Isabel Duarte
Investigador doutorado
Centro de Investigação em Tecnologias e Serviços de Saúde
Centro de Investigação em Tecnologias e Serviços de Saúde
Subsistema
Investigadores
Unidade ID
Centro de Investigação em Tecnologias e Serviços de Saúde
Regime
Exclusividade
Vínculo
CT em Funções Públicas a termo resolutivo certo
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.
Atividades
Atividades
2019/03 - 2023. Curso / Disciplina lecionado. Computational Biology. Ciências Biomédicas - Mecanismos de Doenças (Mestrado). Universidade do Algarve.
2023/05 - Presente. Membro de associação. API | Associação Pattern Institute | Non-profit association for the promotion and development of science. Founding member and Secretary of the board of directors.
2022/05/03 - 2023/05/04. Organização de evento. Dias Abertos da UAlg | Yearly Science Outreach event for high-school students | "Bioinformatics: Discover genes and proteins (10 - 12th grade) (2022). Universidade do Algarve.
2022 - Presente. Orientação. MitoProfiles in Cancer from High Metabolic Rate Organs | Master thesis supervisor.Bioinformática (Mestrado). Coorientador.
2022/12/15 - 2022/12/15. Participação em evento. Cochrane Portugal Annual Meeting 2022 | Real World Data and Evidence-based Decision Making: Present and Future Promises and Challenges . Encontro. 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; Centro de Investigação em Tecnologias e Serviços de Saúde; Cochrane Portugal.
2022/12/07. Apresentação oral de trabalho. DNA sequencing: Techniques and Applications | Masters in Oncobiology. Seminar for OncoLabs2 - Masters in Oncobiology. Universidade do Algarve (Faro, Portugal).
2022/11/30 - 2022/11/30. Participação em evento. Fórum Medicina de Precisão em Oncologia | FMUP. Encontro. Fórum Medicina de Precisão em Oncologia. Universidade do Porto Faculdade de Medicina.
2022/10/26 - 2022/10/28. Organização de evento. Tidy data and visualization with R | 3 day post-graduate course on data analysis and visualization for researchers (13 participants) (2022). Centro de Ciências do Mar.
2022/10/10 - 2022/10/13. Participação em evento. Ibergrid | Innovative Computing and Data Services for Research . Conferência. 11th Iberian Grid Conference. Universidade do Algarve.
2022/09/29 - 2022/09/30. Participação em evento. BioData.pt Infrastructure Status and Development. Encontro. 1st BioData.pt | Elixir | All Hands Meeting . Centro de Ciências do Mar.
2022/09/24. Apresentação oral de trabalho. Bioinformatics in Oncology | LPCC. 4º ENJIO - Encontro Nacional de Jovens Investigadores em Oncologia. Liga Portuguesa Contra o Cancro (Porto, Portugal).
2022/09/24 - 2022/09/24. Participação em evento. Scientific Meeting | Young Cancer Researchers. Encontro. 4º ENJIO - Encontro Nacional de Jovens Investigadores em Oncologia. Liga Portuguesa Contra o Cancro Núcleo Regional do Norte.
2022/04. Apresentação oral de trabalho. Metagenomics: From Environmental Sample to Data Analysis | Masters in Molecular and Microbial Biology. Seminars in Metagenomics - Masters in Molecular and Microbial Biology . Universidade do Algarve (Faro, Portugal).
2022/04/26 - 2022/04/27. Participação em evento. EACR Early Career Researchers' Conference | Interactive, workshop-style meeting for career development in cancer research | 2 day | Virtual Conference . Conferência. 2nd EACR Early Career Researchers' Conference. European Association For Cancer Research.
2022/03. Apresentação oral de trabalho. TEMPORAL CONTROL OF EARLY CHICK EMBRYO DEVELOPMENT: LESSONS FROM IN VIVO REAL-TIME IMAGING. Avian Research Symposium 2022. Roslin Institute.
2022/03. Apresentação oral de trabalho. gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues. Avian Research Symposium 2022. Roslin Institute.
2022/03 - Presente. Membro de associação. EuroScience | European Association for the Advancement of Science and Technology. Full member.
2021/12. Júri de grau académico. Identification of novel key factors of heart development using a systems biology approach. Arguente principal. Rui Sotero Rodrigues Machado (Doutoramento). Universidade do Algarve.
2021/11. Apresentação oral de trabalho. Temporal Control of Early Chick Embryo Development: Lessons form in vivo real-time Imaging. From cells to embryo – 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).
2021/11/22 - 2021/11/24. Participação em evento. EMBL Conference | Cancer Genomics | 2 day | Virtual Conference. Conferência. EMBL Conference: Cancer Genomics. European Molecular Biology Laboratory.
2021/11/18 - 2021/11/19. Participação em evento. Portuguese Society of Human Genetics | 25th Annual Meeting SPGH | 2 day | Virtual Meeting. Encontro. 25th Annual Meeting SPGH. Sociedade Portuguesa de Genetica Humana.
2021/10/14 - 2021/10/15. Participação em evento. II ASPIC-ASEICA International Meeting | Current Trends in Precision Medicine in Cancer | 2 day | Virtual Conference. Conferência. II ASPIC-ASEICA International Meeting - Current Trends in Precision Medicine in Cancer. ASPIC - ASSOCIAÇÃO PORTUGUESA DE INVESTIGAÇÃO EM CANCRO.
2019/09 - 2021/07. Orientação. "ClockOME: Searching for oscillating genes in early vertebrate development" | Masters thesis supervisor.Ciências Biomédicas (Mestrado). Orientador.
2021/07. Apresentação oral de trabalho. ClockOME: Searching for oscillatory genes in early vertebrate development. II International Meeting of the Portuguese Society of Genetics | IMPSG 2021. Portuguese Society of Genetics.
2021/07/31. Júri de grau académico. ClockOME: Searching for oscillatory genes in early vertebrate development. Orientador. Marta Liber (Mestrado). Universidade do Algarve.
2021/07/25 - 2021/07/30. Participação em evento. ISMB ECCB 2021 | Computational Biology | 5 day | Virtual Conference . Conferência. ISMB ECCB 2021. International Society for Computational Biology.
2021/06/23 - 2021/06/24. Participação em evento. COMPBIOMED All-Hands Meeting | 2 day | Virtual Meeting. Encontro. COMPBIOMED All-Hands Meeting .
2021/05/20 - 2021/05/21. Participação em evento. 27th PORTO CANCER MEETING | Stemness & Metastasis: Advances in Research and Clinical Translation | 2 day | Virtual Conference. Conferência. 27th PORTO CANCER MEETING | Stemness & Metastasis: Advances in Research and Clinical Translation. Universidade do Porto Instituto de Investigação e Inovação em Saúde; Universidade do Porto Instituto de Patologia e Imunologia Molecular.
2021/05/18 - 2021/05/19. Participação em evento. EACR | Bioinformatics in Cancer | 2 day | Virtual Conference. Conferência. Bioinformatics in Cancer. European Association For Cancer Research.
2021/02/08 - 2021/02/10. Participação em evento. Genomic Regulation in Cancer | 3 day | Virtual Conference. Conferência. Genomic Regulation 2021: Focus on Cancer. Swiss Institute of Bioinformatics Geneva.
2021/01 - 2021/01. Outro júri / avaliação. 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.
2021/01/26 - 2021/01/28. Participação em evento. Ensembl Browser workshop | 3 day course taught by the EMBL-EBI training team. Oficina (workshop). Ensembl Browser Workshop. European Bioinformatics Institute.
2020 - Presente. Membro de associação. EACR | European Association for cancer Research. EACR Ambassador.
2020/03 - 2020/12. Orientação. Análise da expressão alélica de mutações somáticas em cancro da mama | BSc thesis co-supervisor.Ciências Biomédicas (Licenciatura/Bacharelato). Coorientador.
2020/12/11. Júri de grau académico. The role of TRIB2 in cellular metabolism: Analysis of TRIB2 expression levels in metabolically active tissues. Arguente principal. Vanessa Rodrigues Viegas (Mestrado). Universidade do Algarve.
2020/09/25 - 2020/09/25. Participação em evento. Liga Portuguesa contra o Cancro | Cancer Biology: From Basic to Translational Research | Virtual Conference. Conferência. Cancer Biology: From Basic to Translational Research | Virtual Conference. Liga Portuguesa Contra o Cancro.
2020/06/22 - 2020/06/24. Participação em evento. American Association for Cancer Research | Virtual Annual Meeting II . Conferência. 2020 Virtual Annual Meeting II. American Association for Cancer Research.
2020/06/18 - 2020/06/19. Participação em evento. European Association for Cancer Research | Virtual Congress. Congresso. EACR Virtual Congress 2020. European Association For Cancer Research.
2020/06/03 - 2020/06/03. Participação em evento. European Association for Cancer Research | Virtual Conference on Bioinformatics for Cancer Research. Conferência. EACR Virtual Conference on Bioinformatics for Cancer Research. European Association For Cancer Research.
2020/04. Apresentação oral de trabalho. Metagenomics: Next-Generation Sequencing for the Study of Microbial Communities. Seminars in Metagenomics - Masters in Molecular and Microbial Biology . Universidade do Algarve (Faro, Portugal).
2020/04. Apresentação oral de trabalho. RNA-seq in a nutshell. Seminar for OncoLabs2 - Masters in Oncobiology. Universidade do Algarve (Faro, Portugal).
2020/02/10 - 2020/02/20. Organização de evento. 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). Universidade do Algarve.
2018/09 - 2020/01. Orientação. "Identification and characterization of prophages in Bacteroides spp. isolates from children with type 1 diabetes" | Masters thesis co-supervisor.Biologia Molecular e Microbiana (Mestrado). Coorientador.
2020/01 - Presente. Orientação. "TIMING CELL DIFFERENTIATON: Gene Regulatory Network in Temporal Control of Mesoderm Specification" | PhD thesis co-supervisor.Ciências Biomédicas (Doutoramento). Coorientador.
2019 - 2019. Tutoria. clockOME: Identifying cyclic genes in early vertebrate embryo development using various time-ordering mathematical methods.. Marta Liber.
2015 - 2019. Organização de evento. 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). Centro de Ciências do Mar.
2019. Apresentação oral de trabalho. Genomics: DNA sequencing.. Seminar for OncoLabs2 - Masters in Oncobiology. Universidade do Algarve (Faro, Portugal).
2019. Apresentação oral de trabalho. Chicken miRNA-seq: Understanding the regulation of the Embryo Molecular Clock.. LabClub | CBMR Seminar Series. Universidade do Algarve (Faro, Portugal).
2019/07/03 - 2019/07/05. Participação em evento. Managing single cell transcriptomics data | 3-day Workshop | EBI, Hinxton, UK. Oficina (workshop). Managing single cell transcriptomics data. European Bioinformatics Institute.
2019/06 - 2019/06. Participação em evento. Special DiA Meeting (Development in Action) | Portuguese Society for Developmental Biology (SPBD). Conferência. Special DiA Meeting (Development in Action). Universidade do Algarve.
2019/04. Apresentação oral de trabalho. Metagenomics: Studying and Sequencing Microbial Communities. Seminars in Metagenomics - Masters in Molecular and Microbial Biology . University of Algarve (Faro, Portugal).
2019/03/13 - 2019/03/15. Participação em evento. VIZBI 2019 - EMBO Workshop on Visualising Biological Data | EMBL Advanced Training Centre, Heidelberg, Germany. Conferência. VIZBI 2019 - Visualising Biological Data. European Molecular Biology Laboratory.
2018/09 - 2019/01. Curso / Disciplina lecionado. Bioinformatics (practical classes). Fundamentos de Bioinformática (Licenciatura). Universidade do Algarve.
2018/01 - 2019/01. Outro júri / avaliação. Evaluation of Scientific Posters in Conference | 4th and 5th MEEting of MIM . Universidade do Algarve Departamento de Ciências Biomédicas e Medicina.
2017 - 2018. Orientação. "HoxB genes as potential targets of the Segmentation Clock" | Masters thesis co-supervisor.Biologia Evolutiva e do Desenvolvimento (Mestrado). Coorientador.
2018. Apresentação oral de trabalho. Studying the Regulation of the Embryo Molecular Clock.. CCMar Seminars. CCMar (Faro, Portugal).
2018. Apresentação oral de trabalho. Chicken microRNA-seq: Understanding the regulation of the Embryo Molecular Clock.. 3rd CBMR/ProRegeM Meeting. CBMR (Faro, Portugal).
2018. Apresentação oral de trabalho. RNA-seq.. Seminar for OncoLabs2 - Masters in Oncobiology. Universidade do Algarve (Faro, Portugal).
2018. Apresentação oral de trabalho. Metagenomics: Sequencing Microbial Communities.. Seminars in Metagenomics - Masters in Molecular and Microbial Biology. Universidade do Algarve (Faro, Portugal).
2018 - Presente. Membro de associação. SPDB | Sociedade Portuguesa de Biologia do Desenvolvimento. Membro Associado.
2018 - Presente. Membro de associação. SPB | Sociedade Portuguesa de Botânica. Membro Associado.
2018/11/07 - 2018/11/10. Participação em evento. Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology. Encontro. Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology. Sociedade Portuguesa de Biologia do Desenvolvimento.
2017 - 2017. Organização de evento. CBMR Meeting | Yearly scientific meeting where the CBMR members present and discuss their work developed over the previous year. (2017). Universidade do Algarve Centro de Investigação em Biomedicina.
2017. Apresentação oral de trabalho. RNA-seq and NextGen Sequencing.. Seminar for OncoLabs2 - Masters in Oncobiology. Universidade do Algarve (Faro, Portugal).
2017. Apresentação oral de trabalho. RNA-Seq Explained: Measuring Gene Expression by Sequencing.. Seminar for Gene Expression and Pathology - Masters in Molecular and Microbial Biology. Universidade do Algarve (Faro, Portugal).
2017. Apresentação oral de trabalho. Metagenomics: Sequencing Microbial Communities.. Seminars in Metagenomics - Masters in Molecular and Microbial Biology. Universidade do Algarve (Faro, Portugal).
2017. Apresentação oral de trabalho. RNA-seq for humans (Part 1) | RNA-seq for humans (Part 2). LabClub | CBMR Seminar Series. Universidade do Algarve (Faro, Portugal).
2017/10/01 - 2017/10/02. Participação em evento. EMBL-EBI Bioinformatics Workshop | Bioinformatics tools from EBI and EMBL | Training by Amy Tang. Oficina (workshop). EMBL-EBI Bioinformatics Workshop. Centro de Ciências do Mar.
2016 - 2016. Curso / Disciplina lecionado. Marine Genomics | International workshop. Centro de Ciências do Mar.
2016. Apresentação oral de trabalho. Metagenomics: Sequencing Microbial Communities. Seminars in Metagenomics - Masters in Molecular and Microbial Biology. Universidade do Algarve (Faro, Portugal).
2016/07/01 - 2016/07/01. Participação em evento. CBMR/ProRegeM Annual Meeting | Mechanisms of Disease and Regenerative Medicine. Encontro. 1st CBMR/ProRegeM Annual Meeting. Universidade do Algarve Centro de Investigação em Biomedicina.
2012 - 2015. Curso / Disciplina lecionado. Bioinformatics in Health Sciences | Post-graduate course. Universidade do Minho Instituto de Investigação em Ciências da Vida e Saúde.
2015. Apresentação oral de trabalho. From stem cells 2 heart: Transcriptomics of cardiogenesis.. Molecular Genetics seminars. Universidade do Algarve (Faro, Portugal).
2014. Apresentação oral de trabalho. Past predictions and present analysis: Two examples of bioinformatics at work.. LabClub | CBMR Seminar Series. Universidade do Algarve (Faro, Portugal).
2012 - 2012. Organização de evento. BBC2012 | Benelux Bioinformatics Conference - International conference organized in Nijmegen, The Netherlands. (2012). Radboud Universiteit Centre for Molecular and Biomolecular Informatics.
2012/06/18 - 2012/06/20. Participação em evento. Bioinformatics and Functional Genomics using R and Bioconductor | 3 day hands-on training. Oficina (workshop). Bioinformatics and Functional Genomics using R and Bioconductor. Instituto Gulbenkian de Ciência.
2011. Apresentação oral de trabalho. Evolution of the organellar release factor family: Reinventing genetic codes.. Forum PDBC. IGC (Oeiras, Portugal).
2011. Apresentação oral de trabalho. Origin and evolution of the organellar release factors.. Benelux Bioinformatics Conference (BBC2011). University of Luxembourg (Luxembourg city, Luxemburgo).
2010. Apresentação oral de trabalho. mtRF1: a predicted mitoribosomal rescuing factor.. NCMLS PhD conference. NCMLS (Arnhem, Países Baixos).
2008 - 2009. Orientação. "Predicting novel functional interactions in Iron-Sulfur cluster assembly" | BSc thesis co-supervisor.Licenciatura em Bioinformática (Licenciatura/Bacharelato). Coorientador.
2009. Apresentação oral de trabalho. Psalteriomonas lanterna: a peculiar organism with a peculiar metabolism.. EMBO Eukaryotic Organisms Conference. EMBO (San Feliu de Guixols, Espanha).
2009/06/15 - 2009/06/19. Participação em evento. 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).. Oficina (workshop). IV Course on Molecular Evolution, Phylogenetics, Phylogenomics and Adaptation. Centro de Investigacion Principe Felipe.
2008. Apresentação oral de trabalho. Mitochondria and the origin of eukaryotes.. Forum PDBC. IGC (Oeiras, Portugal).
2008. Apresentação oral de trabalho. Early branching eukaryotes and the evolution of mitochondrion-like organelles.. Benelux Bioinformatics Conference (BBC2008). Maastricht University (Maastricht, Países Baixos).
2004 - 2004. Organização de evento. Seminars in Oncology | One day of oncology-research seminars. (2004). Instituto Português de Oncologia do Porto Francisco Gentil Centro de Investigação.
2002 - 2004. Curso / Disciplina lecionado. Anthropobiology (Practical classes tutor). Biologia e Geologia (Licenciatura). Universidade do Minho.
2003. Apresentação oral de trabalho. O Papel dos Polimorfismos Geneticos no Desenvolvimento de Cancro.. Jornadas de Biologia Aplicada. Universidade do Minho (Braga, Portugal).
Projetos
Projetos
2023 - 2023. MitoProfiles: Gene Expression Landscape in Cancers from High Metabolic Rate Organs, Advanced Computing Projects. Investigador responsável. Centro de Investigação em Tecnologias e Serviços de Saúde.
2019/05 - 2022/05. DEvoCancer: Decoding breast cancer evolution through mutant allele differential expression signatures, FEDER. Bolseiro de Pós-Doutoramento. Universidade do Algarve Centro de Investigação em Biomedicina.
2022/05 - Presente. Cancer Causal Inference, Concurso Estimulo ao Emprego Científico - Individual | 4th Edition. Bolseiro de Investigação. Centro de Investigação em Tecnologias e Serviços de Saúde; Universidade do Algarve.
2016/05 - 2019/04. "TIMING CELL DIFFERENTIATON: Gene Regulatory Network in Temporal Control of Mesoderm Specification". Investigador. Universidade do Algarve Centro de Investigação em Biomedicina.
2014/05 - 2015/10. SPLICE Alternative splicing and its impact on molecular networks during stem cell differentiation. Investigador. Universidade do Algarve Centro de Investigação em Biomedicina.
2012 - 2013. "Modelling the gene regulatory network underlying lineage commitment in human mesenchymal stem cells: Identification of drug targets for the anabolic treatment of degenerative disorders". Investigador. Radboud Universiteit.
2006 - 2009. "Mapping the evolution of the mitochondrial proteome: From its Alpha-proteobacterial ancestor to its current state in Man". Bolseiro de Doutoramento. Radboud Universiteit.
Produções
Prok2EukLateralGeneTransfer | 2018. https://figshare.com/articles/Prok2EukLateralGeneTransfer/7173020. https://doi.org/10.6084/m9.figshare.7173020
FrozenChicken | RData package | 2019. https://github.com/iduarte/FrozenChicken.
DEvoCancerDataset | RData package | 2020. https://github.com/maialab/devocancerMetabricTCGA (Private Repository until publication).
metabricDataset | RData package | 2020. https://github.com/maialab/metabricDataset (Private Repository until publication).
tcgaDataset | RData package | 2020. https://github.com/maialab/tcgaDataset (Private Repository until publication) .
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
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
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)..
Chick Embryo Segmented Region Length | Dataset | 2023. FigShare. https://doi.org/10.6084/m9.figshare.22341070.v3
Barata, Tânia; Duarte, Isabel; Futschik, Matthias. 2023. "Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes". Genes, 14 (3). https://doi.org/10.3390/genes14030745
Duarte, Isabel. 2023. RNA-seq explained | Open presentation. https://doi.org/10.13140/RG.2.2.10629.32481
Duarte, Isabel; Carraco, Gil; de Azevedo, Nayara T. D.; Benes, Vladimir; Andrade, Raquel P.. 2022. "gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues". Scientific Data, 9 (1). https://doi.org/10.1038/s41597-022-01126-7
Correia, Lizelle; Magno, Ramiro; Xavier, Joana M.; de Almeida, Bernardo P.; Duarte, Isabel; Esteves, Filipa; Ghezzo, Marinella; et al. 2022. "Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant". npj Breast Cancer, 8 (1). https://doi.org/10.1038/s41523-022-00435-9
Duarte, Isabel. 2022. Metagenomics | From environmental samples to data analysis | Open presentation. Seminar introducing Metagenomics to master's students. https://doi.org/10.13140/RG.2.2.33044.99202
Duarte, Isabel; Magno, Ramiro. 2022. ualg.dia.aberto | R Package | Bioinformatics interactive tutorial | Scientific outreach for high school students. https://github.com/instructr/ualg.dia.aberto
Duarte, Isabel; Magno, Ramiro. 2022. ualg.compbio | R Package | R programming interactive tutorials. https://github.com/instructr/ualg.compbio
Duarte, Isabel. 2022. DNA sequencing: Techniques and Applications | Open Presentation. Invited seminar for Oncolabs module | Masters in Oncobiology. https://doi.org/10.13140/RG.2.2.17403.39207
Magno, Ramiro; Duarte, Isabel; Maia, Ana-Teresa. 2021. "quincunx: an R package to query, download and wrangle PGS Catalog data". Bioinformatics, 38 (1): 294-296. https://doi.org/10.1093/bioinformatics/btab522
Liber, Marta; Duarte, Isabel; Maia, Ana-Teresa; Oliveira, Hugo Rafael. 2021. "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. doi: 10.3389/fpls.2021.628439
Duarte, Isabel; Magno, Ramiro; Maia, Ana-Teresa. 2021. Monoallelic Expression of Breast Cancer Mutations Reveals Functionally Relevant Cis-Regulation. Em EACR Bioinformatics in Cancer.
Liber, Marta; Magno, Ramiro; Andrade, Raquel P.; Duarte, Isabel. 2021. ClockOME: Searching for oscillatory genes in early vertebrate development. Em II International Meeting of the Portuguese Society of Genetics | IMPSG 2021.
Matos, José; Matos, Isabel; Callha, Manuela; Santos, Pedro; Duarte, Isabel; Cardoso, Yameric; Faleiro, Maria Leonor. 2021. "Insights from Bacteroides Species in Children with Type 1 Diabetes ". Microorganisms. https://doi.org/10.3390/microorganisms9071436
Duarte, Isabel. 2021. gga_mirnOME | R notebook | miRNA Expression data analysis. https://doi.org/10.6084/m9.figshare.14706891.v1
Duarte, Isabel. 2021. Genomics: DNA sequencing | Open Presentation. Introduction to DNA sequencing for master's students. https://doi.org/10.13140/RG.2.2.25791.64165
Duarte, Isabel. 2021. R4Humans & Intro2Transcriptomics | Open tutorial. Brief introduction to R programming and Microarray data analysis using R. Hands-on tutorial. https://doi.org/10.13140/RG.2.2.33341.38885
Duarte, Isabel; Magno, Ramiro; Maia, Ana-Teresa. 2021. Transcriptionally Silenced Mutations in Breast Cancer Driver Genes act as Functional Passengers. Em EMBL Cancer Genomics.
Duarte, Isabel; Magno, Ramiro; Maia, Ana-Teresa. 2021. Monoallelic Expression of Breast Cancer Driver Genes Reveals Functional Passenger Mutations. Em 25th Annual Meeting SPGH.
Duarte, Isabel. 2020. FrozenChicken: Promoting the meta-analysis of chicken microarray data | R Notebook. Open publication describing how the FrozenChicken package was developed. All R code included. https://doi.org/10.5281/ZENODO.3765944
Machado, Susana; Silva, Andreia; De Sousa-Coelho, Ana Luísa; Duarte, Isabel; Grenho, Inês; Santos, Bruno; Mayoral-Varo, Victor; et al. 2020. "Harmine and Piperlongumine Revert TRIB2-Mediated Drug Resistance". Cancers, 12 (12). https://doi.org/10.3390/cancers12123689
Duarte, Isabel. 2020. Introduction to Metagenomics | Open presentation. Introduction to Metagenomics data analysis. https://doi.org/10.13140/RG.2.2.17665.17760
Duarte, Isabel. 2020. RNAseq in a nutshell | Open presentation. Brief explanation about RNA sequencing data analysis. https://doi.org/10.13140/RG.2.2.14309.73441
Duarte, Isabel; Liber, Marta; Andrade, Raquel P.. 2019. FrozenChicken | Promoting the massive meta-analysis of chicken microarray data. Em Special DiA Meeting (Development in Action).
Martins-Jesus, Ana; Maia-Fernandes, Ana; Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.. 2019. Somite formation in the early vertebrate embryo: temporal control and hairy1 oscillations. Em Sinal 2019 - 10th Meeting in Signal Transduction .
Martins-Jesus, Ana P.; Maia-Fernandes, Ana; Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.. 2019. Characterization of early somite formation in the chicken embryo. Em Special DiA Meeting (Development in Action).
Duarte, Isabel; Carraco, Gil; Andrade, Raquel P.. 2019. Are miRNAs important for different paces of the Embryo Clock?. Em European Developmental Biology Congress (EDBC Alicante, Spain).
Carraco, Gil; Duarte, Isabel; Andrade, Raquel P.. 2019. A miR-seq approach to temporal control of Embryo Clock oscillations. Em Special DiA Meeting (Development in Action).
Martins-Jesus, Ana P.; Maia-Fernandes, Ana; Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.. 2019. Temporal control in early chick embryo somite segmentation. Em European Developmental Biology Congress (EDBC Alicante, Spain).
Maia-Fernandes, Ana; Pais-de-Azevedo, Tomás; Martins, G.; Palmeirim, Isabel; Duarte, Isabel; Marreiros, Ana; Andrade, Raquel P.. 2019. A novel morphometric tool describing early chick embryo elongation. Em European Developmental Biology Congress (EDBC Alicante, Spain).
Duarte, Isabel; Carraco, Gil; Andrade, Raquel P.. 2019. gga-miRNome: a miR-Seq approach to temporal control of cell differentiation. Em Portuguese Society for Stem Cells and Cell Therapies (SPCE-TC) 11th International Meeting.
Pais-de-Azevedo, Tomás; Magno, Ramiro; Duarte, Isabel; Palmeirim, Isabel. 2018. "Recent advances in understanding vertebrate segmentation". F1000Research, 7. https://doi.org/10.12688/f1000research.12369.1
Duarte, Isabel; Magno, Ramiro. 2018. Piromyces Laterally Transferred Metabolism | R notebook. https://doi.org/10.6084/m9.figshare.7173173
Duarte, Isabel; Carraco, Gil; Andrade, Raquel P.. 2018. Chicken miRNA-seq: Understanding the regulation of the Embryo Molecular Clock.. Em Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology.
Carraco, Gil; Duarte, Isabel; Andrade, Raquel P.. 2018. RNA-mediated regulation of Embryo Clock expression dynamics.. Em Joint Meeting of the Portuguese, Spanish and French Societies for Developmental Biology.
Magno, Ramiro; Duarte, Isabel. 2018. R for Absolute Beginners | Hands-on Tutorial. R programming introduction for intense 2 day workshop. https://doi.org/10.13140/RG.2.2.23615.36000
Duarte, Isabel. 2017. "The alternative evolutionary fates of mitochondrial proteins". Doutoramento. http://hdl.handle.net/2066/178927
Pinto, José P; Machado, Rui S R; Magno, Ramiro; Oliveira, Daniel V; Machado, Susana; Andrade, Raquel P; Bragança, José; Duarte, Isabel; Futschik, Matthias E. 2017. "StemMapper: a curated gene expression database for stem cell lineage analysis". Nucleic Acids Research, 46 (D1): D788-D793. https://doi.org/10.1093/nar/gkx921
Magno, Ramiro; Duarte, Isabel; Andrade, Raquel P.; Palmeirim, Isabel. 2017. "rdml: A Mathematica package for parsing and importing Real-Time qPCR data". BMC Research Notes, 10 (1). https://doi.org/10.1186/s13104-017-2533-9
Macedo, J. A.; Schrama, D.; Duarte, I.; Tavares, E.; Renaut, J.; Futschik, M. E.; Rodrigues, P. M.; Melo, E. P.. 2017. "Membrane-enriched proteome changes and prion protein expression during neural differentiation and in neuroblastoma cells". BMC Genomics, 18 (1). https://doi.org/10.1186/s12864-017-3694-6
Pinto, Elsa; Anselmo, Marisol; Calha, Manuela; Bottrill, Andrew; Duarte, Isabel; Andrew, Peter W; Faleiro, Maria L. 2017. "The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins". Microbiology, 163 (2): 161-174. https://doi.org/10.1099/mic.0.000412
Bastos, Rita; Duarte, Isabel; Thorsteinsdottir, Solveig ; Andrade, Raquel P.. 2017. Rewinding the Clock: Origin and evolution of the Hairy/Enhancer of split protein family.. Em CBMR Conference.
van Zoelen, Everardus J.; Duarte, Isabel; Hendriks, José M.; van der Woning, Sebastian P.. 2016. "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). https://doi.org/10.1186/s13287-016-0375-3
Pinto, José P.; et al.; Duarte, Isabel; Futschik, Matthias E.. 2016. SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology.. Em INForum.
Machado, Susana; et al.; Duarte, Isabel; Futschik, Matthias E.; Pinto, José P.. 2015. StemChecker : a web-based tool to discover and explore stemness signatures in gene sets.. Em 9th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies.
Machado, Rui S.; Pinto, José P.; Oliveira, Daniel V.; Duarte, Isabel; et al.; Futschik, Matthias E.. 2015. HeartEXpress: A meta-analysis study of stem cell differentiation in the context of cardiogenesis.. Em SPCE-TC.
Oliveira, Daniel V.; Duarte, Isabel; et al.; Futschik, Matthias E.. 2015. From Stem Cells 2 Heart: Finding novel candidate isoforms and genes for cardiomyogenesis. . Em 9th International Meeting of the Portuguese society for Stem cells and Cell therapies.
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.. 2015. "StemChecker: a web-based tool to discover and explore stemness signatures in gene sets". Nucleic Acids Research, 43 (W1): W72-W77. https://doi.org/10.1093/nar/gkv529
Duarte, Isabel; et al.; Futschik, Matthias E.. 2014. From Stem Cells 2 Heart: Elucidating the role of alternative splicing in cardiomyogenesis.. Em Heart without Borders Conference.
Oliveira, Daniel V.; Machado, Rui S.; Pacheco-Leyva, Ivette; Duarte, Isabel; et al.; Futschik, Matthias E.. 2014. From Stem Cells 2 Heart: Finding novel candidate genes for cardiomyogenesis.. Em Heart without Borders Conference.
Huynen, Martijn A.; Duarte, Isabel; Szklarczyk, Radek. 2013. "Loss, replacement and gain of proteins at the origin of the mitochondria". Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1827 (2): 224-231. https://doi.org/10.1016/j.bbabio.2012.08.001
Willems, Peter; Wanschers, Bas F.J.; Esseling, John; Szklarczyk, Radek; Kudla, Urszula; Duarte, Isabel; Forkink, Marleen; et al. 2013. "BOLA1 Is an Aerobic Protein That Prevents Mitochondrial Morphology Changes Induced by Glutathione Depletion". Antioxidants & Redox Signaling, 18 (2): 129-138. https://doi.org/10.1089/ars.2011.4253
Duarte, Isabel; Nabuurs, Sander B.; Magno, Ramiro; Huynen, Martijn. 2012. "Evolution and Diversification of the Organellar Release Factor Family". Molecular Biology and Evolution, 29 (11): 3497-3512. https://doi.org/10.1093/molbev/mss157
Kensche, Philip R; Duarte, Isabel; Huynen, Martijn A. 2012. "A three-dimensional topology of complex I inferred from evolutionary correlations". BMC Structural Biology, 12 (1). https://doi.org/10.1186/1472-6807-12-19
Huynen, Martijn A; Duarte, Isabel; Chrzanowska-Lightowlers, Zofia M A; Nabuurs, Sander B. 2012. "Structure based hypothesis of a mitochondrial ribosome rescue mechanism". Biology Direct, 7 (1). https://doi.org/10.1186/1745-6150-7-14
de Graaf, Rob M.; Ricard, Guenola; van Alen, Theo A.; Duarte, Isabel; Dutilh, Bas E.; Burgtorf, Carola; Kuiper, Jan W. P.; et al. 2011. "The Organellar Genome and Metabolic Potential of the Hydrogen-Producing Mitochondrion of Nyctotherus ovalis". Molecular Biology and Evolution, 28 (8): 2379-2391. https://doi.org/10.1093/molbev/msr059
Duarte, I.; Huynen, Martijn A.. 2011. The Release Factor family: Origin and evolution. Em Benelux Bioinformatics Conference (BBC2011) - Luxembourg city, Luxembourg. https://doi.org/10.1142/9789814542005
Duarte, Isabel; Huynen, Martijn A.. 2010. Origin and evolution of the organellar Release Factors. Em European Conference on Computational Biology (ECCB) - Ghent, Belgium.
Duarte, Isabel; de Graaf, Rob M; van Alen, Theo A; Kuiper, Jan WP; Schotanus, Klaas; Rosenberg, Jörg; Huynen, Martijn A; Hackstein, Johannes HP. 2009. "The hydrogenosomes of Psalteriomonas lanterna". BMC Evolutionary Biology, 9 (1). https://doi.org/10.1186/1471-2148-9-287
Duarte, Isabel; Huynen, Martijn A.. 2009. Mitochondria and the origin of Eukaryotes. Em Intelligent Systems for Molecular Biology (ISMB) and European Conference on Computational Biology (ECCB) - Stockholm, Sweeden.
Duarte, Isabel; Huynen, Martijn A.. 2009. Eukaryotic Iron-Sulfur cluster assembly: Where does it come from?. Em Benelux Bioinformatics Conference (BBC2009) - Liège, Belgium.
Ricard, Guénola; de Graaf, Rob M; Dutilh, Bas E; Duarte, I; van Alen, Theo A; van Hoek, Angela HAM; Boxma, Brigitte; et al. 2008. "Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns". BMC Genomics, 9 (1). https://doi.org/10.1186/1471-2164-9-587
Duarte, Isabel; Huynen, Martijn A.. 2008. Predicting novel functional interactors in Iron-Sulfur cluster assembly. Em Benelux Bioinformatics Conference (BBC2008) - Maastricht, The Netherlands.
Duarte, Isabel; Huynen, Martijn A.. 2008. Phylogenetic study of Eukaryotic Iron-Sulfur cluster assembly proteins. Em NCMLS PhD conference - Arnhem, The Netherlands.
Duarte, Isabel; Huynen, Martijn A.. 2007. Iron-Sulfur cluster biogenesis: Inferring functional interactions. Em NCMLS PhD conference - Arnhem, The Netherlands.
Santos, Alexandra M.; Sousa, Hugo; Pinto, Daniela; Portela, Catarina; Pereira, Deolinda; Catarino, Raquel; Duarte, Isabel; Lopes, Carlos; Medeiros, Rui. 2006. "Linking TP53 codon 72 and P21 nt590 genotypes to the development of cervical and ovarian cancer". European Journal of Cancer, 42 (7): 958-963. https://doi.org/10.1016/j.ejca.2006.01.015
Duarte, Isabel. 2006. "Polimorfismo no promotor do gene TNF-alpha e risco para cancro do colo uterino.". Mestrado.
Duarte, Isabel; Santos, Alexandra; Sousa, Hugo; Catarino, Raquel; Pinto, Daniela; Matos, Ana; Pereira, Deolinda; et al. 2005. "G-308A TNF-a polymorphism is associated with an increased risk of invasive cervical cancer". Biochemical and Biophysical Research Communications, 334 (2): 588-592. https://doi.org/10.1016/j.bbrc.2005.06.137
Duarte, Isabel. 2003. "Polimorfismo associado ao gene TNF-alpha em doentes oncologicos". Licenciatura.
Duarte, Isabel; et al.; Medeiros, Rui. 2003. O Papel do Polimorfismo TNF-alpha (-308) no Desenvolvimento do Cancro da Mama. Em V Congresso Nacional de Senologia.
