Dr. Tomer Kalisky

Single-cell genomics of kidney development, regeneration, and cancer

The Alexander Kofkin Faculty of Engineering


Tomer Kalisky completed his Ph.D. in physics of complex networks with Prof. Shlomo Havlin from Bar-Ilan University. After a postdoc in systems biology with Prof. Uri Alon at the Weizmann Institute and in bioengineering with Prof. Stephen Quake at Stanford, Tomer established his lab for single-cell genomics in the Faculty of Engineering in Bar-Ilan University.


Annual Activity Report, March 2018 – characterizing cancer stem cells in Wilms’ tumor at the single-cell level


The mission of our lab is to understand how tissues and organs are formed in the human body, how they are maintained and regenerated throughout our lifetime, and what causes them to behave badly and create cancer. Two specific aims are: (i) to find markers for tissue-specific and cancer stem cells for regenerative medicine, targeted therapeutics, and early detection, and (ii) 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, thereby creating a “Cell Atlas”. 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.


We are mainly focusing on the kidney - a complex organ composed of many cell types that is responsible for removing waste products from the blood, secreting hormones, regulating electrolyte concentrations, and controlling blood pressure. In a recent study that was done in collaboration with Prof. Benny Dekel from the Sheba Medical Center, we compared the single-cell expression profiles of human fetal kidney cells and Wilms’ tumor patient-derived xenografts, and found that not one – but two cell two populations are required for Wilms’ tumor regeneration. We are now performing single-cell RNA sequencing in order to understand the cross-interactions between these two cell populations in order to find a way to distort them.



2017 All rights to Dangoor Centre for Personalized Medicine, Bar-ilan University.