How does a single genome sequence encode the information to build the enormous complexity of cell types and structures of an adult animal? How are changes in this sequence translated into morphological differences during evolution? These two exciting questions have always been the center of my research. In my lab, we approach these topics focusing on cell and tissue type specific transcriptomes: How are they encoded in the genome? How are they generated during embryogenesis? How do they impact cell function in adult organisms? How do they evolve and how they impact evolution? To answer these questions, we not only study transcriptional regulation, but also other mechanisms that expand transcriptomic diversity, such as alternative splicing and gene duplication.

In particular, we focus on two highly contrasting systems: (i) early mammalian embryogenesis and (ii) vertebrate neural development. These two developmental contexts have radically distinct characteristics. On the one hand, early embryogenesis captures in vivo pluripotency and the first cell fate decisions, involves relatively simple morphogenetic processes, and shows particularly high evolutionary rates. On the other hand, vertebrate brains are extremely complex systems of highly differentiated cell types that develop through very specialized processes (e.g., neuritogenesis, axon guidance, migration, etc.). Furthermore, neural-specific isoforms are exceptionally conserved. Thus, by combining both biological systems we aimed at obtaining highly complementary insights into the roles of transcriptome specificity and diversification in development and evolution. Moreover, these two systems are key to understand two evolutionary transitions we are fascinated about: the origin of vertebrates and the origin of mammals.

To tackle these questions, we combine computational approaches (comparative bulk and single-cell transcriptomics and functional genomics) with experiments using in vitro and in vivo systems (zebrafish, mouse and fruitfly) to investigate how these mechanisms impact embryonic development, adult function, disease and evolution.