Daniel Gonçalves (9D14-B66F-A1CF)

Curriculum Vitae

Daniel Gonçalves

Daniel Gonçalves earned his master's degree in Computer Science and Engineering from Instituto Superior Técnico in November 2020. He has authored five publications in high-impact journals, as the first author for four of them. Prior to this, he obtained a BSc in Informatics Engineering from the University of Aveiro in June 2018. Since September 2021, Daniel has been pursuing a Ph.D. in Computer Science and Engineering, while simultaneously serving as an invited teaching assistant at Instituto Superior Técnico, where he imparts knowledge on computer science topics, particularly information systems. From 2019 to 2022, Daniel held a research fellowship at IDMEC-IST, during which he contributed to a collaborative project with IPO-Porto focused on predicting postoperative complications in cancer patients using machine learning models. His master's thesis was developed within this project, where he played a pivotal role in the development of the IPOscore online platform, aiding oncologists in predicting postoperative complications in cancer patients. Currently, Daniel is an early-stage researcher at INESC-ID, where he is dedicated to his Ph.D. research, focusing on utilizing deep learning for pattern mining in multi-omics data. His research aims to identify potential targets for cancer immunology research, holding promise for advancing cancer treatment strategies. Beyond his research commitments, Daniel is an active participant in seminars, sharing his expertise and insights with colleagues and peers.

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Identification

Personal identification

Full name: Daniel Gonçalves
Gender: Male

Citation names

Gonçalves, Daniel

Author identifiers

Ciência ID: 9D14-B66F-A1CF
ORCID iD: 0000-0001-5388-870X

Email addresses

dmateusgoncalves@tecnico.ulisboa.pt (Professional)
danielmateusgoncalves@gmail.com (Personal)

Telephones

Mobile phone

932283938 (Personal)

Addresses

Rua Luis Pastor de Macedo, 7, 3F, 1750-156, Lisboa, Lisboa, Portugal (Personal)

Websites

https://github.com/danielmg97 (Scholar)
https://scholar.google.pt/citations?user=d9fsjnoAAAAJ&hl (Scholar)

Knowledge fields

Exact Sciences - Computer and Information Sciences - Bioinformatics
Exact Sciences - Computer and Information Sciences - Information Science
Exact Sciences - Computer and Information Sciences - Computer Sciences

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)
Spanish; Castilian	Intermediate (B1)	Intermediate (B1)	Beginner (A1)	Intermediate (B1)
Portuguese (Mother tongue)

Education

	Degree	Classification
2021/09/10 - 2025 Ongoing	Engenharia Informática e de Computadores (Doutoramento) Universidade de Lisboa Instituto Superior Técnico, Portugal "Glycoproteogenomics Characterization in Colorectal Cancer using Deep Learning Approaches " (THESIS/DISSERTATION)
2018/09/12 - 2020/11/20 Concluded	Engenharia Informática e de Computadores (Mestrado) Major in Sistemas Inteligentes Universidade de Lisboa Instituto Superior Técnico, Portugal "Clinical prognosis and risk prediction of postoperative complications in cancer patients" (THESIS/DISSERTATION)	16
2015/09/14 - 2018/06/21 Concluded	Engenharia Informática (Licenciatura) Universidade de Aveiro, Portugal "Catch Me If You Can - Geolocalização entre conhecidos com garantias de privacidade " (THESIS/DISSERTATION)	14

Affiliation

Teaching in Higher Education

	Category Host institution	Employer
2023/09/04 - 2024/08/03	Invited Assistant (University Teacher)	Universidade de Lisboa Instituto Superior Técnico, Portugal
	Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09/19 - 2023/08/19	Invited Assistant (University Teacher)	Universidade de Lisboa Instituto Superior Técnico, Portugal
	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/10/01 - 2022/08/31	Invited Assistant (University Teacher)	Universidade de Lisboa Instituto Superior Técnico, Portugal
	Universidade de Lisboa Instituto Superior Técnico, Portugal

Positions / Appointments

	Category Host institution	Employer
2024/10 - Current	Student Representative - PhD in Computer Science and Engineering	Universidade de Lisboa Instituto Superior Técnico, Portugal

Others

	Category Host institution	Employer
2022/11/01 - Current	Bolseiro de Doutoramento	Fundação para a Ciência e a Tecnologia, Portugal
	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2022/07/15 - 2022/11/15	Bolseiro de Investigação	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2019/10/20 - 2022/07/17	Bolseiro de Investigação	Instituto de Engenharia Mecânica, Portugal
	Universidade de Lisboa Instituto Superior Técnico, Portugal

Projects

Grant

	Designation	Funders
2022/11/01 - Current	Glycoproteogenomics Patterning in Colorectal Cancer using Deep Learning Approaches 2022.12633.BD PhD Student Fellow Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2022/06/15 - 2022/11/15	LAIfeBlood - Inteligência Artificial para a Gestão do Sangue DSAIPA/AI/0033/2019 Research Fellow Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2019/10/20 - 2022/06/14	IPOscore - Predicting the risk of complications of surgical treatment and define prognosis of cancer patients through clinical and biopathological data integration DSAIPA/DS/0042/2018 Research Fellow Instituto de Engenharia Mecânica, Portugal Instituto Português de Oncologia do Porto Francisco Gentil EPE, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Outputs

Publications

Conference paper	Gonçalves, Daniel; Costa, Rafael S.; Henriques, Rui. "Context-situated visualization of biclusters to aid decisions: going beyond subspaces with parallel coordinates". Paper presented in AVI 2022: International Conference on Advanced Visual Interfaces, Roma, 2022. Published • 10.1145/3531073.3531124
Conference poster	Gonçalves, Daniel. "Glycoproteogenomics Characterization in Colorrectal Cancer using Deep Learning Approaches". Paper presented in 19th International Symposium on Intelligent Data Analysis, 2021.
Journal article	Daniel M. Gonçalves; Rui Henriques; Rafael S. Costa. "Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches". Computational and Structural Biotechnology Journal (2023): https://doi.org/10.1016/j.csbj.2023.10.002. Accepted • 10.1016/j.csbj.2023.10.002 Mochão, Hugo; Gonçalves, Daniel; Alexandre, Leonardo; Castro, Carolina; Valério, Duarte; Barahona, Pedro; Moreira-Gonçalves, Daniel; et al. "IPOscore: an interactive web-based platform for postoperative surgical complications analysis and prediction in the oncology domain". Computer Methods and Programs in Biomedicine (2022): 106754. http://dx.doi.org/10.1016/j.cmpb.2022.106754. Published • 10.1016/j.cmpb.2022.106754 Gonçalves, Daniel M.; Henriques, Rui; Costa, Rafael S.. "Predicting Postoperative Complications in Cancer Patients: A Survey Bridging Classical and Machine Learning Contributions to Postsurgical Risk Analysis". Cancers 13 13 (2021): 3217. http://dx.doi.org/10.3390/cancers13133217. Open access • Published • 10.3390/cancers13133217 Gonçalves, Daniel; Henriques, Rui; Santos, Lúcio Lara; Costa, Rafael S.. "On the predictability of postoperative complications for cancer patients: a Portuguese cohort study". BMC Medical Informatics and Decision Making 21 1 (2021): http://dx.doi.org/10.1186/s12911-021-01562-2. Open access • Published • 10.1186/s12911-021-01562-2
Thesis / Dissertation	Gonçalves, Daniel. "Clinical prognosis and risk prediction of postoperative complications in cancer patients". Master, Universidade de Lisboa Instituto Superior Técnico, 2020. https://github.com/danielmg97/master-thesis-iposcore.

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2022/11/28	IPOscore Platform	Workshop Inteligência Artificial - IPO Porto IPO Porto (Porto, Portugal)
2022/03/02	Context-situated visualization of biclusters to aid decisions: going beyond subspaces with parallel coordinates	Research Topics Seminars Professor Francisco Correia dos Santos (Lisbon, Portugal)
2021/05/11	Glycoproteogenomics Characterization in Colorectal Cancer Using Deep Learning (Proposal Presentation)	Systems Biology and Engineering Lab Seminars NOVA School of Science and Technology \| FCT NOVA (Almada, Portugal)
2021/04/28	Glycoproteogenomics Characterization in Colorectal Cancer using Deep Learning Approaches	19th International Symposium on Intelligent Data Analysis IDA Society (Porto, Portugal)
2020/12/04	Clinical prognosis and risk prediction of postoperative complications in cancer patients (IPO - Update 2)	Instituto Português e Oncologia do Porto (Porto, Portugal)
2020/09/30	Clinical prognosis and risk prediction of postoperative complications in cancer patients (SBE - Update)	Systems Biology and Engineering Lab Seminars NOVA School of Science and Technology \| FCT NOVA (Lisboa, Portugal)
2020/05/01	Clinical prognosis and risk prediction of postoperative complications in cancer patients (IPO - Update)	Instituto Português e Oncologia do Porto (Porto, Portugal)
2020/04/08	Clinical prognosis and risk prediction of postoperative complications in cancer patients (SBE)	Systems Biology and Engineering Lab Seminars NOVA School of Science and Technology \| FCT NOVA (Lisboa, Portugal)
2019/11/20	Clinical prognosis and risk prediction of postoperative complications in cancer patients (IPO)	Intituto Português de Oncologia do Porto (Porto, Portugal)

Event organisation

	Event name Type of event (Role)	Institution / Organization
2023/02/02 - Current	PhD Weekly Meetings - weekly one-hour meetings with peer PhD candidates, including a weekly task review and rotating presentation + discussion. (2023/02/02) Other (Co-organisor)
2023/11/06 - 2023/11/09	ER 2023 - The 42nd International Conference On Conceptual Modeling (2023/11/06 - 2023/11/09) Conference (Other)	Universidade de Lisboa Instituto Superior Técnico, Portugal

Event participation

	Activity description Type of event	Event name Institution / Organization
2023/04/27 - 2023/04/27	Workshop on the use of Deep Learning to leverage the study of Genomics presented by Bernardo Almeida, from iMP and University of Vienna, at INESC-ID, Lisbon. Workshop	Decoding the Genome with Deep Learning Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2022/07/11 - 2022/07/15	Monitor at the "Verão na ULisboa" Summer School, representing INESC-ID as a research unit. Other	Summer at ULisboa Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/06/14 - 2021/06/16	This event gathered senior and junior researchers from INESC-ID, ETH Zürich, Inria, and EMBL; in order to share their work in the context of Project OLISSIPO. This project is funded by the European Commission within its H2020 Research and Innovation programme “Spreading Excellence and Widening Participation\|Twinning”, OLISSIPO aims to enhance the competences in Computational Biology at INESC-ID in Lisbon, towards the creation of an international pole of excellence in multi-disciplinary science in Portugal. Meeting	OLISSIPO Week Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Committee member

	Activity description Role	Institution / Organization
2024/04 - Current	PhD Students Volunteer Team	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Conference scientific committee

	Conference name	Conference host
2023/02/15 - 2023/02/15	ISMB ECCB 2023 - Intelligent Systems for Molecular Biology, European Conference on Molecular Biology 2023	Lyon, France

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2023 - 2024	Análise e Integração de Dados (Data Analysis and Integration) 23/24	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - 2024	Administração de Dados e Sistemas de Informação (Data Administration in Information Systems) 23/24	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2022 - 2023	Processamento e Recuperação de Informação (Information Processing and Retrieval) 22/23	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2022 - 2023	Administração de Dados e Sistemas de Informação (Data Administration in Information Systems) 22/23	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022	Processamento e Recuperação de Informação (Information Processing and Retrieval) 21/22	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022	Sistemas de Informação e Bases de Dados (Information Systems and Databases) 21/22	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022	Administração de Dados e Sistemas de Informação (Data Administration in Information Systems) 21/22	(Mestrado)	Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022	Bases de Dados (Databases) 21/22	(Licenciatura)	Universidade de Lisboa Instituto Superior Técnico, Portugal

Mentoring / Tutoring

	Topic	Student name
2022/01/08 - 2022/02/26	AfterSchool by TreeTree2 - Inteligência Artificial 2022	Turma: "Alan Turing"
2021/02/15 - 2021/02/19	Lab Rotation - Integrated Laboratory Practicals II (Data Science Week)	Rodrigo Barriga Alves
2021/02/15 - 2021/02/19	Lab Rotation - Integrated Laboratory Practicals II (Data Science Week)	Joana Pimenta

Distinctions

Other distinction

2022	Diploma de Excelência - Docente Excelente 21/22 Universidade de Lisboa Instituto Superior Técnico, Portugal