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Nuno graduated in Technologic Physics Engineering from Instituto Superior Técnico (Lisbon, Portugal) in 2000. The research on cardiovascular variability associated with the degree's final project took place at the University of Lisbon Medical School, under the supervision of the late Prof. Luis Silva Carvalho. He completed a Graduate Program in Biophysics and Biomedical Engineering at IBEB, Faculty of Sciences of the University of Lisbon in 2001. He did his PhD in Biomedical Sciences at the University of Lisbon Medical School with Carmo Fonseca. Most of the PhD research actually took place at the University of Cambridge with Samuel Aparicio. He also visited the lab of Juan Valcarcel at EMBL for a few months in 2002. His PhD work involved bioinformatics studies on the complexity of splicing and gene expression and his efforts include studies on the evolution of splicing factors and the RNA binding of splicing factors. Nuno was a postdoctoral member of the Computational Biology Group from the University of Cambridge, led by Simon Tavaré and based at the CRUK Cambridge Research Institute, from 2006 to July 2010. His main research in the Computational Biology Group was focused on understanding the complexity of gene expression regulation and its impact on disease mechanisms, namely oncogenesis. Nuno has been interested in the systems-level transcriptional mechanisms underlying mammalian cell specification (often perturbed in carcinomas). In particular, he collaborated with the Odom Group in determining the molecular mechanisms responsible for the stability of transcriptional programs by decoupling the relative contributions of cis and trans effects on histone mark patterning, transcription factor binding, and gene expression, as well as studying the regulation of lineage-specific retrotransposons and repeat elements. Such work involved the analysis, annotation and integration of different sorts of array and sequence information. Nuno was involved in the identification of the most important issues in the analysis of BeadChip information, namely by performing the complete transcriptomic and genomic reannotation of probe sequences, 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. Nuno has collaborated with Roger Palmer in the study of global gene expression patterns in pediatric malignant germ cell tumours. He has also contributed with microarray annotation and sequence analysis for several breast cancer research studies, such as determining molecular classifiers (with the Caldas Lab) and risk-associated SNPs (with the Ponder Lab). Nuno joined the Blencowe Lab at the University of Toronto in August 2010. He was involved in the analysis of mRNA-seq data for the inference of tissue and species specific alternative splicing patterns. He has been awarded a Postdoctoral Fellowship from the Canadian Institutes of Health Research and a Marie Curie International Outgoing Fellowship. Nuno moved in June 2013 to the iMM Lisboa for the return phase of his Marie Curie International Outgoing Fellowship. He was also, from October 2013 to April 2015, an Honorary Senior Research Fellow at the Nuffield Department of Obstetrics and Gynaecology of the University of Oxford. He has been awarded an EMBO Installation Grant and an FCT Investigator Starting Grant and established his own research group at the iMM in the beginning of 2015. Nuno coordinates Bioinformatics Matters, the iMM node of GenomePT. In 2020, he was awarded a 6-year Assistan Researcher contract in FCT's Individual Call to Scientific Employment Stimulus. Nuno is a Guest Associate Professor at the Faculty of Medicine, University of Lisbon, where he teaches Bioinformatics to Masters in Biomedical Engineering, Oncobiology and Biomedical Research.
Identification

Personal identification

Full name
NUNO LUÍS BARBOSA MORAIS

Citation names

  • BARBOSA-MORAIS, NUNO

Author identifiers

Ciência ID
5C19-CA77-A74D
ORCID iD
0000-0002-1215-0538
Google Scholar ID
LS9tM7sAAAAJ
Researcher Id
I-2743-2013
Scopus Author Id
6507555084

Email addresses

  • nmorais@medicina.ulisboa.pt (Professional)

Telephones

Telephone
  • 217999411 (Professional)

Addresses

  • Instituto de Medicina Molecular João Lobo Antunes. Av. Prof. Egas Moniz, Edf. Egas Moniz, Sala P3B-34, 1649-028, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Biology
  • Natural sciences - Biological Sciences - Cell Biology
  • Natural sciences - Biological Sciences - Molecular Biology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Basic Medicine - Human Genetics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Spanish; Castilian Advanced (C1) Proficiency (C2) Upper intermediate (B2) Proficiency (C2) Upper intermediate (B2)
French Elementary (A2) Upper intermediate (B2) Beginner (A1) Intermediate (B1) Beginner (A1)
Education
Degree Classification
2001/10 - 2007/01/30
Concluded
Biomedical Sciences (Doutoramento)
Universidade de Lisboa Faculdade de Medicina, Portugal
"Bioinformatics Studies on the Complexity of Splicing and Gene Expression" (THESIS/DISSERTATION)
Summa Cum Laude (unanimous)
2000/10 - 2001/09
Concluded
Biophysics and Biomedical Engineering (Curso de doutoramento (conclusão de unidades curriculares))
Universidade de Lisboa Faculdade de Ciências, Portugal
19
1995/10 - 2000/10
Concluded
Engenharia Física Tecnológica (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Cardiovascular Variability (review and experimental study)" (THESIS/DISSERTATION)
17
Affiliation

Science

Category
Host institution
Employer
2015/01/01 - Current Principal Investigator (Research) Instituto de Medicina Molecular, Portugal
2013/10/01 - 2015/04/30 Visiting Researcher (Research) University of Oxford, United Kingdom
2013/06/01 - 2014/05/31 Researcher (Research) Instituto de Medicina Molecular, Portugal
2010/08/01 - 2013/05/31 Postdoc (Research) University of Toronto, Canada
2006/08/01 - 2010/07/31 Postdoc (Research) University of Cambridge, United Kingdom
2003/01 - 2005/07 Visiting Researcher (Research) University of Cambridge Department of Oncology, United Kingdom
2002/08 - 2002/08 Visiting Researcher (Research) Institute of Molecular and Cell Biology, Singapore
2002/02 - 2002/05 Visiting Researcher (Research) European Molecular Biology Laboratory, Germany

Teaching in Higher Education

Category
Host institution
Employer
2020/03 - Current Invited Associate Professor (University Teacher) Universidade de Lisboa Faculdade de Medicina, Portugal
1999 - 2001 Trainee Assistant (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
Projects

Grant

Designation Funders
2022 - Current Stem cell toolkit for modelling cerebellar dysfunction in Angelman Syndrome
ASA AWARD
Researcher
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Angelman Syndrome Alliance
Ongoing
2024/10/01 - 2027/09/30 BIOMICS: Fostering Excellent Research, Training and Innovation in Biomedical Data Science
101159926
Principal investigator
Instituto de Medicina Molecular, Portugal
European Commission
Ongoing
2023/03/01 - 2024/08/31 New horizons for Rett syndrome: exploring the role of transposable elements using genetically engineered human stem cell models
2022.02195.PTDC
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2023/03/01 - 2024/08/31 Studying accelerated cognitive decline upon aging in human derived cholinergic neurons
2022.03516.PTDC
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2021/03/29 - 2024/03/28 Regulating meningeal gamma-delta 17 T cell homeostasis: Molecular mechanisms and pathophysiological implications
PTDC/MED-IMU/1988/2020
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/03/15 - 2024/03/14 A subcellular transcriptomics approach to study female gametogenesis
PTDC/BIA-BID/1606/2020
Researcher
Universidade de Aveiro, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/09/01 - 2023/02/28 RiboMed: RNA in disease
Co-Principal Investigator (Co-PI)
Instituto de Medicina Molecular, Portugal
European Commission
Ongoing
2019/03/28 - 2022/03/27 INnovating breast cancer GWAS through inTEgRation of functional GENomics
PTDC/MED-GEN/30895/2017
Researcher
Universidade do Algarve, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2015/01 - 2021/12 Transcriptomic landscapes of cancer: studying the transcriptional etiology of metastization and its implications on personalized therapeutics
3057
Principal investigator
Instituto de Medicina Molecular, Portugal
European Molecular Biology Organization
Ongoing
2018/10 - 2021/09 Deciphering the epigenetic barriers of aging for iPSC reprogramming
PTDC/BIA-MOL/29320/2017
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2018/09 - 2021/08 Physiopathology and clinical implications of the RANK c.1386C>T (R450W) mutation in breast cancer patients
PTDC/MED-ONC/28636/2017
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2018/06 - 2021/06 Programming anti-tumour myeloid cells to improve immunotherapy strategies
PTDC/MED-IMU/30948/2017
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2017/06 - 2021/04 GenomePT - National Laboratory for Genome Sequencing and Analysis
-
Science and Technology Management Fellow
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2015/01 - 2019/12 RNA regulation in cancer: defining the transcriptional etiology of metastasis and its implications on personalized therapeutics
IF/00595/2014
Principal investigator
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2016/12 - 2019/11 Accelerating progress toward the new era of precision medicine
SAICTPAC/0021/2015
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2016/06 - 2019/06 Personalizing cancer therapy through integrated modeling and decision
PTDC/EMS-SIS/0642/2014
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2016/05 - 2019/04 Angiocrine factors as modulators of spinal cord regeneration
PTDC/BIM-MED/3295/2014
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2017 - 2018 (1) Transcriptomic signatures of human organ-specific aging / (2) Bioinformatics applications for analysis and visualization of alternative splicing in biomedical research
YIP Small Grant 2017
Principal investigator
European Molecular Biology Organization
2016 - 2017 Alternative splicing during neuronal development
-
Principal investigator
Instituto de Medicina Molecular, Portugal
Fundação AstraZeneca
2016 - 2017 RNA regulation in colorectal cancer: transcriptomic landscapes of metastasis and their clinical implications
-
Principal investigator
Instituto de Medicina Molecular, Portugal
Instituto de Medicina Molecular
2014/04 - 2015/09 Multiscale modeling for personalized therapy of bone metastasis
EXPL/EMS-SIS/1954/2013
Researcher
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
2011/06 - 2014/05 EVOALTSPLICE - Survey of tissue-specific alternative splicing in vertebrates by high-throughput sequencing: finding the elements of an evolutionary ‘splicing predictor’
274037
Principal investigator
Instituto de Medicina Molecular, Portugal

Terrence Donnelly Centre for Cellular and Biomolecular Research, Canada
European Commission

Contract

Designation Funders
2020/06/01 - 2026/05/31 Unveiling tissue-specific transcriptional signatures of human ageing for therapeutic targeting
CEECIND/00436/2018
Principal investigator
Instituto de Medicina Molecular, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - 2025/12/31 Institute of Molecular Medicine João Lobo Antunes
LA/P/0082/2020
Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2019/12/31 Instituto de Medicina Molecular
UID/BIM/50005/2019
Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2017/04/12 - 2019/09/30 PRECISE-Accelerating progress toward the new era of precision medicine
SAICTPAC/0021/2015
Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2020 - 2022 Sponsored Research Agreement with Limm Therapeutics SA
N/A
Principal investigator
Instituto de Medicina Molecular, Portugal
Concluded
Outputs

Publications

Book chapter
  1. Saraiva-Agostinho, Nuno; Barbosa-Morais, Nuno Luís. "Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics". In Stem Cell Transcriptional Networks, 179-205. Springer US, 2020.
    10.1007/978-1-0716-0301-7_10
  2. Lynch, A.G.; Smith, M.L.; Dunning, M.J.; Cairns, J.M.; Barbosa-Morais, N.L.; Tavaré, S.. "beadarray, BASH and HULK - tools to increase the value of Illumina BeadArray experiments". In Statistical Tools for Challenges in Bioinformatics, 33-37. Leeds University Press, 2009.
    Published
Conference abstract
  1. Xavier, Joana M; Magno, Ramiro; Russel, R; de Almeida, BP; Jacinta-Fernandes, Ana; Duarte, ARB; BARBOSA-MORAIS, NUNO; Maia, Ana-Teresa. "Mapping of cis-regulatory variants by differential allelic expression analysis identifies regulatory variants and target genes of 31 breast cancer risk loci". Paper presented in Bioinformatics in Cancer - Virtual Event: 18 - 19 May 2021, 2021.
    Submitted
Conference poster
  1. Martins, Isaura; Neves-Silva, Dalila; Ascensão-Ferreira, Mariana; Ribeiro, Daniel; Isidro, Ana Filipa; Dias, Ana Filipa; Quitéria, Raquel; et al. Corresponding author: Martins, Isaura. "CD9 and MYLIP as two new vascular players in spinal cord injury". Paper presented in 13th EMBO Young Scientists¿ Forum, 2023.
Journal article
  1. Arthur L Schneider; Rita Martins-Silva; Alexandre Kaizeler; Nuno Saraiva-Agostinho; Nuno L Barbosa-Morais. Corresponding author: Nuno L Barbosa-Morais. "voyAGEr, a free web interface for the analysis of age-related gene expression alterations in human tissues". eLife (2024): https://doi.org/10.7554/eLife.88623.3.
    10.7554/eLife.88623.3
  2. Mariana Ascensao-Ferreira; Rita Martins-Silva; Nuno Saraiva-Agostinho; Nuno L Barbosa-Morais. "betAS: intuitive analysis and visualisation of differential alternative splicing using beta distributions". RNA (2024): https://doi.org/10.1261/rna.079764.123.
    10.1261/rna.079764.123
  3. Martins, Isaura; Neves-Silva, Dalila; Ascensão-Ferreira, Mariana; Dias, Ana Filipa; Ribeiro, Daniel; Isidro, Ana Filipa; Quitéria, Raquel; et al. "Mouse Spinal Cord Vascular Transcriptome Analysis Identifies CD9 and MYLIP as Injury-Induced Players". International Journal of Molecular Sciences 24 7 (2023): 6433. http://dx.doi.org/10.3390/ijms24076433.
    10.3390/ijms24076433
  4. Goulielmaki, Evi; Tsekrekou, Maria; Batsiotos, Nikos; Ascensão-Ferreira, Mariana; Ledaki, Eleftheria; Stratigi, Kalliopi; Chatzinikolaou, Georgia; et al. "The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing". Nature Communications 12 1 (2021): http://dx.doi.org/10.1038/s41467-021-23505-1.
    10.1038/s41467-021-23505-1
  5. Conde, João; Pumroy, Ruth A.; Baker, Charlotte; Rodrigues, Tiago; Guerreiro, Ana; Sousa, Bárbara B.; Marques, Marta C.; et al. "Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression". ACS Central Science 7 5 (2021): 868-881. http://dx.doi.org/10.1021/acscentsci.1c00070.
    10.1021/acscentsci.1c00070
  6. Bordone, Marie C.; Barbosa-Morais, Nuno L.. "Unraveling Targetable Systemic and Cell-Type-Specific Molecular Phenotypes of Alzheimer’s and Parkinson’s Brains With Digital Cytometry". Frontiers in Neuroscience 14 (2020): http://dx.doi.org/10.3389/fnins.2020.607215.
    10.3389/fnins.2020.607215
  7. Rathore, Om S; Silva, Rui D; Ascensao-Ferreira, Mariana; Matos, Ricardo; Carvalho, Celia; Marques, Bruno; Tiago, Margarida N; et al. "NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal-ventral patterning". RNA (2020): rna.077446.120. http://dx.doi.org/10.1261/rna.077446.120.
    10.1261/rna.077446.120
  8. Gomes, Inês; de Almeida, Bernardo P.; Dâmaso, Sara; Mansinho, André; Correia, Inês; Henriques, Sara; Cruz-Duarte, Raquel; et al. "Expression of receptor activator of NFkB (RANK) drives stemness and resistance to therapy in ER+HER2- breast cancer". Oncotarget 11 19 (2020): 1714-1728. http://dx.doi.org/10.18632/oncotarget.27576.
    10.18632/oncotarget.27576
  9. Santos, Alexandra F.; Barbosa-Morais, Nuno L.; Hurlburt, Barry K.; Ramaswamy, Sneha; Hemmings, Oliver; Kwok, Matthew; O’Rourke, Colin; et al. "IgE to epitopes of Ara h 2 enhance the diagnostic accuracy of Ara h 2-specific IgE". Allergy (2020): http://dx.doi.org/10.1111/all.14301.
    10.1111/all.14301
  10. Godinho-Silva, Cristina; Domingues, Rita G.; Rendas, Miguel; Raposo, Bruno; Ribeiro, Hélder; da Silva, Joaquim Alves; Vieira, Ana; et al. "Light-entrained and brain-tuned circadian circuits regulate ILC3s and gut homeostasis". Nature 574 7777 (2019): 254-258. http://dx.doi.org/10.1038/s41586-019-1579-3.
    10.1038/s41586-019-1579-3
  11. Munkley, Jennifer; Li, Ling; Krishnan, S R Gokul; Hysenaj, Gerald; Scott, Emma; Dalgliesh, Caroline; Oo, Htoo Zarni; et al. "Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer". eLife 8 (2019): http://dx.doi.org/10.7554/elife.47678.
    10.7554/elife.47678
  12. de Almeida BP; Vieira AF; Paredes J; Bettencourt-Dias M; BARBOSA-MORAIS, NUNO. "Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome". PLoS Computational Biology 15 3 (2019): e1006832. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006832.
    Open access • Published • https://doi.org/10.1371/journal.pcbi.1006832
  13. Baker, Charlotte; Rodrigues, Tiago; de Almeida, Bernardo P.; Barbosa-Morais, Nuno L.; Bernardes, Gonçalo J.L.. "Natural product–drug conjugates for modulation of TRPV1-expressing tumors". Bioorganic & Medicinal Chemistry (2019): http://dx.doi.org/10.1016/j.bmc.2019.03.025.
    10.1016/j.bmc.2019.03.025
  14. Nuno Saraiva-Agostinho; Nuno L Barbosa-Morais. "psichomics: graphical application for alternative splicing quantification and analysis". Nucleic Acids Research (2019): https://doi.org/10.1093/nar/gky888.
    10.1093/nar/gky888
  15. Rodrigues, Tiago; de Almeida, Bernardo P.; Barbosa-Morais, Nuno L.; Bernardes, Gonçalo J. L.. "Dissecting celastrol with machine learning to unveil dark pharmacology". Chemical Communications (2019): http://dx.doi.org/10.1039/c9cc03116b.
    10.1039/c9cc03116b
  16. Braun, Simon; Enculescu, Mihaela; Setty, Samarth T.; Cortés-López, Mariela; de Almeida, Bernardo P.; Sutandy, F. X.¿ Reymond; Schulz, Laura; et al. "Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis". Nature Communications 9 1 (2018): http://dx.doi.org/10.1038/s41467-018-05748-7.
    10.1038/s41467-018-05748-7
  17. Munkley J; Maia TM; Ibarluzea N; Livermore KE; Vodak D; Ehrmann I; James K; et al. "Androgen-dependent alternative mRNA isoform expression in prostate cancer cells". (2018): http://europepmc.org/abstract/PPR/PPR46476.
    10.12688/f1000research.15604.1
  18. Georgilis A; Klotz S; Hanley CJ; Herranz N; Weirich B; Morancho B; Leote AC; et al. "PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells.". Cancer cell (2018): http://europepmc.org/abstract/med/29990503.
    10.1016/j.ccell.2018.06.007
  19. Leznicki P; Natarajan J; Bader G; Spevak W; Schlattl A; Abdul Rehman SA; Pathak D; et al. "Expansion of DUB functionality generated by alternative isoforms - USP35, a case study.". Journal of cell science (2018): http://europepmc.org/abstract/med/29685892.
    10.1242/jcs.212753
  20. Marteil G; Guerrero A; Vieira AF; de Almeida BP; Machado P; Mendonça S; Mesquita M; et al. "Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation.". Nature communications (2018): http://europepmc.org/abstract/med/29593297.
    10.1038/s41467-018-03641-x
  21. L. M. Gallego-Paez; M. C. Bordone; A. C. Leote; N. Saraiva-Agostinho; M. Ascensão-Ferreira; N. L. Barbosa-Morais. "Alternative splicing: the pledge, the turn, and the prestige". Human Genetics (2017): https://doi.org/10.1007/s00439-017-1790-y.
    10.1007/s00439-017-1790-y
  22. Cardoso, Vânia; Chesné, Julie; Ribeiro, Hélder; García-Cassani, Bethania; Carvalho, Tânia; Bouchery, Tiffany; Shah, Kathleen; et al. "Neuronal regulation of type 2 innate lymphoid cells via neuromedin U". Nature 549 7671 (2017): 277-281. http://dx.doi.org/10.1038/nature23469.
    10.1038/nature23469
  23. Rijo-Ferreira, F.; Pinto-Neves, D.; Barbosa-Morais, N.L.; Takahashi, J.S.; Figueiredo, L.M.. "Trypanosoma brucei metabolism is under circadian control". Nature Microbiology 2 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85015299539&partnerID=MN8TOARS.
    10.1038/nmicrobiol.2017.32
  24. Braunschweig, Ulrich; Barbosa-Morais, Nuno L.; Pan, Qun; Nachman, Emil N.; Alipanahi, Babak; Gonatopoulos-Pournatzis, Thomas; Frey, Brendan; Irimia, Manuel; Blencowe, Benjamin J.. "Widespread intron retention in mammals functionally tunes transcriptomes". Genome Research 24 11 (2014): 1774-1786. http://dx.doi.org/10.1101/gr.177790.114.
    10.1101/gr.177790.114
  25. Pena, Ana C.; Pimentel, Mafalda R.; Manso, Helena; Vaz-Drago, Rita; Pinto-Neves, Daniel; Aresta-Branco, Francisco; Rijo-Ferreira, Filipa; et al. "Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo". Molecular Microbiology 93 4 (2014): 645-663. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000340558600007&KeyUID=WOS:000340558600007.
    10.1111/mmi.12677
  26. Liu, Yu; Noon, Aidan P.; Cabeza, Eduardo Aguiar; Shen, Jess; Kuk, Cynthia; Ilczynski, Christine; Ni, Ruoyu; et al. "Next-generation RNA Sequencing of Archival Formalin-fixed Paraffin-embedded Urothelial Bladder Cancer". European Urology 66 6 (2014): 982-986. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344694300013&KeyUID=WOS:000344694300013.
    10.1016/j.eururo.2014.07.045
  27. Ward, M.C.; Wilson, M.D.; Barbosa-Morais, N.L.; Schmidt, D.; Stark, R.; Pan, Q.; Schwalie, P.C.; et al. "Latent Regulatory Potential of Human-Specific Repetitive Elements". Molecular Cell 49 2 (2013): 262-272. http://www.scopus.com/inward/record.url?eid=2-s2.0-84872815703&partnerID=MN8TOARS.
    10.1016/j.molcel.2012.11.013
  28. Han, H.; Irimia, M.; Ross, P.J.; Sung, H.-K.; Alipanahi, B.; David, L.; Golipour, A.; et al. "MBNL proteins repress ES-cell-specific alternative splicing and reprogramming". Nature 498 7453 (2013): 241-245. http://www.scopus.com/inward/record.url?eid=2-s2.0-84878995293&partnerID=MN8TOARS.
    10.1038/nature12270
  29. Barbosa-Morais, N. L.; Irimia, M.; Pan, Q.; Xiong, H. Y.; Gueroussov, S.; Lee, L. J.; Slobodeniuc, V.; et al. "The Evolutionary Landscape of Alternative Splicing in Vertebrate Species". Science 338 6114 (2012): 1587-1593. http://dx.doi.org/10.1126/science.1230612.
    10.1126/science.1230612
  30. Muralidhar, Balaji; Winder, David; Murray, Matthew; Palmer, Roger; Barbosa-Morais, Nuno; Saini, Harpreet; Roberts, Ian; Pett, Mark; Coleman, Nicholas. "Functional evidence that Drosha overexpression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles". The Journal of Pathology 224 4 (2011): 496-507. http://dx.doi.org/10.1002/path.2898.
    10.1002/path.2898
  31. Dunning, M.J.; Curtis, C.; Barbosa-Morais, N.L.; Caldas, C.; Tavaré, S.; Lynch, A.G.. "The importance of platform annotation in interpreting microarray data". The Lancet Oncology 11 8 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77955262935&partnerID=MN8TOARS.
    10.1016/S1470-2045(10)70115-7
  32. Ahmed, A.A.; Lu, Z.; Jennings, N.B.; Etemadmoghadam, D.; Capalbo, L.; Jacamo, R.O.; Barbosa-Morais, N.; et al. "SIK2 Is a Centrosome Kinase Required for Bipolar Mitotic Spindle Formation that Provides a Potential Target for Therapy in Ovarian Cancer". Cancer Cell 18 2 (2010): 109-121. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955530763&partnerID=MN8TOARS.
    10.1016/j.ccr.2010.06.018
  33. Barbosa-Morais, Nuno L.; Dunning, Mark J.; Samarajiwa, Shamith A.; Darot, Jeremy F. J.; Ritchie, Matthew E.; Lynch, Andy G.; Tavaré, Simon. "A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data". Nucleic Acids Research 38 3 (2009): e17-e17. http://dx.doi.org/10.1093/nar/gkp942.
    10.1093/nar/gkp942
  34. Barbosa-Morais, Nuno L.; Carter, Stephanie; Coleman, Nicholas; Ikelle, Emili; Laskey, Ronald A.; Miller, Richard; Scarpini, Cinzia; White, Victoria. "Isolation of Stool-Derived Mucus Provides a High Yield of Colonocytes Suitable for Early Detection of Colorectal Carcinoma". Cancer Epidemiology Biomarkers & Prevention 18 7 (2009): 2006-2013.
    10.1158/1055-9965.EPI-08-1145
  35. ABCFS; ABCS; AOCS Management Grp; Anton-Culver, Hoda; BBCC; BBCS; BCAC; et al. "Association of ESR1 gene tagging SNPs with breast cancer risk". Human Molecular Genetics 18 6 (2009): 1131-1139.
    10.1093/hmg/ddn429
  36. Lynch, A.G.; Dunning, M.J.; Iddawela, M.; Barbosa-Morais, N.L.; Ritchie, M.E.. "Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms". Statistical Methods in Medical Research 18 5 (2009): 437-452. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349588328&partnerID=MN8TOARS.
    10.1177/0962280208099451
  37. Wilson, M. D.; Barbosa-Morais, N. L.; Schmidt, D.; Conboy, C. M.; Vanes, L.; Tybulewicz, V. L. J.; Fisher, E. M. C.; Tavare, S.; Odom, D. T.. "Species-Specific Transcription in Mice Carrying Human Chromosome 21". Science 322 5900 (2008): 434-438. http://dx.doi.org/10.1126/science.1160930.
    10.1126/science.1160930
  38. Grosso, Ana Rita; Gomes, Anita Q.; Barbosa-Morais, Nuno L.; Caldeira, Sandra; Thorne, Natalie P.; Grech, Godfrey; von Lindern, Marieke; Carmo-Fonseca, Maria. "Tissue-specific splicing factor gene expression signatures". Nucleic Acids Research 36 15 (2008): 4823-4832. http://dx.doi.org/10.1093/nar/gkn463.
    10.1093/nar/gkn463
  39. Dunning, M.J.; Barbosa-Morais, N.L.; Lynch, A.G.; Tavaré, S.; Ritchie, M.E.. "Statistical issues in the analysis of Illumina data". BMC Bioinformatics 9 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-42049089192&partnerID=MN8TOARS.
    10.1186/1471-2105-9-85
  40. Driver, K.E.; Song, H.; Lesueur, F.; Ahmed, S.; Barbosa-Morais, N.I.; Tyrer, J.P.; Ponder, B.A.J.; et al. "Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population". Carcinogenesis 29 2 (2008): 333-341. http://www.scopus.com/inward/record.url?eid=2-s2.0-40549130341&partnerID=MN8TOARS.
    10.1093/carcin/bgm284
  41. Dunning, M.J.; Ritchie, M.E.; Barbosa-Morais, N.L.; Tavaré, S.; Lynch, A.G.. "Spike-in validation of an Illumina-specific variance-stabilizing transformation". BMC Research Notes 1 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-70349604003&partnerID=MN8TOARS.
    10.1186/1756-0500-1-18
  42. Palmer, R.D.; Barbosa-Morais, N.L.; Gooding, E.L.; Muralidhar, B.; Thornton, C.M.; Pett, M.R.; Roberts, I.; et al. "Pediatric malignant germ cell tumors show characteristic transcriptome profiles". Cancer Research 68 11 (2008): 4239-4247. http://www.scopus.com/inward/record.url?eid=2-s2.0-49249104685&partnerID=MN8TOARS.
    10.1158/0008-5472.CAN-07-5560
  43. Conboy, Caitlin M.; Spyrou, Christiana; Thorne, Natalie P.; Wade, Elizabeth J.; Barbosa-Morais, Nuno L.; Wilson, Michael D.; Bhattacharjee, Arindam; et al. "Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor". PLoS ONE 2 10 (2007): e1061. http://dx.doi.org/10.1371/journal.pone.0001061.
    10.1371/journal.pone.0001061
  44. Blenkiron, Cherie; Goldstein, Leonard D; Thorne, Natalie P; Spiteri, Inmaculada; Chin, Suet-Feung; Dunning, Mark J; Barbosa-Morais, Nuno L; et al. "MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype". Genome Biology 8 10 (2007): R214. http://dx.doi.org/10.1186/gb-2007-8-10-r214.
    10.1186/gb-2007-8-10-r214
  45. Adryan, Boris; Barbosa-Morais, Nuno L.; Lynch, Andy G.; Massie, Charles E.; Mills, Ian G.; Neal, David E.; Tran, Maxine G.. "New androgen receptor genomic targets show an interaction with the ETS1 transcription factor". Embo Reports 8 9 (2007): 871-878.
    10.1038/sj.embor.7401046
  46. Chin, Suet F; Teschendorff, Andrew E; Marioni, John C; Wang, Yanzhong; Barbosa-Morais, Nuno L; Thorne, Natalie P; Costa, Jose L; et al. "High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer". Genome Biology 8 10 (2007): R215. http://dx.doi.org/10.1186/gb-2007-8-10-r215.
    10.1186/gb-2007-8-10-r215
  47. Muralidhar, B.; Goldstein, L.D.; Ng, G.; Winder, D.M.; Palmer, R.D.; Gooding, E.L.; Barbosa-Morais, N.L.; et al. "Global microRNA profiles in cervical squamous cell carcinoma depend on Drosha expression levels". Journal of Pathology 212 4 (2007): 368-377. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547114724&partnerID=MN8TOARS.
    10.1002/path.2179
  48. Chin, S.-F.; Wang, Y.; Thorne, N.P.; Teschendorff, A.E.; Pinder, S.E.; Vias, M.; Naderi, A.; et al. "Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers". Oncogene 26 13 (2007): 1959-1970. http://www.scopus.com/inward/record.url?eid=2-s2.0-33947529520&partnerID=MN8TOARS.
    10.1038/sj.onc.1209985
  49. Mollet, Inês; Barbosa-Morais, Nuno L.; Andrade, Jorge; Carmo-Fonseca, Maria. "Diversity of human U2AF splicing factors.". FEBS Journal 273 21 (2006): 4807-4816. http://dx.doi.org/10.1111/j.1742-4658.2006.05502.x.
    10.1111/j.1742-4658.2006.05502.x
  50. Naderi, A; Teschendorff, A E; Barbosa-Morais, N L; Pinder, S E; Green, A R; Powe, D G; Robertson, J F R; et al. "A gene-expression signature to predict survival in breast cancer across independent data sets". Oncogene 26 10 (2006): 1507-1516. http://dx.doi.org/10.1038/sj.onc.1209920.
    10.1038/sj.onc.1209920
  51. Teschendorff, Andrew E.; Naderi, Ali; Barbosa-Morais, Nuno L.; Caldas, Carlos. "PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer". Bioinformatics 22 18 (2006): 2269-2275. http://dx.doi.org/10.1093/bioinformatics/btl174.
    10.1093/bioinformatics/btl174
  52. Stamm, S.; Riethoven, J.J.; Le Texier, V.; Gopalakrishnan, C.; Kumanduri, V.; Tang, Y.; Barbosa-Morais, N.L.; Thanaraj, T.A.. "ASD: a bioinformatics resource on alternative splicing". Nucleic Acids Research 34 90001 (2006): D46-D55. http://dx.doi.org/10.1093/nar/gkj031.
    10.1093/nar/gkj031
  53. Ibrahim, A.E.K.; Thorne, N.P.; Baird, K.; Barbosa-Morais, N.L.; Tavaré, S.; Collins, V.P.; Wyllie, A.H.; Arends, M.J.; Brenton, J.D.. "MMASS: An optimized array-based method for assessing CpG island methylation". Nucleic Acids Research 34 20 (2006): http://www.scopus.com/inward/record.url?eid=2-s2.0-33845643047&partnerID=MN8TOARS.
    10.1093/nar/gkl551
  54. Teschendorff, Andrew E; Naderi, Ali; Barbosa-Morais, Nuno L; Pinder, Sarah E; Ellis, Ian O; Aparicio, Sam; Brenton, James D; Caldas, Carlos. "A consensus prognostic gene expression classifier for ER positive breast cancer". Genome Biology 7 10 (2006): R101. http://dx.doi.org/10.1186/gb-2006-7-10-r101.
    10.1186/gb-2006-7-10-r101
  55. Gama-Carvalho, Margarida; Barbosa-Morais, Nuno L; Brodsky, Alexander S; Silver, Pamela A; Carmo-Fonseca, Maria. "Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors". Genome Biology 7 11 (2006): R113. http://dx.doi.org/10.1186/gb-2006-7-11-r113.
    10.1186/gb-2006-7-11-r113
  56. Barbosa-Morais, N. L.; Carmo-Fonseca, M.; Aparicio, S.. "Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion". Genome Research 16 1 (2005): 66-77. http://dx.doi.org/10.1101/gr.3936206.
    10.1101/gr.3936206
  57. Teschendorff, AE; Wang, YZ; Barbosa-Morais, NL; Brenton, JD; Caldas, C. "A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data". Bioinformatics 21 13 (2005): 3025-3033.
    10.1093/bioinformatics/bti466
  58. Pacheco, TR; Gomes, AQ; Barbosa-Morais, NL; Benes, V; Ansorge, W; Wollerton, M; Smith, CW; Valcarel, J; Carmo-Fonseca, M. "Diversity of vertebrate splicing factor U2AF(35) - Identification of alternatively spliced U2AF1 mRNAs". Journal of Biological Chemistry 279 26 (2004): 27039-27049.
    10.1074/jbc.M402136200
  59. Naderi, A; Ahmed, AA; Barbosa-Morais, NL; Aparicio, S; Brenton, JD; Caldas, C. "Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling". Bmc Genomics 5 (2004):
    10.1186/1471-2164-5-9
Manual
  1. Epifânio da Franca, J.; Barbosa-Morais, N.L.. Handbook of Circuit Theory and Fundamentals of Electronics. Secçãoo de Folhas, Associação de Estudantes do Instituto Superior Técnico. 2001.
    Published
Online resource
  1. Ascensão-Ferreira, Mariana; Martins-Silva, Rita; Saraiva-Agostinho, N.; BARBOSA-MORAIS, NUNO. Corresponding author: BARBOSA-MORAIS, NUNO. betAS: intuitive analysis and visualisation of differential alternative splicing using beta distributions. 2022. compbio.imm.medicina.ulisboa.pt/app/betAS.
  2. Schneider, A.; Saraiva-Agostinho, N.; Barbosa-Morais, N. L.. voyAGEr - analysis of age-related gene expression changes in human tissues. 2021. https://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.
  3. Nuno Saraiva-Agostinho; Nuno L. Barbosa-Morais. psichomics - Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation. 2018. http://bioconductor.org/packages/release/bioc/html/psichomics.html.
  4. Bernardo P. de Almeida; Nuno Saraiva-Agostinho; Nuno L. Barbosa-Morais. cTRAP - Identification of candidate causal perturbations from differential gene expression data. 2018. https://bioconductor.org/packages/release/bioc/html/cTRAP.html.
Preprint
  1. Marín, Nuria Moreno; Marteil, Gaelle; Fresmann, Nora C.; de Almeida, Bernardo P.; Dores, Katharina; Fragoso, Rita; Vaz, Joana Cardoso; et al. "High prevalence and dependence of centrosome clustering in mesenchymal tumors and leukemia". 2023. http://dx.doi.org/10.1101/2023.03.13.532472.
    10.1101/2023.03.13.532472
  2. Sousa, Neuza S.; Bica, Marta; Brás, Margarida F.; Antunes, Inês B.; Encarnação, Isabel A.; Costa, Tiago; Martins, Inês B.; et al. "The immune landscape of murine skeletal muscle regeneration and aging". 2023. http://dx.doi.org/10.1101/2023.11.07.565995.
    10.1101/2023.11.07.565995
Thesis / Dissertation
  1. BARBOSA-MORAIS, NUNO. "Bioinformatics Studies on the Complexity of Splicing and Gene Expression". PhD, Universidade de Lisboa Faculdade de Medicina, 2007.

Intellectual property

Provisional application for patent
  1. 2019. "Methods of cancer treatment".
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/11/07 Disease transcriptomes and cognitive biases Neuroscience Seminar Series
Instituto de Medicina Molecular João Lobo Antunes (Lisbon, Portugal)
2023/09/22 What transcriptomes tell us about human ageing and associated diseases
Center for Neuroscience and Cell Biology (Coimbra, Portugal)
2023/06/27 What makes a good computational biologist? InSilico Club
UCIBIO (Portugal)
2023/03/30 Biologia computacional no estudo do que os transcritomas nos dizem sobre doenças O que há de novo no CAML
Centro Académico de Medicina de Lisboa (Lisbon, Portugal)
2022/11/15 Finding molecular regulators of response to stress and senescence by intelligible analyses of transcriptomes
Department of Biology, University of Minho (Braga, Portugal)
2021/11/19 Bioinformatic analyses of human transcriptomes made intelligible to biologists I Workshop on Systems Medicine
iBiMED - Universidade de Aveiro (Aveiro, Portugal)
2021/05/25 Computational biology in the translation of disease "omics" Department of Bioengineering, Instituto Superior Técnico
Tiago Fernandes (Lisbon, Portugal)
2021/04/21 Making biological big data intelligible to yourself and others TransEvo (DFG Research Training Group on Translational Evolutionary Research) Core Seminar
Kiel Evolution Center, University of Kiel (Kiel, Germany)
2020/11/18 What transcriptomes tell us about diseases
Institute of Biomedicine (iBiMED), University of Aveiro (Aveiro, Portugal)
2020/01/20 What transcriptomes tell us about ageing and associated diseases
Centre of Biological Engineering, University of Minho (Braga, Portugal)
2020/01/16 What transcriptomic data tell us about disease Data Science Portugal
TalkDesk (Lisbon, Portugal)
2019/11/15 Tumour transcriptomes reveal a prognostic alternative splicing signature in colorectal cancer 23rd SPGH Annual Meeting
Sociedade Portuguesa de Genética Humana (Coimbra, Portugal)
2019/10/15 What transcriptomes tell us about ageing and associated diseases RiboMed Kickoff Meeting
(Carcavelos, Portugal)
2019/05/21 What transcriptomes tell us about disease Department of Bioengineering, Instituto Superior Técnico
Tiago Fernandes (Lisboa, Portugal)
2019/05/13 Bioinformatics in the translation of cancer transcriptomics Basel Computational Biology Seminar Series
Maria Katsantoni & Mihaela Zavolan (Biozentrum, University of Basel) (Basel, Switzerland)
2019/05/10 cTRAP: identification of candidate causal perturbations and phenotype-targeting compounds from differential expression data GenomePT Symposium
GenomePT & CIBIO/InBIO (Vairão, Portugal)
2019/03/18 Bioinformatics in the translation of cancer transcriptomics V Semana da Bioengenharia
Instituto Superior Técnico (Lisboa, Portugal)
2019/01/25 CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer VIII National RNA Meeting: ptRNA2019
i3S (Porto, Portugal)
2018/11/06 Biologist-intelligible alternative splicing analysis of RNA-seq data BIRS/CMO workshop on Statistical and Computational Challenges in High-Throughput Genomics with Application to Precision Medicine
(Oaxaca, Mexico)
2018/09/24 What transcriptomes tell us about disease RiboClub Meeting
(Sherbrooke, Canada)
2018/07/25 What transcriptomes tell us about disease MRC London Institute of Medical Sciences
Jesus Gil (United Kingdom)
2018/07/18 CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer 2nd International Caparica Conference in Splicing
(Caparica, Portugal)
2018/05/22 What transcriptomes tell us about disease Department of Bioengineering, Instituto Superior Técnico
Tiago Fernandes (Lisboa, Portugal)
2018/05/16 What transcriptomes tell us about disease EMBO Young Investigator Meeting
IMP (Vienna, Austria)
2018/05/12 Computational biology and what transcriptomes tell us about disease Prossyga 2018
Janssen (Porto, Portugal)
2018/02/06 What transcriptomes tell us about disease ITQB
Isabel Rocha (Oeiras, Portugal)
2017/05/29 Computational biology in the translation of cancer "omics" ReTuBi Joint Summer School
(Lisboa, Portugal)
2017/05/28 Computational biology, splicing, evolution and cancer IHMT PhD students Retreat
IHMT PhD students (Sesimbra, Portugal)
2017/04/05 Alternative splicing landscapes of ageing and neurodegeneration CEDOC
Cláudia Almeida (Lisboa, Portugal)
2017/03/03 Computational Biology: splicing in evolution and disease X Encontro Nacional dos Estudantes de Engenharia Biomédica
(Coimbra, Portugal)
2017/01/19 Profiling alternative splicing in evolution and disease International Institute of Molecular and Cell Biology
Catarina Almeida (Warsaw, Poland)
2017/01/19 My way into Computational Biology Career Path Day, International Institute of Molecular and Cell Biology
Catarina Almeida (Warsaw, Poland)
2016/11/02 Gene splicing in evolution and disease Department of Physics, Instituto Superior Técnico
Luís Melo (Lisboa, Portugal)
2016/10/27 Gene expression profile of Kidney Tumors Novartis Oncology Advanced RCC Preceptorship
Novartis (Lisboa, Portugal)
2016/10/12 Alternative splicing landscapes of cancer Instituto Português de Oncologia
Marta Pojo (Lisboa, Portugal)
2016/09/28 A bioinformatics application for the analysis and visualisation of alternative splicing in cancer 4th Post-EURASNET Symposium
(Poznan, Poland)
2016/09/07 Profiling alternative splicing in evolution and disease 2016 Summer School in Computational Biology
Armindo Salvador (Coimbra, Portugal)
2016/09/01 Alternative splicing landscapes of disease EMBO Young Scientists Forum
(Lisboa, Portugal)
2016/06/28 Alternative splicing landscapes of cancer EMBO YIP Cancer Meeting
FORTH (Heraklion, Greece)
2016/05/13 Alternative splicing landscapes of disease EMBO Young Investigator Meeting
EMBL (Heidelberg, Germany)
2016/05/06 Science & Creativity RedeValor Conference
Reitoria da Universidade de Lisboa (Lisboa, Portugal)
2016/04/17 Alternative splicing and the dynamics of genomes' coding potential 1st BioSAM, Faculty of Sciences, University of Lisbon
(Lisboa, Portugal)
2016/03/03 Biologia Computacional: splicing e cancro IV Jornadas de Bioengenharia
Universidade da Beira Interior (Covilhã, Portugal)
2016/03/02 Computational Biology in the study of Alternative Splicing in Cancer II Semana da Bioengenharia, Instituto Superior Técnico
(Lisboa, Portugal)
2016/01/28 Biologia Computacional no estudo do splicing alternativo em cancro O que há de novo no CAML
Centro Académico de Medicina de Lisboa (Lisbon, Portugal)
2015/12/02 Biologia Computacional: Splicing, Evolução e Cancro Conversas: Oncobiologia
Núcleo de Biologia Celular e Molecular, FCT NOVA (Caparica, Portugal)
2015/05/13 Alternative splicing landscapes of cancer EMBO Young Investigator Meeting
PRBB (Barcelona, Spain)
2015/04/27 Alternative splicing in evolution and cancer ICVS - Life and Health Sciences Research Institute
Agostinho Carvalho (Braga, Portugal)
2014/11/14 Alternative splicing landscapes in clear cell renal cell carcinomas reveal novel candidate markers for prognosis The 4th Global Cancer Genomics Consortium Symposium
Kyoto University (Kyoto, Japan)
2014/05/28 Bioinformática: a nova era III Jornadas de Bioengenharia, Universidade da Beira Interior
(Covilhã, Portugal)
2014/05/12 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data Instituto Gulbenkian de Ciência
(Oeiras, Portugal)
2014/03/18 Biologia Computacional: Splicing, Evolução e Cancro IX Jornadas de Engenharia Biológica, Instituto Superior Técnico
(Lisboa, Portugal)
2014/02/28 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data Bioinformatics Open Days
Universidade do Minho (Braga, Portugal)
2014/02/03 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data Statistics Department, Campinas State University (UNICAMP)
Tatiana Benaglia (Campinas, Brazil)
2013/10/30 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data Computational Biology and Bioinformatics Seminars, iMM
Ana Rita Grosso (Lisboa, Portugal)
2013/09/18 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data The 3rd Global Cancer Genomics Consortium Symposium: From Oncogenomics To Cancer Care - Teaching Workshop
iMM (Lisboa, Portugal)
2013/04/24 Studying the evolution of tissue-specific alternative splicing using RNA-Seq data Toronto Bioinformatics User Group Trainee Seminar
(Toronto, Canada)
2013/03/26 The evolutionary landscape of alternative splicing in vertebrate species Weatherall Institute of Molecular Medicine
Ahmed Ahmed (Oxford, United Kingdom)
2013/03/13 The evolutionary landscape of alternative splicing in vertebrate species Cheriton School of Computer Science
(Waterloo, Canada)
2012/12/20 The evolutionary landscape of alternative splicing in vertebrate species Instituto de Medicina Molecular
Maria Carmo-Fonseca (Lisboa)
2012/12/19 The evolutionary landscape of alternative splicing in vertebrate species BioFIG Seminar - Faculty of Sciences, University of Lisbon
Margarida Gama-Carvalho (Lisboa, Portugal)
2011/11/08 Marie Curie International Fellowships - Case Study Seminar Day - European Programmes for Higher Education and Research: Opportunities for Canadian Institutions
Mélodie Cardin (Toronto, Canada)
2011/07/15 Species-specific differences in alternative splicing are primarily governed by evolutionary changes in cis-regulatory elements ISMB/ECCB 2011 - Special Interest Group: Alternative Splicing
(Vienna, Austria)
2010/06/16 The Illumina Code: are microarrays telling you the whole truth about cancer? 5th CFGBC Symposium "From Array to Understanding Diseases"
(Ljubljana, Slovenia)
2010/05/05 The Illumina Code: are microarrays telling you the whole truth about cancer? Friedrich Miescher Institute for Biomedical Research
Mohamed Bentires-alj (Basel, Switzerland)
2010/04/23 The Illumina Code: are microarrays telling you the whole truth about cancer? 2nd Annual ENBDC Workshop
(Weggis, Switzerland)
2009/12/15 Of trisomic mice and illuminated men Harvard Medical School
Martha Bulik (Boston, United States)
2009/12/09 Of trisomic mice and illuminated men Koshland Hall, U.C. Berkeley
Steven Brenner (Berkeley, United States)
2009/12/04 Of trisomic mice and illuminated men The Donnelly Centre, University of Toronto
Ben Blencowe (Toronto, Canada)
2009/12/03 Of trisomic mice and illuminated men Whitehead Institute for Biomedical Research
Sue Lindquist (Cambridge, United Kingdom)
2009/11/26 Computational Epigenetics Bioinformatics in Genomic and Proteomic Data Conference
(Brno, Czech Republic)
2009/02/18 Determinants of tissue-specific transcriptional regulation in a transplanted chromosome University College London
Andrew Teschendorff (London, United Kingdom)
2009/02/06 Determinants of tissue-specific transcriptional regulation in a transplanted chromosome University of East Anglia
(Norwich, United Kingdom)
2008/10/02 História(s) da Bioinformática Engineering Faculty, Portuguese Catholic University
Pedro Matias (Oeiras, Portugal)
2008/07/22 Determinants of tissue-specific transcriptional regulation in a transplanted chromosome Department of Biology, University of Aveiro
Manuel Santos (Aveiro, Portugal)
2008/07/12 Determinants of tissue-specific transcriptional regulation in a transplanted chromosome First Portuguese Forum on Computational Biology FPBC-2008
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2007/06/30 Computational biology: microarrays and beyond Workshop \Microarrays in Clinical Oncology - promises and pitfalls", Sociedade de Ciências Médicas
(Lisboa, Portugal)
2006/03/15 Differential expansion of splicing factors families in eukaryotes Medical Research Council - Biostatistics Unit
(Cambridge, United Kingdom)
2006/03/15 Bioinformatics: sequence analysis and applications Department of Histopathology and Cytology, University of Cambridge
(Cambridge, United Kingdom)
2002/12/12 Splicing & Bioinformatics Theoretical Immunology Group, Instituto Gulbenkian de Ciência
Francisco Dionisio (Oeiras, Portugal)
2002/12/03 Splicing & Bioinformatics ALGOS Group, INESC
Arlindo Oliveira (Lisboa, Portugal)
2002/10/30 A Gramática dos Genomas 1st Meeting in Biomedical Engineering IST/FML
U. Lisbon Medical School (Lisboa, Portugal)
2002/10/17 História(s) da Biofísica 6a Semana da Física, Instituto Superior Técnico
NFIST (Lisboa, Portugal)
2000/08 Heart Rate Variability: Latest News XV International Conference for Physics Students
(Zadar, Croatia)
1999/08 Breathing Physics XIV International Conference for Physics Students
(Helsinki, Finland)

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2023/03 - Current PhD of Francisca Xara-Brasil (project being written)
Supervisor
Ciências Biomédicas (PhD)
Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Faculdade de Medicina, Portugal
2022/03 - Current p16 as a transcriptomic marker of cell senescence regulation
Supervisor
Ciências Biomédicas (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular, Portugal
2022/03 - Current Uncovering the Stressome: A Computational Approach to Define a Stress Granule Signature and its Implication in Cancer
Supervisor
Ciências Biomédicas
Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular, Portugal
2021 - Current Single-cell transcriptomics in unravelling the complexity of the breast tumour microenvironment
Supervisor
Ciências Biomédicas (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular, Portugal
2020/10 - Current Analysis of the repeatome of the human brain: dynamics of transposable elements during neurodevelopment and in neurodevelopmental diseases
Supervisor of Miguel Casanova
Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - Current When introns behave like exons: intron retention as a mechanism for dynamic regulation of gene expression
Supervisor
Ciências Biomédicas (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular, Portugal
2020/10 - 2024/02/28 Transcriptomic signatures of the INK4A/ARF locus in senescence regulation
Supervisor of José Ferrão
Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017/09 - 2023/05 Developing Web Apps for Analyses of Transcriptomes
Supervisor
Ciências Biomédicas (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular, Portugal
2021/02 - 2021/11 Profiling ageing-associated gene expression alterations in human astrocytes using single cell transcriptomics
Supervisor of Rita Silva
Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2021/03/26 The transcriptional landscape of Alzheimer's and Parkinson's diseases
Supervisor of Marie Catherine Bordone
Ciências Biomédicas (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular, Portugal
2018/07 - 2020/02 Transcriptomic profile comparison between Alzheimer's disease mouse models and human patients
Supervisor
Ciências Biofarmacêuticas (Master)
Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Faculdade de Farmácia, Portugal
2018/10 - 2019/10 Transcriptomic deconvolution of alterations in cellular composition and cell type-specific molecular changes associated with ageing of human tissues
Supervisor
Biotecnologia (Master)
Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
2018/07 - 2019/10 Single-cell transcriptomics in unravelling the molecular complexity of immunity in human disease
Supervisor
Bioinformática e Biologia Computacional (Master)
Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal
2018/02 - 2018/11 Discovery of novel mechanisms of centrosome clustering and their therapeutic value in cancer
Supervisor
Master of Science (Master)
Humboldt-Universität zu Berlin, Germany

Instituto de Medicina Molecular, Portugal
2017 - 2018 Discovery of novel mechanisms of centrosome amplification and their therapeutic value in cancer
Supervisor
Oncobiologia - Mecanismos Moleculares do Cancro (Master)
Universidade do Algarve, Portugal

Instituto de Medicina Molecular, Portugal
2016 - 2016 Genome-wide profiling of alternative splicing in aging across human tissues: Tissue-specific aging signature and contribution of cellular senescence
Supervisor
Engenharia Biológica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Instituto de Medicina Molecular, Portugal
2016 - 2016 Analysis of the contribution of alternative splicing glioma subtype definition
Supervisor
Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal

Instituto de Medicina Molecular, Portugal
2016 - 2016 Alternative splicing during neuronal development
Supervisor
Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Instituto de Medicina Molecular, Portugal
2016 - 2016 Bioinformatics application for analysis and visualisation of alternative splicing in cancer
Supervisor
Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal

Instituto de Medicina Molecular, Portugal
2015 - 2015 Alternative splicing analysis for finding novel molecular signatures in renal carcinomas
Supervisor
Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Instituto de Medicina Molecular, Portugal
2014 - 2014 Analyses of alternative splicing landscapes in clear cell renal cell carcinomas reveal putative novel prognosis factors
Supervisor
Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Event organisation

Event name
Type of event (Role)
Institution / Organization
2023/10/12 - 2023/10/13 EMBO Young Scientists Forum (2023/10/12 - 2023/10/13)
Conference (Co-organisor)
Instituto de Medicina Molecular, Portugal
2022/07/12 - 2022/07/12 RiboMed Satellite Conference on RNA in Disease (2022/07/12 - 2022/07/12)
Symposium
Instituto de Medicina Molecular, Portugal
2012 - 2012 The Donnelly Centre Postdoctoral Fellows' seminar series and symposium (2012 - 2012)
Symposium
Terrence Donnelly Centre for Cellular and Biomolecular Research, Canada
2007/06/30 - 2007/06/30 Microarrays in Clinical Oncology - promises and pitfalls (2007/06/30 - 2007/06/30)
Workshop (Co-organisor)
Instituto de Medicina Molecular, Portugal
2007/06/09 - 2007/06/09 1st Meeting of Portuguese Students and Researchers in the UK, Cambridge (2007/06/09 - 2007/06/09)

Event participation

Activity description
Type of event
Event name
Institution / Organization
2023/11/09 - 2023/11/10 HFP Consulting Leadership and Management Skills Course
Workshop
Instituto de Medicina Molecular, Portugal
2018/06/30 - 2018/07/03 Poster presentation: CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer
Conference
EACR25: 25th Biennial Congress of the European Association for Cancer Research
European Association For Cancer Research, United Kingdom
2018/05/10 - 2018/05/10 Poster presentation: CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer
Congress
3rd ASPIC International Congress
ASPIC - Associação Portuguesa de Investigação em Cancro, Portugal
2017/10/22 - 2017/10/25 Poster presentations: CELF2 at the core of a prognostic alternative splicing signature in colorectal cancer; psichomics - A bioinformatics application for the quantification, analysis and visualisation of alternative splicing from large transcriptomic datasets
Conference
Forty Years of mRNA Splicing
Cold Spring Harbor Laboratory, United States
2016/07/12 - 2016/07/15 Laboratory Management Course
Workshop
European Molecular Biology Organization, Germany
2013/06/11 - 2013/06/16 Poster presentation: The evolutionary landscape of alternative splicing in vertebrate species
Conference
RNA 2013 - The 18th Annual Meeting of the RNA Society (Davos, Switzerland)
RNA Society, United States
2013/01/03 - 2013/01/07 Poster presentation: The evolutionary landscape of alternative splicing in vertebrate species
Symposium
Pacific Symposium of Biocomputing 2013 (Hawaii)
Stanford University, United States
2012/08/19 - 2012/08/23 Poster presentation: The evolutionary landscape of alternative splicing in vertebrate species
Conference
ICSB - The 13th International Conference on Systems Biology
Terrence Donnelly Centre for Cellular and Biomolecular Research, Canada
2011/07/15 - 2011/07/16 Poster presentation: Species-specific differences in alternative splicing are primarily governed by evolutionary changes in cis-regulatory elements
Conference
ISMB/ECCB 2011 - Special Interest Group: Alternative Splicing (Vienna, Austria)
International Society for Computational Biology, United States
2011/05/20 - 2011/06/20 Poster presentation: Establishing determinants of species-specific alternative splicing using mice harboring human chromosome 21
Workshop
Workshop on transcriptional and post-transcriptional regulatory codes
Terrence Donnelly Centre for Cellular and Biomolecular Research, Canada
2011/02/28 - 2011/03/03 Poster presentation: Establishing determinants of species-specific alternative splicing using mice harboring human chromosome 21
Conference
2nd EURASNET Conference on Alternative Splicing (Granada, Spain)
2010/08/12 - 2010/08/15 Poster presentation: Re-annotaion of microarray probes improves the interpretation of cancer gene expression data
Conference
RECOMB 2010 (Lisbon, Portugal)
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2010/06/25 - 2010/06/25 Poster presentation: Re-annotaion of microarray probes improves the interpretation of cancer gene expression data
Symposium
Cambridge Cancer Centre Symposium
Cancer Research UK Cambridge Research Institute, United Kingdom
2010/05/08 - 2010/05/09 Science Communication Workshop
Workshop
PARSUK, United Kingdom
2009/07/06 - 2009/07/08 Poster presentation: Re-annotation of microarray probes improves the interpretation of cancer gene expression data
Conference
Cancer-om-atics: Multilevel interpretation of cancer genome data
Centro Nacional de Investigaciones Oncológicas, Spain
2007/06/10 - 2007/06/15 Poster presentation: Gene Expression Profiles of Pediatric Malignant Germ Cell Tumours
Workshop
Statistics for Biomolecular Data Integration and Modeling - Workshop (Ascona, Switzerland)
Eidgenössische Technische Hochschule Zürich, Switzerland
2004/11/22 - 2004/11/23 Poster presentation: Resemblance between Teleost Gene Duplication and Mammalian Alternative Splicing
Symposium
Symposium on Alternative Transcript Diversity
European Bioinformatics Institute, United Kingdom

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2023/12 Evolutionary dynamics of post-transcriptional regulation mechanisms in vertebrates
(Thesis) Main arguer
Gabriela Santos Rodríguez (PhD)
University of New South Wales, Australia
2023/11/21 Clinical and Molecular Characterization of Sarcomas using Machine Learning with Multiomics Integration
(Thesis) Main arguer
Manuel Sérgio Sokolov Ravasqueira (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/11/21 Detection of aberrant terminal exon usage in RNA sequencing data
(Thesis) Main arguer
Raquel Alves Romão (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/04/20 Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
(Thesis) Main arguer
Ana Pereira de Brito Líbano Monteiro (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/04/17 Towards accreditation in metagenomics for clinical microbiology
Thesis Member
Catarina Inês Marques de Sousa Mendes (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2023/02/22 The roles of tubulin post translational modifications in cancer
(Thesis) Arguer
Danilo da Silva Lopes (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/12/21 A systems approach to the mechanisms of neurodegeneration
(Thesis) Arguer
Marina Luque Garcia-Vaquero (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022/11/30 Disclosing Transcriptomic Signatures of Gliomas Using Sparse Methods
(Thesis) Main arguer
Sofia Matias Coimbra Martins (Master)
Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022/09/14 Unravelling longitudinal mitochondrial DNA mutations in Multiple Sclerosis: Association with disease activity and progression
(Thesis) Arguer
Filipe Carlos Pereira dos Reis Cortes Figueiredo (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2022/04/15 Functional interpretation of transcriptome and translatome dynamics in cancer Marina Reixachs Solé (PhD)
Australian National University, Australia
2022/04/12 SRRM3 regulates a subprogram of highly sensitive microexons important for pancreatic endocrine function
President of the jury
Szymon Piotr Bajew (PhD)
Universitat Pompeu Fabra, Spain

Centre de Regulació Genòmica, Spain
2022/02/09 Unveiling the regulation of germinal centre responses and antibody production by follicular T cells
(Thesis) Arguer
Saumya Dileep Kumar (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2022/01/14 Resolving the complexity of oviduct biology and pathology by comprehensive single-cell sequencing across species
(Thesis) Main arguer
Laura Santana González (PhD)
University of Oxford Nuffield Department of Women's & Reproductive Health, United Kingdom

University of Oxford Balliol College, United Kingdom
2021/12/09 Unveiling the role of cis-regulatory variation in breast cancer aetiology
(Thesis) Arguer
Filipa Alexandra Oleiro Esteves Ribeiros (PhD)
Universidade do Algarve, Portugal
2021/06/22 Effect of the microenvironment on alternative splicing in colorectal cells
(Thesis) Arguer
Joana Filipa de Sousa Pereira (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021/06/16 Gene Expression and Phenotypical Analysis of Winner and Loser Cells Engaged in Cell Competition
(Thesis) Main arguer
Alexandre Miguel Guedes da Silva Afonso (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2021/02/23 Network-based sparse regularization for the identification of disease signatures
(Thesis) Arguer
André Filipe da Silva Veríssimo (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/01/28 VenCode - A versatile entry code for post-DNA delivery identification of target cel
(Thesis) Arguer
André Lopes Martins Macedo (PhD)
Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2020/07/02 Epigenetic hotspots in cancer
(Thesis) Main arguer
Daniel José Formica Pestana (Master)
Universidade do Algarve, Portugal
2020/06/24 Longitudinal analysis of adipocytes and liver gene expression during T. brucei infection
(Thesis) Main arguer
João Francisco Parraga Ribeiro Colaço (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020/02/28 Origin and evolution of neural microexons Antonio Torres Méndez (PhD)
Universitat Pompeu Fabra, Spain

Centre de Regulació Genòmica, Spain
2019/11/13 Identification of common gene signatures in microarray and RNA-sequencing data using network-based regularization
(Thesis) Main arguer
Maria Inês Cotrim de Vilhena Diegues (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019/07/23 Regulation of alternative polyadenylation in Drosophila melanogaster
(Thesis) Main arguer
Marta Sofia dos Santos Oliveira (PhD)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2019/02/14 Alternative splicing dynamics during somatic cell reprogramming
(Thesis) Main arguer
Claudia Vivori (PhD)
Universitat Pompeu Fabra, Spain

Centre de Regulació Genòmica, Spain
2018/12/14 Functional impact of alternative splicing in vertebrate proteomes across tissues and cell types Javier Tapial Rodriguez (PhD)
Universitat Pompeu Fabra, Spain

Centre de Regulació Genòmica, Spain
2018/11/29 On the Origin, Progression, and Evolution of Ovarian Cancer Mohammad KaramiNejadRanjbar (PhD)
University of Oxford, United Kingdom
2018/11/23 Network-based Regularisation for Survival Analysis Pedro Jorge Estrela Martinho (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018/11/15 Astrocyte-specific transcriptomic response to PGC-1alpha isoforms Mariana Messias de Jesus Rufino Ribeiro (Master)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2017/12/04 Modelling cancer progression through joint models for longitudinal and time-to-event data Hugo Daniel Paes Loureiro Santos Ambrósio (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/10/18 Epigenetic Regulation of Signalling Pathways in Pancreatic Cancer Inês Correia da Silva Pires Faleiro (Master)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2017/05/11 Large-scale study of RNA processing alterations in multiple cancers Babita Singh (PhD)
Universitat Pompeu Fabra, Spain

Centre de Regulació Genòmica, Spain
2015/05/20 Outlier Detection in Survival Analysis João Diogo Pinto (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015/01/20 Dissecting Central Nervous System Gene Expression Margherita Francescatto (PhD)
Universidade do Porto, Portugal
2015/01/12 LincRNA profile in clear cell renal cell carcinoma using RNA-seq data Ioana Posa (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal

Instituto de Medicina Molecular, Portugal
2014/12/05 Genome-wide profiling of RNA polymerase II and associated co-transcriptional processes using advanced NET-seq data Tomás Pires de Carvalho Gomes (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal

Association member

Society Organization name Role
2021/11 - Current RNA Society
2021/11 - Current ASPIC - Associação Portuguesa de Investigação em Cancro
2021/11 - Current EACR - European Association for Cancer Research
2010 - Current PAPS - Portuguese-American Post-graduate Society Member of the Executive Committee (2015-2018); Co-leader of the Alumni Chapter (2015-2016); Leader of the Toronto Chapter (2011-2013)
2008 - Current PARSUK - Portuguese Association of Researchers and Students in the UK Member
2003 - Current Cambridge University Portuguese Speakers Society Lifetime member

Committee member

Activity description
Role
Institution / Organization
2022/07 - Current PhD thesis of Marta Andolfato
Member
Instituto de Medicina Molecular, Portugal
2022/05 - Current PhD thesis of Eller Conti
Member
Instituto de Medicina Molecular, Portugal
2021/12 - Current PhD thesis of Jean-Christophe Lone
Member
Instituto de Medicina Molecular, Portugal
2021/11 - Current PhD thesis of Bárbara Teixeira
Member
Instituto de Medicina Molecular, Portugal
2021/01 - Current PhD thesis of Rafael Mamede
Member
Universidade de Lisboa Faculdade de Medicina, Portugal
2021 - Current PhD thesis of Beatriz Silva
Member
Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular, Portugal
2021 - Current PhD thesis of Rui Bernardino
Member
Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2020/01 - Current PhD thesis of Ana Alão Freitas Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/03 - Current PhD thesis of Inês Faleiro Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Faculdade de Medicina, Portugal
2015/01 - Current PhD thesis of Bruno Gonçalves Universidade de Lisboa Faculdade de Medicina, Portugal
2015 - Current Commissioner for the Information Systems Unit Instituto de Medicina Molecular, Portugal
2018/11 - 2023/05 PhD thesis of Federica Mantica Universitat Pompeu Fabra, Spain

Centre de Regulació Genòmica, Spain
2017/03 - 2023/05 PhD thesis of Rita Soares Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Faculdade de Medicina, Portugal
2021/10 - 2023/04 PhD thesis of Inês Mendes
Member
Instituto de Medicina Molecular, Portugal
2016/05 - 2022/02 PhD thesis of Saumya Dileep Kumar Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Faculdade de Medicina, Portugal
2018 - 2022 PhD thesis of Ana Carolina Peixoto
Member
Universidade de Lisboa Instituto Superior Técnico, Portugal
2014 - 2021 PhD thesis of André Veríssimo
Member
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016/03 - 2020/06 PhD thesis of Helena Brigas Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Faculdade de Medicina, Portugal
2015/03 - 2020/01 PhD thesis of Vasco Conceição Instituto de Medicina Molecular, Portugal

Universidade de Lisboa Faculdade de Medicina, Portugal
2014/10 - 2015/11 PhD thesis of Hugo Santos Universidade de Lisboa Faculdade de Ciências, Portugal
2013/12 - 2015 PhD thesis of Fernando Martins Universidade de Lisboa Faculdade de Medicina, Portugal
2012 - 2013 Toronto Bioinformatics User Group (TorBUG) Terrence Donnelly Centre for Cellular and Biomolecular Research, Canada

Consulting

Activity description Institution / Organization
2021 - Current PhD Scholarship reviewer Fundação para a Ciência e a Tecnologia, Portugal
2016 - Current Grant reviewer Medical Research Council, United Kingdom

Agence nationale de la recherche, France

Israel Science Foundation, Israel

Biotechnology and Biological Sciences Research Council, United Kingdom

Fundação para a Ciência e a Tecnologia, Portugal

Worldwide Cancer Research, United Kingdom

Narodowe Centrum Nauki, Poland

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2024/02/06 - Current Systems Biology - Human transcriptomes and cognitive biases Biociências Moleculares (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/12/19 - Current Neuroethics - Biases and incentives in the quest for reproducible science Neurociências (Mestrado integrado) Universidade de Lisboa Faculdade de Medicina, Portugal
2023/10/10 - Current Bioinformatics - Computational biology in the translation of cancer "omics" Investigação Biomédica (Mestrado integrado) Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2023/01/10 - Current Computational biology and what transcriptomes tell us about disease Biomedical and Clinical Science (Doutoramento) Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
2022/10/17 - Current Bioinformatics - Computational biology in the translation of cancer "omics" Investigação Biomédica (Mestrado integrado) Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2022/10/14 - Current Perspectives in Computational Biology - What transcriptomic data tell us about ageing Biologia Computacional e Bioinformática (Mestrado integrado) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/11/19 - Current Perspectives in Computational Biology - What transcriptomic data tell us about ageing Biologia Computacional e Bioinformática (Mestrado) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/01 - Current Bioinformatics Course Investigação Biomédica (Mestrado integrado) Universidade de Lisboa Faculdade de Medicina, Portugal
2019/12 - Current Computational Biology Engenharia Biomédica (Mestrado integrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2018/11 - Current Bioinformatics Course Oncobiologia (Mestrado) Universidade de Lisboa Faculdade de Medicina, Portugal
2023/04/03 - 2023/04/03 Applied Computational Multi-Omics - Biologist-intelligible alternative splicing analysis of RNA-seq data Biologia Computacional e Bioinformática (Mestrado integrado) Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023/02/07 - 2023/02/07 Systems Biology - What (single cell) transcriptomes tell us about human disease Biociências Moleculares (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/11/09 - 2022/11/09 Computational Biology in Cancer - Single cell transcriptomics Neuroscience and Cancer (Doutoramento) Centro Champalimaud, Portugal
2022/06/23 - 2022/06/23 RiboMed Summer School on Modelling Biological Data - Statistical modelling for splicing analyses Instituto de Medicina Molecular, Portugal
2022/04/11 - 2022/04/11 Applied Computational Multi-Omics - Biologist-intelligible alternative splicing analysis of RNA-seq data Biologia Computacional e Bioinformática (Mestrado integrado) Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022/02/17 - 2022/02/17 Computational biology and what transcriptomes tell us about disease Biomedical and Clinical Research (Doutoramento) Instituto de Medicina Molecular, Portugal
2022/02/08 - 2022/02/08 Systems Biology - What (single cell) transcriptomes tell us about human disease Biociências Moleculares (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/01/31 - 2022/01/31 Systems Bioengineering - What (single cell) transcriptomes tell us about human disease Engenharia Biológica (Mestrado integrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2021/10/12 - 2021/10/12 Bioinformatics - Computational biology in the translation of cancer "omics" Investigação Biomédica (Mestrado integrado) Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2021/09/30 - 2021/10/08 Course in “Ageing Cognition” - The CAJAL advanced neuroscience training programme, Bordeaux School of Neuroscience Fédération Bordeaux Neurocampus, France
2021/04/26 - 2021/04/26 Computational biology and what transcriptomes tell us about disease Biomedical and Clinical Research (Doutoramento) Instituto de Medicina Molecular, Portugal
2021/03/15 - 2021/03/15 Computational biology in the translation of disease "omics" Ciências Biofarmacêuticas (Mestrado integrado) Universidade de Lisboa Faculdade de Farmácia, Portugal
2021/02/09 - 2021/02/09 What transcriptomes tell us about diseases Biociências Moleculares (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/10/14 - 2020/10/14 Bioinformatics - Computational biology in the translation of cancer "omics" Investigação Biomédica (Mestrado integrado) Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2020/04/24 - 2020/04/24 Computational biology in the translation of disease "omics" Ciências Biofarmacêuticas (Mestrado) Universidade de Lisboa Faculdade de Farmácia, Portugal
2020/04/23 - 2020/04/23 Computational biology in the translation of disease "omics" Tecnologias Moleculares em Saúde (Mestrado integrado) Instituto Politécnico de Lisboa Escola Superior de Tecnologia da Saúde de Lisboa, Portugal
2020/03/03 - 2020/03/03 Computational biology and what transcriptomes tell us about disease Biomedical and Clinical Research (Doutoramento) Instituto de Medicina Molecular, Portugal
2019/10/18 - 2019/10/18 Bioinformatics - Computational biology in the translation of cancer "omics" Investigação Biomédica (Mestrado integrado) Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2019/10/09 - 2019/10/09 What transcriptomes tell us about ageing and associated diseases Biociências Moleculares (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/05/08 - 2019/05/08 Bioinformatics - Computational biology in the translation of cancer “omics" Ciências Biofarmacêuticas (Mestrado) Universidade de Lisboa Faculdade de Farmácia, Portugal
2018/10/08 - 2018/10/08 Bioinformatics - Computational biology in the translation of cancer "omics" Investigação Biomédica (Mestrado) Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2018/04/05 - 2018/04/05 Bioinformatics - Computational biology in the translation of cancer "omics" Ciências Biofarmacêuticas (Mestrado) Universidade de Lisboa Faculdade de Farmácia, Portugal
2018/01/09 - 2018/01/09 Computational biology and disease transcriptomics Biomedical and Clinical Research (Doutoramento) Instituto de Medicina Molecular, Portugal
2018/01/05 - 2018/01/05 Bioinformatics - Computational biology in the translation of cancer "omics" Investigação Biomédica (Mestrado) Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2017/02/06 - 2017/02/10 Bioinformatics Course PGCD, Graduate Program Science for Development (Curso de doutoramento (conclusão de unidades curriculares)) Instituto Gulbenkian de Ciência, Portugal

Universidade de Cabo Verde, Cape Verde
2017/01/10 - 2017/01/10 Computational biology and disease transcriptomics Biomedical and Clinical Research (Doutoramento) Instituto de Medicina Molecular, Portugal
2016/10/29 - 2016/10/29 Biologia Computacional: splicing & cancro Oncobiologia (Mestrado) Universidade de Lisboa Faculdade de Medicina, Portugal

Instituto de Medicina Molecular, Portugal
2016/03/30 - 2016/03/31 NGS Data Analysis, RNAseq, ChIPseq (Outros) Instituto Gulbenkian de Ciência, Portugal
2016/02/22 - 2016/02/26 Bioinformatics Course PGCD, Graduate Program Science for Development (Curso de doutoramento (conclusão de unidades curriculares)) Instituto Gulbenkian de Ciência, Portugal

Universidade de Cabo Verde, Cape Verde
2016/01/05 - 2016/01/05 Computational biology and disease transcriptomics Biomedical and Clinical Research (Doutoramento) Instituto de Medicina Molecular, Portugal
2015/09/15 - 2015/09/15 RNA-Seq and disease transcriptomics Medicines and Pharmaceutical Innovation (i3DU) (Doutoramento) Universidade de Lisboa Faculdade de Farmácia, Portugal
2015/07/23 - 2015/07/23 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data Bioinformática e Biologia Computacional (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2015/04/21 - 2015/04/22 R and Bioconductor Workshop (Computational Biology course) Ciências Biomédicas (Mestrado integrado) Universidade do Algarve, Portugal
2015/01/30 - 2015/01/30 Alternative splicing in evolution and cancer Integrative Biology and Biomedicine (Doutoramento) Instituto Gulbenkian de Ciência, Portugal
2015/01/07 - 2015/01/07 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data Biomedical and Clinical Research (Doutoramento) Instituto de Medicina Molecular, Portugal
2014/07/17 - 2014/07/17 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data Bioinformática e Biologia Computacional (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2014/04/17 - 2014/04/17 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data BioEngineering - Cell Therapies & Regenerative Medicine (Doutoramento) Instituto de Medicina Molecular, Portugal
2014/02/27 - 2014/02/27 Analysis of Transcriptional Regulation and RNA Processing from RNA-Seq Data Biomedical and Clinical Research (Doutoramento) Instituto de Medicina Molecular, Portugal
2014/01/30 - 2014/01/31 X Summer Bioinformatics Course Bioinformatics Universidade de São Paulo Faculdade de Medicina de Ribeirão Preto, Brazil
2013/07/25 - 2013/07/25 The evolutionary landscape of alternative splicing in vertebrate species Bioinformática e Biologia Computacional (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2010/09/06 - 2010/09/10 Microarray Data Analysis using R and Bioconductor (Outros) Instituto Gulbenkian de Ciência, Portugal
2010/02/24 - 2010/02/26 Microarray Data Analysis using R and Bioconductor University of Cambridge Department of Genetics, United Kingdom
2010/02/02 - 2010/02/02 Microarray and high throughput sequencing data analysis with Bioconductor European Bioinformatics Institute, United Kingdom
2010/01/10 - 2010/01/11 Course in "Microarray Data Analysis using R and BioConductor" M1GPBIDM option Biotechnology Université de Poitiers, France
2009 - 2010 Systems Biology course - Engineering for Life Sciences Engineering Tripos University of Cambridge Department of Engineering, United Kingdom
2007 - 2010 Functional Genomics course MPhil in Computational Biology University of Cambridge Department of Pure Mathematics and Mathematical Statistics, United Kingdom
2009/10/12 - 2009/10/17 EMBO Practical Course on Analysis and Informatics of Microarray Data European Bioinformatics Institute, United Kingdom
2009/09/14 - 2009/09/18 Microarray Data Analysis using R and Bioconductor (Outros) Instituto Gulbenkian de Ciência, Portugal
2009/06/01 - 2009/06/03 Microarray Data Analysis using R and Bioconductor University of Cambridge Department of Genetics, United Kingdom
2009/04/13 - 2009/04/17 Bioinformatics module - Course in "Regulation of Gene Expression" Basic and Applied Biology (Doutoramento) Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal
2009/04/15 - 2009/04/15 Workshop on Gene Expression: From Genes to Systems Basic and Applied Biology (Doutoramento) Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal
2009/03/11 - 2009/03/13 Course in "Analysis of DNA expression microarrays" Computational Biology (Doutoramento) Instituto Gulbenkian de Ciência, Portugal
2009/01/19 - 2009/01/22 Hands-on training at EBI - Transcriptomics European Bioinformatics Institute, United Kingdom
2008/12/01 - 2008/12/03 Microarray Data Analysis using R and Bioconductor Universitetet i Oslo, Norway
2008/09/29 - 2008/10/03 Microarray Data Analysis using R and Bioconductor (Outros) Instituto Gulbenkian de Ciência, Portugal
2008/07/21 - 2008/07/25 Advanced course on mRNA profiling using DNA microarrays Molecular Genomics (Outros) Universidade de Aveiro, Portugal
2007/04 - 2008/02 Four 3-day introductory microarray analysis courses Cancer Research UK Cambridge Research Institute, United Kingdom
2008/01/29 - 2008/01/29 Hands-on training at EBI - Transcriptomics European Bioinformatics Institute, United Kingdom
2007/10/15 - 2007/10/19 Introductory Course on Microarray Data Analysis (Outros) Instituto Gulbenkian de Ciência, Portugal
2007/05/24 - 2007/05/24 R and Bioconductor Microarray Data Analysis (The Norwegian Microarray Consortium) Universitetet i Oslo, Norway
2006/08/28 - 2006/09/01 "Microarray Technology and Bioinformatics" Summer School Università degli Studi di Camerino, Italy
2004/10/13 - 2004/10/19 "Splicing & Bioinformatics" module - Course in "mRNA biogenesis" Biomedicine (Doutoramento) Instituto Gulbenkian de Ciência, Portugal
2004/03/15 - 2004/03/19 "Splicing & Bioinformatics" module - Course in "Genetic Evolution" Basic and Applied Biology (Doutoramento) Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal
2004/01/07 - 2004/01/07 Splicing & Bioinformatics Engenharia Biomédica e Biofísica (Curso de mestrado (conclusão do curso de especialização)) Universidade de Lisboa Faculdade de Ciências, Portugal
2003/10/14 - 2003/10/17 "Splicing & Bioinformatics" module - Course in "mRNA biogenesis" Biomedicine (Doutoramento) Instituto Gulbenkian de Ciência, Portugal
1999 - 2001 Circuit Theory and Fundamentals of Electronics Physics Engineering (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal

Journal scientific committee

Journal title (ISSN) Publisher
2010 - 2022 BMC Bioinformatics (1471-2105) Springer (Biomed Central Ltd.)
2010 - 2021 BMC Cancer (1471-2407) Springer (Biomed Central Ltd.)

Mentoring / Tutoring

Topic Student name
2022/09 - 2022/11 Visiting fellow Claudia Cifuentes
2020/03 - 2021/12 GenomePT Fellowship Rita Belo
2019/03 - 2020/01 Volunteer trainee Ana Sofia Borges
2018/04 - 2018/06 Visiting fellow Javier Tapial
2015/11 - 2018 Postdoc (FCT fellow) co-supervisor Joana Xavier
2015 - 2018 Postdoc supervisor Lina Gallego-Paez
2016/04 - 2016/07 Visiting fellow Juan Carlos Gomez Verjan
2015/07 - 2015/09 Summer trainee Mariana Ascensão Ferreira
2007 - 2007 Summer project of MPhil in Computational Biology, University of Cambridge, UK Julie Addison
2001 - 2002 Mentor of Biomedical Engineering 1st year students 1st year students, Biomedical Engineering - Instituto Superior Técnico

Other jury / evaluation

Activity description Institution / Organization
2023/11/23 - 2023/11/25 Abstract and oral presentation evaluator, 27th Annual Meeting of the Portuguese Human Genetics Society, Lisbon, Portugal Sociedade Portuguesa de Genética Humana, Portugal
2021 - 2021 Abstract evaluator, iMed Conference 13.0 Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
2015/08/05 - 2015/08/08 Poster judge, 5th EMBO Meeting, Birmingham UK European Molecular Biology Organization, Germany
Distinctions

Title

2021 Citizen of Merit
Câmara Municipal de Viana do Castelo, Portugal

Other distinction

2020 FCT Stimulus of Scientific Employment, Individual Support - Assistant Researcher
Fundação para a Ciência e a Tecnologia, Portugal
2014 Investigador FCT - Starting Grant
Fundação para a Ciência e a Tecnologia, Portugal
2014 EMBO Installation Grant
European Molecular Biology Organization, Germany
2011 Marie Curie International Outgoing Fellowship
European Commission, Belgium
2010 CIHR Postdoctoral Fellowship
Canadian Institutes of Health Research, Canada
2005 EMBO Short-Term Fellowship
European Molecular Biology Organization, Germany
2000 Fellowship PRAXIS XXI SFRH/BD (PhD)
Fundação para a Ciência e a Tecnologia, Portugal
2000 Fellowship “Programa de Estágios no Ensino Superior”
European Social Fund, Belgium

Ministério da Educação, Portugal