Identifying conserved and divergent gene expression signatures between in vivo and in vitro models of development with SCOPRO

Supervisor: Dr. Antonio Scialdone

Enrolled since 2019

I completed my Bachelors Degree in Physics from the University of Torino, Italy, in July 2017.  I then obtained a Masters in Physics of Complex Systems from the same university in April 2019. In the summer of 2018, I participated in the Summer Internship Programme at the Helmholtz Zentrum Munich in Antonio Scialdone’s lab. I focused on cell competition in mouse embryo combining the analysis of single-cell RNA-seq data with mathematical modelling.

Cell competition is a biological process whereby cells eliminate their less fitted neighbours. The purpose was to understand the transcriptional features of cells eliminated by competition and what are the roles of cell competition during mammalian development.
I worked on the same project for my masters thesis under the supervision of Dr. Antonio Scialdone and Prof. Michele Caselle. After receiving my masters from the University of Torino, I moved to Munich, in the Scialdone’ s Lab, to start my PhD in May 2019.

During the first months of my PhD, I completed the single-cell RNA-seq data analysis about the cell competition project (pre-print available here).  Since August 2019, I started a new project in collaboration with Maria Elena Torres-Padilla’s lab, about data analysis on 2C- like cells (a rare population of cells displaying molecular features of totipotency that arises in pluripotent embryonic stem (ES) cell culture) in different species.

Current Position

Post-Doctoral Researcher with Helmholtz Munich - Munich, Germany

Team: Institute of Epigenetics and Stem Cells

Team Leader: Dr. Antonio Scialdone


  • Gabriele Lubatti, Marco Stock, Ane Iturbide, Mayra L. Ruiz Tejada Segura, Melina Riepl, Richard C. V. Tyser, Anna Danese, Maria Colomé-Tatché, Fabian J. Theis, Shankar Srinivas, Maria-Elena Torres-Padilla, Antonio Scialdone; CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data. Development 2023; dev.201264.​
  • Lubatti et al. (2022). MitoHEAR: an R package for the estimation and downstream statistical analysis of the mitochondrial DNA heteroplasmy 4 calculated from single- cell datasets. Journal of Open Source Software, 7(74), 4265.
  • Lima, A., Lubatti, G., Burgstaller, J. et al. Cell competition acts as a purifying selection​ to eliminate cells with mitochondrial defects during early mouse development. Nat Metab 3, 1091–1108 (2021).
  • Ane Iturbide, Mayra L Ruiz Tejada Segura, Camille Noll, Kenji​ Schorpp, Ina Rothenaigner, Elias R Ruiz-Morales, Gabriele Lubatti, Ahmed Agami, Kamyar Hadian, Antonio Scialdone, Maria-Elena Torres-Padilla. Retinoic acid signaling is critical during the totipotency window in early mammalian development. Nat Struct Mol Biol 28, 521–532 (2021).