Recent News About
Guy Nir
postdoctoral fellow
Ph.D. in Biophysics, Bar Ilan University
Personal Website and Lab Notebook

The spatiotemporal organization of chromatin is considered to be a fundamental aspect of almost every cellular activity that requires DNA accessibility, including replication, gene expression, homolog pairing and segregation.  In particular, I am interested in visualizing genome organization at different scales using super-resolution microscopy. For example, at, small genomic scales, I will be asking how local sub-chromosomal repositioning can alter genomic activity, such as gene co-regulation. At higher genomic scales, I will be exploring the structural progression of chromatin from its smallest units of function (as small as a single nucleotide, to genes, regulatory regions, and TADs) to the organization of an entire chromosome (telomere to telomere) and, ultimately, the genome.


A Multiplexed DNA FISH strategy for Assessing Genome Architecture in C. elegans.
Fields B. D, Nguyen S. C., Nir G., Kennedy S. bioRxiv (2018).

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.
Guy Nir, Irene Farabella, Cynthia Pérez Estrada, Carl G. Ebeling, Brian J. Beliveau, Hiroshi M. Sasaki, S. Dean Lee, Son C. Nguyen, Ruth B. McCole, Shyamtanu Chattoraj, Jelena Erceg, Jumana AlHaj Abed, Nuno M. C. Martins, Huy Q. Nguyen, Mohammed A. Hannan, Sheikh Russell, Neva C. Durand, Suhas S. P. Rao, Jocelyn Y. Kishi, Paula Soler-Vila, Michele Di Pierro, José N. Onuchic, Steven P. Callahan, John M. Schreiner, Jeff A. Stuckey, Peng Yin, Erez Lieberman Aiden, Marc A. Marti-Renom, C.-ting Wu. PLOS Genetics, December 26, 2018

The role of near-wall drag effect on the dynamics of a tethered DNA under shear flow.
Nir G., Chetrit E., Vivante A., Garini Y., and Berkovich R. Soft Matter, 14, 2219-2226 (2018).

OligoMiner: A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.
Beliveau B. J., Kishi J. Y., Nir G., Sasaki H. M., Saka S. K., Nguyen S. C., Wu C. T., and Yin P. PNAS, (2018).

In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT
Beliveau B.J. *, Boettiger A.N. *, Nir G.*, Bintu B. *, Yin P., Zhuang X., and Wu C.T. Methods Mol. Biol. 1663 231-252 (2017).[*Co-first authors].

Dynamic analysis of a diffusing particle in a trapping potential.
Nir G., Lindner M. and Garini Y. in Protein Interactions, J. Cai and R. E. Wang, Editors. InTech. p. 369-400 (2012).

Protein-DNA Interactions Studies with Single Tethered Molecule Techniques.
M. Lindner, G. Nir, A. Vivante, I. T. Young and Y. Garini. In Physical Review E, 87, 022716 (2013).

Plasmonic Scattering as an Efficient Tool for a Force-Free Technique to Follow Single DNA Molecules.
Lindner M., Nir G. and Garini Y. The Open Optics Journal, 5, 12-16 (2011)

Nano-optics methods for studying DNA-protein interactions.
Lindner M., Nir G. and Garini Y. in Recent Advances in Nano-Technology, Z. Zalevsky, Editor. VDM Verlag: Saarbrücken. p. 155-192 (2011).

HU protein induces incoherent DNA persistence length.
Nir G., Lindner M., Dietrich H. R. C., Girshevitz O., Vorgias C. E. and Garini Y. Biophysical Journal 100, 784-790 (2011).

Force-free measurements of the conformations of DNA molecules tethered to a wall.
Lindner M*., Nir G*., Medalion S., Dietrich H. R. C., Rabin Y. and Garini Y., Physical Review E 83, 011916 (2011). [*Co-first authors].

Studies of single molecules at their natural form.
Lindner M., Nir G., Dietrich H. R. C., Young I. T., Tauber E., Bronshtein I., Altman L. and Garini Y. Israel Journal of Chemistry 49, 283-291 (2009).