Nir's Research Lab


For a complete list of publications: Google Scholar profile

  1. Harris H, Gu H, Olshansky M, Wang A, Farabella I, Eliaz Y, Kalluchi A, Krishna A, Jacobs M, Cauer G, Pham M, Rao S, Dudchenko O, Omer A, Mohajeri K, Kim S, Nichols M, Davis E, Gkountaroulis D, Udupa D, Aiden A, Corces V, Phanstiel D, Noble W, Nir G, Di Pierro M, Seo J, Talkowski M, Aiden E, Rowley M. Chromatin alternates between A and B compartments at kilobase scale for subgenic organization. Nature Communications.14(1), 3303 (2023).
  2. Flores V, Farabella I, Nir G. Genome-wide tracing to decipher nuclear organization. Curr Opin Cell Biol. 82, 102175 (2023).
  3. Yeh SC, Strilets T, Tan WL, Castillo D, Medkour H, Rey-Cadilhac F, Serrato-Pomar IM, Rachenne F, Chowdhury A, Chuo V, Azar SR, Singh MK, Hamel R, Missé D, Kini RM, Kenney LJ, Vasilakis N, Marti-Renom MA, Nir G, Pompon J, Garcia-Blanco MA. The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity. PLoS Pathog. 19(3), e1011224 (2023).
  4. Nussinov R., Jang H., Nir G., Tsai C.-J., Cheng F., Open Structural Data in Precision Medicine, Annual Review of Biomedical Data Science, 5, 95-117 (2022).
  5. Nussinov R., Jang H., Nir G., Tsai C.-J., Cheng F., A new precision medicine initiative at the dawn of exascale computing, Sig. Transduct. Target Ther. 6, 3 (2021).
  6. Nguyen H. Q*., Chattoraj S*., Castillo D*., Nguyen S. C., Nir G., Lioutas A., Hershberg E. A., Martins N. M. C., Reginato P. L., Hannan M., Beliveau B. J., Church G. M., Daugharthy E.R., Marti-Renom M. A., and Wu C-t., 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing, Nat. Methods 17, 822-832 (2020).
  7. Erceg J.*, AlHaj Abed J.*, Goloborodko A.*, Lajoie B., Fudenberg G., Abdennur N., Imakaev M., McCole R., Nguyen S., Saylor W., Joyce E., Senaratne N., Hannan M., Nir G., Dekker J., Mirny L., and Wu C-t., The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nat. Comms, 10 (1), 1-13 (2019).
  8. Fields B. D, Nguyen S. C., Nir G., Kennedy S., A Multiplexed DNA FISH strategy for Assessing Genome Architecture in C. elegans, eLife, 8, e42823 (2019).
  9. Guy Nir, Irene Farabella, Cynthia Pérez Estrada, Carl G. Ebeling, Brian J. Beliveau, Hiroshi M. Sasaki, Soun H. 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, and Wu C-t. Walking along chromosomes with super-resolution microscopy, contact maps, and integrative modeling, PLoS Genet. 14(12), e1007872 (2018).
  10. G. Nir, E. Chetrit, A. Vivante, Y. Garini, and R. Berkovich, The role of near-wall drag effect on the dynamics of a tethered DNA under shear flow, Soft Matter, 14, 2219-2226 (2018).
    Our paper was also chosen to be presented on the cover: http://pubs.rsc.org/en/content/articlelanding/2018/sm/c8sm90049c#!divAbstract
  11. Brian J Beliveau, Joceyln Y Kishi, Guy Nir, Hiroshi M Sasaki, Sinem K Saka, Son C Nguyen, Chao-ting Wu , Peng Yin, OligoMiner: A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes, PNAS (2018).
  12. B.J. Beliveau*, A.N. Boettiger,* G. Nir*, B. Bintu*, P. Yin, X. Zhuang, C.T. Wu, In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT, Methods Mol. Biol. 1663, 231-252 (2017)
  13. M. Lindner, G. Nir, A. Vivante, I. T. Young and Y. Garini,  Dynamic analysis of a diffusing particle in a trapping potential. Physical Review E, 87, 022716 (2013).
  14. G. Nir, M. Lindner and Y. Garini, Protein-DNA Interactions Studies with Single Tethered Molecule Techniques, in Protein Interactions, J. Cai and R. E. Wang, Editors. (2012), InTech. p. 369-400.
  15. M. Lindner, G. Nir and Y. Garini, Plasmonic Scattering as an Efficient Tool for a Force-Free Technique to Follow Single DNA Molecules. The Open Optics Journal, 5, 12-16 (2011).
  16. M. Lindner, G. Nir and Y. Garini, Nano-optics methods for studying DNA-protein interactions, in Recent Advances in Nano-Technology, Z. Zalevsky, Editor. VDM Verlag: Saarbrücken. p. 155-192. (2011)
  17. G. Nir, M. Lindner, H. R. C. Dietrich, O. Girshevitz, C. E. Vorgias and Y. Garini. HU protein induces incoherent DNA persistence length. Biophysical Journal, 100, 784-790 (2011).
  18. M. Lindner, G. Nir, S. Medalion, H. R. C. Dietrich, Y. Rabin and Y. Garini. Force-free measurements of the conformations of DNA molecules tethered to a wall. Physical Review E, 83, 011916 (2011).
  19. M. Lindner, G. Nir, H. R. C. Dietrich, I. T. Young, E. Tauber, I. Bronshtein, L. Altman and Y. Garini. Studies of single molecules at their natural form. Israel Journal of Chemistry, 49, 283-291 (2009).