Exploring the Epigenome by Multiplexed Physical Mapping of Individual Chromosomes

Project Information

MultiplexGenomics

Grant agreement ID: 817811

DOI

10.3030/817811

Project closed

EC signature date 14 February 2019

Start date 1 October 2019

End date 31 March 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 750 000,00

EU contribution

€ 2 750 000,00

Coordinated by

TEL AVIV UNIVERSITY
Israel

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (14)

Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays

Author(s): Gil Nifker; Assaf Grunwald; Sapir Margalit; Zuzana Tulpova; Yael Michaeli; Hagai Har-Gil; Noy Maimon; Elad Roichman; Leonie Schütz; Elmar Weinhold; Yuval Ebenstein
Published in: ACS nano 17(10), 9178-9187 (2023). doi:10.1021/acsnano.2c12755, Issue 4, 2023, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.2c12755

Multimodal single-molecule microscopy with continuously controlled spectral resolution

Author(s): Jonathan Jeffet; Ariel Ionescu; Yael Michaeli; Dmitry Torchinsky; Eran Perlson; Timothy D. Craggs; Yuval Ebenstein
Published in: Biophysical Journal, Issue 1, 2021, ISSN 2667-0747
Publisher: Elsevier BV
DOI: 10.1016/j.bpr.2021.100013

From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing

Author(s): Noa Gilat, Dena Fridman, Hila Sharim, Sapir Margalit, Natalie R. Gassman, Yael Michaeli, Yuval Ebenstein
Published in: Biophysical Reports, 2021, ISSN 2667-0747
Publisher: The Biophysical Society
DOI: 10.1016/j.bpr.2021.100017

Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping

Author(s): Sapir Margalit, Zuzana Tulpová, Tahir Detinis Zur, Yael Michaeli, Jasline Deek, Gil Nifker, Rita Haldar, Yehudit Gnatek, Dorit Omer, Benjamin Dekel, Hagit Baris Feldman, Assaf Grunwald, Yuval Ebenstein
Published in: NAR Genomics and Bioinformatics, Issue 7, 2025, ISSN 2631-9268
Publisher: Oxford University Press (OUP)
DOI: 10.1093/nargab/lqae190

Optical genome and epigenome mapping of clear cell renal cell carcinoma

Author(s): Sapir Margalit, Zuzana Tulpová, Yael Michaeli, Tahir Detinis Zur, Jasline Deek, Sivan Louzoun-Zada, Gil Nifker, Assaf Grunwald, Yuval Scher, Leonie Schütz, Elmar Weinhold, Yehudit Gnatek, Dorit Omer, Benjamin Dekel, Eitan Friedman, Yuval Ebenstein
Published in: NAR Cancer, Issue 7, 2025, ISSN 2632-8674
Publisher: Oxford University Press (OUP)
DOI: 10.1093/narcan/zcaf008

Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution

Author(s): Sapir Margalit, Yotam Abramson, Hila Sharim, Zohar Manber, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Hayk Barseghyan, Ran Elkon, Roded Sharan, Yuval Ebenstein
Published in: Bioinformatics, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab306

Single-molecule toxicogenomics: Optical genome mapping of DNA-damage in nanochannel arrays

Author(s): Tahir Detinis Zur, Sapir Margalit, Jonathan Jeffet, Assaf Grunwald, Sivan Fishman, Zuzana Tulpová, Yael Michaeli, Jasline Deek, Yuval Ebenstein
Published in: DNA Repair, Issue 146, 2025, Page(s) 103808, ISSN 1568-7864
Publisher: Elsevier BV
DOI: 10.1016/j.dnarep.2025.103808

Chemo-Enzymatic Fluorescence Labeling Of Genomic DNA For Simultaneous Detection Of Global 5-Methylcytosine And 5-Hydroxymethylcytosine

Author(s): Sigal Avraham, Dr. Leonie Schütz, Dr. Larissa Käver, Dr. Andreas Dankers, Sapir Margalit, Dr. Yael Michaeli, Dr. Shahar Zirkin, Dr. Dmitry Torchinsky, Dr. Noa Gilat, Omer Bahr, Gil Nifker, Prof. Maya Koren-Michowitz, Prof. Elmar Weinhold, Prof. Yuval Ebenstein
Published in: ChemBioChem, 2023, Page(s) e202300400, ISSN 1439-7633
Publisher: Wiley-VCH
DOI: 10.1002/cbic.202300400

Machine-Learning-Based Single-Molecule Quantification of Circulating MicroRNA Mixtures

Author(s): Jonathan Jeffet; Sayan Mondal; Amit Federbush; Nadav Tenenboim; Miriam Neaman; Jasline Deek; Yuval Ebenstein; Yohai Bar-Sinai
Published in: Crossref, Issue 1, 2023, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/acssensors.3c01234

Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping

Author(s): Tslil Gabrieli, Yael Michaeli, Sigal Avraham, Dmitry Torchinsky, Sapir Margalit, Leonie Schutz, Matyas Juhasz, Ceyda Coruh, Nissim Arbib, Zhaohui Sunny Zhou, Julie A. Law, Elmar Weinhold and Yuval Ebenstein
Published in: Nucleic Acids Research, 2022, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac460

Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale

Author(s): Jonathan Jeffet, Sapir Margalit, Yael Michaeli, Yuval Ebenstein
Published in: Essays in Biochemistry, Issue 65/1, 2021, Page(s) 51-66, ISSN 0071-1365
Publisher: Portland Press, Ltd.
DOI: 10.1042/ebc20200021

Effective training of nanopore callers for epigenetic marks with limited labelled data

Author(s): Brian Yao, Chloe Hsu, Gal Goldner, Yael Michaeli, Yuval Ebenstein and Jennifer Listgarten
Published in: Open Biology, 2024, ISSN 2046-2441
Publisher: Royal Society Publishing
DOI: 10.1098/rsob.230449

DeepQR: single-molecule QR codes for optical gene-expression analysis

Author(s): Jonathan Jeffet, Barak Hadad, Sahar Froim, Kawsar Kaboub, Keren M. Rabinowitz, Jasline Deek, Sapir Margalit, Iris Dotan, Alon Bahabad, Yuval Ebenstein
Published in: Nanophotonics, 2024, ISSN 2192-8606
Publisher: Walter de Gruyter GmbH
DOI: 10.1515/nanoph-2024-0236

Single-molecule approaches for DNA damage detection and repair: A focus on Repair Assisted Damage Detection (RADD)

Author(s): Tahir Detinis Zur; Jasline Deek; Yuval Ebenstein
Published in: Crossref, Issue 3, 2023, ISSN 1568-7864
Publisher: Elsevier BV
DOI: 10.1016/j.dnarep.2023.103533

Other (3)

A Spectral Image Scanning Microscope for Multi-Color High-Resolution Imaging

Author(s): Lanna Bram, Ofir Tal-Friedman, Neta Fibeesh, Yohai Bar-Sinai, Eli Flaxer, Yael Roichman, Uri Ashery, Yuval Ebenstein, Jonathan Jeffet
Published in: 2025
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.05.14.653993

Write and read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing

Author(s): Uri Bertocchi, Assaf Grunwald, Gal Goldner, Eliran Eitan, Sigal Avraham, Jasline Deek, Yael Michaeli, Brian Yao, Jennifer Listgarten, Jared T. Simpson, Winston Timp, Yuval Ebenstein
Published in: 2025
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.04.14.648727

Nanopore callers for epigenetics from limited supervised data

Author(s): Yao B; Chloe Ching-Yun Hsu; Goldner G; Yael Michaeli; Yuval Ebenstein; Jennifer Listgarten
Published in: Issue 1, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.06.17.448800

Intellectual Property Rights

Patent (1)

DETECTION OF BASE MODIFICATIONS BY ENHANCING ELECTRICAL CONTRAST IN NANOPORES

Application/Publication number: 20 23050792
Date: 2023-07-31
Applicant(s): TEL AVIV UNIVERSITY