Dr Nuno L. Barbosa-Morais

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CV / Publications (by topic)

• Transcriptional regulation (publications)
  Nuno has been interested in the systems-level transcriptional mechanisms underlying mammalian cell specification (often perturbed in carcinomas). In particular, he has been collaborating 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 involves the analysis, annotation and integration of different sorts of array and sequence information.
  
  
• Splicing (publications)
  Motivated by examples of resemblance between mammalian alternative splicing and gene duplication in teleosts, Nuno is particularly interested in unveiling the features shared by the transcription and splicing regulatory circuitries, thereby shedding some light on the mechanisms responsible for the association between aberrant splicing and cancer. His efforts include studies on the evolution of splicing factors, the RNA binding of splicing factors, and the expression profiling of splicing factors in myogenesis (mostly in collaboration with the Carmo-Fonseca lab, based at the Institute of Molecular Medicine in Lisbon). He is now involved in the analysis of mRNA-seq data for the inference of tissue and species specific alternative splicing patterns.
  
  
• Microarray analysis (publications)
  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.
  
  
• Cancer biology (publications)
  Nuno has been collaborating 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).