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João A. I. Miranda is a PhD candidate in Biochemistry/Systems Biology at BioISI, Faculdade de Ciências, Universidade de Lisboa (FCUL). At the RNA Systems Biology Lab, BioISI, he has been researching cancer biology using computational approaches, including network science, mathematical modelling, and machine learning. More recently, he was contracted as a research trainee within the scope of the project “SKINDEV: Skin Microbial Devices” at FCUL, with the aim of developing a mathematical model of Cutibacterium acnes metabolism. He was the recipient of a research grant within the scope of the project FAIRification of YEASTRACT+ to Support Yeast-based Bioeconomy and Health at INESC-ID Lisboa. During 2024, he lectured mathematical modelling and analysis of gene regulatory networks as a teaching assistant at FCUL. His most recent work entitled “When neighbours play a role: a systems-level analysis of protein interactions conditioning cancer driver mutation effects” was recently published in the Proceedings of the National Academy of Sciences (PNAS). He has an MSc degree in Biochemistry and Biomedicine.
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Identification

Personal identification

Full name
João André Isidoro Miranda

Author identifiers

Ciência ID
B915-D668-DF0C
Scopus Author Id
59126128900

Knowledge fields

  • Natural sciences - Biological Sciences - Biochemistry
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences - Molecular Biology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Upper intermediate (B2) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2024/11 - 2028
Ongoing
 Bioquímica (Doutoramento)
Major in Biologia de Sistemas
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2023
Concluded
 Bioquímica e Biomedicina (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Understanding Metastasis Organotropism Patterns Through Within-cell and Between-cells Molecular Interaction Networks" (THESIS/DISSERTATION)
 19
2020
Concluded
 Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
 16
Affiliation

Science

Category
Host institution 		Employer
2025/10/16 - Current Research Trainee (Research) FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
2024/12/01 - 2025/09/30 Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2023 - 2024 Research Trainee (Research) Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2024/02/01 - 2024/07/31 Invited Assistant (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa, Portugal
Projects

Grant

Designation Funders
2024/12/01 - 2025/09/30 FAIRY - FAIRification of YEASTRACT+ to Support Yeast-based Bioeconomy and Health
GRANT AGREEMENT 101129751
Integration into Research Grant Fellow

Contract

Designation Funders
2025/10/16 - Current SKIN MICROBIAL DEVICES (SKINDEV)
10062857
Researcher
UK Research and Innovation
Outputs

Publications

Conference abstract
  1. Vital, Márcia; Miranda, João A. I.; CARROLO, Margarida; António Quintela; Francisco R. Pinto. "The Neighbour Effect: How Interacting Proteins Influence Driver Mutations and Cancer Patient Outcomes". Paper presented in Bioinformatics Open Days 2025, XIV Edition, Braga, 2025.
    Published
  2. Vital, Márcia; Miranda, João A. I.; CARROLO, Margarida; António Quintela; Francisco R. Pinto. Corresponding author: Francisco R. Pinto. "When neighbours play a role: The importance of interacting proteins in the tumorigenic effect of cancer driver genes". Paper presented in V International Congress in Health Sciences Research 2025: From molecule to community, Covilhã, 2025.
    Published
  3. Vital, Márcia; Miranda, João A. I.; CARROLO, Margarida; Francisco R. Pinto. Corresponding author: Vital, Márcia. "Identification of tissue specific dependencies between cancer driver gene mutations and their interactors abundances". Paper presented in XII National Congress of Biochemistry, Aveiro, 2024.
  4. Miranda, João A. I.; CARROLO, Margarida; Francisco R. Pinto; António Quintela. Corresponding author: Miranda, João A. I.. "Understanding Metastasis Organotropism Patterns Through Within-cell and Between cells Molecular Interaction Networks". Paper presented in Champalimaud Research Symposium: The Ecology of Cancer—understanding and targeting cancer-host interactions, Lisboa, 2024.
  5. Miranda, João A. I.; Francisco R. Pinto. Corresponding author: Miranda, João A. I.. "Understanding Metastasis Organotropism Patterns Through Within-cell and Between-cells Molecular Interaction Networks". Paper presented in 13th EMBO Young Scientists’ Forum, Lisboa, 2023.
  6. M. Carrolo; J.A.I. Miranda; A.F.R. Coelho; A. Quintela; F.R. Pinto. "57P Metastasis organotropism: Unveiling associated proteins using network biology". 2023.
    10.1016/j.annonc.2023.09.1558
  7. CARROLO, Margarida; Guilherme Vilhais; Miranda, João A. I.; Francisco R. Pinto; António Quintela. "Cavitating pulmonary metastases associated with improved survival in pancreatic ductal adenocarcinoma cancer patients". Paper presented in 20º Congresso Nacional de Oncologia, Estoril, 2023.
    Published
  8. Filipa V.M.A. Pereira; Miranda, João A. I.; Alexandre F.R. Coelho; Fiviano L. Santos; Paulo R.C. Lopes; CARROLO, Margarida; Francisco R. Pinto. Corresponding author: Francisco R. Pinto. "Exploring cancer tissue specificities through protein physical interaction networks". Paper presented in 8th International Iberian Biophysics Congress, Bilbao, 2022.
    Published
Journal article
  1. João A. I. Miranda; Márcia F. S. Vital; Margarida Carrolo; António Quintela; Francisco R. Pinto. "When neighbors play a role: A systems-level analysis of protein interactions conditioning cancer driver mutation effects". Proceedings of the National Academy of Sciences (2025): https://doi.org/10.1073/pnas.2501925122.
    10.1073/pnas.2501925122
  2. Carrolo, Margarida; Miranda, Joao A. I.; Vilhais, Guilherme; Quintela, Antonio; Fontes e Sousa, Mario; Costa, Diogo Alpuim; Pinto, Francisco R.. "Metastatic organotropism: a brief overview". Frontiers in Oncology (2024): https://publons.com/wos-op/publon/66061957/.
    10.3389/FONC.2024.1358786
  3. M. Carrolo; M. Vital; J. Miranda; A. Quintela; F. Pinto. "71P When neighbors play a role: The importance of interacting proteins in the tumorigenic effect of cancer driver genes". ESMO Open (2024): https://publons.com/wos-op/publon/71333603/.
    10.1016/J.ESMOOP.2024.103815
Preprint
  1. Márcia FS Vital; João AI Miranda; Margarida Carrolo; António Quintela; Francisco R Pinto. "When neighbours play a role: a systems-level analysis of protein interactions conditioning cancer driver mutation effects". 2025. https://doi.org/10.1101/2025.01.18.633728.
    10.1101/2025.01.18.633728
Thesis / Dissertation
  1. "Understanding Metastasis Organotropism Patterns Through Within-cell and Between-cells Molecular Interaction Networks". Master, Universidade de Lisboa Faculdade de Ciências, 2023. http://hdl.handle.net/10451/60536.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2025/03/26 The Neighbour Effect: How Interacting Proteins Influence Driver Mutations and Cancer Patient Outcomes Bioinformatics Open Days 2025, XIV Edition
University of Minho, Gualtar Campus (Braga, Portugal)
2025/03/21 When neighbours play a role: The importance of interacting proteins in the tumorigenic effect of cancer driver genes V International Congress in Health Sciences Research 2025: From molecule to community
RISE-Health@UBI (Covilhã, Portugal)
2023/07/13 Understanding Metastasis Organotropism Patterns Through Within-cell and Between-cells Molecular Interaction Networks 3rd Chem&Biochem Students Meeting
Faculdade de Ciências da Universidade de Lisboa - Departamento de Química e Bioquímica (Lisboa, Portugal)

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2024/02/22 - 2024/07/31 Bioquímica Experimental IV Bioquímica (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
Distinctions

Award

2023 Best Flash Pitch Communication at the 3rd Chem&Biochem Students Meeting
Universidade de Lisboa Faculdade de Ciências, Portugal