Genomic diagnostics beyond the sequence

Livrables

Expanded database of plasmids from clinical isolates

Expanded database of unsequenced plasmids. An expanded database with >100 previously non-sequenced plasmids from clinical isolates, each plasmid with its clinical phenotype.

Fully sequenced and validated database of bacterial DNA

Fully validated database of sequenced bacterial DNA. A database of sequenced bacterial DNA, both chromosomal and plasmids, that has been validated with experiments on >20 of the plasmids and >20 of the bacterial strains in the database.

Dissemination plan

Toolbox for identification of bacteria and plasmids

Comprehensive toolbox for identification of bacteria and plasmids. Fully working and validated software as well as experimental protocols adapted to clinical situations for identification of barcode patterns along DNA for both bacterial identification and characterization of antibiotic resistance

Project logo, leaflets, presentation & website
International conference

Publications

Epigenetic Optical Mapping of 5-Hydroxymethylcytosine in Nanochannel Arrays

Auteurs: Tslil Gabrieli, Hila Sharim, Gil Nifker, Jonathan Jeffet, Tamar Shahal, Rani Arielly, Michal Levi-Sakin, Lily Hoch, Nissim Arbib, Yael Michaeli, Yuval Ebenstein
Publié dans: ACS Nano, 2018, ISSN 1936-0851
Éditeur: American Chemical Society
DOI: 10.1021/acsnano.8b03023

A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA

Auteurs: Jochem Deen, Su Wang, Sven Van Snick, Volker Leen, Kris Janssen, Johan Hofkens, Robert K Neely
Publié dans: Nucleic Acids Research, Numéro 46/11, 2018, Page(s) e64-e64, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gky184

Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers

Auteurs: Noa Gilat, Tzlil Tabachnik, Amit Shwartz, Tamar Shahal, Dmitry Torchinsky, Yael Michaeli, Gil Nifker, Shahar Zirkin, Yuval Ebenstein
Publié dans: Clinical Epigenetics, Numéro 9/1, 2017, ISSN 1868-7075
Éditeur: Springer Verlag
DOI: 10.1186/s13148-017-0368-9

Sensing Native Protein Solution Structures Using a Solid-state Nanopore: Unraveling the States of VEGF

Auteurs: Nitinun Varongchayakul, Diana Huttner, Mark W. Grinstaff, Amit Meller
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-018-19332-y

Optical DNA mapping in nanofluidic devices: principles and applications

Auteurs: Vilhelm Müller, Fredrik Westerlund
Publié dans: Lab on a Chip, Numéro 17/4, 2017, Page(s) 579-590, ISSN 1473-0197
Éditeur: Royal Society of Chemistry
DOI: 10.1039/c6lc01439a

Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach

Auteurs: Albertas Dvirnas, Christoffer Pichler, Callum L. Stewart, Saair Quaderi, Lena K. Nyberg, Vilhelm Müller, Santosh Kumar Bikkarolla, Erik Kristiansson, Linus Sandegren, Fredrik Westerlund, Tobias Ambjörnsson
Publié dans: PLOS ONE, Numéro 13/3, 2018, Page(s) e0193900, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0193900

Open channel deterministic lateral displacement for particle and cell sorting

Auteurs: Trung S. H. Tran, Bao D. Ho, Jason P. Beech, Jonas O. Tegenfeldt
Publié dans: Lab Chip, Numéro 17/21, 2017, Page(s) 3592-3600, ISSN 1473-0197
Éditeur: Royal Society of Chemistry
DOI: 10.1039/C7LC00707H

Broad spectrum detection of DNA damage by Repair Assisted Damage Detection (RADD)

Auteurs: Nathaniel W. Holton, Yuval Ebenstein, Natalie R. Gassman
Publié dans: DNA Repair, Numéro 66-67, 2018, Page(s) 42-49, ISSN 1568-7864
Éditeur: Elsevier BV
DOI: 10.1016/j.dnarep.2018.04.007

Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools

Auteurs: Karolin Frykholm, Lena K. Nyberg, Fredrik Westerlund
Publié dans: Integrative Biology, Numéro 9/8, 2017, Page(s) 650-661, ISSN 1757-9694
Éditeur: Royal Society of Chemistry
DOI: 10.1039/c7ib00085e

Real-time visualization and sub-diffraction limit localization of nanometer-scale pore formation by dielectric breakdown

Auteurs: Adam Zrehen, Tal Gilboa, Amit Meller
Publié dans: Nanoscale, Numéro 9/42, 2017, Page(s) 16437-16445, ISSN 2040-3364
Éditeur: Royal Society of Chemistry
DOI: 10.1039/c7nr02629c

Chapter Fourteen - Single-Molecule Characterization of DNA–Protein Interactions Using Nanopore Biosensors

Auteurs: A.H. Squires, T. Gilboa, C. Torfstein, N. Varongchayakul, A. Meller
Publié dans: Methods in Enzymology, 2017, Page(s) 353-385, ISSN 0076-6879
Éditeur: Academic Press
DOI: 10.1016/bs.mie.2016.08.010

Methyltransferase-directed covalent coupling of fluorophores to DNA

Auteurs: Milena Helmer Lauer, Charlotte Vranken, Jochem Deen, Wout Frederickx, Willem Vanderlinden, Nathaniel Wand, Volker Leen, Marcelo H. Gehlen, Johan Hofkens, Robert K. Neely
Publié dans: Chemical Science, Numéro 8/5, 2017, Page(s) 3804-3811, ISSN 2041-6520
Éditeur: Royal Society of Chemistry
DOI: 10.1039/C6SC04229E

Irys Extract

Auteurs: Rani Arielly, Yuval Ebenstein
Publié dans: Bioinformatics, Numéro 34/1, 2017, Page(s) 134-136, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx437

Noise reduction in single time frame optical DNA maps

Auteurs: Paola C. Torche, Vilhelm Müller, Fredrik Westerlund, Tobias Ambjörnsson
Publié dans: PLOS ONE, Numéro 12/6, 2017, Page(s) e0179041, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0179041

Methyltransferase-Directed Labeling of Biomolecules and its Applications

Auteurs: Jochem Deen, Charlotte Vranken, Volker Leen, Robert K. Neely, Kris P. F. Janssen, Johan Hofkens
Publié dans: Angewandte Chemie International Edition, Numéro 56/19, 2017, Page(s) 5182-5200, ISSN 1433-7851
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201608625

Separation of pathogenic bacteria by chain length

Auteurs: Jason P. Beech, Bao Dang Ho, Geneviève Garriss, Vitor Oliveira, Birgitta Henriques-Normark, Jonas O. Tegenfeldt
Publié dans: Analytica Chimica Acta, Numéro 1000, 2018, Page(s) 223-231, ISSN 0003-2670
Éditeur: Elsevier BV
DOI: 10.1016/j.aca.2017.11.050

Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores

Auteurs: Tal Gilboa, Chen Torfstein, Matyas Juhasz, Assaf Grunwald, Yuval Ebenstein, Elmar Weinhold, Amit Meller
Publié dans: ACS Nano, Numéro 10/9, 2016, Page(s) 8861-8870, ISSN 1936-0851
Éditeur: American Chemical Society
DOI: 10.1021/acsnano.6b04748

Super-Resolution Genome Mapping in Silicon Nanochannels

Auteurs: Jonathan Jeffet, Asaf Kobo, Tianxiang Su, Assaf Grunwald, Ori Green, Adam N. Nilsson, Eli Eisenberg, Tobias Ambjörnsson, Fredrik Westerlund, Elmar Weinhold, Doron Shabat, Prashant K. Purohit, Yuval Ebenstein
Publié dans: ACS Nano, Numéro 10/11, 2016, Page(s) 9823-9830, ISSN 1936-0851
Éditeur: American Chemical Society
DOI: 10.1021/acsnano.6b05398

Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

Auteurs: Lena K. Nyberg, Saair Quaderi, Gustav Emilsson, Nahid Karami, Erik Lagerstedt, Vilhelm Müller, Charleston Noble, Susanna Hammarberg, Adam N. Nilsson, Fei Sjöberg, Joachim Fritzsche, Erik Kristiansson, Linus Sandegren, Tobias Ambjörnsson, Fredrik Westerlund
Publié dans: Scientific Reports, Numéro 6, 2016, Page(s) 30410, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/srep30410

Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping

Auteurs: Vilhelm Müller, Nahid Karami, Lena K. Nyberg, Christoffer Pichler, Paola C. Torche Pedreschi, Saair Quaderi, Joachim Fritzsche, Tobias Ambjörnsson, Christina Åhrén, Fredrik Westerlund
Publié dans: ACS Infectious Diseases, Numéro 2/5, 2016, Page(s) 322-328, ISSN 2373-8227
Éditeur: ACS Publications
DOI: 10.1021/acsinfecdis.6b00017

Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping

Auteurs: Vilhelm Müller, Fredrika Rajer, Karolin Frykholm, Lena K. Nyberg, Saair Quaderi, Joachim Fritzsche, Erik Kristiansson, Tobias Ambjörnsson, Linus Sandegren, Fredrik Westerlund
Publié dans: Scientific Reports, Numéro 6, 2016, Page(s) 37938, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/srep37938

Light-Enhancing Plasmonic-Nanopore Biosensor for Superior Single-Molecule Detection

Auteurs: Ossama N. Assad, Tal Gilboa, Joshua Spitzberg, Matyas Juhasz, Elmar Weinhold, Amit Meller
Publié dans: Advanced Materials, 2016, Page(s) 1605442, ISSN 0935-9648
Éditeur: United Nations Industrial Developement Organization
DOI: 10.1002/adma.201605442

Single-molecule protein sensing in a nanopore: a tutorial

Auteurs: Nitinun Varongchayakul, Jiaxi Song, Amit Meller, Mark W. Grinstaff
Publié dans: Chemical Society Reviews, Numéro 47/23, 2018, Page(s) 8512-8524, ISSN 0306-0012
Éditeur: Royal Society of Chemistry
DOI: 10.1039/c8cs00106e

Analytical epigenetics: single-molecule optical detection of DNA and histone modifications

Auteurs: Christian Heck, Yael Michaeli, Ilko Bald, Yuval Ebenstein
Publié dans: Current Opinion in Biotechnology, Numéro 55, 2019, Page(s) 151-158, ISSN 0958-1669
Éditeur: Elsevier BV
DOI: 10.1016/j.copbio.2018.09.006

Hypersensitive quantification of global 5-hydroxymethylcytosine by chemoenzymatic tagging

Auteurs: Tamar Shahal, Omri Koren, Gabi Shefer, Naftali Stern, Yuval Ebenstein
Publié dans: Analytica Chimica Acta, Numéro 1038, 2018, Page(s) 87-96, ISSN 0003-2670
Éditeur: Elsevier BV
DOI: 10.1016/j.aca.2018.08.035

Microfluidic DNA combing for parallel single-molecule analysis

Auteurs: Shuyi Wu, Jonathan Jeffet, Assaf Grunwald, Hila Sharim, Noa Gilat, Dmitry Torchinsky, Quanshui Zheng, Shahar Zirkin, Luping Xu, Yuval Ebenstein
Publié dans: Nanotechnology, Numéro 30/4, 2019, Page(s) 045101, ISSN 0957-4484
Éditeur: Institute of Physics Publishing
DOI: 10.1088/1361-6528/aaeddc

Optically-Monitored Nanopore Fabrication Using a Focused Laser Beam

Auteurs: Tal Gilboa, Adam Zrehen, Arik Girsault, Amit Meller
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-018-28136-z

DNA barcodes for rapid, whole genome, single-molecule analyses

Auteurs: Nathaniel O Wand, Darren A Smith, Andrew A Wilkinson, Ashleigh E Rushton, Stephen J W Busby, Iain B Styles, Robert K Neely
Publié dans: Nucleic Acids Research, 2019, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz212

Enzyme-free optical DNA mapping of the human genome using competitive binding

Auteurs: Vilhelm Müller, Albertas Dvirnas, John Andersson, Vandana Singh, Sriram KK, Pegah Johansson, Yuval Ebenstein, Tobias Ambjörnsson, Fredrik Westerlund
Publié dans: Nucleic Acids Research, 2019, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz489

Long-read single-molecule maps of the functional methylome

Auteurs: Hila Sharim, Assaf Grunwald, Tslil Gabrieli, Yael Michaeli, Sapir Margalit, Dmitry Torchinsky, Rani Arielly, Gil Nifker, Matyas Juhasz, Felix Gularek, Miguel Almalvez, 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, Y
Publié dans: Genome Research, Numéro 29/4, 2019, Page(s) 646-656, ISSN 1088-9051
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.240739.118

Droits de propriété intellectuelle

METHODS OF DETECTING 5-HYDROXYMETHYLCYTOSINE AND DIAGNOSING OF CANCER

Numéro de demande/publication: WO 2017081689
Date: 2017-05-18