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I hold a Master of Science degree in Biomedical Engineering from Instituto Superior Técnico (IST) and I am currently completing the first year of the Doctoral Program in Biomedical Engineering at the same institution. During my master’s degree, I majored in Regenerative Medicine and Tissue Engineering, while also pursuing topics such as bioinformatics, machine learning and algorithms and their applications to biomedical research. The combination of these two areas of expertise was the foundation of my master’s thesis project entitled “Unsupervised machine learning approaches for whole transcriptome analysis of human pluripotent stem cell differentiation into cardiomyocytes”. This thesis, graded 19/20, presented a novel methodology, comprising several unsupervised learning algorithms, to study the transcriptomic changes of stem cell cardiac differentiation, from a whole transcriptome point of view. This work is now published in Scientific Reports, a peer-reviewed open-access journal from the Nature Portfolio. Beyond these achievements, my master's thesis was developed in the scope of the FCT-funded project SMART, a collaboration between the Pattern and Image Analysis Group (PIA-Lx) from IT – Instituto de Telecomunicações, and the Stem Cell Engineering Research Group of Institute for Bioengineering and Biosciences (iBB-SCERG). From September 2022 to August 2023, while I was a researcher in the PIA group, I incorporated pseudotime analysis in the unsupervised workflow for transcriptome analysis from my master. This work gave rise to the publication of a peer-reviewed full paper in the International Joint Conference on Biomedical Engineering Systems and Technologies and an oral presentation at the co-located Conference on Bioinformatics Models, Methods and Algorithms. Since November 2023 I have been a researcher of the SCERG-iBB team. My focus is to improve the unsupervised whole transcriptome analysis tool so that it can be used for a wider range of applications. This led me to dive into the field of cellular agriculture, broadening even further my knowledge. During the past year, I embraced the challenge of being a teaching assistant for the Introduction to Biomedical Engineering and Machine Learning in Bioengineering courses. My roles are to teach practical classes about clustering and biomedical data analysis and propose and supervise course projects. Through this experience, I improved my communication skills and helped Regenerative Medicine, Biomedical and Biological Engineering students apply machine learning algorithms to study gene expression data from real-world problems. Besides developing technical and scientific skills during my studies I interned at the Gastroenterology and Hepatology Service at Hospital de Santa Maria, where I was able to be in close contact with healthcare professionals and patients, following the process of diagnosis and treatment up close. Being passionate about communication, I was an IST ambassador. My role as ambassador was to help and guide potential IST undergraduate candidates in getting to know the institution and the courses it offers. To diversify my range of knowledge, I participated in the IST management challenge - Best of Class edition sponsored by EDP and conquered third place in this management competition thus securing the sponsorship of STAPLES to compete in the Global Management Challenge.
Identificação

Identificação pessoal

Nome completo
Sofia de Pinto e Lobo da Silva Agostinho

Nomes de citação

  • Agostinho, Sofia P.
  • Sofia, Agostinho

Identificadores de autor

Ciência ID
F415-77C3-CB7B
ORCID iD
0000-0002-7254-7916

Endereços de correio eletrónico

  • sofia.p.agostinho@tecnico.ulisboa.pt (Profissional)

Moradas

  • Instituto de Telecomunicações (IT), Av. Rovisco Pais 1, Torre Norte Piso 10, 1049-001, Lisboa, Lisboa, Portugal (Profissional)
  • iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Lisboa, Portugal (Profissional)

Websites

Domínios de atuação

  • Ciências da Engenharia e Tecnologias

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português (Idioma materno)
Inglês Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Formação
Grau Classificação
2023/09/13 - 2027/09/13
Em curso
Programa Doutoral em Engenharia Biomédica (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09/01 - 2023/08/31
Concluído
Diploma de Formação Avançada em Metodologias e Técnicas de Investigação Científica (Pós-Graduação)
Universidade de Lisboa Instituto Superior Técnico, Portugal
20/20
2022/07/01
Concluído
Engenharia Biomédica (Mestrado)
Especialização em Regenerative Medicine and Tissue Engineering
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Unsupervised machine learning approaches for whole transcriptome analysis of human pluripotent stem cell differentiation into cardiomyocytes" (TESE/DISSERTAÇÃO)
17/20
2022/03/01
Concluído
Machine Learning, Maths & Ethics: Hands-on (MOOC Tecnico course) (Outros)
Universidade de Lisboa Instituto Superior Técnico, Portugal
95%
2021/03/05
Concluído
Epigenetics: Foundations (MOOC Tecnico course) (Outros)
Universidade de Lisboa Instituto Superior Técnico, Portugal
91%
2017/09/05 - 2020/07/15
Concluído
Ciências de Engenharia - Engenharia Biomédica (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
14/20
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento
Empregador
2023/11/01 - 2024/08/31 Investigador (Investigação) Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2022/09/01 - 2023/08/31 Investigador (Investigação) Instituto de Telecomunicações Lisboa, Portugal
Instituto de Telecomunicações Lisboa, Portugal
(...)
Projetos

Bolsa

Designação Financiadores
2023/11/01 - 2024/08/31 VitaminSea
22-CM-PT-DG-1-317
Bolseiro de Investigação
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2022/09/01 - 2024/06/30 SMART - New technologies for Stem cell Manufacturing bioprocess monitoring and ARTificial intelligence-based modeling
PTDC/EQU-EQU/3853/2020
Bolseiro de Investigação
Instituto de Telecomunicações Lisboa, Portugal

Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
Produções

Publicações

Artigo em conferência
  1. Agostinho, Sofia P.; Cabral, Joaquim; Fred, Ana; Rodrigues, Carlos. Autor correspondente: Agostinho, Sofia P.. "Unsupervised Cardiac Differentiation Stage Portraying and Pseudotime Mapping Based on Gene Expression Data". Trabalho apresentado em International Joint Conference on Biomedical Engineering Systems and Technologies, 2023.
    Publicado • 10.5220/0011892200003414
Artigo em revista
  1. Agostinho, Sofia P.; Branco, Mariana A.; Nogueira, Diogo E.S.; Diogo, Maria Margarida; Joaquim M.S. Cabral; Rodrigues, Carlos A.V.. Autor correspondente: Agostinho, Sofia P.. "Unsupervised Analysis of Whole Transcriptome Data from Human Pluripotent Stem Cells Cardiac Differentiation". Scientific Reports 14 3110 (2024): https://www.nature.com/articles/s41598-024-52970-z.
    Acesso aberto • Publicado • https://doi.org/10.1038/s41598-024-52970-z
Poster em conferência
  1. Agostinho, Sofia P.; Joaquim M.S. Cabral; Ana L. N. Fred; Carlos A. V. Rodrigues. Autor correspondente: Agostinho, Sofia P.. "Unsupervised Analysis of Whole Transcriptome Data from Pluripotent Stem Cells". Trabalho apresentado em III iBB WORKSHOP, 2023.
  2. Agostinho, Sofia P.; Joaquim M.S. Cabral; Ana L. N. Fred; Carlos A. V. Rodrigues. Autor correspondente: Agostinho, Sofia P.. "Unsupervised Analysis of Whole Transcriptome Data from Pluripotent Stem Cells". Trabalho apresentado em 1st International Conference of the Portuguese Association for Cellular Agriculture, 2023.
  3. Agostinho, Sofia P.; Branco, Mariana A.; Nogueira, Diogo E.S.; Diogo, Maria Margarida; Joaquim M.S. Cabral; Ana L. N. Fred; Carlos A. V. Rodrigues. "Unsupervised machine learning for whole transcriptome analysis of pluripotent stem cells cardiac differentiation". Trabalho apresentado em 2nd iBB Workshop, 2022.
Tese / Dissertação
  1. "Unsupervised machine learning approaches for whole transcriptome analysis of human pluripotent stem cell differentiation into cardiomyocytes". Mestrado, Universidade de Lisboa Instituto Superior Técnico, 2022. https://fenix.tecnico.ulisboa.pt/cursos/mebiom21/dissertacao/846778572214169.
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2023/02/16 Unsupervised Cardiac Differentiation Stage Portraying and Pseudotime Mapping Based on Gene Expression Data 14th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2023)
NSTICC - Institute for Systems and Technologies of Information, Control and Communication (Lisbon, Portugal)

Participação em evento

Descrição da atividade
Tipo de evento
Nome do evento
Instituição / Organização
2024/06/10 - 2024/06/14 Accepted for the Advanced Training Program Systems biology: from large datasets to biological insight at EMBL-EBI
Outro
Systems biology: from large datasets to biological insight
European Bioinformatics Institute, Reino Unido
2023/11/13 - 2023/11/13 Poster presentation and participation at the III iBB Workshop. This event, which gathered all the iBB research groups, included presentations of the current research being undertaken at the research units, several keynote lectures, an alumni session and, a round table on "What is the vision for the future of iBB regarding funding opportunities, career development and links within i4HB".
Oficina (workshop)
III iBB WORKSHOP
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2023/09/07 - 2023/09/08 Poster presentation at the inaugural International Conference of CellAgri Portugal. This conference took place at the International Iberian Nanotechnology Laboratory in Braga and the main goal was to foster and encourage the collaborative development of cellular agriculture within Portugal, while also sharing the latest scientific and innovative advancements related to cellular agriculture products, such as cultivated meat, fish, milk, collagen, leather, fur, wool, and hair, both nationally and internationally.
Conferência
1st International Conference of the Portuguese Association for Cellular Agriculture
International Iberian Nanotechnology Laboratory, Portugal
2023/02/22 - 2023/02/24 Attended the 12th International Conference on Pattern Recognition Applications and Methods (ICPRAM 2023) as Conference Delegate. The International Conference on Pattern Recognition Applications and Methods is a major point of contact between researchers, engineers and practitioners in the areas of Pattern Recognition and Machine Learning, both from theoretical and application perspectives.
Conferência
12th International Conference on Pattern Recognition Applications and Methods (ICPRAM 2023)
Instituto Para Os Sistemas e Tecnologias de Informação Controlo e Comunicação, Portugal
2023/02/16 - 2023/02/18 Attended the 16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC23). The purpose of BIOSTEC is to bring together researchers and practitioners, including engineers, biologists, health professionals and informatics/computer scientists, interested in both theoretical advances and applications of information systems, artificial intelligence, signal processing, electronics and other engineering tools in knowledge areas related to biology and medicine.
Conferência
16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC23)
Instituto Para Os Sistemas e Tecnologias de Informação Controlo e Comunicação, Portugal
2022/12/19 - 2022/12/19 The i4HB kick-off meeting took place on 19th December gathering researchers from the 3 units that integrate the associate laboratory, Institute for Bioengineering and Biosciences (iBB), Institute for System Engineering and Computers-Microsystems and Nanotechnologies (INESC.MN) and Applied Biomolecular Sciences Unit (UCIBIO). The program of the meeting included sessions about the i4HB Thematic Lines, scientific flash presentations with discussion, a round table session dedicated to career development, poster sessions and time for networking
Encontro
i4HB Kick-off Meeting
Institute for Health and Bioeconomy (i4HB), Portugal
2022/09/23 - 2022/09/23 Poster presentation and participation at the 2nd iBB Workshop. This event, which gathered the four iBB research groups, included presentations of the current research being undertaken at the research units, several keynote lectures, a round table on challenges in health and bioeconomy, and a career development session.
Conferência
2nd iBB Workshop
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2022/07/12 - 2022/07/14 Attended the 3rd International Conference on Deep Learning Theory and Applications (DeLTA 2022) as Conference Delegate. This conference focuses in Deep Learning and Big Data Analytics, the two major topics of data science nowadays, and Machine-Learning and Artificial Intelligence which are pervasive in most real-world applications scenarios.
Conferência
3rd International Conference on Deep Learning Theory and Applications (DeLTA 2022)
Instituto Para Os Sistemas e Tecnologias de Informação Controlo e Comunicação, Portugal

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2023/09/11 - 2023/12/28 Machine Learning in Bioengineering Mestrado em Engenharia Biomédica (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/05/01 - 2023/06/30 Introdução à Engenharia Biomédica Licenciatura em Engenharia Biomédica (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal

Tutoria

Tópico Nome do aluno
2023/09/21 - Atual Master thesis entitled "New strategies for biosurfactant bioprocess monitoring and control using machine learning" Carolina Alexandra Jorge Vares
2023/09/15 - Atual Master thesis entitled "Analysis of transcriptomic data from stem cell differentiation in bioreactors using Machine Learning" Afonso Nuno Ribeiro da Silva Mangas Reis
2022/12/19 - 2023/11/14 Master thesis entitled "An integrated Unsupervised Machine Learning Workflow for Transcriptome Analysis: A Case study in Cardiac Differentiation" Inês Sofia Martins Pereira Soares
2023/09/11 - 2023/11/10 Course Project on Gene Expression Data for Brain Region Classification Inês Brites, Inês Marques, Sofia Rebola, Tomás Talento
2023/09/11 - 2023/11/10 Course Project on Prediction of Human Induced Pluripotent Stem Cell Cardiac Differentiation Outcome Pelin Akça, Elena Knollhuber, Robert Spornraft
2023/09/11 - 2023/11/10 Course Project on Classification of Human Pluripotent Stem Cell Cardiac Differentiation Outcome Carolina Vares, Miguel Leonardo, Oriana Pinto
2023/09/11 - 2023/11/10 Course Project on Characterization of brain regions through gene expression data using different clustering methods Isabel Campagnolo, Bernardo Baptista, Cristiana Violante, João Flor
2023/09/11 - 2023/11/10 Course Project on Gene Expression Data for Brain Region Classification Constança Pinto, Inês Castelhano, Margarida Carvalho, Teresa Porqueddu
2022/10/05 - 2022/11/11 Course Project on Gene Selection vs. Feature Extraction for Time Series Cardiomyocyte Differentiation RNA-seq Beatriz Fernandes, Inês Martins, Miguel Amil, Inês Silva
2022/10/03 - 2022/11/11 Course Project on Using gene expression data for brain region classification: Analysis of different classification techniques Augusto Marques, Carolina Cruz, Laura Quintas, Teresa Ribeiro
2022/10/03 - 2022/11/11 Course Project on Supervised Learning Approaches For COVID-19 Severity Prediction Maria Inês Neves, Matilde Lopes, Beatriz Carvalho, André Carneiro
2022/10/03 - 2022/11/11 Course Project on Clustering Analysis of Brain Gene Samples Paola de Gouveia, Marta Serra, Ricardo Amaral, Sara Sebastião
2022/10/03 - 2022/11/11 Course Project on Unsupervised Analysis of Gene Signatures for Cardiomyocyte Differentiation Derived From hiPSCs and hESCs Ana Rita Varela, Ana Matilde Silvano, Diogo Engrácia
Distinções

Prémio

2018 3rd Place at the IST Management Challenge - Best of Class Edition
Instituto Superior Técnico Departamento de Engenharia e Gestão, Portugal

EDP, Portugal