Prof. Yuval Ebenstein

School of Chemistry
ביה"ס לכימיה סגל אקדמי בכיר
Prof. Yuval Ebenstein
Phone: 03-6408901
Office: Ornstein - Chemistry, 312


Our lab specializes in many areas of optical imaging and spectroscopy with emphasis on single molecule detection and development of imaging based techniques. Our research is focused on the application of novel imaging and optical detection approaches to genomic studies and biomarker detection. We are developing new spectroscopy and microscopy methodologies that combine advanced optics with tools and reagents from the realm of nano-technology. In addition, we have great interest in developing unique biochemistries for genomic analysis that are based on chemo-enzymatic reactions.


Research in the lab currently focuses on three fields of interest:


Single molecule genomics by optical mapping:

We create optical barcodes containing genetic and epigenetic information by labeling long chromosomal DNA molecules with fluorescent markers. Nano-fluidic channels are used to stretch the DNA by flow or electric field and the barcode is directly visualized by single molecule imaging. We are aiming to apply SR imaging techniques in order to increase the resolution and allow detection of genomic aberrations.


Epigenetic analysis technologies:

Epigenetics is one of the most exciting and fast growing fields in biology. It links biological signatures with mental or environmental conditions previously not believed to be quantified by physical means. We develop new methods for sequencing, targeted and global analysis of various epigenetgic markers. We use these novel methods in order to study epigenetic alterations related to disease. We are also very interested in the physiological interface between nature and nurture, biology and psychology, body and spirit.


High-throughput single molecule detection:

We develop optical methods and nano-biosensors for detection of rare analytes and weakly interacting biomolecules. Our emphasis is on ultrasensitive detection and quantification of clinical biomarkers. To achieve this aim we are developing a micro-lens-array based optical setup that can detect single molecule fluorescence from hundreds of confocal excitation volumes in parallel.
We are also active in development of single-molecule counting schemes and development of high resolution imaging techniques and specialized contrast agents that utilize fluorescence, plasmonics and energy transfer for super-resolution (SR) imaging. 



  • Ph.D., Physical Chemistry, Hebrew University, Jerusalem, Israel, 2007

  • Ms.S., Physical Chemistry, Hebrew University, Jerusalem, Israel, 2001

  • BS.c., Physics and Chemistry, Hebrew University, Jerusalem, Israel, 2000

Academic Appointments

  • Founder and Academic director, Tel-Aviv University, Entrepreneurship and Innovation Center, Tel-Aviv, Israel, 2018-Present

  • Associate professor, Tel-Aviv University, Department of Chemical Physics, School of Chemistry, Tel-Aviv, Israel, 2016-Present

  • Senior lecturer, Department of Chemical Physics, School of Chemistry, Tel Aviv University, Tel Aviv, Israel, 2011-2016

  • The Raymond and Beverly Sackler Career Development Chair - 2014, 2013-2014

  • Postdoctoral research fellow, under the supervision of Prof. Shimon Weiss, Department of Chemistry and Biochemistry, DOE Institute for Genomics and Proteomics – UCLA, Los Angeles, USA, 2006-2011

Top Ten Publications


  1. Jonathan Jeffet (ST), Asaf Kobo (ST), Tianxiang Su (ST), Assaf Grunwald (ST), Ori Green (ST), Adam N. Nilsson (ST), Eli Eisenberg (ST), Tobias Ambjörnsson (CI), Fredrik Westerlund (CI), Elmar Weinhold (CI), Doron Shabat (CI), Prashant K. Purohit (CI), and Yuval Ebenstein* (PI), Super-Resolution Genome Mapping in Silicon Nanochannels. ACS Nano (2016), 10 (11), 9823–9830

  2. Noa Gilat (ST), Tzlil Tabachnik (ST), Amit Shwartz (ST), Tamar Shahal (CI), Dmitry Torchinsky (ST), Yael Michaeli (CI), Gil Nifker (ST), Shahar Zirkin* (CI) and Yuval Ebenstein* (PI), Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers. Clinical epigenetics (2017), 9(1), 70. DOI:10.1186/s13148-017-0368-9.

  3. Tslil Gabrieli (ST), Hila Sharim (ST), Dena Fridman (ST), Nissim Arbib, Yael Michaeli (CI) and Yuval Ebenstein* (PI), Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH). Nucleic Acids Research (2018),46, 14, e87.  DOI: 10.1093/nar/gky411.

  4. Tslil Gabrieli (ST), Hila Sharim (ST), Gil Nifker (ST), Jonathan Jeffet (ST), Tamar Shahal (CI), Rani Arielly (ST), Michal Levy-Sakin, Lily Hoch, Nissim Arbib, Yael Michaeli (CI) and Yuval Ebenstein* (PI), Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays. ACS Nano (2018), 12, 7, 7148–7158. DOI: 10.1021/acsnano.8b03023.

  5. Hila Sharim(ST), Assaf Grunwald(ST), Tslil Gabrieli(ST), Yael Michaeli(T), Sapir Margalit(ST), Dmitry Torchinsky(ST), Rani Arielly(ST), Gil Nifker(ST), Matyas Juhasz, Felix Gularek, Miguel Almalve, Brandon Dufault, Sreetama Sen Chandra, Alexander Liu, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Kathryn R Wagner, Jonathan Pevsner, Jeff Reifenberger, Ernest T Lam, Alex R Hastie, Han Cao, Hayk Barseghyan, Elmar Weinhold*(PI) and Yuval Ebenstein*(PI), Long-read single-molecule maps of the functional methylome. Genome Research (2019) 29:646–656. DOI: 10.1101/gr.240739.118.

  6. Nikhil Jain, Tamar Shahal(T), Tslil Gabrieli(ST), Noa Gilat(ST), Dmitry Torchinsky(ST), Yael   Michaeli(T), Viola Vogel and Yuval Ebenstein*(PI), Global Modulation in DNA Epigenetics during Pro- Inflammatory Macrophage Activation. Epigenetics (2019), 14, 12, 1183-1193. doi:10.1080/15592294.2019.1638700.

  7. Dmitry Torchinsky(ST), Yael Michaeli(T), Natalie R. Gassman and Yuval Ebenstein*(PI), Simultaneous detection of multiple DNA damage types by multi-colour fluorescent labelling. Chemical Communications (2019), 55, 11414-11417.

  8. Sapir Margalit(ST), Sigal Avraham(ST), Tamar Shahal(T), Yael Michaeli(T), Noa Gilat(ST), Prerna Magod, Michal Caspi, Shelly Loewenstein, Guy Lahat, Dinorah Friedmann‐Morvinski, Revital Kariv, Rina Rosin‐Arbesfeld, Shahar Zirkin(T)  and Yuval Ebenstein* (PI), 5‐hydroxymethylcytosine as a clinical biomarker: Fluorescence‐based assay for high‐throughput epigenetic quantification in human tissues. International Journal of Cancer (2020),146, 1, 115-122.

  9. Noa Gilat(ST), Dmitry Torchinsky(ST), Sapir Margalit(ST), Yael Michaeli(T), Sigal Avraham(ST), Hila Sharim(ST), Nadav Elkoshi, Carmit Levy, Shahar Zirkin(ST), Yuval Ebenstein*(PI), Rapid Quantification of Oxidation and UV Induced DNA Damage by Repair Assisted Damage Detection-(Rapid RADD). Anal Chem (2020), 92, 14, 9887–9894. https:/

  10. Christian Heck (PD), Dmitry Torchinsky(ST), Gil Nifker(ST), Felix Gularek(ST) , Yael Michaeli(T), Elmar Weinhold , Yuval Ebenstein*(PI) , Label as you fold: methyltransferase-assisted functionalization of DNA nanostructures. Nanoscale (2020), 12, 20287-20291 (2020). DOI: 10.1039/d0nr03694c.



ERC consolidator grant (PI) 2019-2024                                                                                    €2,750,000                                                                 

“MultiplexGenomics: Exploring the Epigenome by Multiplexed Physical Mapping of Individual Chromosomes” 

EU consortium grant (coordinator) 2015-2019                                                                          €1,100,000                                                             

“Genomic diagnostics beyond the sequence”    

ERC starter grant 2013-2019                                                                                                       €1,700,000                                                           

“Beads on String Genomics: Experimental Toolbox for Unmasking Genetic/ Epigenetic Variation in Genomic DNA and Chromatin”  



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