Publications

For a complete list of publications: Google Scholar profile

📧 co-corresponding authors
* of equal contribution

  1. Yeqiao Zhou*,  Atishay Jay*,  Noah Burget,  Tobias Friedrich,  Sora Yoon,  Jessica Alsing,  Guy Nir,  Rudolf Grosschedl,  Golnaz Vahedi & Robert B. Faryabi. Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation, Nature Cell Biology, 2025. doi: https://doi.org/10.1038/s41556-025-01827-2
    * These authors have contributed equally
  2. Vivante A, Dwivedi N, Sheetz M, Nir G. Restored rigidity sensing fails to induce anoikis in cancer cells due to Akt activation and cell–cell interactions, bioRxiv, June 16, 2025
  3. Bo Zhao, Chae Yun Cho, Lingqun Ye, Tula Keal, Thomas Mitchell, Ines Martin-Barrio, Christina Abi Faraj, Mesut Unal, Jessica Alsing, Nora M. Lawson, Ellie Rahm Kim, Francisco Chavez, Kristy Mendoza Rangel, Sanjay K. Singh, Joseph H. McCarthy, David M. Ashley, W. K. Alfred Yung, Vinay Puduvalli, Guy Nir, Jeffrey S. Weinberg, Linghua Wang, Keith L. Ligon, Giannicola Genovese, Peter Van Loo, P. Andrew Futreal, Jason T. Huse, Jesse R. Dixon, Frederick F. Lang, Kadir C. Akdemir. Oncogenic drivers shape the tumor microenvironment in human gliomas, bioRxiv, May 21, 2025
  4. 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. 2023/06; 14(1):3303. doi: 10.1038/s41467-023-38429-1.
  5. Flores V, Farabella I📧, Nir G📧. Genome-wide tracing to decipher nuclear organization. Curr Opin Cell Biol. 2023 May 30;82:102175. doi: 10.1016/j.ceb.2023.102175. [Epub ahead of print] Review. PubMed PMID: 37263058.
  6. 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. 2023 Mar;19(3):e1011224. doi: 10.1371/journal.ppat.1011224. eCollection 2023 Mar. PubMed PMID: 36996041; PubMed Central PMCID: PMC10062553.
  7. Nussinov R., Jang H., Nir G., Tsai C.-J., Cheng F., Open Structural Data in Precision Medicine, Annual Review of Biomedical Data Science (2022).
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. Nir G*, Farabella I*, Pérez Estrada C*, Ebeling CG*, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet. 2018 Dec;14(12):e1007872. doi: 10.1371/journal.pgen.1007872. eCollection 2018 Dec. PubMed PMID: 30586358; PubMed Central PMCID: PMC6324821.
  13. 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, 2018, 14, 2219-2226.
    Our paper was also chosen to be presented on the cover: http://pubs.rsc.org/en/content/articlelanding/2018/sm/c8sm90049c#!divAbstract
  14. 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.
  15. 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)
  16. 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).
  17. 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.
  18. 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).
  19. M. Lindner, G. Nir and Y. Garini, Nano-optics methods for studying DNA-protein interactions, in Recent Advances in Nano-Technology, Z. Zalevsky, Editor. (2011), VDM Verlag: Saarbrücken. p. 155-192.
  20. 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).
  21. 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).
  22. 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).