Single cell genomics

In my lab we are interested single-cell genomics. In particular, in developing new single-cell technologies and computational strategies that will facilitate new insights into complex biological mechanisms involved in organ development, regeneration, and cancer.

Tissues and organs in the human body are composed of hundreds of different cell types. A network of well-controlled interactions between these different cell types is responsible for proper organ formation and tissue regeneration throughout our lifetime. In a complex disease such as cancer, genetic and epigenetic aberrations distort the repertoire cell types and the interactions between them in a way that is not well understood and that can vary widely between different individuals.

In my lab we want to understand how tissues and organs are formed, how they are maintained and regenerated throughout our lifetime, and what causes them to behave badly and create cancer. Three specific aims are: (i) to identify and characterize cellular and molecular mechanism controlling development, regeneration, and tumorigenesis; (ii) to find markers for tissue-specific and cancer stem cells for regenerative medicine, targeted therapeutics, and early detection; (iii) to understand tumor heterogeneity, that is, how tumors differ from patient to patient, in order to design personalized treatment strategies.

To this end, we use single-cell technologies and next-generation sequencing. We dissociate a tissue or tumor into single cells and measure gene expression and sequence information from each individual cell. Then, we use computational algorithms to identify and characterize the different cells types and to understand their roles, fate trajectories, and network of interactions. Our overall goal is to comprehensively profile embryonic, adult, and diseased tissues at the single-cell level in order to reveal the cellular and molecular mechanism underlying development, regeneration, and disease.