Publications

Publicationseminars/conferences | Patent | Thesis

2017 | 2016 |2015 | 2014 |2013 | 2012 | 2011 | prior 2010

2017

An in vivo binding assay for RNA-binding proteins based on repression of a reporter gene
Noa KatzBeate KaufmannRoni CohenOz SolomonOrna AtarZohar YakhiniSarah Goldberg,Roee Amit
(In Review)

Synthetic protein-sensing riboswitches
Noa KatzBeate KaufmannRoni CohenOz SolomonOrna AtarZohar YakhiniSarah GoldbergRoee Amit
(In Review)

Demonstration of de novo chemotaxis in E. coli using a real-time, quantitative, and digital-like approach
Tzila Davidov, Naor Granik, Sharbel Zahran, Inbal Adir, Ofek Elul, Tal Fried, Asif Gil, Bar Mayo, Shilo Ohayon, Shiran Sarig, Nofar Shasha, Shirane Tsedef, Shani Weiner, Michal Brunwasser-Meirom, Alexandra Ereskovsky, Noa Katz, Beate Kaufmann, Yuri Haimov, Heidi Leonard, Ester Segal, Roee Amit
(In Review)

Short CT-rich motifs encoded within σ54 promoters insulate downstream genes from transcriptional read-through Cell Reports, 21 (3), 845-858 (2017)
Lior Levy, Leon Anavy, Oz Solomon, Roni Cohen, Shilo Ohayon, Orna Atar, Sarah Goldberg, Zohar Yakhini, Roee Amit

A Looping-Based Model for Quenching Repression
PLOS. Comp. Biol., (2017), Yaroslav Pollak, Sarah Goldberg, Roee Amit

2016

Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repressionNat. Commun. 7:10407  (2016).
Michal Brunwasser-Meirom, Yaroslav Pollak, Sarah Goldberg, Lior Levy, Orna Atar, Roee Amit

A protrusion can “eclipse” looping of a long self-avoiding chain(2016)
Yaroslav Pollak, Sarah Goldberg, Roee Amit

 

2015

Anti-Cooperative and Cooperative protein-protein interactions between TetR isoforms in Synthetic Enhancers”, Journal of Computational Biology, Vol 19 (2012) 115-125
Amit R

2014

Self-avoiding wormlike chain model for double-stranded-DNA loop formation“, Physical Review  E 90,052602 (2014), Yaroslav Pollak, Sarah Goldberg, Roee Amit,

2012

Anti-Cooperative and Cooperative protein-protein interactions between TetR isoforms in Synthetic Enhancers”, Journal of Computational Biology, Vol 19 (2012) 115-125
Amit R

Towards Synthetic Gene Circuits with Enhancers: Biology’s Multi-input Integrators”, Subcellular Biochemistry, Vol 64 (2012) 3-20.
Amit R

2011

Building Enhancers from the Ground Up: A Synthetic Biology Approach, Cell, 146 (2011) 1-14.
Amit R, Garcia HG, Phillips R, and Fraser SE

 Prior 2010

Single molecule elasticity measurements: a biophysical approach to bacterial nucleoid organization”, Biophys J. 87 (2004) 1392-3.
Amit R, Oppenheim AB, and Stavans J

Direct observation of RuvAB-catalyzed branch migration of single Holliday junctions”, Proc. Nat. Acad. Sci. USA, 101 (2004) 11605-10.
Amit R, Gileadi O, and Stavans J

Increase bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor, Biophys J. 84 (2003) 2467.
Amit R, Oppenheim AB, and Stavans J

Compaction of single DNA molecules induced by binding of integration host factor (IHF), Proc. Nat. Acad. Sci. USA 98 (2001) 10
Ali BMJ, Amit R, Braslavsky I, Oppenheim AB, Gileadi O, and Stavans J

Objective-type dark-field illumination for scattering from microbeads, Appl. Opt. 40 (2001) 5650-7.
Braslavsky I, Amit R, Ali BMJ, Gileadi O, Oppenheim AB, and Stavans J

seminars/confrences

Synthetic biology games with RNA in bacteria
7th annual Winter q-bio meeting in Hawaii
Feb.  2017

A looping based model for quenching repression
Israel Biophysical Society Meeting
Oct. 2016

Using synthetic enhancers to reveal a mechanism for quenching repression
Conference: Systems Biology: Global Regulation of Gene Expression
Venue: Windham Resort, Puerto Rico
Feb. 2015

Synthetic Genomics
Agilent Technologies, Santa Clara
November, 2014

Towards a Set of Design Rules for Bacterial (or possibly all) Enhancers
Center for Synthetic Biology, MIT
June, 2013

Towards a set of Design rules for Bacterial Enhancers
Roee AmitConference: Regulation of gene expression from a distance – Exploring mechanisms.
Royal Society’s KAVLI center.
Seminar Date: 25 Oct, 2012

Synthetic Enhancers: Building Enhancers from the ground up
Seminar Date: 27 Apr, 2011
Biophysics Group Seminar, Technion

Patent

US provisional patent 62/396,167

Thesis

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