My CV

Isabel Duarte (PhD) - Junior Researcher
Faculty of Sciences and Technology (building 8, room 3.14)
University of Algarve, Faro - Portugal
Phone: + 351 289 800 100 (extension 7177)
Institutional website: UAlg
Scientific profile: Google scholar | ORCID | CienciaVitae
Social media: LinkedIn
Contact me: giduarte at ualg dot pt


Academic degrees

2017

  • PhD in Medical Sciences | Radboud Universiteit (Nijmegen, The Netherlands)

2005-2006

  • PhD program in Computational Biology | Instituto Gulbenkian de Ciência (Oeiras, Portugal)

2006

  • Master in Oncology | Universidade do Porto (Porto, Portugal)

2003

  • BSc in Applied Biology | Universidade do Minho (Braga, Portugal)


Current position

2022 – present

  • Junior researcher | CINTESIS - Universidade do Algarve (Faro, Portugal) |
    CEEC Project | Causal Inference in Cancer | Research fellow contract
Previous positions

2019 – 2022

  • Bioinformatics researcher | CINTESIS - Universidade do Algarve (Faro, Portugal)
    FCT Project | DEvoCancer: Decoding breast cancer evolution through mutant allele differential expression signatures | Post-doc research contract

2018 – 2019

  • Invited Assistant Professor | Faculty of Medicine and Biomedical Sciences - Universidade do Algarve - Faro, Portugal
    Lecturer in Computational Biology

2016 – 2019

  • Bioinformatics researcher | CBMR - Universidade do Algarve - Faro, Portugal
    FCT Project | ClockOME: Gene Regulatory Network in Temporal Control of Mesoderm Specification | Research grant

2014 – 2015

  • Bioinformatics researcher | CBMR - Universidade do Algarve - Faro, Portugal
    FCT Project | SPLICE: Alternative splicing and its impact on molecular networks during stem cell differentiation | Research grant

2012 - 2013

  • Bioinformatics expert | Radboud University (The Netherlands) & University of Birmingham (United Kingdom) & University of Jena (Germany)
    European ERASysBio+ project | LINCONET: Modelling the gene regulatory network underlying lineage commitment in human Mesenchymal Stem Cells | Research grant

2005

  • Lab researcher | Thomas Jefferson University - Philadelphia, USA
    Daniel Baugh Institute for Functional Genomics and Computational Biology | Masters degree student

2002 –2005

  • Lab researcher | Instituto Português de Oncologia Francisco Gentil (IPO) - Porto, Portugal
    Molecular Pathology Lab | Masters degree student

2002-2004

  • Practical classes assistant | Universidade do Minho - Braga, Portugal
    Antropobiology course | Practical classes instructor


Skills & Competences

  • Informatics

    R (software environment for statistical computing and graphics) • Perl (scripting language) • Bash (Unix command processor shell) • MySQL (open source database) • Linux (Operating System)

  • Bioinformatics

    Data science • Next Generation sequencing (OMICs) • R/Bioconductor • BigData management • Statistics • Phylogenomics • Comparative genomics • Genome annotation

  • Natural languages

    Portuguese | Native language

    English | Full professional proficiency


Teaching

2018 - 2023 | Computational Biology

  • Masters in Biomedical Sciences | Faculty of Medicine and Biomedical Sciences - Universidade do Algarve - Faro, Portugal

2017 - present | RNA-seq | Invited Yearly Seminar

  • Masters in Oncobiology | Faculty of Medicine and Biomedical Sciences - Universidade do Algarve - Faro, Portugal

2017 - present | Metagenomics | Invited Yearly Seminar

  • Masters in Molecular and Microbial Biology | Faculty of Sciences and Technology - Universidade do Algarve - Faro, Portugal

2018 - 2019 | Bioinformatics

  • BSc in Biomedical Sciences | Faculty of Medicine and Biomedical Sciences - Universidade do Algarve - Faro, Portugal


Selected publications | Peer-reviewed Journals

  • Maia-Fernandes AC, Martins-Jesus A, Borralho-Martins N, Pais-de-Azevedo T, Magno R, Duarte I, Andrade RP. Spatio-temporal dynamics of early somite segmentation in the chicken embryo. PLoS ONE. 2024. (doi: https://doi.org/10.1371/journal.pone.0297853)

  • Barata Tânia, Duarte Isabel, Futschik ME. Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes. Genes. 2023. https://doi.org/10.3390/genes14030745

  • Lizelle Correia*, Ramiro Magno*, Joana M. Xavier, Bernardo P. de Almeida, Isabel Duarte, Filipa Esteves, Marinella Ghezzo, Matthew Eldridge, Chong Sun, Astrid Bosma, Lorenza Mittempergher, Ana Marreiros, Rene Bernards, Carlos Caldas, Suet-Feung Chin, Ana-Teresa Maia. Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant. NPJ Breast Cancer. 2022. (doi: https://doi.org/10.1038/s41523-022-00435-9)

  • Duarte Isabel*, Carraco G*, Andrade RP. gga-miRNOME, A microRNA-sequencing dataset from chick embryo development. Nature Scientific Data. 2022. (doi: https://doi.org/10.1038/s41597-022-01126-7)

  • Duarte Isabel*, Magno R*, Maia AT. quincunx: an R package to query, download and wrangle PGS Catalog data. Bioinformatics. 2021. (doi: https://doi.org/10.1093/bioinformatics/btab522)

  • José Matos, Isabel Matos, Manuela Calha, Pedro Santos, Isabel Duarte, Yameric Cardoso, and Maria L. Faleiro. Insights from Bacteroides Species in Children with Type 1 Diabetes. Microorganisms. 2021. (doi: https://doi.org/10.3390/microorganisms9071436)

  • Liber M, Duarte Isabel, Maia AT, Oliveira HR. 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: https://10.3389/fpls.2021.628439)

  • Machado S, Silva A, De Sousa-Coelho AL, Duarte Isabel, Grenho I, Santos B, Mayoral-Varo V, Megias D, Sánchez-Cabo F, Dopazo A, Ferreira BI, Link W. Harmine and Piperlongumine Revert TRIB2-Mediated Drug Resistance. Cancers. 2020. (doi: https://doi.org/10.3390/cancers12123689)

  • Pais-de-Azevedo T, Magno R, Duarte Isabel and Palmeirim I. Recent advances in understanding vertebrate segmentation. F1000 Research. 2018. (PMID: 29416855)

  • Pinto JP, Machado RSR, Magno R, Oliveira DV, Machado S, Andrade RP, Bragança J, Duarte I and Futschik ME. StemMapper: a curated gene expression database for stem cell lineage analysis. Nucleic Acids Research. 2017. (PMID: 29045725)

  • Magno R, Duarte Isabel, Andrade RP and Palmeirim I. rdml: A Mathematica package for parsing and importing Real-Time qPCR data. BMC Research Notes. 2017. (PMID: 28606167)

  • Macedo JA, Schrama D, Duarte Isabel, Tavares E, Renaut J, Futschik ME, Rodrigues PM and Melo EP. Membrane-enriched Proteomic changes Associated with Prion protein expression during Neural Differentiation and in Neuroblastoma Cells. BMC Genomics. 2017. (PMID: 28431525)

  • Pinto E, Anselmo M, Calha M, Bottrill A, Duarte Isabel, Andrew PW and Faleiro ML. The Intestinal Proteome of Diabetic and Control children are Enriched with Different Microbial and Host proteins. Microbiology (UK). 2017. (PMID: 28270263)

  • van Zoelen EJ, Duarte Isabel, Hendriks JM and van der Woning SP. TGFB-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. 2016. (PMID: 27562730)

  • Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RS, Machado S, Pacheco-Leyva I, Duarte Isabel and Futschik ME. StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. Nucleic Acids Research. 2015. (PMID: 26007653)

  • Huynen MA, Duarte Isabel and Szklarczyk R. Loss, replacement and gain of proteins at the origin of the mitochondria. Biochimica et Biophysica Acta - Bioenergetics. 2013. (PMID: 22902511)

  • Willems P, Wanschers B, Esseling J, Szklarczyk R, Kudla U, Duarte Isabel, Forkink M, Nooteboom M, Swarts H, Gloerich J, Nijtmans L, Koopman W and Huynen MA. BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion. Antioxidants & Redox Signaling. 2013. (PMID: 22746225)

  • Kensche PR, Duarte Isabel and Huynen MA. A three-dimensional topology of complex I inferred from evolutionary correlation. BMC Structural Biology. 2012. (PMID: 22857522)

  • Duarte Isabel, Naaburs SB, Magno R and Huynen MA. Evolution and diversification of the organellar release factor family. Molecular Biology and Evolution. 2012. (PMID: 22688947)

  • Huynen MA, Duarte Isabel, Chrzanowska-Lightowlers ZM and Naaburs SB. Structure based hypothesis of a mitochondrial ribosome rescue mechanism. Biologyl Direct. 2012. (PMID: 22569235)

  • de Graaf RM, Ricard G, van Alen TA, Duarte Isabel, Dutilh BE, Burgtorf C, Kuiper JW, van der Staay GW, Tielens AG, Huynen MA, Hackstein JH. The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis. Molecular Biology and Evolution. 2011. (PMID: 21378103)

  • Duarte Isabel*, de Graaf RM*, van Alen TA, Kuiper JW, Schotanus K, Rosenberg J, Huynen MA, Hackstein JH. The hydrogenosomes of Psalteriomonas lanterna. BMC Evolutionary Biology. 2009. (PMID: 20003182)

  • Ricard G, de Graaf RM, Dutilh BE, Duarte Isabel, van Alen TA, van Hoek AH, Boxma B, van der Staay GW, Moon-van der Staay SY, Chang WJ, Landweber LF, Hackstein JH, Huynen MA. Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. BMC Genomics. 2008. (PMID: 19061489)

  • Santos AM, Sousa H, Pinto D, Portela C, Pereira D, Catarino R, Duarte Isabel, Lopes C, Medeiros R. Linking TP53 codon 72 and P21 nt590 genotypes to the development of cervical and ovarian cancer. European Journal of Cancer. 2006. (PMID: 16542834)

  • Duarte Isabel, Santos AM, Sousa H, Catarino R, Pinto D, Matos A, Pereira D, Moutinho J, Canedo P, Machado JC, Medeiros R. G-308A TNF-alpha Polymorphism is Associated with an Increased Risk of Invasive Cervical Cancer. Biochemical and Biophysical Research Communications. 2005. (PMID: 16009345)


Pre-print publications

  • Duarte Isabel*, Liber M*, Magno R, Andrade RP. FrozenChicken: Promoting the meta-analysis of chicken microarray data. bioRxiv. 2021. (doi: https://doi.org/10.1101/2021.02.25.432894)

  • Duarte Isabel and Huynen MA. Contribution of Lateral Gene Transfer to the evolution of the eukaryotic fungus Piromyces sp. E2: Massive bacterial transfer of genes involved in carbohydrate metabolism. bioRxiv. 2019. (doi: https://doi.org/10.1101/514042)


Software packages & Open code

  • R Package | Duarte Isabel | SomiteExploreR | 2023 https://github.com/iduarte/SomiteExplorerR

  • R Package | Duarte Isabel, Magno Ramiro | ualg.dia.aberto | Bioinformatics interactive tutorial | Scientific outreach for high school students. 2022 https://github.com/instructr/ualg.dia.aberto

  • R Package | Duarte Isabel, Magno Ramiro | ualg.compbio | R programming interactive tutorials. 2022 https://github.com/instructr/ualg.compbio

  • R Package | Magno Ramiro, Duarte Isabel, Maia Ana-Teresa | quincunx | Analysis of Polygenic Risk Scores. 2021 https://github.com/maialab/quincunx

  • R notebook | Duarte Isabel | gga_mirnOME | miRNA Expression data analysis 2021 https://doi.org/10.6084/m9.figshare.14706891.v1

  • R notebook | Duarte Isabel, Magno Ramiro | Piromyces Laterally Transferred Metabolism. 2018 https://doi.org/10.6084/m9.figshare.7173173


Datasets | Published, Managed & Analysed

  • Chick Embryo Segmented Region Length Measurements data | Ana Cristina Maia-Fernandes, Ana Martins-Jesus, Tomas Pais-de-Azevedo, Ramiro Magno, Isabel Duarte, Raquel P Andrade | 2023 https://doi.org/10.6084/m9.figshare.22341070.v3

  • microRNA-seq data | Duarte Isabel | gga_mirnOME Expression | miRNA Expression datasets from chick embryonic tissues | 2021 https://doi.org/10.6084/m9.figshare.14706867.v2

  • microRNA-seq data | Duarte Isabel | gga_mirnOME Novel | Novel Predicted miRNAs and Expression values from chick embryonic tissues | 2021 https://doi.org/10.6084/m9.figshare.14901102.v1

  • RData package | Duarte Isabel, Magno Ramiro | gga.mirnas.qpcr | Data from the qPCR validation of miRNAs from gga_mirnOME | 2021 https://github.com/iduarte/gga.mirnas.qpcr (Private Repository until publication)

  • RData package | Duarte Isabel | DEvoCancerDataset | Breast Cancer genomics and transcriptomics | 2020 https://github.com/maialab/devocancerMetabricTCGA (Private Repository until publication)

  • RData package | Duarte Isabel | metabricDataset | Breast Cancer genomics and transcriptomics | 2020 https://github.com/maialab/metabricDataset (Private Repository until publication)

  • RData package | Duarte Isabel | tcgaDataset | Breast Cancer genomics and transcriptomics | 2020 https://github.com/maialab/tcgaDataset (Private Repository until publication)

  • RData package | Duarte Isabel | FrozenChicken | Transcriptomics data for normalization of chicken microarray meta-analyses | 2019 https://github.com/iduarte/FrozenChicken

  • Comparative genomics data | Duarte Isabel | Prok2EukLateralGeneTransfer | 2018 https://doi.org/10.6084/10.6084/m9.figshare.7173020


* Equal contribution

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