Publications | Patents | Theses

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 Biotechnology37(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 & Engineering5(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 Biology7(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 Reports21(3), pp.845-858.

A Looping-Based Model for Quenching Repression (PDF)
Pollak, Y., Goldberg, S. and Amit, R., 2017. PLoS Computational Biology13(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 Communications7, 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 E90(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 Biology19(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. Cell146(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 Journal87(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 Sciences101(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 Journal84(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 Sciences98(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 optics40(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