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Francisca Gaspar Vieira is a ELLIS PhD student at Heidelberg University, advised by Dr. Britta Velten (Centre for Organismal Studies, Heidelberg University) and co-advised by Dr. Julio Saez-Rodriguez (EMBL's European Bioinformatics Institute). Francisca is a fellow member of the PhD program of the European Laboratory for Learning and Intelligent Systems (ELLIS) and of the Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp), where she is developing statistical methods and computational tools for the inference and comparison of perturbation responses from single-cell CRISPR screens across different biological contexts with a particular focus on time course data. Francisca holds an Integrated Master’s degree in Biological Engineering and a second Master's degree in Computational Biology and Bioinformatics. In her first master’s thesis, she spent six months in the Laboratory of Gene Technology in KU Leuven investigating bacteriophage genomics and biocontrol, while during the second master’s thesis she explored multi-omics integration and classification of glioma types. Francisca was also a researcher at NOVA School of Science and Technology, NOVA University of Lisbon, where she aimed to identify the biomolecular mechanisms and processes driving human disease, discover new therapeutic targets, perform patient stratification, predict patient outcomes and optimize early detection, by studying and developing cutting-edge machine learning and statistical tools.
Identification

Personal identification

Full name
Francisca Manuel Gaspar Vieira

Citation names

  • Francisca G. Vieira

Author identifiers

Ciência ID
5612-F0EA-BE7E
ORCID iD
0000-0002-9767-4356
Google Scholar ID
vOar1y4AAAAJ&hl
Scopus Author Id
58246152500

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Mathematics - Statistics and Probability

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Elementary (A2) Elementary (A2) Elementary (A2) Elementary (A2) Elementary (A2)
German Elementary (A2) Elementary (A2) Elementary (A2) Elementary (A2) Elementary (A2)
Education
Degree Classification
2024/09 - 2027
Ongoing
Bioinformatics (Doktor (PhD))
Universität Heidelberg Centre for Organismal Studies, Germany
2021/09 - 2023/11/13
Concluded
Biologia Computacional e Bioinformática (Mestrado integrado)
Major in Biosystems Simulation for Life and Health Sciences
Universidade Nova de Lisboa, Portugal
"Unveiling Novel Glioma Biomarkers through Multi-omics Integration and Classification" (THESIS/DISSERTATION)
20
2016/09 - 2021/11
Concluded
Engenharia Biológica (Mestrado integrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Genomic Characterization of Three Novel Acidovorax Phage Genera and Their Potential in Phage Biocontrol " (THESIS/DISSERTATION)
17
Affiliation

Science

Category
Host institution
Employer
2024/09 - Current Researcher (Research) Universität Heidelberg Centre for Organismal Studies, Germany
2023/08/01 - 2024/07/31 Research Assistant (Research) Universidade Nova de Lisboa Unidade de Investigação e Desenvolvimento em Engenharia Mecânica e Industrial, Portugal
2022/07/15 - 2022/10/15 Research Assistant (Research) Universidade Nova Centro de Matemática e Aplicações, Portugal
2020/03 - 2020/06 Research Trainee (Research) Universidade de Lisboa Computer and Robot Vision Laboratory, Portugal

Others

Category
Host institution
Employer
2023/06/01 - Current Member of PerMediK Action European Cooperation in Science and Technology, Belgium
2023/01/01 - 2023/08/01 Programming Teacher Algorithmics Lisbon - Programming School, Portugal
2022/10/01 - 2023/01/01 Machine Learning Instructor TreeTree2, Portugal
Projects

Grant

Designation Funders
2023/08/01 - Current OMICs approaches to reveal the anticancer properties of Virgin Olive Oil
Research Fellow
Fundação para a Ciência e a Tecnologia
2022/07 - 2022/10 ARTIFICIAL INTELLIGENCE ON THE MANAGEMENT OF THE DEGREE OF READINESS IN URBAN FIREFIGHTING
Research Fellow
Universidade Nova Centro de Matemática e Aplicações, Portugal
Fundação para a Ciência e a Tecnologia

Contract

Designation Funders
2023/01 - 2024/02 Multi-omic networks in gliomas
Researcher
Fundação para a Ciência e a Tecnologia
Outputs

Publications

Journal article
  1. Dominique Holtappels; Francisca G. Vieira; Marleen Voet; Marta Vallino; Johan Van Vaerenbergh; Rob Lavigne; Jeroen Wagemans. "Characterization of four Acidovorax phages and their potential in phage biocontrol for lambs lettuce seed decontamination". Microbiology Spectrum 0 0 (2024): e00993-24. https://journals.asm.org/doi/abs/10.1128/spectrum.00993-24.
    10.1128/spectrum.00993-24
  2. Francisca G Vieira; Regina Bispo; Marta B Lopes. "Integration of Multi-Omics Data for the Classification of Glioma Types and Identification of Novel Biomarkers". Bioinformatics and Biology Insights 18 (2024): 11779322241249563-11779322241249563. https://doi.org/10.1177/11779322241249563.
    10.1177/11779322241249563
  3. Regina Bispo; Francisca G. Vieira; Clara Yokochi; Filipe J. Marques; Pedro Espadinha-Cruz; Alexandre Penha; António Grilo. "Using spatial point process models, clustering and space partitioning to reconfigure fire stations layout". International Journal of Data Science and Analytics (2023): http://dx.doi.org/10.1007/s41060-023-00455-z.
    10.1007/s41060-023-00455-z
  4. Bispo,R.; Francisca G. Vieira; Nádia Bachir; Pedro Espadinha-Cruz; José Pedro Lopes; Alexandre Penha; Filipe J. Marques; António Grilo. "Spatial modelling and mapping of urban fire occurrence in Portugal". Fire Safety Journal (2023): 103802-103802. http://dx.doi.org/10.1016/j.firesaf.2023.103802.
    10.1016/j.firesaf.2023.103802
Preprint
  1. Francisca G. Vieira; Regina Bispo; Marta B. Lopes. "Integration of Multi-omics Data for the Classification of Glioma Types and Identification of Novel Biomarkers". 2023. https://doi.org/10.1101/2023.12.22.572983.
    10.1101/2023.12.22.572983
Thesis / Dissertation
  1. "Unveiling Novel Glioma Biomarkers through Multi-omics Integration and Classification". Master, Universidade Nova de Lisboa, 2023. http://hdl.handle.net/10362/160879.
  2. "Genomic Characterization of Three Novel Acidovorax Phage Genera and Their Potential in Phage Biocontrol". Master, Universidade de Lisboa Instituto Superior Técnico, 2021. https://fenix.tecnico.ulisboa.pt/cursos/mebiol/dissertacao/1972678479054999.

Other

Other output
  1. Using spatial point process models, clustering and space partitioning to reconfigure fire stations layout. 2023. Bispo, R.; Vieira, F.G.; Yokochi, C.; Marques, F.J.; Espadinha-Cruz, P.; Penha, A.; Grilo, A.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85166952869&partnerID=MN8TOARS.
    10.21203/rs.3.rs-3170443
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/10/12 Classification and Survival Analysis of Multi-Omics Data for the Identification of Novel Diagnostic and Prognostic Biomarkers in Glioma XXVI Congress of the Portuguese Statistical Society
Portuguese Statistical Society (Guimarães, Portugal)
2023/03/13 Integration of Multi-omics Data for the Classification of Glioma Subtypes and Identification of Novel Biomarkers. XII Edition of the Bioinformatics Open Days
University of Minho (Braga, Portugal)

Event organisation

Event name
Type of event (Role)
Institution / Organization
2020 - 2021 Organization of the program "CoLab Sessions": program of semiannual internships for higher education students. (2020 - 2021)
Workshop (Member of the Organising Committee)
IEEE-IST Engineering in Medicine and Biology Society, Portugal

Event participation

Activity description
Type of event
Event name
Institution / Organization
2024/10/07 - 2024/10/11 Participation in Romberg Course by Dr. Tiangang Cui (University of Sydney): The overall aim of this course was to study matrix computations that lie at the core of a wide variety of applications in machine learning and data science: Introduction to the mathematical theory of computational linear algebra, including methods for solving linear systems of equations, least-squares problems, eigenvalue problems, and other matrix decompositions.
Workshop
Romberg Course: Computational Linear Algebra for Machine Learning
Universität Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Germany
2024/09/09 - 2024/09/11 The HGS MathComp Annual Retreat features workshops to improve academic practice and chances for Fellows to present their current research. Workshops attended: Effective Software Testing; Career Development, SAP Coding Interview.
Meeting
HGS MathComp Annual Retreat 2024
Universität Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Germany
2024/02/06 - 2024/02/09 Attendance of the international "OLISSIPO School on Mathematical modelling of inter-cell and communities interactions with a focus on metabolism". Lecturers: Prof. Jörg Stelling (ETH Zürich), Prof. Jürgen Zanghellini (University of Vienna), Prof. Kiran Patil (University of Cambridge), Prof. Steffen Klamt (Max Planck Institute for Dynamics of Complex Technical Systems).
Workshop
OLISSIPO School on Mathematical modelling of inter-cell and communities interactions with a focus on metabolism
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2023/10/11 - 2023/10/14 Participation in the Workshop "Joint Models for Longitudinal and Survival Data" by Pedro Miranda Afonso (Erasmus Medical Center Rotterdam): Introduction of joint analysis of longitudinal and survival data and practical examples using the R library JMbayes2.
Workshop
Joint Models for Longitudinal and Survival Data
Universidade do Minho, Portugal

Sociedade Portuguesa de Estatística, Portugal
2023/09/14 - 2023/09/16 Attendance of the international "Training School for Big Data collection, handling, Bioinformatics tools for Big data Analysis", in Athens, Greece, with a fully funded grant/scholarship by COST (European Cooperation in Science and Technology).
Workshop
Training School for Big Data collection, handling, Bioinformatics tools for Big data Analysis
2023/07/05 - 2023/07/13 Participation in the workshop entitled "Bioinformatics tools for multi-omics analysis", by Sonia Tarazona (Universitat Politècnica de València): Estimation of statistical power in multi-omics studies and generation of multi-omics regulatory networks for gene expression.
Workshop
NOVAMATH Thematic Weeks 2023 - Mathematical Models in Health
Universidade Nova Centro de Matemática e Aplicações, Portugal
2023/05/11 - 2023/05/12 Participation in the Workshop: "Single-Cell", by Donnacha Fitzgerald, Hosna Baniadam, Harald Vöhringer, Petr Smirnov (EMBL): The aim of this workshop was to introduce single-cell (including multi-omic and spatial) methods, what can be achieved with them and principles for their analysis.
Workshop
OLISSIPO Workshop - EMBL Training: Single-Cell
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

European Molecular Biology Laboratory, Germany
2023/05/10 - 2023/05/10 Participation in the Workshop: "Drug Synergy", by Petr Smirnov (EMBL): Introduced the fundamental concepts behind analysing drug combination experiments on immortalised cancer cell lines; discussed common models for assessing drug synergy, and introduced R/Bioconductor tools implementing these methods. A hands-on analysing public drug combination data was included.
Workshop
OLISSIPO Workshop - EMBL Training: Drug Synergy
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

European Molecular Biology Laboratory, Germany
2023/04/27 - 2023/04/27 Participation in the OLISSIPO Workshop: "Decoding the genome with deep learning", Bernardo Almeida (University of Vienna): Training and interpretation of deep learning models to predict regulatory activities and gene expression from DNA sequences.
Workshop
OLISSIPO Workshop: Decoding the genome with deep learning
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2023/03/18 - 2023/03/18 Participation in the Workshop: "The Importance of Machine Learning in Structural Biology", by Irina Moreira, Catarina Marques-Pereira and Luana Afonso (University of Coimbra): Training and evaluating different machine learning and deep learning models with structural biology data.
Workshop
The Importance of Machine Learning in Structural Biology
Universidade do Minho, Portugal
2022/09/14 - 2022/09/14 Attendance of the Workshop in Statistics for Health, Public Health and Surveillance Problems.
Conference
II Workshop in Statistics for Health, Public Health and Surveillance Problems
Universidade Nova Centro de Matemática e Aplicações, Portugal
Distinctions

Award

2024 Academic Merit Scholarship for Higher Education Students
Universidade Nova de Lisboa, Portugal
2024 Best Student Award in MSc. in Computational Biology and Bioinformatics 2022/2023
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2024 Best Science Student Award 2022/2023
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2024 Best Faculty Student Award 2022/2023
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023 Congress Participation Grant
Sociedade Portuguesa de Estatística, Portugal
2022 Huawei Merit Scholarship
Huawei Portugal, Portugal
2022 IST Mention of Academic Excellence
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 IST Mention of Academic Merit
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 IST Mention of Academic Merit
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 Best in Class BCG
Boston Consulting Group, United States

Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 EDP-Best of Class
EDP, Portugal