BAR-ILAN INSTITUTE OF NANOTECHNOLOGY & ADVANCED MATERIALS | 2019 ANNUAL REPORT

Dr. Tomer Kalisky Faculty of Engineering Member of BINA, Nano-Medicine Center Research Areas • Biochips & Sensors • Disease Treatment • Drug Delivery • Genomics, Proteomics & Glycomics • Imaging Abstract Single-cell genomics of kidney development, regeneration, and cancer 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 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. 69 Publications 2018 and 2019 • Y Frenkel, Y Xie, HY Hwang, B Kalisky, “Magnetism and Conductivity Along Structural Domain Walls of SrTiO3”, Journal of Superconductivity and Novel Magnetism, 1-3, 2019 . • DV Christensen, Y Frenkel, YZ Chen, YW Xie, ZY Chen, Y Hikita, A Smith, L Klein, HY Hwang, N Pryds, B Kalisky, “Strain-tunable magnetism at oxide domain walls”, Nature Physics 15 (3), 269, 2019 . • Y Shperber, N Vardi, E Persky, S Wissberg, ME Huber, B Kalisky, “Scanning SQUID microscopy in a cryogen-free cooler”, Review of Scientific Instruments 90 (5), 053702, 2019 . • E. Persky and B. Kalisky, “Scanning SQUID View of Oxide Interfaces,” Adv. Mater., 30 (41), p. 1706653, May 2018 . • E Persky, N Vardi, Y Shperber, B Kalisky, “Improving the sensitivity of scanning probe microscopy with mechanical vibrations”, Applied Physics Letters 113 (17), 173101, 2018 . • S Wissberg, A Frydman, B Kalisky, “Local view of superconducting fluctuations”, Applied Physics Letters 112 (26), 262602, 2018 . • DV Christensen, Y Frenkel, P Schütz, F Trier, S Wissberg, R Claessen, B Kalisky, A Smith, YZ Chen, Nini Pryds, “Electron Mobility in Ѕ −Al 2 O 3 /SrTiO 3 ”, Physical Review Applied 9 (5), 054004, 2018 . • H. Khan, Y. Loh, A. Kerman, A. Frydman, and B. K., “Imaging Quantum Fluctuations Near Criticality,” Nature Physics, 14 (12), 1205, 2018 . • D. V. Christensen, Y. Frenkel, Y. Z. Chen, Y. W. Xie, Z. Y. Chen, Y. Hikita, A. Smith, L. Klein, H. Y. Hwang, N. Pryds and B. Kalisky, “Strain- tunable magnetism at oxide domain walls”, Nature physics, 2018 . Books Y. Frenkel and B. Kalisky, “Scanning SQUID measurements of oxide interfaces,” in Metal Oxide-Based Thin Film Structures, pp. 225–242, 2018 . 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. . 2D embedding of single cell gene expression profiles in the developing embryonic kidney Publications 2018 and 2019 • DAD Munro, Y Wineberg, J Tarnick, CS Vink, Z Li, C Pridans, E Dzierzak, T Kalisky, P Hohenstein, J A Davies, “Macrophages restrict the nephrogenic field and promote endothelial connections during kidney development”, eLife 8, e43271, 2019 . • T Ling, Y Birger, MJ Stankiewicz, N Ben-Haim, T Kalisky, A Rein, E Kugler, W Chen, C Fu, K Zhang, H Patel, J W Sikora, Y A Goo, N Kelleher, L Zou, S Izraeli, J D Crispino, “Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis”, Blood 134 (19), 1619- 1631, 2019 . • T Ling, Y Birger, M Stankiewicz, N Ben- Haim, I Kanter, T Kalisky, AR Gil, Neil L Kelleher, Lihua Zou, Shai Izraeli, John D Crispino, “Global Chromatin Occupancy and Epigenetic Signature Analysis Reveal New Insights into the Function of GATA1 N-Terminus in Erythropoiesis”, Blood 132 (Suppl 1), 533-533, 2018 . • H Golan, R Shukrun, R Caspi, E Vax, N Pode-Shakked, S Goldberg, Oren Pleniceanu, Dekel D Bar-Lev, Michal Mark- Danieli, Sara Pri-Chen, Jasmine Jacob- Hirsch, Itamar Kanter, Ariel Trink, Ginette Schiby, Ron Bilik, Tomer Kalisky, Orit Harari-Steinberg, Amos Toren, Benjamin Dekel, “In vivo expansion of cancer stemness affords novel cancer stem cell