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Aparicio</a>. He also visited the lab of <ahref="https://www.crg.eu/juan_valcarcel">Juan Valcárcel</a> at
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<ahref="http://www.embl.de/" target="_blank" rel="noopener">EMBL</a> Heidelberg for a few months in 2002.
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His PhD work involved bioinformatics studies on the complexity of splicing and gene expression,
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His PhD work involved <ahref="nuno/Thesis.pdf" target="_blank" rel="noopener">bioinformatics studies on the complexity of splicing and gene expression</a>,
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including studies on
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<ahref="http://www.ncbi.nlm.nih.gov/pubmed/16344558" target="_blank" rel="noopener">the evolution of splicing factors</a>
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and
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<ahref="http://www.ncbi.nlm.nih.gov/pubmed/17137510" target="_blank" rel="noopener">the RNA binding of splicing factors</a>.
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<ahref="https://doi.org/10.1101/gr.3936206" target="_blank" rel="noopener">the evolution of splicing factors</a>.
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</p>
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<p>
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Nuno was a postdoctoral member of the Computational Biology Group at the University of Cambridge,
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led by Professor Simon Tavaré and based at the
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<ahref="http://www.cambridgecancer.org.uk/" target="_blank" rel="noopener">CRUK Cambridge Research Institute</a>,
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led by <ahref="https://tavarelab.cancerdynamics.columbia.edu/">Simon Tavaré</a> and based at the
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<ahref="https://www.cruk.cam.ac.uk/" target="_blank" rel="noopener">CRUK Cambridge Research Institute</a>,
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from 2006 to July 2010. His main research was focused on understanding the complexity of gene
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expression regulation and its impact on disease mechanisms, namely oncogenesis. He collaborated
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with the Odom Group in determining the molecular mechanisms responsible for the stability of
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transcriptional programs, studying the regulation of lineage-specific retrotransposons and
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repeat elements. He also contributed to the
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<ahref="http://www.ncbi.nlm.nih.gov/pubmed/19923232" target="_blank" rel="noopener">complete transcriptomic and genomic reannotation of Illumina BeadArray probe sequences</a>
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and numerous cancer research studies.
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with the <ahref="https://www.dkfz.de/en/employees/duncan-odom">Odom
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Group</a> in determining the molecular mechanisms responsible for the stability of
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transcriptional programs by <a
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href="https://doi.org/10.1126/science.1160930">decoupling the
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relative contributions of <i>cis</i< and <i>trans</i> effects on
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histone mark patterning, transcription factor binding, and gene
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expression</a>, as well as studying the regulation of
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lineage-specific retrotransposons and repeat elements. Such work
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involved the analysis, annotation and integration of different
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sorts of array and sequence information.
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<BR>He also contributed to the <ahref="https://doi.org/10.1093/nar/gkp942" target="_blank" rel="noopener">complete transcriptomic and genomic reannotation of Illumina BeadArray probe sequences</a>, as the original annotation is shown to bias the interpretation of cancer data. This is part of a general pipeline for microarray probe reannotation. Nuno's efforts have also contributed for the development of several microarray-related methodologies.
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In Cambridge, Nuno has also contributed with <ahref="https://pubmed.ncbi.nlm.nih.gov/?term=barbosa-morais+n+%26+((caldas+c+%26+cancer[title])+|+coleman+n+|+ponder+b)&sort=date">microarray annotation and sequence analysis for several cancer research studies</a>.
at the University of Toronto in August 2010, where he was involved in
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<ahref="http://www.sciencemag.org/content/338/6114/1587.abstract" target="_blank" rel="noopener">the analysis of mRNA-seq data for the inference of tissue- and species-specific alternative splicing patterns</a>.
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He was awarded a Postdoctoral Fellowship from the
@@ -427,20 +434,19 @@ <h1 class="nuno-hero-name">Nuno L. Barbosa-Morais</h1>
and an FCT Investigator Starting Grant, establishing
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his independent research group at GIMM in early 2015. In 2020, he was awarded a 6-year
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and an FCT Investigator Starting Grant, establishing his independent research group in early 2015 at the iMM (now GIMM), where he was based until 2025. In 2020, he was awarded a 6-year
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Assistant Researcher contract in FCT's Individual Call to Scientific Employment Stimulus.
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</p>
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<p>
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Nuno is an Invited Associate Professor at the
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<ahref="https://www.medicina.ulisboa.pt/en" target="_blank" rel="noopener">Faculty of Medicine, University of Lisbon</a>,
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where he teaches Bioinformatics to Masters students in Biomedical Engineering, Oncobiology,
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Nuno was an Invited Associate Professor at the
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<ahref="https://www.medicina.ulisboa.pt/en" target="_blank" rel="noopener">Faculty of Medicine, University of Lisbon</a> from 2020 to 2025,
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where he taught Bioinformatics to Masters students in Biomedical Engineering, Oncobiology,
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and Biomedical Research.
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</p>
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<p>
@@ -496,13 +502,38 @@ <h1 class="nuno-hero-name">Nuno L. Barbosa-Morais</h1>
Martins-Silva R, Kaizeler A, <strong>Barbosa-Morais NL</strong>.
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"<ahref="https://doi.org/10.1093/nargab/lqag057" target="_blank" rel="noopener">Exploring molecular signatures of senescence with markeR, an R toolkit for evaluating gene sets as phenotypic markers.</a>"
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<em>NAR Genomics and Bioinformatics</em>, 2026 Jun 8;8(2):lqag057.
Soares MVD, Gómez VE, Azevedo RI, Pereira PNG, Velázquez TC, Mendes L, Alho AC, García-Guerrero E, Garcia-Calderón CB, Tharmaratnam K, Cabral IA, Ribeiro AC, Juncal C, Roncon S, Pais AT, Gil AR, Espada E, Rodrigues A, Garção A, Yaspo ML, Warnatz HJ, Lehrach H, Ward L, <strong>Barbosa-Morais NL</strong>, Quintas AM, Palmela P, Caldas C, Ferreira R, Leite L, Martins C, Lourenço F, Moreno R, Campilho F, Cheyne CP, Garcia-Fiñana M, Campos A, Baron F, Arpinati M, Hoffmann P, Edinger M, Koreth J, Ritz J, Vaz CP, Perez-Simon JA, Lacerda JF.
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"<ahref="https://doi.org/10.1182/bloodadvances.2025017996" target="_blank" rel="noopener">Phase 1/2 trials of donor regulatory T cells for the treatment of steroid-refractory chronic graft-versus-host disease.</a>"
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<em>Blood Advances</em>, 2026 May 12;10(9):2904-2915.
Wagner V, Bousset L, Ascensão-Ferreira M, Sun B, Barragan Avila JE, Kaizeler A, Martins-Silva R, Rahbari M, Fernández-Vaquero M, Haston S, Tinti M, Pombo J, Khadayate S, Roth S, Schürch CM, Martínez-Barbera JP, Bahat A, Wee KB, Morton JP, Malek N, Innes AJ, Vernia S, <strong>Barbosa-Morais NL</strong>, Gallage S, Heikenwalder M, Gil J.
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"<ahref="https://doi.org/10.1038/s41467-026-71564-z" target="_blank" rel="noopener">Spliceosome induction is a druggable dependency of RAS-driven senescence and cancer.</a>"
Jardim C*, Bica M*, Reis-Sobreiro M, da Mota AT, Lopes R, Pinto M, Sousa NS, Mensurado S, Boekhoff H, Scolaro T, Reugebrink M, Gonçalves-Sousa N, Kubo H, Gomes CM, Brito C, Arguello R, Leites EP, Morais VA, Silva-Santos B, <strong>Barbosa-Morais NL</strong><sup>+</sup>, Serre K.
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"<ahref="https://doi.org/10.1158/2326-6066.CIR-24-0797" target="_blank" rel="noopener">Sustained macrophage reprogramming is required for CD8 T cell-dependent long-term tumor eradication.</a>"
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<em>Cancer Immunology Research</em>, 2025 Jun 5; in press.
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<em>Cancer Immunology Research</em>, 2025 Aug 1;13(8):1207-1225.
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