
Bolseiro de Doutoramento
Instituto Gulbenkian de Ciência, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído

Projeto

Designação Financiadores
2018/04/01 - 2020/02/01 LARGE TRIAL TO DEVELOP A LOW COST, MASS MARKET, NON-INVASIVE, URINARY, PRENATAL DIAGNOSTICS TEST FOR THE CHINESE MARKET
11223-2
Investigador
MAP Sciences Ltd, Reino Unido
 Innovate UK
Concluído
2009/02 - 2011/03/31 RECONSTRUCTION AND SYSTEMS ANALYSIS OF THE REACTION NETWORKS OF REACTIVE OXYGEN, NITROGEN AND SULFUR SPECIES IN REPRESENTATIVE PHYSIOLOGICAL SYSTEMS
PTDC/QUI/70523/2006
Bolseiro de Investigação
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
Produções

Publicações

Artigo em conferência
  1. Ricardo Jorge Pais; Tiago Alexandre Pais; Uraquitan Lima Filho. "Bespoke Biomarker Combinations for Cancer Survival Prognosis Using Artificial Intelligence on Tumour Transcriptomics". 2025.
    10.3390/msf2025037018
  2. Ricardo Pais; Amanda Carneiro; Yolanda Zendzela; Yosra Sdiri; Tidiana Rodrigues; Maria Guilhermina Moutinho; Tabisam Khan; Markella Mikkelsen. "Facilitating NGS-Based Screening of Genetic Disorders Using -AI-Driven Bioinformatics". 2023.
    10.3390/msf2023022039
  3. Ricardo Jorge Pais; Filipa Lopes; Inês Parreira; Márcia Silva; Mariana Silva; Maria Guilhermina Moutinho. "Predicting Cancer Prognostics from Tumour Transcriptomics Using an Auto Machine Learning Approach". 2023.
    10.3390/msf2023022006
Artigo em revista
  1. Uraquitan Lima Filho; Tiago Alexandre Pais; Ricardo Jorge Pais. "Visualising the Truth: A Composite Evaluation Framework for Score-Based Predictive Model Selection". BioMedInformatics (2025): https://doi.org/10.3390/biomedinformatics5030055.
    10.3390/biomedinformatics5030055
  2. Ricardo Jorge Pais; João Botelho; Vanessa Machado; Gil Alcoforado; José João Mendes; Ricardo Alves; Lucinda J. Bessa. "Exploring AI-Driven Machine Learning Approaches for Optimal Classification of Peri-Implantitis Based on Oral Microbiome Data: A Feasibility Study". Diagnostics (2025): https://doi.org/10.3390/diagnostics15040425.
    10.3390/diagnostics15040425
  3. Bessa, L.J.; Egas, C.; Pires, C.; Proença, L.; Mascarenhas, P.; Pais, R.J.; Barroso, H.; et al. "Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study". Frontiers in Cellular and Infection Microbiology 15 (2025): http://www.scopus.com/inward/record.url?eid=2-s2.0-105004196813&partnerID=MN8TOARS.
    10.3389/fcimb.2025.1543100
  4. João Dourado Santos; Daniel Sobral; Miguel Pinheiro; Joana Isidro; Carlijn Bogaardt; Miguel Pinto; Rodrigo Eusébio; et al. "INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance". Genome Medicine (2024): http://dx.doi.org/10.1186/s13073-024-01334-3.
    10.1186/s13073-024-01334-3
  5. Filho, U.L.; Pais, T.A.; Pais, R.J.. "Facilitating “Omics” for Phenotype Classification Using a User-Friendly AI-Driven Platform: Application in Cancer Prognostics". BioMedInformatics 3 4 (2023): 1071-1082. http://www.scopus.com/inward/record.url?eid=2-s2.0-85180449506&partnerID=MN8TOARS.
    10.3390/biomedinformatics3040064
  6. Ricardo J. Pais. "Predictive Modelling in Clinical Bioinformatics: Key Concepts for Startups". BioTech (2022): https://doi.org/10.3390/biotech11030035.
    10.3390/biotech11030035
  7. Ricardo J. Pais; Raminta Zmuidinaite; Jonathan C. Lacey; Christian S. Jardine; Ray K. Iles. "A Rapid and Affordable Screening Tool for Early-Stage Ovarian Cancer Detection Based on MALDI-ToF MS of Blood Serum". Applied Sciences 12 6 (2022): 3030-3030. https://doi.org/10.3390/app12063030.
    10.3390/app12063030
  8. Pais, Ricardo J.. "Simulation of multiple microenvironments shows a pivot role of RPTPs on the control of Epithelial-to-Mesenchymal Transition". Biosystems 198 (2020): 104268-104268. http://dx.doi.org/10.1016/j.biosystems.2020.104268.
    10.1016/j.biosystems.2020.104268
  9. Ricardo J. Pais; Ray K. Iles; Raminta Zmuidinaite. "MALDI-ToF Mass spectra phenomic analysis for human disease diagnosis enabled by cutting-edge data processing pipelines and bioinformatic tools". Current Medicinal Chemistry (2020): https://doi.org/10.2174/0929867327666201027154257.
    10.2174/0929867327666201027154257
  10. Ricardo J. Pais; Fady Sharara; Raminta Zmuidinaite; Stephen Butler; Sholeh Keshavarz; Ray Iles. "Bioinformatic identification of euploid and aneuploid embryo secretome signatures in IVF culture media based on MALDI-ToF mass spectrometry". Journal of Assisted Reproduction and Genetics (2020): https://doi.org/10.1007/s10815-020-01890-8.
    10.1007/s10815-020-01890-8
  11. Ricardo J. Pais; Nuno Taveira. "Predicting the evolution and control of the COVID-19 pandemic in Portugal [version 2; peer review: 2 approved]". (2020): https://f1000research.com/articles/9-283/v2.
    10.12688/f1000research.23401.2
  12. Ricardo J. Pais; Nuno Taveira. "Predicting the evolution and control of the COVID-19 pandemic in Portugal [version 1; peer review: awaiting peer review]". (2020): https://f1000research.com/articles/9-283/v1.
    10.12688/f1000research.23401.1
  13. Pais, Ricardo. "The importance of gestational age in first trimester, maternal urine MALDI-Tof MS screening tests for Down Syndrome". Annals of Proteomics and Bioinformatics (2019): http://dx.doi.org/10.29328/journal.apb.1001008.
    Publicado • 10.29328/journal.apb.1001008
  14. Pais, Ricardo. "Rapid, Affordable and Efficient Screening of Multiple Blood Abnormalities Made Possible Using an Automated Tool for MALDI-ToF Spectrometry Analysis". Applied Sciences (2019): http://dx.doi.org/10.3390/app9234999.
    10.3390/app9234999
  15. Fady I. Sharara; Stephen A. Butler; Raminta Zmuidinaite; Pais, Ricardo J.; Sholeh Keshavarz; Ray Kurse Iles. "BESST, a Non-Invasive Computational Tool for Embryo Selection Using Mass Spectral Profiling of Embryo Culture Media". Reproductive Health 5 1 (2019): 59-60.
    Publicado
  16. Pais, Ricardo. "An automated workflow for MALDI-ToF mass spectra pattern identification on large data sets: An application to detect aneuploidies from pregnancy urine". Informatics in Medicine Unlocked (2019): http://dx.doi.org/10.1016/j.imu.2019.100194.
    10.1016/j.imu.2019.100194
  17. Thapper, A.; Rizzi, A.C.; Brondino, C.D.; Wedd, A.G.; Pais, R.J.; Maiti, B.K.; Moura, I.; Pauleta, S.R.; Moura, J.J.G.. "Copper-substituted forms of the wild type and C42A variant of rubredoxin". Journal of Inorganic Biochemistry 127 (2013): 232-237. http://www.scopus.com/inward/record.url?eid=2-s2.0-84884413851&partnerID=MN8TOARS.
    10.1016/j.jinorgbio.2013.06.003
  18. Pais, Ricardo J.; António E. Ferreira; Armindo Salvador; Fernando Antunes. "Kinetic Modeling of Reactive Oxygen Species in the Ancient Ocean: the Evolutionary Origin of Oxidative Stress". Free Radical Biology and Medicine 51 (2011): S143-S144.
    Publicado
Artigo em revista (magazine)
  1. Pais, Ricardo J.. "Bioinformatics and predictive modelling as tools for clinical diagnostics", Omnia-Health DIGITAL PATHOLOGY, 2020, https://insights.omnia-health.com/laboratory/bioinformatics-and-predictive-modelling-tools-clinical-diagnostics.
Capítulo de livro
  1. Pais, Ricardo J.; Zmuidinaite, Raminta; Iles, Ray K.; Butler, Stephen A.. "hCGßcf as a quality control marker for urine mass spectrometry analysis". In 100 Years of Human Chorionic Gonadotropin, 139-147. London, Reino Unido: Elsevier, 2020.
    10.1016/b978-0-12-820050-6.00012-6
  2. Zmuidinaite, Raminta; Iles, Ray K.; Pais, Ricardo J.; Butler, Stephen A.. "Detection and quantification of hCG and its isoforms with MALDI-ToF mass spectrometry". In 100 Years of Human Chorionic Gonadotropin, 75-85. Elsevier, 2020.
    10.1016/b978-0-12-820050-6.00008-4
  3. Pais, R.J.; Zmuidinaite, R.; Iles, R.K.; Butler, S.A.. "hCGßcf as a quality control marker for urine mass spectrometry analysis". 139-147. 2020.
  4. Zmuidinaite, R.; Iles, R.K.; Pais, R.J.; Butler, S.A.. "Detection and quantification of hCG and its isoforms with MALDI-ToF mass spectrometry". 75-85. 2020.
Pré-impressão
  1. Uraquitan Lima Filho; Tiago Alexandre Pais; Ricardo Jorge Pais. "Visualising the Truth: A Composite Evaluation Framework for Score-Based Predictive Models Selection". 2025. https://doi.org/10.20944/preprints202506.1803.v1.
    10.20944/preprints202506.1803.v1
  2. Ricardo Jorge Pais; João Botelho; Vanessa Machado; Gil Alcoforado; José João Mendes; Ricardo Alves; Lucinda J. Bessa. "Exploring AI-Driven Machine Learning Approaches for Optimal Classification of Peri-Implantitis Based on Oral Microbiome Data: A Feasibility Study". 2025. https://doi.org/10.20944/preprints202501.0529.v1.
    10.20944/preprints202501.0529.v1
  3. Uraquitan Lima Filho; Tiago Alexandre Pais; Ricardo Jorge Pais. "Facilitating “Omics” to Phenotype Classification Using a User-Friendly AI-Driven Platform: Application to Cancer Prognostics". 2023. https://doi.org/10.20944/preprints202308.1712.v1.
    10.20944/preprints202308.1712.v1

Outros

Outra produção
  1. Predicting the evolution and control of COVID-19 pandemic in Portugal.. 2020. Ricardo Jorge Pais; Nuno Taveira. https://doi.org/10.1101/2020.03.28.20046250.
    10.1101/2020.03.28.20046250
  2. Simulation of multiple microenvironments shows a putative role of RPTPs on the control of Epithelial-to-Mesenchymal Transition. 2019. Ricardo Jorge Pais. https://doi.org/10.1101/609263.
    10.1101/609263
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2020/10/20 Application of AI & big data to the medical lab, how to do and is it time? MedLab Asia
Informa Markets (Taiwan)
2020/02/05 Advancing care through personalised diagnostics using bioinformatics and predictive modelling tools. Laboratory Inovation
Medlab , UK (Dubai)
2020/02/05 The bioinformatics and automated processing of phenomic data in personalised diagnostics - A working example of mass spectral pattern recognition Molecular Diagnostics & Genetics
Medlab (Dubai, Emiratos Árabes Unidos)
2019/09/20 Blastocyst and embryo screening selection tool (BESST): an ultrafast non-invasive embryo selection test for use immediately prior to embryo transfer ESHRE 2019
(Viena)

Consultoria / Parecer

Descrição da atividade Instituição / Organização
2019/09/16 - 2020/02/24 Consulting activities in the field of Informatics, Data science and Python programming. Growin Insights SA, Portugal
2016/07/01 - 2018/05/01 Data analysis and quality assessment of multiple cosmetics products from a Portuguese company. Scientific advisory regarding production protocols and their optimal design. Da Minha Casinha Cosmetica Natural Biologica, Portugal

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2019/11/16 - 2019/12/16 Bioinformatica Análises Clínicas (Mestrado integrado) Egas Moniz Cooperativa de Ensino Superior CRL, Portugal

Tutoria

Tópico Nome do aluno
2019/03/01 - 2019/09/01 Hb Analyzer Software development in Python Christian Jardine