Disease Transcriptomics

We are a group of researchers applying mostly computational approaches, particularly those involving the analysis of high-throughput genomic and transcriptomic data, to fundamental questions in biomedical research. We have a long-term interest in the systems-level transcriptional regulation underlying mammalian cell specification, often perturbed in disease.

We aim to understand how RNA-level (transcription initiation, splicing, etc) changes in (mostly) human tissues increase proneness to diseases, namely cancer, neurodegenerative disorders and other ageing-related pathologies.

We thereby aim to identify molecular targets for functional exploration in vitro and in vivo. We also combine molecular and clinical information for the unveiling of novel candidate prognostic factors and therapeutic targets. Along the way, we develop some tools for assisting non-computational scientists in their analyses of transcriptomic data. We coordinate BIOMICS, a Twinning project funded by the European Union aiming at "Fostering Excellent Research, Training and Innovation in Biomedical Data Science".

  • Horizon Europe Twinning – BIOMICS: Fostering Excellent Research, Training and Innovation in Biomedical Data Science.
    Learn more here.
  • Horizon Europe – EvoMG-DN: Evolutionary Medical Genomics Doctoral Network.
    Learn more here.
  • Jardim C, Bica M, Reis-Sobreiro M, Teixeira da Mota A, Lopes R, Pinto MF, Sousa NS, Mensurado S, Boekhoff H, Scolaro T, Reugebrink M, Goncalves-Sousa N, Kubo H, Gomes CM, Brito C, Argüello RJ, Leites EP, Morais VA, Silva-Santos B, Barbosa-Morais NL, Serre K. Sustained Macrophage Reprogramming Is Required for CD8+ T cell-Dependent Long-Term Tumor Eradication. Cancer Immunol Res. 2025 Aug 1;13(8):1207-1225. doi: 10.1158/2326-6066.CIR-24-0797.
  • Schneider AL, Martins-Silva R, Kaizeler A, Saraiva-Agostinho N, Barbosa-Morais NL. voyAGEr, a free web interface for the analysis of age-related gene expression alterations in human tissues. Elife. 2024 Mar 28;12:RP88623. doi: 10.7554/eLife.88623.
  • Ascensão-Ferreira M, Martins-Silva R, Saraiva-Agostinho N, Barbosa-Morais NL. betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions. RNA. 2024 Mar 18;30(4):337-353. doi: 10.1261/rna.079764.123.
  • Bordone MC, Barbosa-Morais NL. Unraveling Targetable Systemic and Cell-Type-Specific Molecular Phenotypes of Alzheimer's and Parkinson's Brains With Digital Cytometry. Front Neurosci. 2020 Dec 9;14:607215. doi: 10.3389/fnins.2020.607215.
  • Rathore OS, Silva RD, Ascensão-Ferreira M, Matos R, Carvalho C, Marques B, Tiago MN, Prudêncio P, Andrade RP, Roignant JY, Barbosa-Morais NL, Martinho RG. NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal-ventral patterning. RNA. 2020 Dec;26(12):1935-1956. doi: 10.1261/rna.077446.120.
  • Munkley J, Li L, Krishnan SRG, Hysenaj G, Scott E, Dalgliesh C, Oo HZ, Maia TM, Cheung K, Ehrmann I, Livermore KE, Zielinska H, Thompson O, Knight B, McCullagh P, McGrath J, Crundwell M, Harries LW, Daugaard M, Cockell S, Barbosa-Morais NL, Oltean S, Elliott DJ. Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer. Elife. 2019 Sep 3;8:e47678. doi: 10.7554/eLife.47678.
  • de Almeida BP, Vieira AF, Paredes J, Bettencourt-Dias M, Barbosa-Morais NL. Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome. PLoS Comput Biol. 2019 Mar 11;15(3):e1006832. doi: 10.1371/journal.pcbi.1006832.
  • Saraiva-Agostinho N, Barbosa-Morais NL. psichomics: graphical application for alternative splicing quantification and analysis. Nucleic Acids Res. 2019 Jan 25;47(2):e7. doi: 10.1093/nar/gky888.
  • 2026: Oncology Research Grant, Portuguese League Against Cancer - Southern Regional Center / Benfica Foundation [Francisca Xara-Brasil and Nuno B. Morais]
  • 2026: Best Poster Presentation by a 4th year PhD student, CAML & GIMM PhD Meeting [Rita M. Silva]
  • 2024: University of Lisbon/Caixa Geral de Depósitos Scientific Award – Biomedical Sciences [Nuno B. Morais]
  • 2023: Best Graphical Poster, XVI CAML PhD Students Meeting [Rita M. Silva]
  • 2022: Best Beginner Presentation, XV CAML PhD Students Meeting [Rita M. Silva]
  • 2022: Best Master Thesis Award, Institute of Molecular Medicine João Lobo Antunes [Rita M. Silva]
  • 2015-2021: EMBO (European Molecular Biology Organization) Installation Grant [Nuno B. Morais]
  • Manuel Irimia – CRG/UPF Barcelona, Spain
  • Pedro Beltrão – ETH Zürich, Switzerland
  • Jesús Gil – Imperial College London, UK
  • Verena Wagner – M3 Tübingen, Germany
  • Vera Martins – University Hospital Ulm, Germany
  • Gonçalo Bernardes – University of Cambridge, UK
  • Vanessa Morais – Lisbon School of Medicine, Portugal
  • Sandra Casimiro – GIMM, Portugal

Principal Investigator

Nuno Barbosa Morais
Principal Investigator

Team

Diana Vieira
Post-doc Researcher
Jacek Marzec
Post-doc Researcher
Rita Silva
PhD Student
Alexandre Kaizeler
PhD Student
Francisca Xara-Brasil
PhD Student
Daniel Marques
MSc Student