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Hi, this is the website of the NanoBioPhotonix Lab in Tel-Aviv university. 

The main focus of the group is Single-molecule genomics but we have activity also in development of new optical detection schemes and novel imaging techniques. We explore genomes utilizing tools and reagents from the realm of nano-technology. We try learning new things about these systems by zooming in on individuals - single cells, single chromosomes and single molecules. Research in the lab is highly multi and inter disciplinary and our team is composed of chemists, biologists and physicists who are interested in learning from each other and doing some great (but sometimes risky...) stuff at the very forefront of science.



Media coverage of our work 


18 May 2023

Our lab hit the evening news!

Article published in Biophysical Reports


8 December 2021

Mapping DNA damage and its repair has immense potential in understanding environmental exposures, their genotoxicity, and their impact on human health. Monitoring changes in genomic stability also aids in the diagnosis of numerous DNA-related diseases, such as cancer, and assists in monitoring their progression and prognosis. Developments in recent years have enabled unprecedented sensitivity in quantifying the global DNA damage dose in cells via fluorescence-based analysis down to the single-molecule level. However, genome-wide maps of DNA damage distribution are challenging to produce. Here, we describe the localization of DNA damage and repair loci by repair-assisted damage detection sequencing (RADD-seq).

Article published in Bioinformatics


12 July 2021

While promoter methylation is associated with reinforcing fundamental tissue identities, the methylation status of distant enhancers was shown by genome-wide association studies to be a powerful determinant of cell-state and cancer. With recent availability of long reads that report on the methylation status of enhancer–promoter pairs on the same molecule, we hypothesized that probing these pairs on the single-molecule level may serve the basis for detection of rare cancerous transformations in a given cell population. We explore various analysis approaches for deconvolving cell-type mixtures based on their genome-wide enhancer–promoter methylation profiles.

Sapir won the Women of chemistry Forum Award 


20 July 2021

Sapir won for her work on Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution


Sapir won the David and Paulina Trotsky Foundation Award 


6 April 2021

Sapir won for her work on Single-cell level epigenetic analysis in distal regulatory elements


Noa won the Avital and Eran Rabani award


29 April 2021

Noa won this award for her work on Rapid-RADD DNA Damage Detection, Designed to be used as a method of quantifying DNA damage for multiple DNA samples in one.


Goodbye from Tamar


29 April 2021

Saying good bye to Dr. Tamar Shahal who will be moving on in her Career.

Good Luck!

Jonathan won the excellence award for teaching and research


3 May 2021

Jonathan has won the Excellence award for teaching and research from the school of Physics and Astronomy 


Article published in Essays Biochem


16 April2021

The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information conten

Article published in BiorXiv


29 January 2021

Motivation While promoter methylation is associated with reinforcing fundamental tissue identities, the methylation status of distant enhancers was shown by genome-wide association studies to be a powerful determinant of cell-state and cancer. With recent availability of long-reads that report on the methylation status of enhancer-promoter pairs on the same molecule, we hypothesized that probing these pairs on the single-molecule level may serve the basis for detection of rare cancerous transformations in a given cell population. We explore various analysis approaches for deconvolving cell-type mixtures based on their genome-wide enhancer-promoter methylation profiles.

Sigal presented in the CBRC 3rd virtual seminar


14 October 2020

Rapid quantification of 5mC and 5hmC on multi-sample array slides

Gal presented a poster in the Retreat of the Edmond J. Safra Center for Bioinformatics


24 May 2020

Using nanopore sequencing to detect base modifications

Jonathan presented in SPAOM2020


24 November 2020

Multi-Model Single-Molecule Imaging with continuously controlled spectral-resolution Microscopy

Article published in Nanoscale

1 October 2020

Non-DNA labels are key components for the construction of functional DNA nanostructures. Here, we present a method to graft covalent labels onto DNA origami nanostructures in an enzymatic one-pot reaction. The DNA methyltransferase M.TaqI labels the DNA nanostructures with azide groups, which serve as universal attachment points via click chemistry. Direct labeling with fluorescent dyes is also demonstrated. The procedure yields structures with high fluorescence intensities and narrow intensity distributions. In combination with UV crosslinking it enables the creation of temperature-stable, intense fluorescent beacons.

Article published in Translational Oncology

8 July 2020

Ionizing radiation (IR) is a common mode of cancer therapy, where DNA damage is the major reason of cell death. Here, we use an assay based on fluorescence imaging of single damaged DNA molecules isolated from radiated lymphocytes, to quantify IR induced DNA damage. The assay uses a cocktail of DNA-repair enzymes that recognizes and excises DNA lesions and then a polymerase and a ligase incorporate fluorescent nucleotides at the damage sites, resulting in a fluorescent “spot” at each site. The individual fluorescent spots can then be counted along single stretched DNA molecules and the global level of DNA damage can be quantified. Our results demonstrate that inclusion of the human apurinic/apyrimidinic endonuclease 1 (APE1) in the enzyme cocktail increases the sensitivity of the assay for detection of IR induced damage significantly. This optimized assay also allowed detection of a cooperative increase in DNA damage when IR was combined with mild hyperthermia, which is sometimes used as an adjuvant in IR therapy. Finally, we discuss how the method may be used to identify patients that are sensitive to IR and other types of DNA damaging agents.

24 June 2020

Knowing the amount and type of DNA damage is of great significance for a broad range of clinical and research applications. However, existing methods either lack in their ability to distinguish between types of DNA damage, or are limited in their sensitivity and reproducibility. The method described herein enables rapid and robust quantification of type-specific single-strand DNA damage. The method is based on Repair-Assisted Damage Detection (RADD) by which fluorescent nucleotides are incorporated into DNA damage sites using type-specific repair enzymes. Up to 90 DNA samples are then deposited on a multi-well glass slide, and analyzed by a conventional slide scanner for quantification of DNA damage levels. Accurate and sensitive measurements of oxidative or UV-induced DNA damage levels and repair kinetics are presented for both in-vitro and in-vivo models.Add News Story here

2 September 2019

Herein we present an assay allowing concurrent detection of oxidative DNA damage and photoproducts. We apply DNA repair enzymes specific for each lesion type to incorporate spectrally distinct fluorescent nucleotides, enabling simultaneous quantification of the lesions on individual DNA molecules. We follow the repair of both damage types in skin cells exposed to artificial sunlight.

Our research was mentioned in the TAU Annual Report 2018

2 September 2018

Check out the TAU Annual Report 2018 - and you'll find our research on pages 32-33!

Article Published in Analytica Chimica Acta: "Hypersensitive quantification of global 5-hydroxymethylcytosine by chemoenzymatic tagging"

22 August 2018

One of the challenges associated with detecting 5hmC levels is its extremely low content, especially in blood. Detecting 5hmC levels in blood samples for diagnosis of leukemia and other blood malignancies presents a unique challenge. To overcome these difficulties we introduce a simple chemoenzymatic method for specifically tagging 5hmC, resulting in an eight-fold increase in detection sensitivity. We demonstrate that we could quantitatively detect 5hmC levels in various human tissues, including blood samples from healthy individuals and leukemia patients, using the most basic quadrupole mass-analyzer instrument and only 200 ng of DNA. The limit of detection (LOD) of our technique is 0.001% 5hmC from 300 ng DNA, sufficient for future mass-spectroscopy based diagnostics of diseases associated with low 5hmC levels such as leukemia

Check out this GEN Insight & Intelligence about us

28 June 2018

New Approach to Nanopore Sequencing That Is Sure to CATCH Your Interest 

Article Published in "ACS Nano": Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays

20 June 2018

The epigenetic mark 5-hydroxymethylcytosine (5-hmC) is linked to gene regulation, development, and disease. In particular, its levels dramatically decline in many cancers, potentially serving as an epigenetic biomarker.

We present a long-read, highly sensitive single-molecule mapping technology that generates hybrid genetic/epigenetic profiles of native chromosomal DNA. The single-molecule concept provides information on the distribution and coexistence of 5-hmC signals at multiple genomic loci on the same genomic DNA molecule, revealing long-range correlations and cell-to-cell epigenetic variation.

To view the paper in open access click the "Read More" button below

Shavuot Picnic

21 May 2018

The annual lab picnic in celebration of Shavuot holiday

Article Published in "Nucleic Acids Research": Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)

21 May 2018

Here, we optimized Cas9-Assisted Targeting of CHromosome segments (CATCH) for nanopore sequencing of the breast cancer gene BRCA1. The CATCH enrichment scheme only requires knowledge of the target flanking sequence for Cas9 cleavage while providing contiguous data across both coding and non-coding sequence and holds promise for characterization of complex disease-related or highly variable genomic regions.

To view the paper in open access click the "Read More" button below

Article Published in "DNA Repair": Broad spectrum detection of DNA damage by Repair Assisted Damage Detection (RADD)

27 April 2018

Numerous methods to characterize the formation of DNA adducts and their retention for risk assessment have been developed. Here, we describe a new methodology, Repair Assisted Damage Detection (RADD), which utilizes a DNA damage processing repair enzyme cocktail to detect and modify sites of DNA damage for a subsequent gap filling reaction that labels the DNA damage sites. 

To view the paper click the "Read More" button below

Congratulations to Dr. Tamar Shahal for Best Poster Award in Isranalytica 2018!

January 24, 2018

Our work on Optical Methylation Mapping featured in Bionano Genomics article

December 16, 2017

Read Bionano Genomics' article "Optical Methylation Mapping Made Simple" featuring our lab's work

Listen to the podcast about our work on Mendelspod!

December 12, 2017

Come listen to (or read) the Mendelspod podcast about out lab's work! 

Noa's participation in a conference of the XIN project at Tsinghua University, China

September 2017

Noa presented an abstract in a conference of the XIN project at Tsinghua University, Beijing, China. Noa used single-molecule fluorescence imaging to detect chemical changes in individual DNA molecules and showed she can detect colon and blood cancer with extreme sensitivity.

Her work was recently published in the journal Clinical Epigenetics: "Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers".

Click the "Read More" button to see the paper. 

Dima's working visit to the University of Minnesota

August 2017

Dima has recently received the Prof. Rahamimoff Travel Grant for Young Scientists from the BSF United States – Israel Binational Foundation, for a working visit to University of Minnesota at Prof. Kevin Dorfman's lab. During his stay from 26.7.17-24.8.17, he was trained on fabricating nano-fluidic devices in fused silica that utilizing electricity enable the manipulation and imaging of single DNA molecules.


In the figure: DNA molecules labeled with YOYO-1 as imaged in a fabricated device. Each white line represents an individual DNA molecule in a 100nm channel.

Gil's participation in EUROCARB 2017, Barcelona

June 2017

The EUROCARB 2017 program consolidated the interplay between the chemistry and biology communities, and reinforced the needed interaction between glycochemistry, glycobiology, and applied glycosciences.


Gil gave a talk titled "UDP-sugar derivative as a key substrate for DNA epigenetic modification labeling"

Article published in "Clinical Epigenetics": Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers

July 14, 2017

Using a single-molecule approach, we observed a significantly reduced level of 5hmC in blood and colon cancers, and could distinguish between colon tumor and colon tissue adjacent to the tumor based on the global levels of this molecular biomarker.


To view the paper in open access click the "Read More" button below

Participation in Xin Innovation Forum 2017

July 4, 2017

Congrats  to Noa for being invited to participate in the Xin Innovation Forum 2017, which will be held in Beijing this September!

Dima is awarded the Prof. Rahamimoff Travel Grant for Young Scientists of the US-Israel Binational Science Foundation (BSF)

July 4, 2017

Congratulations to our very own Dima, for being selected to receive the Prof. Rahamimoff Travel Grant for Young Scientists of the US-Israel Binational Science Foundation (BSF)

Targeted Purification with CRISPR/Cas9: CATCH

June 29, 2017

CRISPR/Cas9 can be used to design targeted purification of large genomic regions or genes.  This in vitro application with Cas9, termed CATCH, can enhance study of structural variation and provide valuable phasing information.

Check out our attention score for the CATCH paper in biorxivs!

March 14, 2017

Our innovative targeting method - CHromosome segments Assisted targeting of Cas9 (CATCH) for long read nanopore sequencing and optical mapping - received high attention score in bioRxiv!

- It's in the top 5% of all research outputs scored by Altmetric 

- Has high attention score compared to outputs of the same age and source (98th percentile)

- ans high attention score compared to outputs of the same age (97th percentile)

A new article about us in Adjacent Government Magazine!

February 2017

Check out the article about our lab in the February issue of Adjacent Government Magazine.

To read the article click the button below or the pic!

Irys Extract software released

February 14, 2017

The software tool for people who work in bioinformatics and genomics and use the Irys platform from BioNano Genomics allows easy access to the raw data in the form of cropped images and genetically aligned intensity profiles.

Collaboration with the Jaroslav Dolezel lab from the Institute of Experimental Botany

November 14, 2016

We have recently welcomed Zuzana from the Centre of Plant Structural and Functional Genomics in the Czech Republic, to work on the CATCH technique in our lab.

Published a paper in IOPScience Methods and Applications in Fluorescence

October 7, 2016

To read our article about Simple and cost-effective fluorescent labeling of 5-hydroxymethylcytosine, click the "Read More" button below:

Comgrats to Dima and Jonthan for winning 3rd and 1st poster prizes at the i-core meeting!

September 27, 2016

Another paper published in ACS Nano

September 19, 2016

To read our article about Super-Resolution Genome Mapping in Silicon Nanochannels, click the "Read More" button below:

Published a paper in ACS Nano in collaboration with Amit Meller's lab in the Technion

August 31, 2016

Read our article "Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores" (click the "Read More" Button)


Lab meeting invaded by Pokemon!

July 19, 2016

Click "Read More" to see who came to visit the lab meeting!

Signed the first license for our CATCH technology with Sage Science!

July 13, 2016

Happy to update you that we have signed the first license for our CATCH technology with Sage Science, a US-based company which develops DNA and protein fractionation systems for the life sciences research markets.

Lab trip - Sea Turtle Rescue Center

July 7, 2016

Click the "Read More" button to see the photos from our Lab trip to the Israel Sea Turtle Rescue and Rehabilitation Center!


Article about Nanosubs published in Organic Letters

June 13, 2016

Check out the new article about Nanosubs that got published in Organic Letters: Synthesis and Photostability of Unimolecular Submersible Nanomachines: Toward Single-Molecule Tracking in Solution

Congratulations to Tslil for winning Best Poster Award at the CRISPR 2016!

May 25, 2016

Another award-winning poster by our very own Tslil Gabrieli!


The BeadsOnString Project in Adjacent Government Magazine

May 2016

Read about the BeadsOnString Project in the May 2016 edition of Adjacent Government

Congratulations to Tslil for winning Best Poster Award in Nano-Israel 2016!

February 23, 2016

Lab Picnic

February 26, 2016

The lab's picnic out at the TAU botanic gardens was deemed a great success!

For photos click the "Read More" button below

Beads On String Project in EU Research Magazine

December 2015

Read the article about the Beads On String Project in the EU Research Magazine!

 (pages 10-11)

Sizing femtogram amounts of dsDNA by single-molecule counting

September 13, 2015

Modern molecular-biology applications raise renewed interest in sizing minute-amounts of DNA. In this work we utilize single-molecule imaging with in situ size calibration to accurately analyze the size and mass distribution of DNA samples. We exploit the correlation between DNA length and its fluorescence intensity after staining in order to assess the length of individual DNA fragments by fluorescence microscopy. Synthetic reference DNA standards are added to the investigated sample before staining and serve as internal size calibrators, supporting a robust assay for accurate DNA sizing. Our results demonstrate the ability to reconstruct the exact length distribution in a complex DNA sample by sizing a subset containing only femtogram amounts of DNA, thus, outperforming microfluidic gel electrophoresis which is the currently accepted gold standard. This assay may find useful applications for genetic analysis where the exact size distribution of DNA molecules is critical and the availability of genetic material is limited.

Baby Boom! Congratulations to the Fishmans & the Shahals!

September 12, 2015

Congratulations to Tamar Shahal & Sivan Fishman,

on the safe arrival of your baby boy & baby girl (respectively) into the world, and in a 5-minute difference! 

May Babyhood be filled with lots of joy and make lots of wonderful memories. 

We wish you all the best!

CRISPR-Cas9- Assisted Targeting of CHromosome segments (CATCH)

July 21 2015

Cas9 can be engineered to cut specific genomic loci. In our new paper accepted to Nature Communications, two such enzymes are used in-vitro in order to cut-out any genomic region of interest for further downstream applications with the selected region.

Together with our colleagues from Prof. Ting Zhu’s lab in Tsinghua University of Beijing we utilize this approach to isolate specific gene clusters up to 200 kbp and clone them into BAC vectors. 

Major research bottleneck solved!

July 3rd 2015

In a new paper in ChemBioChem we report on a One-Pot Chemoenzymatic Cascade for Labelling of the Epigenetic Marker 5-Hydroxymethylcytosine. In a joint project with Dr. Micha Fridman from the organic chemistry department we found an elegant way of utilizing enzymes to assist in the preparation of a key reagent for 5-hmC labeling. 

Nucleic Acid Research (NAR) gets impact factor of 9.112

July 1, 2015

NARs impact factor crossed the 9 line. This is a testemony to the growing interest in nucleic acids and the quality science published in NAR.

We like this journal!

In a new paper we show how DNA mapping can distinguish between viruses

May 15, 2015

Research of microbiological environments displays a growing scientific interest, unmasking their great variability and specifically characterizing their population has applications for public health and biotechnological development. In our recent paper "Bacteriophage strain typing by rapid single molecule analysis" published in the journal Nucleic Acid Research, we show that we can identify single short genomes of bacteriophages. We fluorescently label  the genomes in a sequence specific manner and measure the amplitude modulations of the  fluorescent signal along stretched DNA. These modulations displays organism specific  pattern and can refer as finger print for identification. This research can be applied to study and characterization of biological samples with unknown contents.

Our lab was awarded 1.1 million Euros for developing next generation diagnostic tools

April 15, 2015

We are the coordinators of the BeyonSeq consortium!

With only 1.9% success rate, we were lucky to be awarded six and a half million Euros to be shared between 7 research groups, to develop single-molecule diagnostic technologies in various areas.

The unifying theme is the analysis of individual DNA molecules.

Collaboration published in Nature Nanotechnology

March 16, 2015

A paper titled "Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson–Crick base pairing" was published by The Gazit lab and we had the pleasure to help. While imaging these interesting self assembled structures we found that they emit light across the visible spectrum. We also helped analyzing the growth dynamics and with the qualitative model for the intersting light emission effects

High throughput quantification of 5hmC - Published in Ananlytical Chemistry

August 5, 2014

We further developed our method for optical detection of 5hmC to be compatible with measurements on a multiwell plate. Now ~350 samples can be measured simultaneously. We demonstrate a measurement of 190 mouse tissue samples.

Lighting up individual DNA damage sites by in-vitro repair synthesis

May 13, 2014

Our work on direct visualization of DNA damage was just accepted to JACS.
We repair extracted genomic DNA in a tube containing a cocktail of repair enzymes and fluorescent nucleotides. Damaged DNA lights up as it is repaired and is visualized as fluorescent spots along the DNA molecules.

Toward Single-Molecule Optical Mapping of the Epigenome

Our new review is out in ACS NANO. We show exciting preliminary results of engineered 5hmC patterns on Lambda DNA. Individual molecules are stretched and imaged in silicon nano-channel arrays.

I've been told that it's important to show off our winning of an ERC starters grant...

November 29, 2013

We got 1.63 million Euros for our project: Beads on String Genomics: Experimental Toolbox for Unmasking Genetic / Epigenetic Variation in Genomic DNA and Chromatin.

Our work featured in

September 1, 2013

Shining a Light on 5-hmC: Direct Labeling and Optical Detection of DNA Hydroxymethylation.

Spotlight item on about our epigenetic labeling method

July 24, 2013

Optical detection of epigenetic marks.

Our paper featured in

July 20, 2013

Optical Detection Adds Color to 5hmC Analysis.

Optical detection of epigenetic marks: sensitive quantification and direct imaging of individual hydroxymethylcytosine bases

July 15, 2013

The first 100% independent work from our lab and the first of its kind observation of individual epigenetic modifications in genomic DNA. Just published on the front cover of Chemical Communications.

Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy

July 15, 2013

We were very happy to be invited to write this short review for a special issue on bio-nano-technology in Current opinion in biotechnology. It really gave us the opportunity to see what was going on in the field and to refine our opinion on where this technology is going.

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