Publications | Patents | Theses
2022
Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes
Naor Granik, Noa Katz, Or Willinger, Sarah Goldberg and Roee Amit. Nature Communications (2022)
Molecular and experimental tools to design synthetic enhancers
Inbal Vaknin and Roee Amit. Current Opinion in Biotechnology 76 (2022): 102728.
A Cell-Free Assay for Rapid Screening of Inhibitors of hACE2-Receptor–SARS-CoV-2-Spike
Nanami Kikuchi, Or Willinger, Naor Granik, Reut Gal, Noa Navon, Shanny Ackerman, Ella Samuel, Tomer Antman, Noa Katz, Sarah Goldberg, and Roee Amit. ACS synthetic biology (2021).
2021
An Oligo-Library-Based Approach for Mapping DNA-DNA Triplex Interactions In Vitro (PDF)
Beate Kaufmann, Or Willinger, Nanami Kikuchi, Noa Navon, Lisa Kermas, Sarah Goldberg and Roee Amit, 2021. ACS Synthetic Biology
Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes (PDF)
Noa Katz, Eitamar Tripto, Naor Granik, Sarah Goldberg, Orna Atar, Zohar Yakhini, Yaron Orenstein and Roee Amit, 2021. Nature Communications, 12-1576.
2019
Data storage in DNA with fewer synthesis cycles using composite DNA letters (PDF)
Anavy, L., Vaknin, I., Atar, O., Amit, R. and Yakhini, Z., 2019. Nature Biotechnology, 37(10), pp.1229-1236.
An Assay for Quantifying Protein-RNA Binding in Bacteria
Katz, N., Cohen, R., Atar, O., Goldberg, S. and Amit, R., 2019. JoVE (Journal of Visualized Experiments), (148), p.e59611.
Synthetic 5’ UTRs can either up- or down-regulate expression upon RBP binding (PDF)
Katz, N., Cohen, R., Solomon, O., Kaufmann, B., Atar, O., Yakhini, Z., Goldberg, S. and Amit, R., 2019. Cell Systems 9(1), pp.93-106.
Designing Bacterial Chemotactic Receptors Guided by Photonic Femtoliter Well Arrays for Quantifiable, Label-Free Measurement of Bacterial Chemotaxis (PDF)
Davidov, T., Granik, N., Zahran, S., Leonard, H., Adir, I., Elul, O., Fried, T., Gil, A., Mayo, B., Ohayon, S. and Sarig, S., 2019. ACS Biomaterials Science & Engineering, 5(2), pp.603-612.
2018
An in Vivo Binding Assay for RNA-Binding Proteins Based on Repression of a Reporter Gene (PDF)
Katz, N., Cohen, R., Solomon, O., Kaufmann, B., Atar, O., Yakhini, Z., Goldberg, S. and Amit, R., 2018. ACS Synthetic Biology, 7(12), pp.2765-2774.
2017
A Synthetic Oligo Library and Sequencing Approach Reveals an Insulation Mechanism Encoded within Bacterial σ54 Promoters (PDF)
Levy, L., Anavy, L., Solomon, O., Cohen, R., Brunwasser-Meirom, M., Ohayon, S., Atar, O., Goldberg, S., Yakhini, Z. and Amit, R., 2017. Cell Reports, 21(3), pp.845-858.
A Looping-Based Model for Quenching Repression (PDF)
Pollak, Y., Goldberg, S. and Amit, R., 2017. PLoS Computational Biology, 13(1), p.e1005337.
2016
Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression (PDF)
Brunwasser-Meirom, M., Pollak, Y., Goldberg, S., Levy, L., Atar, O. and Amit, R., 2016. Nature Communications, 7, p.10407.
2014
Self-avoiding wormlike chain model for double-stranded-DNA loop formation (PDF)
Pollak, Y., Goldberg, S. and Amit, R., 2014. Physical Review E, 90(5), p.052602.
2012 and Prior
Anti-Cooperative and Cooperative protein-protein interactions between TetR isoforms in Synthetic Enhancers (PDF)
Amit, R., 2012. Journal of Computational Biology, 19(2), pp.115-125.
Towards Synthetic Gene Circuits with Enhancers: Biology’s Multi-input Integrators (PDF)
Amit, R., 2012. In Reprogramming Microbial Metabolic Pathways (pp. 3-20). Springer, Dordrecht.
Building Enhancers from the Ground Up: A Synthetic Biology Approach (PDF)
Amit, R., Garcia, H.G., Phillips, R. and Fraser, S.E., 2011. Cell, 146(1), pp.105-118.
Single molecule elasticity measurements: a biophysical approach to bacterial nucleoid organization (PDF)
Amit, R., Oppenheim, A.B. and Stavans, J., 2004. Biophysical Journal, 87(2), p.1392.
Direct observation of RuvAB-catalyzed branch migration of single Holliday junctions (PDF)
Amit, R., Gileadi, O. and Stavans, J., 2004. Proceedings of the National Academy of Sciences, 101(32), pp.11605-11610.
Increase bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor (PDF)
Amit, R., Oppenheim, A.B. and Stavans, J., 2003. Biophysical Journal, 84(4), pp.2467-2473.
Compaction of single DNA molecules induced by binding of integration host factor (IHF) (PDF)
Ali, B.J., Amit, R., Braslavsky, I., Oppenheim, A.B., Gileadi, O. and Stavans, J., 2001. Proceedings of the National Academy of Sciences, 98(19), pp.10658-10663.
Objective-type dark-field illumination for scattering from microbeads (PDF)
Braslavsky, I., Amit, R., Ali, B.J., Gileadi, O., Oppenheim, A. and Stavans, J., 2001. Applied optics, 40(31), pp.5650-5657.
Patents
Composition and method for treating androgen-dependent disorders – US 10240132B2
Theses
Development of a Fluorescent Repressor Operator System (FROS) Based on LexA for DNA Labeling in Live Cells
M.Sc. thesis, Noa Navon
Protein-RNA interactions: Synthetic Biology applications
Ph.D. thesis, Noa Katz
Characterization of Intracellular Transcription and Diffusion Kinetics
M.Sc. thesis, Naor Granik
Understanding regulation of translation through RNA structure and investigating regulatory synthetic long non-coding RNA (slncRNAs)
M.Sc. thesis, Roni Cohen
Deciphering triplex formation using a synthetic biology-inspired and deep-sequencing approach
Ph.D. thesis, Beate Kaufmann
Studying Looping-Based Transcriptional Regulation Using Synthetic Biology Tools
Ph.D. thesis, Michal Brunwasser-Meirom
Using Synthetic Biology to Investigate And Utilize The Human Skin Microbiome
M.Sc. thesis, Alexey Tomsov
Enhancer Modeling by Monte-Carlo Simulations
Ph.D. thesis, Yaroslav Pollak
Novel Frontier in Gene Regulation via Expression of T7 Bacteriophage RNA polymerase in Yeast
M.Sc. thesis, Inbal Vaknin
Reconstructing and Discovering New σ54 Regulation Mechanisms in a High Throughput Manner
M.Sc. thesis, Lior Levy
Design and characterization of a fluorescent protein-based imaging system for RNA in live cells
M.Sc. thesis, Aya Friedman