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Isabel Duarte is a Junior Researcher at Universidade do Algarve affiliated with CINTESIS (Center for Health Technology and Services Research). She has published over 25 articles in international journals, and developed several R packages with software tools for the biomedical community, transcriptomics cancer datasets, and participated in the design and development of 2 online databases with stem-cell transcriptomics analyses. She also developed interactive R tutorials for university students, and for science outreach for high-schoolers. She uses Bioinformatics/Computational Biology as a way of answering biologically relevant questions. She is passionate about Open Science and is always keen on establishing new collaborations. *** EDUCATION *** She holds a PhD in Medical Sciences by the Radboud Universiteit Nijmegen (The Netherlands); a Masters in Oncology by ICBAS - Universidade do Porto (Portugal); and a Science degree in Applied Biology by Universidade do Minho Braga (Portugal). *** RESEARCH INTERESTS *** Her research interests are focused on understanding how gene expression profiles translate into robust genetic modules that explain the phenotypic plasticity observed in healthy and diseased cells, particularly cancer. Such genetic modules hold the promise to be used as markers for precision medicine (diagnostic/prognostic classifiers of cellular phenotypic potential). *** PREVIOUS RESEARCH *** She has used OMICs datasets to study breast cancer, genetic regulation in early vertebrate embryo development, in stem cell differentiation, and in mitochondrial evolution. *** CURRENT RESEARCH *** She is starting her independent research line studying cancer causality using Structural Causal Models. She has been awarded a 6 year Junior Researcher grant, within FCT's CEEC 2020 call, to pursue this research. *** TEACHING *** She teaches Computational Biology at the Universidade do Algarve, and she organizes yearly courses on R programming.
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Identification

Personal identification

Full name
Guilhermina Isabel dos Santos Duarte

Citation names

  • Duarte, Isabel

Author identifiers

Ciência ID
ED15-7F67-7B64
ORCID iD
0000-0003-0060-2936
Google Scholar ID
620YlxwAAAAJ
Scopus Author Id
56991285300

Email addresses

  • giduarte@ualg.pt (Professional)

Websites

Knowledge fields

  • Medical and Health Sciences
  • Medical and Health Sciences - Clinical Medicine - Oncology
  • Natural sciences - Biological Sciences - Genetics and Heredity
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2023/08 - 2023/09
Concluded
 Statistics and Data Science Foundations (Pós-Graduação)
Major in Data Science and Statistics
LinkedIn Learning, United States
2017/12/13
Concluded
 Medical Sciences (Doutoramento)
Radboud Universiteit, Netherlands
"The alternative evolutionary fates of mitochondrial proteins" (THESIS/DISSERTATION)
 n/a
2005/09 - 2006/09
Concluded
 Programa de Doutoramento em Biologia Computacional (Curso de doutoramento (conclusão de unidades curriculares))
Major in Biologia Computacional
Instituto Gulbenkian de Ciência, Portugal
 n/a
2006/02
Concluded
 Oncologia (Mestrado)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
"Polimorfismo no promotor do gene TNF-alpha e risco para cancro do colo uterino" (THESIS/DISSERTATION)
 Muito Bom
2003/02
Concluded
 Biologia Aplicada (Licenciatura)
Universidade do Minho Escola de Ciências, Portugal
"Polimorfismo associado ao gene TNF-alpha em doentes oncológicos" (THESIS/DISSERTATION)
 15 valores
Affiliation

Science

Category
Host institution 		Employer
2019/05 - Current Contracted Researcher (Research) Universidade do Algarve, Portugal
Centro de Investigação em Tecnologias e Serviços de Saúde, Portugal
2014/05 - 2019/10 Researcher (Research) Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
2012/07/01 - 2013/04/30 Contracted Researcher (Research) Radboud Universiteit, Netherlands
2003/01/01 - 2005/08/31 Research Trainee (Research) Instituto Português de Oncologia do Porto Francisco Gentil Centro de Investigação, Portugal
2005/03/01 - 2005/07/31 Research Trainee (Research) Thomas Jefferson University College of Biomedical Sciences, United States

Teaching in Higher Education

Category
Host institution 		Employer
2018/09 - 2023/12 Invited Assistant (University Teacher) Universidade do Algarve, Portugal
Universidade do Algarve Departamento de Ciências Biomédicas e Medicina, Portugal
2002 - 2004 Tutor (University Teacher) Universidade do Minho, Portugal

Positions / Appointments

Category
Host institution 		Employer
2023/05 - Current Vice-Director Pattern Institute, Portugal
Pattern Institute, Portugal

Others

Category
Host institution 		Employer
2024/02 - Current Editorial Board of Genomics Analysis | Review Editor Frontiers in Bioinformatics, Switzerland
2006/11 - 2012/01 PhD Student Radboud Universiteit Centre for Molecular and Biomolecular Informatics, Netherlands
2005/09 - 2006/09 PhD Program in Computational Biology (PDBC) Instituto Gulbenkian de Ciência, Portugal
Projects

Grant

Designation Funders
2024 - 2024 CaCau: Cancer Causality | Phase 1 | Advanced Computational Resources Grant
2023.09536.CPCA.A1
Principal investigator
Centro de Investigação em Tecnologias e Serviços de Saúde, Portugal

Universidade do Algarve, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2023 - 2023 MitoProfiles: Gene Expression Landscape in Cancer from High Metabolic Rate Organs | Advanced Computational Resources Grant
2022.46814.CPCA.A0
Principal investigator
Centro de Investigação em Tecnologias e Serviços de Saúde, Portugal

Universidade do Algarve, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/05 - 2022/05 DEvoCancer: Decoding breast cancer evolution through mutant allele differential expression signatures
ALG-01-0145-FEDER-31477
Post-doc Fellow
Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2016/05 - 2019/04 Timing Cell Differentiation: Gene Regulatory Network in Temporal Control of Mesoderm Specification
PTDC/BEX-BID/5410/2014
Researcher
Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2014/05 - 2015/10 SPLICE Alternative splicing and its impact on molecular networks during stem cell differentiation
PTDC/BIA-GEN/116519/2010
Researcher
Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2012 - 2013 LINCONET
LINCONET
Researcher
Radboud Universiteit, Netherlands
 Horizon 2020
Concluded
2006 - 2009 Mapping the evolution of the mitochondrial proteome: From its Alpha-proteobacterial ancestor to its current state in Man
SFRH/BD/32959/2006
PhD Student Fellow
Radboud Universiteit, Netherlands
 Fundação para a Ciência e a Tecnologia
Concluded
2005 - 2005 TNF-alpha polymorphisms and risk for cervical cancer
TNFalpha
Master Student Fellow
Thomas Jefferson University Sidney Kimmel Medical College, United States
 Liga Portuguesa Contra o Cancro Núcleo Regional do Norte
Concluded

Contract

Designation Funders
2022/05 - Current CaCau: Cancer Causal Inference
2021.00238.CEECIND
Research Fellow
Centro de Investigação em Tecnologias e Serviços de Saúde, Portugal

Universidade do Algarve, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2020/03/31 Centre for Biomedical Research
UID/BIM/04773/2019
Researcher
Universidade do Algarve, Portugal

Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference poster
  1. Duarte, Isabel; Magno, Ramiro; Maia, Ana-Teresa. "Silent but Significant: Uncovering the Passenger Role of Transcriptionally Silenced Mutations in Breast Cancer Drivers". Paper presented in 6th ASPIC International Conference, 2024.
  2. Duarte, Isabel; Magno, Ramiro; Maia, Ana-Teresa. "Transcriptionally Silenced Mutations in Breast Cancer Driver Genes act as Functional Passengers". Paper presented in EMBL Cancer Genomics, 2021.
  3. Duarte, Isabel; Magno, Ramiro; Maia, Ana-Teresa. "Monoallelic Expression of Breast Cancer Driver Genes Reveals Functional Passenger Mutations". Paper presented in 25th Annual Meeting SPGH, 2021.
  4. Liber, Marta; Magno, Ramiro; Andrade, Raquel P.; Duarte, Isabel. "ClockOME: Searching for oscillatory genes in early vertebrate development". Paper presented in II International Meeting of the Portuguese Society of Genetics | IMPSG 2021, 2021.
  5. Duarte, Isabel; Magno, Ramiro; Maia, Ana-Teresa. "Monoallelic Expression of Breast Cancer Mutations Reveals Functionally Relevant Cis-Regulation". Paper presented in EACR Bioinformatics in Cancer, 2021.
  6. Martins-Jesus, Ana; Maia-Fernandes, Ana; Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.. "Somite formation in the early vertebrate embryo: temporal control and hairy1 oscillations". Paper presented in Sinal 2019 - 10th Meeting in Signal Transduction, 2019.
  7. Duarte, Isabel; Carraco, Gil; Andrade, Raquel P.. "Are miRNAs important for different paces of the Embryo Clock?". Paper presented in European Developmental Biology Congress (EDBC Alicante, Spain), 2019.
  8. Martins-Jesus, Ana P.; Maia-Fernandes, Ana; Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.. "Temporal control in early chick embryo somite segmentation". Paper presented in European Developmental Biology Congress (EDBC Alicante, Spain), 2019.
  9. Maia-Fernandes, Ana; Pais-de-Azevedo, Tomás; Martins, G.; Palmeirim, Isabel; Duarte, Isabel; Marreiros, Ana; Andrade, Raquel P.. "A novel morphometric tool describing early chick embryo elongation". Paper presented in European Developmental Biology Congress (EDBC Alicante, Spain), 2019.
  10. Duarte, Isabel; Carraco, Gil; Andrade, Raquel P.. "gga-miRNome: a miR-Seq approach to temporal control of cell differentiation". Paper presented in Portuguese Society for Stem Cells and Cell Therapies (SPCE-TC) 11th International Meeting, 2019.
  11. Duarte, Isabel; Liber, Marta; Andrade, Raquel P.. "FrozenChicken | Promoting the massive meta-analysis of chicken microarray data". Paper presented in Special DiA Meeting (Development in Action), 2019.
  12. Martins-Jesus, Ana P.; Maia-Fernandes, Ana; Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.. "Characterization of early somite formation in the chicken embryo". Paper presented in Special DiA Meeting (Development in Action), 2019.
  13. Carraco, Gil; Duarte, Isabel; Andrade, Raquel P.. "A miR-seq approach to temporal control of Embryo Clock oscillations". Paper presented in Special DiA Meeting (Development in Action), 2019.
  14. Duarte, Isabel; Carraco, Gil; Andrade, Raquel P.. "Chicken miRNA-seq: Understanding the regulation of the Embryo Molecular Clock.". Paper presented in Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology, 2018.
  15. Carraco, Gil; Duarte, Isabel; Andrade, Raquel P.. "RNA-mediated regulation of Embryo Clock expression dynamics.". Paper presented in Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology, 2018.
  16. Duarte, Isabel; Carraco, Gil; Andrade, Raquel P.. "A microRNA OMICS approach to understand the temporal control of the embryo molecular clock". Paper presented in Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology, 2018.
  17. Bastos, Rita; Duarte, Isabel; Thorsteinsdottir, Solveig ; Andrade, Raquel P.. "Rewinding the Clock: Origin and evolution of the Hairy/Enhancer of split protein family.". Paper presented in CBMR Conference, 2017.
  18. Pinto, José P.; et al.; Duarte, Isabel; Futschik, Matthias E.. "SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology.". Paper presented in INForum, 2016.
  19. Machado, S.; Kalathur, R.K.; Oliveira, DV; Barata, T.; Machado, RS; Pacheco-Leyva, Ivette; Duarte, Isabel; Futschik, Matthias; Pinto, JP. "StemCellNet: an interactive platform for network-oriented investigations in stem cell biology.". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies., 2015.
  20. Machado, Susana; et al.; Duarte, Isabel; Futschik, Matthias E.; Pinto, José P.. "StemChecker : a web-based tool to discover and explore stemness signatures in gene sets.". Paper presented in 9th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, 2015.
  21. Machado, Rui S.; Pinto, José P.; Oliveira, Daniel V.; Duarte, Isabel; et al.; Futschik, Matthias E.. "HeartEXpress: A meta-analysis study of stem cell differentiation in the context of cardiogenesis.". Paper presented in SPCE-TC, 2015.
  22. Oliveira, Daniel V.; Duarte, Isabel; et al.; Futschik, Matthias E.. "From Stem Cells 2 Heart: Finding novel candidate isoforms and genes for cardiomyogenesis.". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies, 2015.
  23. Duarte, Isabel; et al.; Futschik, Matthias E.. "From Stem Cells 2 Heart: Elucidating the role of alternative splicing in cardiomyogenesis.". Paper presented in Heart without Borders Conference, 2014.
  24. Oliveira, Daniel V.; Machado, Rui S.; Pacheco-Leyva, Ivette; Duarte, Isabel; et al.; Futschik, Matthias E.. "From Stem Cells 2 Heart: Finding novel candidate genes for cardiomyogenesis.". Paper presented in Heart without Borders Conference, 2014.
  25. Duarte, I.; Huynen, Martijn A.. "The Release Factor family: Origin and evolution". Paper presented in Benelux Bioinformatics Conference (BBC2011) - Luxembourg city, Luxembourg, 2011.
    10.1142/9789814542005
  26. Duarte, Isabel; Huynen, Martijn A.. "Origin and evolution of the organellar Release Factors". Paper presented in European Conference on Computational Biology (ECCB) - Ghent, Belgium, 2010.
  27. Duarte, Isabel; Huynen, Martijn A.. "Mitochondria and the origin of Eukaryotes". Paper presented in Intelligent Systems for Molecular Biology (ISMB) and European Conference on Computational Biology (ECCB) - Stockholm, Sweeden, 2009.
  28. Duarte, Isabel; Huynen, Martijn A.. "Eukaryotic Iron-Sulfur cluster assembly: Where does it come from?". Paper presented in Benelux Bioinformatics Conference (BBC2009) - Liège, Belgium, 2009.
  29. Duarte, Isabel; Huynen, Martijn A.. "Predicting novel functional interactors in Iron-Sulfur cluster assembly". Paper presented in Benelux Bioinformatics Conference (BBC2008) - Maastricht, The Netherlands, 2008.
  30. Duarte, Isabel; Huynen, Martijn A.. "Phylogenetic study of Eukaryotic Iron-Sulfur cluster assembly proteins". Paper presented in NCMLS PhD conference - Arnhem, The Netherlands, 2008.
  31. Duarte, Isabel; Huynen, Martijn A.. "Iron-Sulfur cluster biogenesis: Inferring functional interactions". Paper presented in NCMLS PhD conference - Arnhem, The Netherlands, 2007.
  32. Duarte, Isabel; et al.; Medeiros, Rui. "O Papel do Polimorfismo TNF-alpha (-308) no Desenvolvimento do Cancro da Mama". Paper presented in V Congresso Nacional de Senologia, 2003.
Journal article
  1. Maia-Fernandes, Ana; Martins-Jesus, Ana; Borralho-Martins, Nísia; Pais de Azevedo, Tomás Augusto Barreiros ; Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.. "Spatio-temporal dynamics of early somite segmentation in the chicken embryo". PLOS ONE 19 4 (2024): e0297853. http://dx.doi.org/10.1371/journal.pone.0297853.
    Open access • Published • 10.1371/journal.pone.0297853
  2. Barata, Tânia; Duarte, Isabel; Futschik, Matthias. "Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes". Genes 14 3 (2023): 745. http://dx.doi.org/10.3390/genes14030745.
    Open access • Published • 10.3390/genes14030745
  3. Correia, Lizelle; Magno, Ramiro; Xavier, Joana M.; de Almeida, Bernardo P.; Duarte, Isabel; Esteves, Filipa; Ghezzo, Marinella; et al. "Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant". npj Breast Cancer 8 1 (2022): http://dx.doi.org/10.1038/s41523-022-00435-9.
    Open access • Published • 10.1038/s41523-022-00435-9
  4. Duarte, Isabel; Carraco, Gil; de Azevedo, Nayara T. D.; Benes, Vladimir; Andrade, Raquel P.. "gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues". Scientific Data 9 1 (2022): http://dx.doi.org/10.1038/s41597-022-01126-7.
    Open access • 10.1038/s41597-022-01126-7
  5. Magno, Ramiro; Duarte, Isabel; Maia, Ana-Teresa. "quincunx: an R package to query, download and wrangle PGS Catalog data". Bioinformatics 38 1 (2021): 294-296. http://dx.doi.org/10.1093/bioinformatics/btab522.
    Open access • Published • 10.1093/bioinformatics/btab522
  6. Matos, José; Matos, Isabel; Callha, Manuela; Santos, Pedro; Duarte, Isabel; Cardoso, Yameric; Faleiro, Maria Leonor. "Insights from Bacteroides Species in Children with Type 1 Diabetes". Microorganisms (2021): https://doi.org/10.3390/microorganisms9071436.
    Open access • Published
  7. Liber, Marta; Duarte, Isabel; Maia, Ana-Teresa; Oliveira, Hugo Rafael. "The history of lentil (Lens culinaris subsp. culinaris) domestication and spread as revealed by Genotyping-by-Sequencing of wild and landrace accessions". Frontiers in Plant Science (2021): doi: 10.3389/fpls.2021.628439.
    Published
  8. Machado, Susana; Silva, Andreia; De Sousa-Coelho, Ana Luísa; Duarte, Isabel; Grenho, Inês; Santos, Bruno; Mayoral-Varo, Victor; et al. "Harmine and Piperlongumine Revert TRIB2-Mediated Drug Resistance". Cancers 12 12 (2020): 3689. http://dx.doi.org/10.3390/cancers12123689.
    Published • 10.3390/cancers12123689
  9. Pais-de-Azevedo, Tomás; Magno, Ramiro; Duarte, Isabel; Palmeirim, Isabel. "Recent advances in understanding vertebrate segmentation". F1000Research 7 (2018): 97. http://dx.doi.org/10.12688/f1000research.12369.1.
    Published • 10.12688/f1000research.12369.1
  10. Pinto, José P; Machado, Rui S R; Magno, Ramiro; Oliveira, Daniel V; Machado, Susana; Andrade, Raquel P; Bragança, José; Duarte, Isabel; Futschik, Matthias E. "StemMapper: a curated gene expression database for stem cell lineage analysis". Nucleic Acids Research 46 D1 (2017): D788-D793. http://dx.doi.org/10.1093/nar/gkx921.
    Published • 10.1093/nar/gkx921
  11. Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.; Palmeirim, Isabel. "rdml: A Mathematica package for parsing and importing Real-Time qPCR data". BMC Research Notes 10 1 (2017): 208. http://dx.doi.org/10.1186/s13104-017-2533-9.
    Open access • Published • 10.1186/s13104-017-2533-9
  12. Macedo, J. A.; Schrama, D.; Duarte, I.; Tavares, E.; Renaut, J.; Futschik, M. E.; Rodrigues, P. M.; Melo, E. P.. "Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells". BMC Genomics 18 1 (2017): 319. http://dx.doi.org/10.1186/s12864-017-3694-6.
    Open access • Published • 10.1186/s12864-017-3694-6
  13. Pinto, Elsa; Anselmo, Marisol; Calha, Manuela; Bottrill, Andrew; Duarte, Isabel; Andrew, Peter W; Faleiro, Maria L. "The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins". Microbiology 163 2 (2017): 161-174. http://dx.doi.org/10.1099/mic.0.000412.
    Published • 10.1099/mic.0.000412
  14. van Zoelen, Everardus J.; Duarte, Isabel; Hendriks, José M.; van der Woning, Sebastian P.. "TGFß-induced switch from adipogenic to osteogenic differentiation of human mesenchymal stem cells: identification of drug targets for prevention of fat cell differentiation". Stem Cell Research & Therapy 7 1 (2016): 123. http://dx.doi.org/10.1186/s13287-016-0375-3.
    Open access • Published • 10.1186/s13287-016-0375-3
  15. Pinto, José P.; Kalathur, Ravi K.; Oliveira, Daniel V.; Barata, Tânia; Machado, Rui S.R.; Machado, Susana; Pacheco-Leyva, Ivette; Duarte, Isabel; Futschik, Matthias E.. "StemChecker: a web-based tool to discover and explore stemness signatures in gene sets". Nucleic Acids Research 43 W1 (2015): W72-W77. http://dx.doi.org/10.1093/nar/gkv529.
    10.1093/nar/gkv529
  16. Huynen, Martijn A.; Duarte, Isabel; Szklarczyk, Radek. "Loss, replacement and gain of proteins at the origin of the mitochondria". Biochimica et Biophysica Acta (BBA) - Bioenergetics 1827 2 (2013): 224-231. http://dx.doi.org/10.1016/j.bbabio.2012.08.001.
    Open access • Published • 10.1016/j.bbabio.2012.08.001
  17. Willems, Peter; Wanschers, Bas F.J.; Esseling, John; Szklarczyk, Radek; Kudla, Urszula; Duarte, Isabel; Forkink, Marleen; et al. "BOLA1 Is an Aerobic Protein That Prevents Mitochondrial Morphology Changes Induced by Glutathione Depletion". Antioxidants & Redox Signaling 18 2 (2013): 129-138. http://dx.doi.org/10.1089/ars.2011.4253.
    Published • 10.1089/ars.2011.4253
  18. Duarte, Isabel; Nabuurs, Sander B.; Magno, Ramiro; Huynen, Martijn. "Evolution and Diversification of the Organellar Release Factor Family". Molecular Biology and Evolution 29 11 (2012): 3497-3512. http://dx.doi.org/10.1093/molbev/mss157.
    Open access • Published • 10.1093/molbev/mss157
  19. Kensche, Philip R; Duarte, Isabel; Huynen, Martijn A. "A three-dimensional topology of complex I inferred from evolutionary correlations". BMC Structural Biology 12 1 (2012): 19. http://dx.doi.org/10.1186/1472-6807-12-19.
    Published • 10.1186/1472-6807-12-19
  20. Huynen, Martijn A; Duarte, Isabel; Chrzanowska-Lightowlers, Zofia M A; Nabuurs, Sander B. "Structure based hypothesis of a mitochondrial ribosome rescue mechanism". Biology Direct 7 1 (2012): 14. http://dx.doi.org/10.1186/1745-6150-7-14.
    Open access • Published • 10.1186/1745-6150-7-14
  21. de Graaf, Rob M.; Ricard, Guenola; van Alen, Theo A.; Duarte, Isabel; Dutilh, Bas E.; Burgtorf, Carola; Kuiper, Jan W. P.; et al. "The Organellar Genome and Metabolic Potential of the Hydrogen-Producing Mitochondrion of Nyctotherus ovalis". Molecular Biology and Evolution 28 8 (2011): 2379-2391. http://dx.doi.org/10.1093/molbev/msr059.
    Open access • Published • 10.1093/molbev/msr059
  22. Duarte, Isabel; de Graaf, Rob M; van Alen, Theo A; Kuiper, Jan WP; Schotanus, Klaas; Rosenberg, Jörg; Huynen, Martijn A; Hackstein, Johannes HP. "The hydrogenosomes of Psalteriomonas lanterna". BMC Evolutionary Biology 9 1 (2009): 287. http://dx.doi.org/10.1186/1471-2148-9-287.
    Open access • Published • 10.1186/1471-2148-9-287
  23. Ricard, Guénola; de Graaf, Rob M; Dutilh, Bas E; Duarte, I; van Alen, Theo A; van Hoek, Angela HAM; Boxma, Brigitte; et al. "Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns". BMC Genomics 9 1 (2008): 587. http://dx.doi.org/10.1186/1471-2164-9-587.
    Open access • Published • 10.1186/1471-2164-9-587
  24. Santos, Alexandra M.; Sousa, Hugo; Pinto, Daniela; Portela, Catarina; Pereira, Deolinda; Catarino, Raquel; Duarte, Isabel; Lopes, Carlos; Medeiros, Rui. "Linking TP53 codon 72 and P21 nt590 genotypes to the development of cervical and ovarian cancer". European Journal of Cancer 42 7 (2006): 958-963. http://dx.doi.org/10.1016/j.ejca.2006.01.015.
    Published • 10.1016/j.ejca.2006.01.015
  25. Duarte, Isabel; Santos, Alexandra; Sousa, Hugo; Catarino, Raquel; Pinto, Daniela; Matos, Ana; Pereira, Deolinda; et al. "G-308A TNF-a polymorphism is associated with an increased risk of invasive cervical cancer". Biochemical and Biophysical Research Communications 334 2 (2005): 588-592. http://dx.doi.org/10.1016/j.bbrc.2005.06.137.
    Published • 10.1016/j.bbrc.2005.06.137
Online resource
  1. Duarte, Isabel; Magno, Ramiro. ualg.dia.aberto | R Package | Bioinformatics interactive tutorial | Scientific outreach for high school students. 2022. https://github.com/instructr/ualg.dia.aberto.
  2. Duarte, Isabel; Magno, Ramiro. ualg.compbio | R Package | R programming interactive tutorials. 2022. https://github.com/instructr/ualg.compbio.
  3. Duarte, Isabel. gga_mirnOME | R notebook | miRNA Expression data analysis. 2021. https://doi.org/10.6084/m9.figshare.14706891.v1.
    10.6084/m9.figshare.14706891.v1
  4. Duarte, Isabel; Magno, Ramiro. Piromyces Laterally Transferred Metabolism | R notebook. 2018. https://doi.org/10.6084/m9.figshare.7173173.v2.
    10.6084/m9.figshare.7173173
Preprint
  1. Duarte, Isabel; Liber, Marta; Magno, Ramiro; Andrade, Raquel P. (2312-360B-227A). "FrozenChicken: Promoting the meta-analysis of chicken microarray data". 2021. https://doi.org/10.1101/2021.02.25.432894.
    10.1101/2021.02.25.432894
  2. Duarte, Isabel; Huynen, Martijn A.. "Contribution of Lateral Gene Transfer to the evolution of the eukaryotic fungus Piromyces sp. E2: Massive bacterial transfer of genes involved in carbohydrate metabolism". 2019. http://dx.doi.org/10.1101/514042.
    10.1101/514042
Thesis / Dissertation
  1. Duarte, Isabel. "The alternative evolutionary fates of mitochondrial proteins". PhD, Radboud Universiteit, 2017. http://hdl.handle.net/2066/178927.
  2. Duarte, Isabel. "Polimorfismo no promotor do gene TNF-alpha e risco para cancro do colo uterino.". Master, Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, 2006.
  3. Duarte, Isabel. "Polimorfismo associado ao gene TNF-alpha em doentes oncologicos". Degree, Universidade do Minho, 2003.

Other

Dataset
  1. Duarte, Isabel. Prok2EukLateralGeneTransfer | 2018. https://figshare.com/articles/Prok2EukLateralGeneTransfer/7173020.
    10.6084/m9.figshare.7173020
  2. Duarte, Isabel. FrozenChicken | RData package | 2019. https://github.com/iduarte/FrozenChicken.
  3. Duarte, Isabel. DEvoCancerDataset | RData package | 2020. https://github.com/maialab/devocancerMetabricTCGA (Private Repository until publication).
  4. Duarte, Isabel. metabricDataset | RData package | 2020. https://github.com/maialab/metabricDataset (Private Repository until publication).
  5. Duarte, Isabel. tcgaDataset | RData package | 2020. https://github.com/maialab/tcgaDataset (Private Repository until publication).
  6. Duarte, Isabel. gga_mirnOME Expression | microRNA-seq | miRNA Expression datasets from chick embryonic tissues | 2021. https://doi.org/10.6084/m9.figshare.14706867.v1.
    https://doi.org/10.6084/m9.figshare.14706867.v2
  7. Duarte, Isabel. gga_mirnOME Novel | microRNA-seq | Novel Predicted miRNAs and Expression values from chick embryonic tissues | 2021. https://doi.org/10.6084/m9.figshare.14901102.v1.
    https://doi.org/10.6084/m9.figshare.14901102.v1
  8. Duarte, Isabel; Magno, Ramiro. gga.mirnas.qpcr | RData package | Data from the qPCR validation of miRNAs from gga_mirnOME | 2021. https://github.com/iduarte/gga.mirnas.qpcr (Private Repository until publication)..
  9. Maia-Fernandes, Ana; Martins-Jesus, Ana; Pais de Azevedo, Tomás Augusto Barreiros ; Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.. Chick Embryo Segmented Region Length | Dataset | 2023. FigShare.
    https://doi.org/10.6084/m9.figshare.22341070.v3
Other output
  1. DNA sequencing: Techniques and Applications | Open presentation. 2023. Duarte, Isabel. http://dx.doi.org/10.13140/RG.2.2.16220.56969.
    http://dx.doi.org/10.13140/RG.2.2.16220.56969
  2. RNA-seq explained | Open presentation. 2023. Duarte, Isabel. http://dx.doi.org/10.13140/RG.2.2.10629.32481.
    http://dx.doi.org/10.13140/RG.2.2.10629.32481
  3. DNA sequencing: Techniques and Applications | Open Presentation. Invited seminar for Oncolabs module | Masters in Oncobiology. 2022. Duarte, Isabel. https://www.researchgate.net/publication/366089681_DNA_sequencing_Techniques_and_Applications.
    10.13140/RG.2.2.17403.39207
  4. Metagenomics | From environmental samples to data analysis | Open presentation. Seminar introducing Metagenomics to master's students. 2022. Duarte, Isabel. https://www.researchgate.net/publication/360261349_Metagenomics_From_environmental_samples_to_data_analysis.
    10.13140/RG.2.2.33044.99202
  5. Genomics: DNA sequencing | Open Presentation. Introduction to DNA sequencing for master's students. 2021. Duarte, Isabel. http://dx.doi.org/10.13140/RG.2.2.25791.64165.
    10.13140/RG.2.2.25791.64165
  6. R4Humans & Intro2Transcriptomics | Open tutorial. Brief introduction to R programming and Microarray data analysis using R. Hands-on tutorial. 2021. Duarte, Isabel. http://dx.doi.org/10.13140/RG.2.2.33341.38885.
    10.13140/RG.2.2.33341.38885
  7. FrozenChicken: Promoting the meta-analysis of chicken microarray data | R Notebook. Open publication describing how the FrozenChicken package was developed. All R code included. 2020. Duarte, Isabel. https://zenodo.org/record/3765944#.YB7JMWPLewQ.
    10.5281/ZENODO.3765944
  8. Introduction to Metagenomics | Open presentation. Introduction to Metagenomics data analysis. 2020. Duarte, Isabel. http://dx.doi.org/10.13140/RG.2.2.17665.17760.
    10.13140/RG.2.2.17665.17760
  9. RNAseq in a nutshell | Open presentation. Brief explanation about RNA sequencing data analysis. 2020. Duarte, Isabel. http://dx.doi.org/10.13140/RG.2.2.14309.73441.
    10.13140/RG.2.2.14309.73441
  10. Piromyces Laterally Transferred Metabolism. The purpose of this analysis is to find if the connectivity of metabolic genes that are predicted to be Lateral Transfers from Bacteria to Piromyces is significantly different from what could be expected from randomly choosing edges (which correspond to enzymes) from the whole metabolic map.. 2018. Duarte, Isabel; Magno, Ramiro. https://doi.org/10.6084/m9.figshare.7173173.v2.
    10.6084/m9.figshare.7173173.v2
  11. R for Absolute Beginners | Hands-on Tutorial. R programming introduction for intense 2 day workshop. 2018. Magno, Ramiro; Duarte, Isabel. https://www.researchgate.net/publication/331209857_R_for_Absolute_Beginners_-_Hands-on_R_Tutorial.
    DOI: 10.13140/RG.2.2.23615.36000
Software
  1. Duarte, Isabel; Magno, Ramiro. "tdp43 | R package". Universidade do Algarve. GitHub | https://github.com/patterninstitute/tdp43 (Private Repository until publication). 2023.
  2. Duarte, Isabel. "MitoCarta | R Package". Universidade do Algarve. GitHub | https://github.com/MitoProfiles/MitoCarta. 2023.
  3. Duarte, Isabel. "SomiteExploreR | R package". Universidade do Algarve. GitHub | https://github.com/iduarte/SomiteExplorerR. 2023.
  4. Magno, Ramiro; Duarte, Isabel; Maia, Ana-Teresa. "agvgd: An R Implementation of the Align-GVGD Method". 0.1.2. Pattern Institute. R. 2022.
  5. Magno, Ramiro; Duarte, Isabel; Maia, Ana-Teresa. "protean: Sequence Profiles of OncoKB Genes". 0.1.2. Pattern Institute. R. 2022.
  6. Duarte, Isabel. "quincunx | R package | Broad analysis of Polygenic Risk Scores". Universidade do Algarve. CRAN. 2021.
    https://doi.org/10.1093/bioinformatics/btab522
  7. Magno, Ramiro; Duarte, Isabel; Maia, Ana-Teresa. "grantham: calculate the Grantham Distance". 0.1.1. Pattern Institute. R. 2021.
  8. Magno, Ramiro; Duarte, Isabel; Maia, Ana-Teresa. "ensemblr: R Client for the Ensembl REST API". 0.1.0. Pattern Institute. R. 2019.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/09/24 Bioinformatics in Oncology | LPCC (Portuguese Cancer League) | Keynote 4º ENJIO - Encontro Nacional de Jovens Investigadores em Oncologia
Liga Portuguesa Contra o Cancro (Porto, Portugal)
2022/03 Temporal Control of Early Chick Embryo Development: Lessons form in vivo real-time Imaging | ARS 2022 | Selected Avian Research Symposium 2022
Roslin Institute
2022/03 gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues | Selected Avian Research Symposium 2022
Roslin Institute
2021/11 Temporal Control of Early Chick Embryo Development: Lessons form in vivo real-time Imaging | SFBD & SBCF 2021 | Selected From cells to embryos Patterning and Self-Organization
Multi-Organization Thematic Institute Cell Biology, Development & Evolution (ITMO-BCDE) & French Society of Developmental Biology (SFBD) & French Society of Cell Biology (SBCF)
2021/07 ClockOME: Searching for oscillatory genes in early vertebrate development | Selected II International Meeting of the Portuguese Society of Genetics | IMPSG 2021
Portuguese Society of Genetics
2019 Chicken miRNA-seq: Understanding the regulation of the Embryo Molecular Clock | Invited LabClub | CBMR Seminar Series
Universidade do Algarve (Faro, Portugal)
2018 Studying the Regulation of the Embryo Molecular Clock | Keynote CCMar Seminars
CCMar (Faro, Portugal)
2018 Chicken microRNA-seq: Understanding the regulation of the Embryo Molecular Clock | Selected 3rd CBMR/ProRegeM Meeting
CBMR (Faro, Portugal)
2017 RNA-seq for humans - Part 1 | RNA-seq for humans - Part 2 | Invited LabClub | CBMR Seminar Series
Universidade do Algarve (Faro, Portugal)
2015 From stem cells 2 heart: Transcriptomics of cardiogenesis | Keynote Molecular Genetics seminars
Universidade do Algarve (Faro, Portugal)
2014 Past predictions and present analysis: Two examples of bioinformatics at work | Invited LabClub | CBMR Seminar Series
Universidade do Algarve (Faro, Portugal)
2011 Evolution of the organellar release factor family: Reinventing genetic codes | Invited Forum PDBC
IGC (Oeiras, Portugal)
2011 Origin and evolution of the organellar release factors | Selected Benelux Bioinformatics Conference (BBC2011)
University of Luxembourg (Luxembourg city, Luxembourg)
2010 mtRF1: a predicted mitoribosomal rescuing factor | Selected NCMLS PhD conference
NCMLS (Arnhem, Netherlands)
2009 Psalteriomonas lanterna: a peculiar organism with a peculiar metabolism | Awarded Best Young Researcher Talk | Selected EMBO Eukaryotic Organisms Conference
EMBO (San Feliu de Guixols, Spain)
2008 Mitochondria and the origin of eukaryotes | Invited Forum PDBC
IGC (Oeiras, Portugal)
2008 Early branching eukaryotes and the evolution of mitochondrion-like organelles | Selected Benelux Bioinformatics Conference (BBC2008)
Maastricht University (Maastricht, Netherlands)
2003 O Papel dos Polimorfismos Geneticos no Desenvolvimento de Cancro | Invited Jornadas de Biologia Aplicada
Universidade do Minho (Braga, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2020/01 - Current Timing Cell Differentiation: Gene Regulatory Network in Temporal Control of Mesoderm Specification | PhD thesis co-supervisor
Co-supervisor
 Ciências Biomédicas (PhD)
Universidade do Algarve, Portugal
2022/09 - 2023/12 MitoProfiles: Cancer mitochondrial profiles in high metabolic rate organs | Master thesis supervisor
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2019/09 - 2021/07 ClockOME: Searching for oscillating genes in early vertebrate development | Masters thesis supervisor
Supervisor
 Ciências Biomédicas (Master)
Universidade do Algarve, Portugal
2020/03 - 2020/12 Análise da expressão alélica de mutações somáticas em cancro da mama | BSc thesis co-supervisor
Co-supervisor
 Ciências Biomédicas (Degree)
Universidade do Algarve, Portugal
2018/09 - 2020/01 Identification and characterization of prophages in Bacteroides spp. isolates from children with type 1 diabetes | Masters thesis co-supervisor
Co-supervisor
 Biologia Molecular e Microbiana (Master)
Universidade do Algarve, Portugal
2008 - 2009 Predicting novel functional interactions in Iron-Sulfur cluster assembly | BSc thesis co-supervisor
Co-supervisor
 Licenciatura em Bioinformática (Degree)
Universidade Católica Portuguesa Centro Regional do Porto, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2023/10/31 - 2023/11/03 R-Mind: Unlocking the Potential of R Data Analysis for Biomolecular Research | 3-days international workshop | ESN-ISN Neurochemistry School 2023 (2023/10/31 - 2023/11/03)
Workshop (Member of the Organising Committee)
 Universidade do Algarve, Portugal
2022/05/03 - 2023/05/04 Dias Abertos da UAlg | Yearly Science Outreach event for high-school students | "Bioinformatics: Discover genes and proteins (10 - 12th grade) (2022/05/03 - 2023/05/04)
Other (Other)
 Universidade do Algarve, Portugal
2023/05/02 - 2023/05/02 Publication-ready graphs using R | 1-day international workshop | ENCODS2023 (2023/05/02 - 2023/05/02)
Workshop (Other)
 Universidade do Algarve, Portugal
2022/10/26 - 2022/10/28 Tidy data and visualization with R | 3 day post-graduate course on data analysis and visualization for researchers (13 participants) (2022/10/26 - 2022/10/28)
Workshop (Member of the Organising Committee)
 Centro de Ciências do Mar, Portugal
2020/02/10 - 2020/02/20 Dia Aberto da UAlg 2020 | Science outreach event for high-school students | 2 Bioinformatics activities: "Mystery at the airpoirt: Searching for the guilty protein" (9th and 10th grade); and "Discover the mysterious gene" (11th and 12th grade) (2020/02/20 - 2020/02/20)
Other (Other)
 Universidade do Algarve, Portugal
2015 - 2019 R for absolute beginners | 2 day post-graduate introductory workshop on R programming and basic statistical analysis using R. Organized yearly. Over 125 total participants. (2015 - 2019)
Workshop (Member of the Organising Committee)
 Centro de Ciências do Mar, Portugal
2017 - 2017 CBMR Meeting | Yearly scientific meeting where the CBMR members present and discuss their work developed over the previous year. (2017 - 2017)
Meeting (Member of the Organising Committee)
 Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
2016 - 2016 Marine Genomics | International workshop (2016 - 2016)
Workshop (Co-organisor)
 Centro de Ciências do Mar, Portugal
2012 - 2012 BBC2012 | Benelux Bioinformatics Conference - International conference organized in Nijmegen, The Netherlands. (2012 - 2012)
Conference (Member of the Organising Committee)
 Radboud Universiteit Centre for Molecular and Biomolecular Informatics, Netherlands
2004 - 2004 Seminars in Oncology | One day of oncology-research seminars. (2004 - 2004)
Conference (Member of the Organising Committee)
 Instituto Português de Oncologia do Porto Francisco Gentil Centro de Investigação, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2024/01/29 - 2024/01/30 Ready for BioData Management: Intensive Course
Workshop
 Ready for BioData Management: Intensive Course
Centro de Ciências do Mar, Portugal

BioData.pt, Portugal
2023/11/15 - 2023/11/17 EMBL | Cancer genomics
Conference
 EMBL Cancer Genomics
European Molecular Biology Laboratory, Germany
2023/11/02 - 2023/11/09 Inteligência Artificial Generativa na Educação: Desafios, oportunidades e preocupações
Seminar
 Inteligência Artificial Generativa na Educação: Desafios, oportunidades e preocupações
Universidade do Algarve, Portugal
2023/10/19 - 2023/10/20 Jornadas interinstitucionais de desenvolvimento pedagógico | Avaliação da Aprendizagem – para onde queremos ir? | Avaliação objetiva de apresentações orais: Estratégias e Processos
Seminar
 Jornadas interinstitucionais de desenvolvimento pedagógico
Universidade de Aveiro, Portugal
2023/09/18 - 2023/09/18 The Future of Graduate Education | Conference | Chairing of the session: Tools for transparent and reproducible science
Conference
 The Future of Graduate Education
Instituto Gulbenkian de Ciência, Portugal
2023/09/11 - 2023/09/15 Open Research Summer School 2023 | LMU Open Science Center (Ludwig-Maximilians-Universitat Munchen, Germany)
Workshop
 Open Research Summer School 2023
Ludwig-Maximilians-Universität München, Germany
2023/07/18 - 2023/07/21 EMBL | Theory and concepts in biology
Conference
 EMBL | Theory and concepts in biology
European Molecular Biology Laboratory, Germany
2023/06/27 - 2023/06/28 EACR Early Career Researchers' Conference | Workshop-style meeting for career development in cancer research | Virtual
Conference
 3rd EACR Early Career Researchers' Conference
European Association For Cancer Research, United Kingdom
2022/12/15 - 2022/12/15 Cochrane Portugal Annual Meeting 2022 | Real World Data and Evidence-based Decision Making: Present and Future Promises and Challenges
Meeting
 Cochrane Portugal Annual Meeting 2022 | Real World Data and Evidence-based Decision Making: Present and Future Promises and Challenges
Universidade do Porto Faculdade de Medicina, Portugal

Centro de Investigação em Tecnologias e Serviços de Saúde, Portugal

Cochrane Portugal, Portugal
2022/11/30 - 2022/11/30 Fórum Medicina de Precisão em Oncologia | FMUP
Meeting
 Fórum Medicina de Precisão em Oncologia
Universidade do Porto Faculdade de Medicina, Portugal
2022/10/10 - 2022/10/13 Ibergrid | Innovative Computing and Data Services for Research
Conference
 11th Iberian Grid Conference
Universidade do Algarve, Portugal
2022/09/29 - 2022/09/30 BioData.pt Infrastructure Status and Development
Meeting
 1st BioData.pt | Elixir | All Hands Meeting
Centro de Ciências do Mar, Portugal
2022/09/24 - 2022/09/24 Scientific Meeting | Young Cancer Researchers
Meeting
 4º ENJIO - Encontro Nacional de Jovens Investigadores em Oncologia
Liga Portuguesa Contra o Cancro Núcleo Regional do Norte, Portugal
2022/04/26 - 2022/04/27 EACR Early Career Researchers' Conference | Interactive, workshop-style meeting for career development in cancer research | 2 day | Virtual Conference
Conference
 2nd EACR Early Career Researchers' Conference
European Association For Cancer Research, United Kingdom
2021/11/22 - 2021/11/24 EMBL Conference | Cancer Genomics | 2 day | Virtual Conference
Conference
 EMBL Conference: Cancer Genomics
European Molecular Biology Laboratory, Germany
2021/11/18 - 2021/11/19 Portuguese Society of Human Genetics | 25th Annual Meeting SPGH | 2 day | Virtual Meeting
Meeting
 25th Annual Meeting SPGH
Sociedade Portuguesa de Genetica Humana, Portugal
2021/10/14 - 2021/10/15 II ASPIC-ASEICA International Meeting | Current Trends in Precision Medicine in Cancer | 2 day | Virtual Conference
Conference
 II ASPIC-ASEICA International Meeting - Current Trends in Precision Medicine in Cancer
ASPIC - ASSOCIAÇÃO PORTUGUESA DE INVESTIGAÇÃO EM CANCRO, Portugal
2021/07/25 - 2021/07/30 ISMB ECCB 2021 | Computational Biology | 5 day | Virtual Conference
Conference
 ISMB ECCB 2021
International Society for Computational Biology, United States
2021/06/23 - 2021/06/24 COMPBIOMED All-Hands Meeting | 2 day | Virtual Meeting
Meeting
 COMPBIOMED All-Hands Meeting
2021/05/20 - 2021/05/21 27th PORTO CANCER MEETING | Stemness & Metastasis: Advances in Research and Clinical Translation | 2 day | Virtual Conference
Conference
 27th PORTO CANCER MEETING | Stemness & Metastasis: Advances in Research and Clinical Translation
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal

Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2021/05/18 - 2021/05/19 EACR | Bioinformatics in Cancer | 2 day | Virtual Conference
Conference
 Bioinformatics in Cancer
European Association For Cancer Research, United Kingdom
2021/02/08 - 2021/02/10 Genomic Regulation in Cancer | 3 day | Virtual Conference
Conference
 Genomic Regulation 2021: Focus on Cancer
Swiss Institute of Bioinformatics Geneva, Switzerland
2021/01/26 - 2021/01/28 Ensembl Browser workshop | 3 day course taught by the EMBL-EBI training team
Workshop
 Ensembl Browser Workshop
European Bioinformatics Institute, United Kingdom
2020/09/25 - 2020/09/25 Liga Portuguesa contra o Cancro | Cancer Biology: From Basic to Translational Research | Virtual Conference
Conference
 Cancer Biology: From Basic to Translational Research | Virtual Conference
Liga Portuguesa Contra o Cancro, Portugal
2020/06/22 - 2020/06/24 American Association for Cancer Research | Virtual Annual Meeting II
Conference
 2020 Virtual Annual Meeting II
American Association for Cancer Research, United States
2020/06/18 - 2020/06/19 European Association for Cancer Research | Virtual Congress
Congress
 EACR Virtual Congress 2020
European Association For Cancer Research, United Kingdom
2020/06/03 - 2020/06/03 European Association for Cancer Research | Virtual Conference on Bioinformatics for Cancer Research
Conference
 EACR Virtual Conference on Bioinformatics for Cancer Research
European Association For Cancer Research, United Kingdom
2019/07/03 - 2019/07/05 Managing single cell transcriptomics data | 3-day Workshop | EBI, Hinxton, UK
Workshop
 Managing single cell transcriptomics data
European Bioinformatics Institute, United Kingdom
2019/06 - 2019/06 Special DiA Meeting (Development in Action) | Portuguese Society for Developmental Biology (SPBD)
Conference
 Special DiA Meeting (Development in Action)
Universidade do Algarve, Portugal
2019/03/13 - 2019/03/15 VIZBI 2019 - EMBO Workshop on Visualising Biological Data | EMBL Advanced Training Centre, Heidelberg, Germany
Conference
 VIZBI 2019 - Visualising Biological Data
European Molecular Biology Laboratory, Germany
2018/11/07 - 2018/11/10 Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology
Meeting
 Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology
Sociedade Portuguesa de Biologia do Desenvolvimento, Portugal
2017/10/01 - 2017/10/02 EMBL-EBI Bioinformatics Workshop | Bioinformatics tools from EBI and EMBL | Training by Amy Tang
Workshop
 EMBL-EBI Bioinformatics Workshop
Centro de Ciências do Mar, Portugal
2016/07/01 - 2016/07/01 CBMR/ProRegeM Annual Meeting | Mechanisms of Disease and Regenerative Medicine
Meeting
 1st CBMR/ProRegeM Annual Meeting
Universidade do Algarve Centro de Investigação em Biomedicina, Portugal
2012/06/18 - 2012/06/20 Bioinformatics and Functional Genomics using R and Bioconductor | 3 day hands-on training
Workshop
 Bioinformatics and Functional Genomics using R and Bioconductor
Instituto Gulbenkian de Ciência, Portugal
2009/06/15 - 2009/06/19 Course on Molecular Evolution, Phylogenetics, Phylogenomics and Adaptation | Five-day course teaching the basic concepts from comparative genomics, evolutionary biology and hypothesis testing (theoretical and computer practicals sessions).
Workshop
 IV Course on Molecular Evolution, Phylogenetics, Phylogenomics and Adaptation
Centro de Investigacion Principe Felipe, Spain

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023/12/21 MitoProfiles: Cancer mitochondrial profiles in high metabolic rate organs
Supervisor
 Catarina Gomes Ferreira (Master)
Universidade do Minho, Portugal
2021/12 Identification of novel key factors of heart development using a systems biology approach
(Thesis) Main arguer
 Rui Sotero Rodrigues Machado (PhD)
Universidade do Algarve, Portugal
2021/07/31 ClockOME: Searching for oscillatory genes in early vertebrate development
Supervisor
 Marta Liber (Master)
Universidade do Algarve, Portugal
2020/12/11 The role of TRIB2 in cellular metabolism: Analysis of TRIB2 expression levels in metabolically active tissues
(Thesis) Main arguer
 Vanessa Rodrigues Viegas (Master)
Universidade do Algarve, Portugal

Association member

Society Organization name Role
2023/05 - Current API | Associação Pattern Institute | Non-profit association for the promotion and development of science Founding member
2022/03 - Current EuroScience | European Association for the Advancement of Science and Technology Full member
2020 - Current EACR | European Association for cancer Research EACR Ambassador
2018 - Current SPBD | Portuguese Society for Developmental Biology Membro Associado
2018 - Current SPB | Portuguese Society for Botany Membro Associado

Committee member

Activity description
Role 		Institution / Organization
2023/12 - 2024 Work group for AI in Pedagogical Innovation at UAlg
Member
 Universidade do Algarve, Portugal
2023/11 - 2023/12 Electoral Commission for UAlg Workers
Member
 Universidade do Algarve, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2019/03 - 2023 Computational Biology Ciências Biomédicas - Mecanismos de Doenças (Mestrado) Universidade do Algarve, Portugal
2019 - 2023 DNA sequencing: Techniques and Applications | Yearly Invited Seminar in OncoLabs | Masters in Oncobiology Oncobiologia - Mecanismos Moleculares do Cancro (Mestrado) Universidade do Algarve, Portugal
2017 - 2023 RNA-seq and NextGen Sequencing | Yearly Invited Seminar for OncoLabs2 | Masters in Oncobiology Oncobiologia - Mecanismos Moleculares do Cancro (Mestrado integrado) Universidade do Algarve, Portugal
2016 - 2022 Metagenomics: Sequencing Microbial Communities | Yearly Invited Seminar in Metagenomics | Masters in Molecular and Microbial Biology Biologia Molecular e Microbiana (Mestrado integrado) Universidade do Algarve, Portugal
2018/09 - 2019/01 Bioinformatics (practical classes) Fundamentos de Bioinformática (Licenciatura) Universidade do Algarve, Portugal
2017 - 2017 RNA-Seq Explained: Measuring Gene Expression by Sequencing | Invited Seminar for Gene Expression and Pathology | Masters in Molecular and Microbial Biology Biologia Molecular e Microbiana (Mestrado integrado) Universidade do Algarve, Portugal
2012 - 2015 Bioinformatics in Health Sciences | Post-graduate course (Pós-Graduação) Universidade do Minho Instituto de Investigação em Ciências da Vida e Saúde, Portugal
2002 - 2004 Anthropobiology (Practical classes) | BSc BioGeo Biologia e Geologia (Licenciatura) Universidade do Minho, Portugal
2002 - 2004 Antropobiology (Practical classes) | BSc BioApplied Biologia Aplicada (Licenciatura) Universidade do Minho, Portugal

Mentoring / Tutoring

Topic Student name
2019 - 2019 clockOME: Identifying cyclic genes in early vertebrate embryo development using various time-ordering mathematical methods. Marta Liber
2017 - 2018 Biologia Evolutiva e do Desenvolvimento | HoxB genes as potential targets of the Segmentation Clock Rita Bastos

Other jury / evaluation

Activity description Institution / Organization
2023/11 - 2024/01 Evaluation member | Application for Master's fellowship | Project 2022.02380.PTDC PLEIREG Universidade do Algarve, Portugal
2021/01 - 2021/01 Membro de Painel de Avaliação | Concurso para atribuição de bolsa de Mestre | Projeto POCI-01-0145-FEDER-022184 "GenomePT" no âmbito do Programa CRESC ALGARVE 2020 e pela FCT Universidade do Algarve, Portugal
2018/01 - 2019/01 Evaluation of Scientific Posters in Conference | 4th and 5th MEEting of MIM Universidade do Algarve Departamento de Ciências Biomédicas e Medicina, Portugal
Distinctions

Award

2009 Outstanding Young Investigator Award
American Society for Microbiology, United States

Other distinction

2023 First Honourable Mention | Molecular Oncology Writing Competition: Uniting disciplines to tackle cancer
FEBS Press, United States