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 Professor 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 then did his PhD in Biomedical Sciences at the Instituto de Medicina Molecular / University of Lisbon Medical School with Professor Maria do Carmo Fonseca. Most of the PhD research actually took place at the University of Cambridge with Dr. 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 Professor 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 Dr 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 [presentation video].

Nuno moved in June 2013 to the iMM 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 (press release) 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, and iMM's participation in Nuno also coordinates the Computational Biology efforts of the iMM-Laço Hub. In 2020, he was awarded a 6-year Assistan Researcher contract in FCT's Individual Call to Scientific Employment Stimulus. Nuno is an Invited Associate Professor at the Faculty of Medicine, University of Lisbon, where he teaches Bioinformatics to Masters in Biomedical Engineering, Oncobiology and Biomedical Research.