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João Carneiro (JC) is a data scientist, computational researcher, and bioinformatician with a robust academic background and extensive experience in developing and deploying advanced analytics solutions. He has a degree in Biology at University of Porto (UP) and a master's in forensic genetics (UP). JC finished his Biology PhD thesis in 2013 at UP and the Institute of Molecular Pathology and Immunology of UP. His thesis was related to molecular dynamics simulations of non-B DNA conformations. JC received a 2014 Foundation for Science and Technology (FCT) postdoctoral fellowship to study the influence of non-B DNA conformations on mtDNA rearrangements at Interdisciplinary Centre of Marine and Environmental Research (CIIMAR). JC was subsequently a contracted researcher at CIIMAR under DL57/2016. JC is now a researcher at the Centre of Molecular and Environmental Biology (CBMA) at the University of Minho. JC recently concluded the courses Molecular Dynamics and Structure-based Virtual Screening (National Infrastructure for Distributed Computing - INCD) and the E-learning course - Machine Learning (ML) with Python: A Practical Introduction (IBM). He maintains 6 online databases (e.g. https://cyanobioactivedb.jc-biotechaiteam.com/, https://rhdv-primers-identification-db.jc-biotechaiteam.com/). EbolaID and CoV2ID are part of the Portuguese distributed infrastructure for biological data through BioData.pt. JC maintains one catalogue of reference sequences for transgenic elements. JC was involved in a project financed by the FCT RESEARCH 4 COVID-19 call (029_596289414). He participated in the project "Development of the CoV2ID platform for sharing data on COVID-19 detection and treatment protocols" funded by the European Union (Brussels, BE). He was awarded the project "Understanding non-B mtDNA conformations using molecular dynamics simulations" from FCT Advanced Computing Projects A2 typology (2021.09782.CPCA). He also integrates the team of the project "Biomarkers of health and performance in aquacultured fish: the application of antibody-based biosensors" funded by FCT (2022.07659.PTDC). He is also involved in the project Vírus4Health (monitoring the presence of SARS-CoV-2 in wastewater) at CIIMAR in collaboration with Águas do Porto. JC also coordinates the project "Machine Learning Models to Predict Plastic Degrading Enzymes with Application in Blue Biotechnology" and participates in the COST action CA21162 - Establishing a Pan-European Network on Computational Redesign of Enzymes (COZYME). JC collaborates with the Sérgio Sousa group at BioSIM, Biomedicine department, Faculty of Medicine of UP. This collaboration resulted in 4 published papers related to computational analysis of 3D models of proteins and DNA using molecular dynamics and ML models of biochemical datasets. He started a recent collaboration with Manuel Simões from LEPABE at the Faculty of Engineering of the UP regarding the development of ML algorithms for the prediction of biochemical properties of compounds with application in biotechnology. JC advised multiple students in bioinformatics over the past 5 years. He has supervised 7 MSc students, and co-supervised 1 MSc and 1 PhD. He cooperated with 126 collaborators for the co-authorship of scientific papers. He published 31 articles in peer review journals (Scopus h-index=11, 18 Q1), including 3 in NAR (IF=19.6), 1 in MBE (IF=8.8), 1 in MER (IF=8.6), and 1 in ER (8.4). He published 30 posters, 4 conference papers and 2 preprints. JC has delivered 7 oral presentations in national and international conferences. He organized one international event and participated in 21 events. JC participated as a team member in 8 funded research projects, including the MARINFO consortium. He is the PI of 2 competitive projects. He secured more than 90K euros in grants and more than 15K euros in projects as PI.
Identification

Personal identification

Full name
JOÃO MIGUEL SOTTO MAIOR FARIA CARNEIRO

Citation names

  • Carneiro, João

Author identifiers

Ciência ID
361E-93D9-D467
ORCID iD
0000-0002-5153-2395
Google Scholar ID
https://scholar.google.com/citations?user=6Ty_qiEAAAAJ&hl=en
Researcher Id
A-6289-2009
Scopus Author Id
37057156500

Email addresses

  • joaomiguelsov@gmail.com (Professional)
  • jcarneiro@ciimar.up.pt (Professional)

Addresses

  • CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental. Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n , 4450-208, Matosinhos, Matosinhos, Portugal (Professional)
  • CBMA - Centro de Biologia Molecular e Ambiental, Departamento de Biologia, University of Minho, Edifício n.º 18 Campus de Gualtar, 4710-057, Braga, Braga, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Other Medical Sciences - Forensic Science
  • Natural sciences - Biological Sciences - Genetics and Heredity

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Proficiency (C2) Advanced (C1) Proficiency (C2) Advanced (C1)
Portuguese (Mother tongue)
Education
Degree Classification
2024/08/01 - 2024/08
Ongoing
Data Analytics Basics for Everyone (Outros)
International Business Machines Corporation (IBM), United States
2024/07 - 2024/08
Ongoing
Agile and Scrum Fundamentals (Outros)
IBM, United States
2024/07 - 2024/08
Ongoing
Management - Becoming an Effective Leader (Outros)
Doane University, United States
2024/07/05 - 2024/07/20
Concluded
Python Basics for Data Science (Outros)
International Business Machines Corp, United States
100 (0-100)
2024/06 - 2024/07
Ongoing
5-week Data Science Bootcamp (Outros)
AI Planet, Belgium
2024/06/27 - 2024/06/27
Concluded
How FAIRsharing helps you enable FAIR: focus on standards, repositories and policies (Workshop) (Outros)
ELIXIR-UK, United Kingdom
2024/06/05 - 2024/06/05
Attended
Career Development Strategies in the US and Europe: Insights Across Borders! (Outros)
Chaperone, Portugal
2023/05/25 - 2023/05/25
Concluded
Graphical Design Workshop (Outros)
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2022/11/10 - 2022/11/10
Concluded
Course on Grant Proposal writing (Outros)
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2022/09/28 - 2022/09/28
Concluded
Molecular Dynamics (Outros)
Major in Molecular Dynamics
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal

Infraestrutura Nacional de Computação Distribuída, Portugal
2022/09/27 - 2022/09/27
Concluded
Structure-based Virtual Screening (Outros)
Major in Structure-based Virtual Screening
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal

Infraestrutura Nacional de Computação Distribuída, Portugal
2021/05/19 - 2021/06/07
Concluded
E-learning course - Machine Learning with Python: A Practical Introduction (Outros)
IBM, United States
Completed and approved
2016/11/15 - 2016/12/02
Concluded
E-learning Course "Analysis of Data from Molecular Techniques of the BioMarPT project - Learning to know the marine environment of Portugal" (Outros)
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
93/100
2013/07/09
Concluded
Doutoramento em Biologia/PhD in Biology (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
"The Role of Non-coding DNA Structural Information in Phylogeny, Evolution and Disease" (THESIS/DISSERTATION)
Approved with distinction unanimously
2008/12/17
Concluded
Genética forense/Forensic genetics (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
"Forensic applicability of phylogenetic analyses in mtDNA" (THESIS/DISSERTATION)
15
2007/05/02 - 2007/05/04
Concluded
Bioinformatics Course, 2-4 May 2007 (Outros)
Major in Bioinformatics
Universidade do Minho, Portugal
2006/07/01
Concluded
Biologia animal aplicada/Applied animal biology (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal
12
2006/03/31 - 2006/04/01
Concluded
ABZ da Genética Humana (Outros)
Major in Identificação Genética
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Approved
Affiliation

Science

Category
Host institution
Employer
2024/10/22 - Current Researcher (Research) Universidade do Minho, Portugal
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2018/09/01 - 2024/08/31 Contracted Researcher (Research) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2015/04/01 - 2018/08/31 Postdoc (Research) Fundação para a Ciência e a Tecnologia, Portugal
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2007/04/01 - 2010/03/31 Researcher (Research) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2006/09/01 - 2007/03/31 Research Trainee (Research) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal

Others

Category
Host institution
Employer
2014/04/15 - 2015/03/31 Bolseiro de Investigação (BI licenciado)/Research fellow Project: "Structure of the HIV genome: novel frameworks for clinical diagnosis and anti-retroviral therapeutics"- com a referência "VIH/SAU/001 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2013/10/01 - 2013/12/31 Bolseiro de Investigação/Research fellow Project: Correlations between non-B 3D structure conformations, primary DNA sequence and flanking regions using molecular dynamics simulations. Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
2010/04/01 - 2013/07/09 Bolseiro de doutoramento/Doctoral fellow Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Projects

Contract

Designation Funders
2024/10/14 - Current Plastizyme - Blue Bio Value Ideation 2024 (PI)
Principal investigator
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Oceano Azul Foundation, Portugal

BLUEBIO ALLIANCE (BBA), Portugal

MAZE Impact , Portugal
Oceano Azul Foundation

BLUEBIO ALLIANCE (BBA)

MAZE Impact

CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental
Ongoing
2023/03/12 - Current Biomarkers of health and performance in aquacultured fish: the application of antibody based biosensors (Team member) Funding: 249k Eur
2022.07659.PTDC
Researcher
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Fundação para a Ciência e a Tecnologia
2021/01/01 - 2025/12/31 Centro de Investigação Marinha e Ambiental
Centro de Ciências do Mar, Portugal

Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2023/05 - 2024/05 Machine Learning Models to Predict Plastic Degrading Enzymes with Application in Blue Biotechnology (PI) Funding: 10k Eur
Not available
Principal investigator
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental
2022/02/21 - 2023/07/31 Understanding non-B mtDNA conformations using molecular dynamics simulations (PI)
2021.09782.CPCA
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2020/05/01 - 2021/03/31 Development of the CoV2ID platform for sharing data on COVID-19 detection and treatment protocols (Team member)
60
Researcher
European Union
Concluded
2020/05/18 - 2020/08/18 2020: Portuguese Science and Technology Foundation RESEARCH 4 COVID-19 call (029_596289414) Implementation of rapid endpoint PCR systems for SARS-CoV-2 detection in conventional molecular biology laboratories (Team member)
029_596289414
Researcher
Fundação para a Ciência e a Tecnologia
2019/01/01 - 2019/12/31 Centro Interdisciplinar de Investigação Marinha e Ambiental
UID/Multi/04423/2019
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016/01 - 2019/07 MarInfo - Integrated Platform for Marine Data Acquisition and Analysis (Team member)
Provided by PTCRIS: NORTE-01-0145-FEDER-000031
Researcher
Fundação para a Ciência e a Tecnologia
2014/03 - 2016/02 Structure of the HIV genome: novel frameworks for clinical diagnosis and anti-retroviral therapeutics
Co-Principal Investigator (Co-PI)
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/05 - 2013/11 The causes and consequences of mitochondrial DNA deletions in animal cells (Team member)
Researcher
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/05 - 2013/07 CO-EVOLUTIONARY STUDY OF NAD BIOCHEMICAL NETWORKS (CO-PI)
Co-Principal Investigator (Co-PI)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/05 - 2013/04 Search for genomic structural variants in azoospermia: a study in the Portuguese population (Team member)
Co-Principal Investigator (Co-PI)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2011/01/01 - 2012/12/31 Projecto Estratégico - LA 3 - 2011-2012
PEst-C/SAU/LA0003/2011
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2023/03/08 - Current COST action - CA21162 - Establishing a Pan-European Network on Computational Redesign of Enzymes (COZYME)
CA21162
Researcher
European Union, Belgium
Ongoing
Outputs

Publications

Conference abstract
  1. Boazinha, João Pedro; Carneiro, João; Cerqueira, Nuno M. F. S. A.; Sousa, Sérgio F.. "Creation of a 3D-Molecular Database of Voltage-gate Sodium Channels". Paper presented in 6th Meeting of Medicinal Biotechnology, Porto, 2024.
  2. Carneiro, João; Brooke E. Hjelm; Filipe Pereira. "Gibbs Free Energy Variation Analysis of Breakpoint Regions from MtDNA Human Brain Deletions". Paper presented in 10th edition of Bioinformatics Open Days, 2021.
    10.13140/RG.2.2.16891.64803
  3. Cláudia Moreira; Filipe Pereira; João Carneiro; Luísa Azevedo; Isabel Pereira-Castro; Luci Conceição; Manuel Mota; Barbara van Asch; António Amorim. "Genetic diversity within the mitochondrial genome of Bursaphelenchus xylophilus. Cláudia Moreira, Filipe Pereira, Luís Fonseca, João Carneiro, Luísa Azevedo, Isabel Pereira-Castro, Luci Conceição, Manuel Mota, Isabel Abrantes, Barbara van Asch, António Amorim". Paper presented in XLIII ONTA Annual Meeting, Coimbra, Portugal, Coimbra, 2011.
    Published
  4. CARNEIRO, JOÃO. "The mitochondrial genome of Bursaphelenchus xylophilus, the pinewood nematode. Cláudia Moreira, Filipe Pereira, Luís Fonseca, Raquel Silva, João Carneiro, Luísa Azevedo, Isabel Pereira-Castro, Luci Conceição, Manuel Mota, Isabel Abrantes, Barbara van Asch, António Amorim". Paper presented in 30th International ESN Symposium, Vienna, Austria; 09/2010, Vienna, 2010.
    Published
Conference poster
  1. Clara Cerqueira; Mariana Fernandes; Diogo Pratas; Sérgio F. Sousa; CARNEIRO, JOÃO. "Otimização de Enzimas Degradadoras de Plástico Utilizando Machine Learning e Modelação 3D". Paper presented in Ciência 2024 - +Ciência para Uma Só Saúde e bem-estar global, July 3rd to 5th at the Centro de Congressos da Alfândega do Porto, 2024.
  2. Margarida Cardeano Pinheiro; Joana Abrantes; Diogo Pratas; Ana M Lopes; CARNEIRO, JOÃO. "Diversidade genómica e potencial zoonótico do vírus da hepatite E em coelhos europeus: Implicações para abordagens de diagnóstico e terapêuticas". Paper presented in Ciência 2024 - +Ciência para Uma Só Saúde e bem-estar global, July 3rd to 5th at the Centro de Congressos da Alfândega do Porto, 2024.
  3. Rafael Primo Vieira; Diogo Pratas; CARNEIRO, JOÃO; Sérgio F. Sousa. "In-silico aptamer development approach through machine learning". Paper presented in Ciência 2024 - +Ciência para Uma Só Saúde e bem-estar global, July 3rd to 5th at the Centro de Congressos da Alfândega do Porto, 2024.
  4. Rafael Primo Vieira; Diogo Pratas; CARNEIRO, JOÃO; Sérgio F. Sousa. "Developing a machine learning model for in-silico aptamer development". Paper presented in Encontro de Investigação Jovem da U.Porto (IJUP), 8-10 May 2024, 2024.
  5. Margarida Cardeano Pinheiro; Mariana Fernandes; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Decoding the Genomic Diversity of Hepatitis E Virus in European Rabbits: A Step Towards Understanding Zoonotic Transmission". Paper presented in The 20th Portugaliæ Genetica: DNA - Ancient and New 21-22 March 2024, 2024.
  6. Clara Cerqueira; Margarida Cardeano Pinheiro; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Evolutionary Insights into Plastic-Degrading Enzymes: A Data-Driven Approach to Bioremediation". Paper presented in The 20th Portugaliæ Genetica: DNA - Ancient and New 21-22 March 2024, 2024.
  7. Mariana Fernandes; Clara Cerqueira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. "Exploring the Evolution of PET-Degrading Enzymes: Insights from Sequence Alignment and Phylogenetic Analysis". Paper presented in The 20th Portugaliæ Genetica: DNA - Ancient and New 21-22 March 2024, 2024.
  8. Margarida Cardeano Pinheiro; Rafael Vieira; Abrantes, Joana; Diogo Pratas; Ana M Lopes; Carneiro, João. "Exploring the Genomic Diversity of Hepatitis E Virus in European Rabbits: A Search for Optimal Primers". Paper presented in Bioinformatics Open Days XIII Edition 14-16 March 2024, 2024.
  9. Clara Cerqueira; E11D-C109-D995; Sousa, Sérgio F.; Pratas, Diogo; Carneiro, João. "Creating a Comprehensive Database of Plastic Degrading Enzymes for Machine Learning Applications". Paper presented in Bioinformatics Open Days XIII Edition 14-16 March 2024, 2024.
  10. Mariana Fernandes; Clara Cerqueira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. "Unifying Information on Plastic Degrading Enzymes Across Different Databases". Paper presented in Bioinformatics Open Days XIII Edition 14-16 March 2024, 2024.
  11. Rafael Primo Vieira; Margarida Cardeano Pinheiro; Diogo Pratas; CARNEIRO, JOÃO; Sérgio F. Sousa. "Bridging Aptamer Information: Standardization and Curation of Diverse Databases". Paper presented in Bioinformatics Open Days XIII Edition 14-16 March 2024, 2024.
  12. Carneiro, Filipa; Lopes, Ana M; Abrantes, Joana; CARNEIRO, JOÃO. "RHDV database: computational approaches to build a primer database". Paper presented in The International Meeting of the Portuguese Society of Genetics (IMPSG), 2023.
  13. Carneiro, Filipa; Ana M Lopes; Joana Abrantes; CARNEIRO, JOÃO. "Experimental validation of promising RHDV identification primers from Literature and In-silico databases". Paper presented in Blue Think Conference 2023, 2023.
  14. Carneiro, Filipa; Ana M Lopes; Joana Abrantes; CARNEIRO, JOÃO. "Phylogenetic Conservation Scores to Select Primers for RHDV Identification". Paper presented in Conference: International Virus Bioinformatics Meeting 2023, 2023.
  15. Renato Soares; Sérgio F. Sousa ; Diogo Pratas; Sérgio Crisóstomo; CARNEIRO, JOÃO. "An Automatic Workflow to build a Database of Cyanobacterial Bioactive Compounds with applications in Blue Biotechnology". Paper presented in IJUP – Investigação Jovem da U.Porto 2023, 2023.
  16. João Carneiro; Francisco Pascoal; Miguel Semedo; Diogo Pratas; Maria Paola Tomasino; Adriana Rego; Maria De Fátima Carvalho; Ana P Mucha; Catarina Magalhães. "A computational approach to improve wastewater human pathogens detection". 2022.
    10.13140/RG.2.2.13262.33600
  17. Rita P. Magalhães; Victor de La Oliva; Carneiro, João; Sousa, Sérgio F.. "Optimization of Classification Models for Identification of Ligand-Target Inhibition Pairs in Biofilm Formation in P. aeruginosa". Paper presented in Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE), 2021.
    10.13140/RG.2.2.26841.39526
  18. Rita Magalhães; Victor de La Oliva; Carneiro, João; Sérgio F. Sousa. "Development of a Classification Model for the Identification of Targets to Known P.aeruginosa Biofilm Formation Inhibitors". Paper presented in Machine Learning in Quantum Physics and Chemistry Summer School (August 24th to September 3rd ), organized by the Faculty of Physics of the University of Warsaw, Poland., 2021.
  19. Dulce Quelhas; M. Martins; Carneiro, João; Jaeken, J.; Sousa, Sérgio F.; Azevedo, Luísa. "Effects of PMM2 single and double variants on protein stability and substrate interaction". Paper presented in Scientific CDG Symposium - Virtual Symposium 23-24 June 2021, 2021.
  20. André Ferreira; Filipe Pereira; Luísa Azevedo; Carneiro, João. "Detection methods of intraspecific variability in human highly infectious viruses". Paper presented in IJUP 2021 - Encontro de Investigação Jovem, 2021.
    10.13140/RG.2.2.25594.82885
  21. André Pina; Sérgio F. Sousa ; Carneiro, João. "3D Prediction of Non-B DNA Conformations Associated with MtDNA Genomic Instability". Paper presented in 10th edition of Bioinformatics Open Days, 2021.
    10.13140/RG.2.2.20561.66406
  22. Iolanda Soares; Luísa Azevedo; CARNEIRO, JOÃO. "Improving the identification of species using mitochondrial DNA information". Paper presented in IJUP 2020, 2020.
  23. CARNEIRO, JOÃO; Matthias Bernt; Filipe Pereira. "G-Quadruplexes are putatively involved in MtDNA Evolutionary Rearrangements in Chordata". Paper presented in XV Encontro Nacional de Biologia Evolutiva, 2019.
  24. Morteza Hosseini; Diogo Pratas; António Manuel Amorim dos Santos; CARNEIRO, JOÃO. "Improving the Detection of MtDNA Rearrangements using a Fast and Accurate Algorithm". Paper presented in XV Encontro Nacional de Biologia Evolutiva, 2019.
  25. João Carneiro. "Unravelling the role of non-B DNA conformations in mitochondrial genome rearrangements. João Carneiro, Matthias Bernt, Filipe Pereira". Paper presented in MitoPorto – Advances in Mitochondrial Research. 26 May 2017. Porto, Portugal., 2017.
  26. João Carneiro; Filipe Pereira; António Amorim; Irina de Sousa Moreira; Maria João Ramos. "The single-stranded structural conformations of STRs during replication. João Carneiro, Filipe Pereira, António Amorim, Irina de Sousa Moreira, Maria João Ramos". Paper presented in 15th Portugaliæ Genetica, 22 and 23 March 2012, Porto, Portugal, 2012.
  27. Ana Carolina Silva; João Carneiro; António Amorim; Luísa Azevedo. "The association between Alu distribution along the Xp21.2-Xp11.4 region and deleterious rearrangements. Ana Carolina Silva, João Carneiro, António Amorim, Luisa Azevedo". Paper presented in 15th Portugaliæ Genetica, 22 and 23 March 2012. Porto, Portugal., 2012.
  28. Raquel M. Silva; Ana Moleirinho; João Carneiro; Rune Matthiesen; Luísa Azevedo; António Amorim. "Widespread distribution of Nampt orthologues across non-vertebrate species. - Raquel M Silva, Ana Moleirinho, João Carneiro, Rune Matthiesen, Luísa Azevedo and António Amorim.". Paper presented in Portugaliae Genetica 13th. Edition - 2010, March 18-19. Porto, Portugal, 2010.
  29. CARNEIRO, JOÃO. "Extensive rearrangement of the mitochondrial genome of Bursaphelenchus xylophilus, the pinewood nematode. Cláudia Moreira, Filipe Pereira, Luís Fonseca, João Carneiro, Luísa Azevedo, Isabel Pereira-Castro, Luci Conceição, Manuel Mota, Isabel Abrantes, Barbara van Asch, António Amorim.". Paper presented in Portugaliae Genetica 13th. Edition - 2010, March 18-19. Porto, Portugal., 2010.
  30. Ana Moleirinho; Barbara van Asch; João Carneiro; Filipe Pereira; António Amorim; Luísa Azevedo. "Gene losses: casualities without causality?". Paper presented in Portugaliae Genética 11ºedition: “Tales of comparative genomics and evolution”. March 27 and 28. 2008. Porto. Portugal, IPATIMUP, 2008.
  31. João Carneiro; António Amorim. "Impact of silent genes in kinship probability calculations. João Carneiro, António Amorim.". Paper presented in II Encontro Nacional de Pós-Graduação em Ciências Biológicas. 4, 5 e 6 de June. 2007. Porto, Portugal., 2007.
  32. Filipe Pereira; João Carneiro; David C. Samuels; António Amorim. "A highly conserved hexanucleotide motif triggers the formation of tandem repeats in the mammalian mitochondrial DNA control region. Filipe Pereira, João Carneiro, David C. Samuels, António Amorim.". Paper presented in I Encontro Nacional de Pós-Graduação em Ciências Biológicas & V Simpósio de Pós-Graduação do Departamento de Biologia da Universidade de Aveiro. 2, 3 and 4 de May. 2006. Aveiro, Portugal., 2006.
    10.12702/viii.simposfloresta.2014.78-679-1
Journal article
  1. Mónica Lopes-Marques; Matthew Mort; João Carneiro; António Azevedo; Andreia P Amaro; David N Cooper; Luísa Azevedo. "Meta-analysis of 46,000 germline de novo mutations linked to human inherited disease". Human Genomics 18 (2024): 20-20. https://doi.org/10.1186/s40246-024-00587-8.
    10.1186/s40246-024-00587-8
  2. Walid Zeghbib; Fares Boudjouan; João Carneiro; Ana L.S. Oliveira; Sérgio F. Sousa; Manuela Estevez Pintado; Asma Ourabah; Vitor Vasconcelos; Graciliana Lopes. "LC-ESI-UHR-QqTOF-MS/MS profiling and anti-inflammatory potential of the cultivated Opuntia ficus-indica (L.) mill. and the wild Opuntia stricta (haw.) haw. fruits from the Algerian region". Food Chemistry (2024): 140414-140414. https://www.sciencedirect.com/science/article/pii/S0308814624020648.
    https://doi.org/10.1016/j.foodchem.2024.140414
  3. João Carneiro; Francisco Pascoal; Miguel Semedo; Diogo Pratas; Maria Paola Tomasino; Adriana Rego; Carvalho MF; Ana Paula Mucha; Catarina Magalhães. "Mapping human pathogens in wastewater using a metatranscriptomic approach". Environmental Research (2023): 116040-116040. http://dx.doi.org/10.1016/j.envres.2023.116040.
    10.1016/j.envres.2023.116040
  4. João Carneiro; Rita P. Magalhães; Victor M. de la Oliva Roque; Manuel Simões; D. Pratas; Sergio F. Sousa. "TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa". Journal of Computer-Aided Molecular Design (2023): http://dx.doi.org/10.1007/s10822-023-00505-5.
    10.1007/s10822-023-00505-5
  5. André F. Pina; Sérgio F. Sousa; Luísa Azevedo; João Carneiro. "Non-B DNA conformations analysis through molecular dynamics simulations". Biochimica et Biophysica Acta (BBA) - General Subjects (2022): 130252-130252. http://dx.doi.org/10.1016/j.bbagen.2022.130252.
    10.1016/j.bbagen.2022.130252
  6. Fares Boudjouan; walid zeghbib; João Carneiro; Raquel Silva; João Morais; Vitor Vasconcelos; Graciliana Lopes. "Comparison Study on Wild and Cultivated Opuntia sp.: Chemical, Taxonomic, and Antioxidant Evaluations". Agriculture (2022): https://www.mdpi.com/2077-0472/12/11/1755.
    10.3390/agriculture12111755
  7. Quelhas, D.; Carneiro, J.; Lopes-Marques, M.; Jaeken, J.; Martins, E.; Rocha, J.F.; Teixeira Carla, S.S.; et al. "Assessing the effects of PMM2 variants on protein stability". Molecular Genetics and Metabolism (2021): http://dx.doi.org/10.1016/j.ymgme.2021.11.002.
    10.1016/j.ymgme.2021.11.002
  8. Serrano, Catarina; Teixeira, Carla S. S.; Cooper, David N.; Carneiro, João; Lopes-Marques, Mónica; Stenson, Peter D.; Amorim, António; et al. "Compensatory epistasis explored by molecular dynamics simulations". Human Genetics 140 9 (2021): 1329-1342. http://dx.doi.org/10.1007/s00439-021-02307-x.
    10.1007/s00439-021-02307-x
  9. Carneiro, João; C. Gomes; Cátia Couto; Filipe Pereira. "CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2". bioRxiv (2020): https://doi.org/10.1101/2020.04.19.048991.
    Published
  10. CARNEIRO, JOÃO; Santos, Chiara; Pereira, Filipe. "A web-based platform of nucleotide sequence alignments of plants". bioRxiv (2019): http://dx.doi.org/10.1101/617035.
    Open access • Published • 10.1101/617035
  11. Pratas, Diogo; Hosseini, Morteza; Grilo, Gonçalo; Pinho, Armando; Silva, Raquel; Caetano, Tânia; Carneiro, João; Pereira, Filipe. "Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard". Genes 9 9 (2018): 445. http://dx.doi.org/10.3390/genes9090445.
    10.3390/genes9090445
  12. Carneiro, João; Resende, Adriana; Pereira, Filipe. "The HIV oligonucleotide database (HIVoligoDB)". Database 2017 (2017): http://dx.doi.org/10.1093/database/bax005.
    10.1093/database/bax005
  13. Moreira, Filipa; Carneiro, João; Pereira, Filipe. "A proposal for standardization of transgenic reference sequences used in food forensics". Forensic Science International: Genetics 29 (2017): e26. http://www.sciencedirect.com/science/article/pii/S1872497317301060.
    https://doi.org/10.1016/j.fsigen.2017.04.022
  14. Carneiro, João; Pereira, Filipe. "EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment". PLOS Neglected Tropical Diseases 10 7 (2016): e0004757. http://dx.doi.org/10.1371/journal.pntd.0004757.
    10.1371/journal.pntd.0004757
  15. Froufe, Elsa; Gan, Han Ming; Lee, Yin Peng; Carneiro, João; Varandas, Simone; Teixeira, Amílcar; Zieritz, Alexandra; Sousa, Ronaldo; Lopes-Lima, Manuel. "The male and female complete mitochondrial genome sequences of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798) (Bivalvia: Unionidae)". Mitochondrial DNA Part A 27 5 (2015): 3571-3572. http://dx.doi.org/10.3109/19401736.2015.1074223.
    10.3109/19401736.2015.1074223
  16. Damas, J.; Samuels, D.C.; Carneiro, J.; Amorim, A.; Pereira, F.. "Mitochondrial DNA Rearrangements in Health and Disease-A Comprehensive Study". Human Mutation 35 1 (2014): 1-14. http://www.scopus.com/inward/record.url?eid=2-s2.0-84890797290&partnerID=MN8TOARS.
    10.1002/humu.22452
  17. Damas, Joana; Carneiro, João; Amorim, António; Pereira, Filipe. "MitoBreak: the mitochondrial DNA breakpoints database". Nucleic Acids Research 42 D1 (2013): D1261-D1268. http://dx.doi.org/10.1093/nar/gkt982.
    10.1093/nar/gkt982
  18. Teixeira-Silva, A.; Silva, R.M.; Carneiro, J.; Amorim, A.; Azevedo, L.. "The Role of Recombination in the Origin and Evolution of Alu Subfamilies". PLoS ONE 8 6 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84878637862&partnerID=MN8TOARS.
    10.1371/journal.pone.0064884
  19. Carneiro, J.; Duarte-Pereira, S.; Azevedo, L.; Castro, L.F.C.; Aguiar, P.; Moreira, I.S.; Amorim, A.; Silva, R.M.. "The Evolutionary Portrait of Metazoan NAD Salvage". PLoS ONE 8 5 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84878391235&partnerID=MN8TOARS.
    10.1371/journal.pone.0064674
  20. Pereira, V.; Gusmão, L.; Valente, C.; Pereira, R.; Carneiro, J.; Gomes, I.; Morling, N.; Amorim, A.; João Prata, M.. "Refining the genetic portrait of Portuguese Roma through X-chromosomal markers". American Journal of Physical Anthropology 148 3 (2012): 389-394. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862586987&partnerID=MN8TOARS.
    10.1002/ajpa.22061
  21. Van Asch, B.; Pereira, F.; Santos, L.S.; Carneiro, J.; Santos, N.; Amorim, A.. "Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds". Animal Genetics 43 1 (2012): 35-41. http://www.scopus.com/inward/record.url?eid=2-s2.0-84855642252&partnerID=MN8TOARS.
    10.1111/j.1365-2052.2011.02222.x
  22. Carneiro, J.; Pereira, F.; Amorim, A.. "SPInDel: A multifunctional workbench for species identification using insertion/deletion variants". Molecular Ecology Resources 12 6 (2012): 1190-1195. http://www.scopus.com/inward/record.url?eid=2-s2.0-84867506608&partnerID=MN8TOARS.
    10.1111/1755-0998.12011
  23. Damas, J.; Carneiro, J.; Gonçalves, J.; Stewart, J.B.; Samuels, D.C.; Amorim, A.; Pereira, F.. "Mitochondrial DNA deletions are associated with non-B DNA conformations". Nucleic Acids Research 40 16 (2012): 7606-7621. http://www.scopus.com/inward/record.url?eid=2-s2.0-84869477659&partnerID=MN8TOARS.
    10.1093/nar/gks500
  24. Van Asch, B.; Pereira, R.; Carneiro, J.; Amorim, A.. "Population assignment in seven Portuguese dog breeds and Iberian wolves". Forensic Science International: Genetics Supplement Series 3 1 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-82455210828&partnerID=MN8TOARS.
    10.1016/j.fsigss.2011.10.019
  25. Van Asch, B.; Silva Santos, L.; Carneiro, J.; Pereira, F.; Amorim, A.. "Identification of mtDNA lineages of Sus scrofa by multiplex single base extension for the authentication of processed food products". Journal of Agricultural and Food Chemistry 59 13 (2011): 6920-6926. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960067625&partnerID=MN8TOARS.
    10.1021/jf201283r
  26. Moleirinho, A.; Carneiro, J.; Matthiesen, R.; Silva, R.M.; Amorim, A.; Azevedo, L.. "Gains, losses and changes of function after gene duplication: Study of the metallothionein family". PLoS ONE 6 4 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79955562969&partnerID=MN8TOARS.
    10.1371/journal.pone.0018487
  27. Pereira, Filipe; Carneiro, João; Barbara van Asch. "A guide for mitochondrial DNA analysis in non-human forensic investigations". Open Forensic Science Journal 3 (2010): 33-44. https://benthamopen.com/ABSTRACT/TOFORSJ-3-33.
    Open access • Published
  28. Raquel M. Silva; Filipe Pereira; João Carneiro; Olimpia Sobral; Rui Ribeiro; António Amorim; Amadeu M V M Soares; Isabel Lopes. "Microevolution in a natural population of Daphnia longispina exposed to acid mine drainage.". Interdisciplinary Studies on Environmental Chemistry—Biological Responses to Contaminants, Eds., N. Hamamura, S. Suzuki, S. Mendo, C. M. Barroso, H. Iwata and S. Tanabe (2010): 213-218.
    Open access • Published
  29. Pereira, F.; Carneiro, J.; Matthiesen, R.; Van Asch, B.; Pinto, N.; Gusmão, L.; Amorim, A.. "Identification of species by multiplex analysis of variable-length sequences". Nucleic Acids Research 38 22 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78650444073&partnerID=MN8TOARS.
    10.1093/nar/gkq865
  30. Azevedo, L.; Carneiro, J.; van Asch, B.; Moleirinho, A.; Pereira, F.; Amorim, A.. "Epistatic interactions modulate the evolution of mammalian mitochondrial respiratory complex components". BMC Genomics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-67650927396&partnerID=MN8TOARS.
    10.1186/1471-2164-10-266
  31. Pereira, F.; Soares, P.; Carneiro, J.; Pereira, L.; Richards, M.B.; Samuels, D.C.; Amorim, A.. "Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region". Molecular Biology and Evolution 25 12 (2008): 2759-2770. http://www.scopus.com/inward/record.url?eid=2-s2.0-56449124495&partnerID=MN8TOARS.
    10.1093/molbev/msn225
  32. Pereira, F.; Carneiro, J.; Amorim, A.. "Identification of species with DNA-based technology: Current progress and challenges". Recent Patents on DNA and Gene Sequences 2 3 (2008): 187-200. http://www.scopus.com/inward/record.url?eid=2-s2.0-70350236393&partnerID=MN8TOARS.
  33. Pereira, F.; Carneiro, J.; Soares, P.; Maciel, S.; Nejmeddine, F.; Lenstra, J.A.; Gusmão, L.; Amorim, A.. "A multiplex primer extension assay for the rapid identification of paternal lineages in domestic goat (Capra hircus): Laying the foundations for a detailed caprine Y chromosome phylogeny". Molecular Phylogenetics and Evolution 49 2 (2008): 663-668. http://www.scopus.com/inward/record.url?eid=2-s2.0-55149091106&partnerID=MN8TOARS.
    10.1016/j.ympev.2008.08.026
  34. Amorim, A.; Carneiro, J.. "The impact of silent alleles in kinship probability calculations". Forensic Science International: Genetics Supplement Series 1 1 (2008): 638-639. http://www.scopus.com/inward/record.url?eid=2-s2.0-50349102395&partnerID=MN8TOARS.
    10.1016/j.fsigss.2007.10.024
Online resource
  1. Clara Cerqueira; Mariana Fernandes; Joana Rocha; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. Plastizyme: a central Hub for plastic biodegradation research. 2024. https://ml3denzymeoptimization.jc-biotechaiteam.com/.
  2. Margarida Cardeano Pinheiro; Abrantes, Joana; Lopes, Ana M; Pratas, Diogo; Carneiro, João. HEV in European Rabbits Resource Hub. 2024. https://rhev-primers-identification-db.jc-biotechaiteam.com/.
  3. Rafael Primo Vieira; Pratas, Diogo; Sousa, Sérgio F.; Carneiro, João. AptaCom: Bridging aptamer knowledge. 2024. http://jc-biotechaiteam.com/AptaCom.
  4. Carneiro, Filipa; Carneiro, João. RHDV Database: a freely accessible database that sorts the oligonucleotides (primers) used in the reverse transcription (RT)-PCR for the detection and identification of RHDV. 2023. https://rhdv-primers-identification-db.jc-biotechaiteam.com/.
  5. Renato Soares; Carneiro, João. CyanoBioActivedb: Database of bioactive compounds derived from cyanobacteria. 2023. https://cyanobioactivedb.jc-biotechaiteam.com/.
  6. Carneiro, João; C. Gomes; Cátia Couto; Filipe Pereira. CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2. 2020. http://dx.doi.org/10.1101/2020.04.19.048991.
    10.1101/2020.04.19.048991
  7. Filipa Moreira; CARNEIRO, JOÃO; Filipe Pereira. Catalogue of reference sequences for transgenic elements in Genetically Modified (GM) plants. 2017. http://portugene.com/GMOTables/cgi-bin/GMOTablesHome.cgi.
  8. CARNEIRO, JOÃO. PlantAligDB: A database of curated nucleotide sequence alignments for plants. 2017. http://plantaligdb.portugene.com/cgi-bin/PlantAligDB_home.cgi.
  9. CARNEIRO, JOÃO; Filipe Pereira. HIVoligoDB - The HIV oligonucleotide database. 2017. http://portugene.com/HIVoligoDB/cgi-bin/HIVoligoDB_home.cgi.
  10. CARNEIRO, JOÃO; Filipe Pereira. EbolaID DATABASE PROJECT. 2016. http://ebolaid.portugene.com/cgi-bin/EbolaID_home.cgi.
Thesis / Dissertation
  1. CARNEIRO, JOÃO. "The Role of Non-coding DNA Structural Information in Phylogeny, Evolution and Disease". PhD, Universidade do Porto Faculdade de Ciências, 2013.
  2. CARNEIRO, JOÃO. "Forensic applicability of phylogenetic analyses in mtDNA". Master, Universidade do Porto Faculdade de Ciências, 2008.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/09/29 AI-Powered Workflows in Biotechnology: From Environmental Remediation to Health Meeting Centre for Molecular and Environmental Biology (CBMA) at the University of Minho
Centre for Molecular and Environmental Biology (CBMA) at the University of Minho (Braga, Portugal)
2024/09/09 Models to Predict Plastic Degrading Enzymes with Application in Blue Biotechnology CIIMAR Annual Meeting
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) (Matosinhos, Portugal)
2023/10/18 Models to Predict Plastic Degrading Enzymes with Application in Blue Biotechnology UMIB 2023 seminars
Institute for the Biomedical Sciences “Abel Salazar” (ICBAS) (Porto, Portugal)
2023/05/12 A Computational Approach to Build a RHDV Primer Database from the Literature IJUP – Young Research at the University of Porto
University of Porto (Porto, Portugal)
2021/05/06 Gibbs Free Energy Variation Analysis of Breakpoint Regions from MtDNA Human Brain Deletions 10th edition of Bioinformatics Open Days, 2021.
University of Minho, Braga (Braga, Portugal)
2019/11/25 Dissecting the role of non-B DNA conformations in mitochondrial DNA rearrangements in the human brain 1st BioSIM Cycle of Conferences
Biomedicine department of the Faculty of Medicine of the University of Porto (Porto, Portugal)
2018/03/22 Mitochondrial DNA evolutionary breakpoints are associated with non-B DNA conformations 18th Portugaliæ Genetica-Genetic Diversity in Structure and Regulation, Oral Presentation, 22 & 23 March 2018
i3S - Instituto de Investigação e Inovação em Saúde (Porto, Portugal)
2012/05 The role of non-coding DNA structural information in phylogeny, evolution and disease - João Carneiro - May 2012 Conference: Conference: Cycle of Conferences 2012 - Theoretical Chemistry and Computational Biochemistry Group DQB/FCUP
Universidade do Porto Faculdade de Ciências (Porto, Portugal)
2010/03/18 A new method for detection of compositional strand asymmetries in vertebrate mitochondrial genomes” Fonseca MM, Carneiro J, Pereira F, Amorim A, Roca-Pardiñas, Posada D, Harris DJ Portugaliae Genetica 13th. Edition - 2010, March 18-19. Porto, Portugal.
Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto (Porto, Portugal)
2007/08/21 The impact of silent alleles in kinship probability calculations – (0-42)22nd. João Carneiro, António Amorim Congress of the International Society for Forensic Genetics 21–25 August 2007 - Copenhagen - Denmark
International Society for Forensic Genetics (Copenhagen, Denmark)
2006/03/16 A highly conserved hexanucleotide motif triggers the formation of tandem repeats in the mammalian mitochondrial DNA control region. Filipe Pereira, João Carneiro, David C. Samuels, António Amorim. Portugaliae Genética 9ºedition: “Genes and Populations in Health and disease”. IPATIMUP March 16, 17 and 18. 2006. Porto. Portugal.
Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto (Porto, Portugal)

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2024/10 - Current A User-friendly bioinformatic tool for transcriptomic data analysis -to create proxy gene expression profiles of highly restricted or endangered species.
Co-supervisor
Mestrado em Bioinformática e Biologia Computacional (Master)
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2024/09 - Current Algae and Plastic Pollution: A Computational Study on Enzyme-Based Biodegradation Mechanisms
Supervisor
Mestrado em Bioinformática e Biologia Computacional (Master)
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2024/09 - Current Development of a computational toolbox for data integration in environmental pathways analysis
Co-supervisor
Mestrado em Bioinformática e Biologia Computacional (Master)
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2024/09 - Current Leveraging Genomic Databases for Enhanced Identification and Therapeutic Strategies against Highly Infectious Viruses: A Comparative Study of HIV, Ebola, and SARS-CoV-2
Supervisor
Mestrado em Bioinformática e Biologia Computacional (Master)
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
2023/12 - Current Development of In Silico Simulation Protocols for Selective Inhibition of Voltage-Gate Sodium Channels
Co-supervisor
Doctoral Program in Sustainable Chemistry (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2023/10 - Current Machine Learning-Enhanced Optimization of Plastic-Degrading Enzymes for Sustainable Ocean Cleanup
Supervisor
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2023/10 - Current Designing Optimal 3D Enzyme Computational Models for Efficient Plastic Degradation
Supervisor
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2023/10 - Current Genomic Diversity and Zoonotic Potential of Hepatitis E Virus in European Rabbits: Implications for Diagnostic and Therapeutic Approaches
Supervisor
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2023/10 - Current Designing In-Silico Aptamers for Potential Use in Marine Bioremediation
Co-supervisor
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2022/10 - 2023/11/27 Identification of Rabbit Hemorrhagic Disease Virus using a Computational Approach
Supervisor
Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2022/10 - 2023/07/24 Improving a Database of Cyanobacterial Bioactive Compounds for Therapeutic Approaches in Human Diseases
Supervisor
Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2021/01/06 - 2021/12/03 An automatic algorithm to design primers for identification of highly infectious viruses using inter and intra-specific genome conservation scores
Supervisor
Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2019/10 - 2020/10/31 Improving the identification of species using intra- specific mitochondrial DNA information
Supervisor
Genética Forense (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Event organisation

Event name
Type of event (Role)
Institution / Organization
2023/07/31 - 2023/08/04 ALGAS MARINHAS – DA PRAIA AO LABORATÓRIO - CIIMAR - CENTRO INTERDISCIPLINAR DE INVESTIGAÇÃO MARINHA E AMBIENTAL (2023/07/31)
Workshop (Co-organisor)
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2012/06/21 - 2012/06/21 II PhD Forum - "Organizing principles: cell and tissue dynamics, from fundamental biology to disease" (2012/06/21 - 2012/06/21)
Meeting (Member of the Organising Committee)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal

Event participation

Activity description
Type of event
Event name
Institution / Organization
2024/02/01 - Current 6th European COZYME webinar
Seminar
6th European COZYME webinar
COST (European Cooperation in Science and Technology), Belgium
2024/11/13 - 2024/11/14 Workshop Oxford Nanopore Technologies (ONT)
Workshop
Workshop Oxford Nanopore Technologies (ONT)
Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal
2024/07/03 - 2024/07/05 Presentation of the master students (Bioinformatics and Computational Biology) thesis results in the Ciência 2024 - +Ciência para Uma Só Saúde e bem-estar global, July 3rd to 5th at the Centro de Congressos da Alfândega do Porto
Conference
Ciência 2024 - +Ciência para Uma Só Saúde e bem-estar global, July 3rd to 5th at the Centro de Congressos da Alfândega do Porto
University of Porto, Portugal

Fundação para a Ciência e a Tecnologia, Portugal

Ciência Viva, Portugal

Governo da República Portuguesa, Portugal
2024/05/08 - 2024/05/10 Presentation of the master students (Bioinformatics and Computational Biology) thesis results in the Encontro de Investigação Jovem da U.Porto (IJUP), 8-10 May 2024
Meeting
Encontro de Investigação Jovem da U.Porto (IJUP), 8-10 May 2024
Universidade do Porto Faculdade de Economia, Portugal
2024/03/21 - 2024/03/22 Presentation of the master students (Bioinformatics and Computational Biology) thesis results in the 20th Portugaliæ Genetica: DNA - Ancient and New 21-22 March 2024
Conference
The 20th Portugaliæ Genetica: DNA - Ancient and New 21-22 March 2024
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2024/03/14 - 2024/03/16 Presentation of the master students (Bioinformatics and Computational Biology) thesis results in the Bioinformatics Open Days XIII Edition 14-16 March 2024
Conference
Bioinformatics Open Days XIII Edition 14-16 March 2024
2023/10/19 - 2023/10/20 IV Encontro Internacional da Sociedade Portuguesa de Genética IV Encontro Internacional da Sociedade Portuguesa de Genética
Universidade do Minho, Portugal
2023/09/13 - 2023/09/13 Participation in the Blue Think Conference (BTC) 2023
Meeting
Blue Think Conference (BTC) 2023
CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2023/07/20 - 2023/07/20 LAGovírus emergentes na bacia do MEDiterrâneo: desenvolvimento e otimização de metodologias para deteção e controlo de agentes patogénicos
Meeting
LAGovírus emergentes na bacia do MEDiterrâneo
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
2023/07/06 - 2023/07/07 3rd European COZYME webinar
Seminar
3rd European COZYME webinar
COST (European Cooperation in Science and Technology), Belgium
2023/07/05 - 2023/07/07 The 2023 edition of the Science Meeting will be held on July 5, 6 and 7 in Aveiro, at the University Field of Santiago. It will be the first time that the event is held outside Lisbon, this time under the title "Science and the Ocean Beyond the Horizon", focusing on the ocean and waters.
Meeting
Science Meeting 2023: "Science and the Ocean Beyond the Horizon"
Universidade de Aveiro, Portugal
2022/03/24 - 2022/03/25 19th Portugaliæ Genetica - Phenotypic Manifestation of Genetic Heterogeneity
Conference
19th Portugaliæ Genetica - Phenotypic Manifestation of Genetic Heterogeneity
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2021/10/07 - 2021/10/08 e - Conference on Innovation in Microbial Control
Conference
e - Conference on Innovation in Microbial Control
Universidade do Porto Faculdade de Engenharia, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
2021/09/23 - 2021/09/24 Participation in the Blue Think Conference (BTC) - annual meeting organised by the Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) PhD Students Committee.
Meeting
Blue Think Conference 2021
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2019/12/04 - 2019/12/06 Attendance at TiBE 2019 - BIODIVERSITY, ECOLOGY AND EVOLUTION IN MEDITERRANEAN ECOSYSTEMS
Conference
Trends in Biodiversity and Evolution Conferences 2019
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
2019/11/14 - 2019/11/15 Presentation of the posters: “G-quadruplexes ares putatively involved in mtDNA rearrangements in Chordata” and “Improving the detection of mtDNA rearrangements using a fast and accurate algorithm”
Meeting
XV Encontro Nacional de Biologia Evolutiva
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2018/07/13 - 2018/07/13 MitoPorto - Mitochondrial evolution, metabolism and disease.
Symposium
International symposium - MitoPorto - Mitochondrial evolution, metabolism and disease.
Universidade do Porto, Portugal
2018/03/22 - 2018/03/23 18th Portugaliæ Genetica - Genetic Diversity in Structure and Regulation
Conference
18th Portugaliæ Genetica-Genetic Diversity in Structure and Regulation
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2017/05/26 - 2017/05/26 MitoPorto – Advances in Mitochondrial Research. Porto, Portugal
Symposium
MitoPorto – Advances in Mitochondrial Research.
Universidade do Porto, Portugal
2014/03/20 - 2014/03/21 16th Portugaliæ Genetica
Meeting
16th Portugaliæ Genetica
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2011/03/17 - 2011/03/18 14th Portugaliæ Genetica
Meeting
14th Portugaliæ Genetica - Models organisms: humans et al.
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2010/03/18 - 2010/03/19 13th Portugaliæ Genetica
Meeting
13th Portugaliæ Genetica
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2009/03/19 - 2009/03/20 12th Portugaliæ Genetica
Meeting
12th Portugaliæ Genetica
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2008/03/27 - 2008/03/28 11th Portugaliæ Genetica
Meeting
11th Portugaliæ Genetica
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2007/03/22 - 2007/03/24 10th Portugaliæ Genetica
Meeting
10th Portugaliæ Genetica
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2006/03/16 - 2006/03/18 9th Portugaliæ Genetica
Meeting
Portugaliae Genética 9ºedition: ¿Genes and Populations in Health and disease¿. IPATIMUP March 16, 17 and 18. 2006. Porto. Portugal.
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2005/03/17 - 2005/03/19 8th Portugaliæ Genetica - One Evolution, Four Modes of Inheritance
Meeting
One Evolution, Four Modes of Inheritance
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2023/11/27 Identification of Rabbit Hemorrhagic Disease Virus using a Computational Approach
Supervisor
Filipa Alexandra Tavares Carneiro (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2023/11/22 Understanding the Molecular Basis Behind Congenital Disorders of Glycosylation
(Thesis) Main arguer
Tiago André Cunha Oliveira (Master)
Escola Superior de Saúde do Politécnico do Porto, Portugal
2023/07/24 Improving a Database of Cyanobacterial Bioactive Compounds for Therapeutic Approaches in Human Diseases
Supervisor
Renato Jorge Sousa Soares (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2023/04/26 In Silico Identification of Protein Targets Associated to the Insecticide Activity of Natural Products
(Thesis) Main arguer
Maria Francisca Fernandes de Araújo (Master)
Universidade do Minho, Portugal
2021/12/03 An automatic algorithm to design primers for identification of highly infectious viruses using inter and intra-specific genome conservation scores
Supervisor
André Rafael Ferreira (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2015/12/14 In vitro detection of non-canonical mitochondrial DNA conformations
(Thesis) Main arguer
João Pedro Silva Monteiro (Master)
Universidade do Porto Faculdade de Ciências, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2023/10/24 - Current BMC genomics (ISSN: 1471-2164) Springer Nature
2023/07 - Current Scientific Reports (Sci Rep) ( 2045-2322) Springer Nature
2023/01 - Current Biofouling journal (1029-2454) Taylor and Francis

Committee member

Activity description
Role
Institution / Organization
2023/10 - Current Committee for Blue Biotechnology, Environment, and Health Seminars at CIIMAR
Member
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Consulting

Activity description Institution / Organization
2020/05/14 - Current Metatranscriptomes analysis in the project Vírus4Health (monitor the presence of SARS-CoV-2 in wastewater). Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2024/05/17 - 2024/05/17 Master Students Workshop UIDB_(COB) - Posters and graphical abstract design Posters and graphical abstract design (Outros) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2024/04/05 - 2024/04/05 Master Students Workshop UIDB_(COB) - Computational Enzyme optimization - Workshop using computational tools for enzyme optimization and machine learning models. Enzyme kinetics, reaction mechanisms, and the use of computational tools like machine learning to predict and enhance enzyme activity. (Outros) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2024/01/15 - 2024/01/15 Master Students Workshop UIDB_(COB) - Machine Learning Models Workshop using computational tools for data analysis. (Outros) CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Evaluation committee

Activity description
Role
Institution / Organization Funding entity
2020/06 - 2020/07 BYT PhD Jury Evaluation - 2020 (graduate program that immerses you in high level original research and rigorous scientific learning for a full doctorate at CIIMAR)
Evaluator
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2020/04/30 Interview Agência Lusa "Ferramenta criada na U.Porto pode melhorar deteção do SARS-CoV-2" Agência Lusa

Interview (tv / radio show)

Program Topic
2017/04/04 - Current Antena 1 Interview for Antena 1 regarding EbolaID database.

Mentoring / Tutoring

Topic Student name
2021/05/31 - 2021/06/18 "Development of a Classification Model for the Identification of Targets to Known P.aeruginosa Biofilm Formation Inhibitors" Rita Prata Barbedo Magalhães

Other jury / evaluation

Activity description Institution / Organization
2022/07/13 - 2022/07/13 Jury of the defense exams for the course project in Medicinal Biotechnology Escola Superior de Saúde do Politécnico do Porto, Portugal
2021/02/10 - 2021/02/10 Meeting-interview referring to the development of the work of student Cláudia Tatiana Freitas Vieira, from the Doctoral Program in Biomedicine, Faculty of Medicine of the University of Porto. Universidade do Porto Faculdade de Medicina, Portugal
2018/10/30 - 2018/10/30 Avaliação do trabalho desenvolvido no Ano Probatório do aluno de doutoramento / Evaluation of the work developed in the Probationary Year of the doctoral student João Pedro Silva Monteiro: "Dissecting the mitochondrial DNA replisome of Neurospora crassa". Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2018/10/30 - 2018/10/30 Avaliação do trabalho desenvolvido no Ano Probatório da aluna de doutoramento / Evaluation of the work developed in the Probationary Year of the doctoral student Filipa Isabel Menezes Moreira: "Unravelling the role of topoisomerases in mitochondrial DNA rearrangements". Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal