Identification of the origin of cellular heterogeneity in mammalian development through single cell transcriptomics

Supervisor: Dr. Antonio Scialdone

Enrolled from 2018 - 2023

I completed my undergraduate degree in Biological Sciences at the University of Alberta in Canada. There, my final project focused on novel gene identification in congenital abnormalities of kidney and urinary tract disease through whole-exome sequencing analysis. I continued my scientific education through a Master’s degree program in Bioinformatics at the University of Copenhagen. During my master’s thesis, I focused on data-driven mathematical modeling of the gene regulatory network of mammalian circadian clock at the Institute for Theoretical Biology in Berlin. After that I joined Helmholtz Munich to do PhD at the Institute of Epigenetics and Stem Cells under the supervision of Dr. Antonio Scialdone. My PhD project involves elucidation of cell-fate decision through single-cell transcriptomics analysis. The goal of my PhD project is to identify the origin of cellular heterogeneity in mammalian (human and mouse) development through single cell transcriptomics. Using the advantages of this new technique, my aim is to computationally determine the molecular state of the cells that arise during cell fate decision in mammalian heart. Single cell genomics data can help to identify regulatory mechanisms, functional domains in the genome, and spatio-temporal events that can be associated with cellular heterogeneity.

Current Position

Post-Doctoral Researcher with the Max Delbrück Center - Berlin, Germany


  • Lubatti, G., Mahammadov, E., & Scialdone, A. (2022). MitoHEAR: an R package for the estimation and​ downstream statistical analysis of the mitochondrial DNA heteroplasmy calculated from single-cell​ datasets. Journal of Open Source Software, 7(74), 4265. ​
  • Nakatani, T., Lin, J., Ji, F., Ettinger, A., Pontabry, J., Tokoro, M., Altamirano-Pacheco, L., Fiorentino, J.,​ Mahammadov, E., Hatano, Y., Van Rechem, C., Chakraborty, D., Ruiz-Morales, E. R., Arguello Pascualli,​ P. Y., Scialdone, A., Yamagata, K., Whetstine, J. R., Sadreyev, R. I., & Torres-Padilla, M.-E. (2022). DNA​ replication fork speed underlies cell fate changes and promotes reprogramming. Nature​ Genetics, 54(3), 318–327.
  • Tyser, R. C. V., Mahammadov, E., Nakanoh, S., Vallier, L., Scialdone, A., & Srinivas, S. (2021). Single-cell​ transcriptomic characterization of a gastrulating human embryo. Nature, 600(7888), 285–289.​​
  • Lima, A., Lubatti, G., Burgstaller, J., Hu, D., Green, A. P., Di Gregorio, A., Zawadzki, T., Pernaute, B.,​ Mahammadov, E., Perez-Montero, S., Dore, M., Sanchez, J. M., Bowling, S., Sancho, M., Kolbe, T.,​ Karimi, M. M., Carling, D., Jones, N., Srinivas, S., … Rodriguez, T. A. (2021). Cell competition acts as a​ purifying selection to eliminate cells with mitochondrial defects during early mouse​ development. Nature Metabolism, 3(8), 1091–1108. ​