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  1. 1.   Crystal Structure of an i-Motif from the HRAS Oncogene Promoter
  2. Li, Kevin S; Jordan, Deondre; Lin, Linda Y; McCarthy, Sawyer E; Schneekloth,Jay; Yatsunyk, Liliya A
  3. Angewandte Chemie (International ed. in English). 2023, Mar 30; e202301666.
  1. 2.   dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data
  2. Ou, Jianhong; Liu, Haibo; Nirala, Niraj K.; Stukalov, Alexey; Acharya,Usha; Green, Michael R.; Zhu, Lihua Julie
  3. PLOS ONE. 2020, NOV 6; 15(11):
  1. 3.   SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations
  2. Liao, Tsung-Jen; Jang,Hyunbum; Fushman, David; Nussinov,Ruth
  3. The Journal of chemical physics. 2020, Jul 28; 153(4): 045106.
  1. 4.   High-Affinity Interactions of the nSH3/cSH3 Domains of Grb2 with the C-Terminal Proline-Rich Domain of SOS1
  2. Liao,Tsung-Jen; Jang,Hyunbum; Nussinov,Ruth; Fushman, David
  3. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2020, Feb 19; 142: 3401-3411.
  1. 5.   Effect of Calcium Carbonate Encapsulation on the Activity of Orally Administered CpG Oligonucleotides
  2. Kayraklioglu, Neslihan; Scheiermann, Julia; Alvord, W. Gregory; Klinman, Dennis
  3. MOLECULAR THERAPY-NUCLEIC ACIDS. 2017, Sep 15; 8: 243-249.
  1. 6.   MDM1 is a microtubule-binding protein that negatively regulates centriole duplication
  2. Van de Mark, D.; Kong, D.; Loncarek, J.; Stearns, T.
  3. Molecular Biology of the Cell. 2015, 1-Nov; 26(21): 3788-802.
  1. 7.   Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement
  2. Tuncbag, N.; Keskin, O.; Nussinov, R.; Gursoy, A.
  3. Proteins-Structure Function and Bioinformatics. 2012, Apr; 80(4): 1239-1249.
  1. 8.   The acceleration of wound healing in primates by the local administration of immunostimulatory CpG oligonucleotides
  2. Yamamoto, M.; Sato, T.; Beren, J.; Verthelyi, D.; Klinman, D. M.
  3. Biomaterials. 2011, Jun; 32(18): 4238-4242.
  1. 9.   Crystallographic and Functional Analysis of the ESCRT-I/HIV-1 Gag PTAP Interaction
  2. Im, Y. J.; Kuo, L.; Ren, X. F.; Burgos, P. V.; Zhao, X. Z.; Liu, F.; Burke, T. R.; Bonifacino, J. S.; Freed, E. O.; Hurley, J. H.
  3. Structure. 2010, Nov; 18(11): 1536-1547.
  1. 10.   Why Does Binding of Proteins to DNA or Proteins to Proteins Not Necessarily Spell Function?
  2. Ma, B. Y.; Tsai, C. J.; Pan, Y. P.; Nussinov, R.
  3. Acs Chemical Biology. 2010, Mar; 5(3): 265-272.
  1. 11.   Short- and long-term changes in gene expression mediated by the activation of TLR9
  2. Klaschik, S.; Tross, D.; Shirota, H.; Klinman, D. M.
  3. Molecular Immunology. 2010, Mar; 47(6): 1317-1324.
  1. 12.   Immunostimulatory CpG oligonucleotides: Effect on gene expression and utility as vaccine adjuvants
  2. Klinman, D. M.; Klaschik, S.; Tomaru, K.; Shirota, H.; Tross, D.; Ikeuchi, H.
  3. Vaccine. 2010, Feb; 28(8): 1919-1923.
  1. 13.   Accelerated wound healing mediated by activation of Toll-like receptor 9
  2. Sato, T.; Yamamoto, M.; Shimosato, T.; Klinman, D. M.
  3. Wound Repair and Regeneration. 2010, Nov-Dec; 18(6): 586-593.
  1. 14.   Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels
  2. Jang, H.; Arce, F. T.; Capone, R.; Ramachandran, S.; Lal, R.; Nussinov, R.
  3. Biophysical Journal. 2009, Dec 2; 97(11): 3029-37.
  1. 15.   Structure of the Taz2 domain of p300: insights into ligand binding
  2. Miller, M.; Dauter, Z.; Cherry, S.; Tropea, J. E.; Wlodawer, A.
  3. Acta crystallographica. Section D, Biological crystallography. 2009, Dec; 65(Pt 12): 1301-8.
  1. 16.   Signaling dynamics of the KSR1 scaffold complex
  2. McKay, M. M.; Ritt, D. A.; Morrison, D. K.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2009, Jul 7; 106(27): 11022-7.
  1. 17.   A suppressive oligodeoxynucleotide inhibits ocular inflammation
  2. Fujimoto, C.; Klinman, D. M.; Shi, G.; Yin, H.; Vistica, B. P.; Lovaas, J. D.; Wawrousek, E. F.; Igarashi, T.; Chan, C. C.; Gery, I.
  3. Clinical and Experimental Immunology. 2009 156(3): 528-534.
  1. 18.   Contribution of IRF-3 mediated IFN beta production to DNA vaccine dependent cellular immune responses
  2. Shirota, H.; Petrenko, L.; Hattori, T.; Klinman, D. M.
  3. Vaccine. 2009 27(15): 2144-2149.
  1. 19.   Global changes in gene expression and synergistic interactions induced by TLR9 and TLR3
  2. Tross, D.; Petrenko, L.; Klaschik, S.; Zhu, Q.; Klinman, D. M.
  3. Molecular Immunology. 2009 46(13): 2557-2564.
  1. 20.   Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler
  2. Bindewald, E.; Grunewald, C.; Boyle, B.; O'Connor, M.; Shapiro, B. A.
  3. Journal of Molecular Graphics & Modelling. 2008 27(3): 299-308.
  1. 21.   RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
  2. Bindewald, E.; Hayes, R.; Yingling, Y. G.; Kasprzak, W.; Shapiro, B. A.
  3. Nucleic Acids Research. 2008 36: D392-D397.
  1. 22.   Structure-activity relationship studies for the peptide portion of the bladder epithelial cell antiproliferative factor from interstitial cystitis patients
  2. Kaczmarek, P.; Keay, S. K.; Tocci, G. M.; Koch, K. R.; Zhang, C. O.; Barchi, J. J.; Grkovic, D.; Guo, L.; Michejda, C. J.
  3. Journal of Medicinal Chemistry. 2008 51(19): 5974-5983.
  1. 23.   Protected aminooxyprolines for expedited library synthesis: Application to Tsg101-directed proline-oxime containing peptides
  2. Liu, F.; Stephen, A. G.; Fisher, R. J.; Burke, T. R.
  3. Bioorganic & Medicinal Chemistry Letters. 2008 18(3): 1096-1101.
  1. 24.   Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study
  2. Zanuy, D.; Rodriguez-Ropero, F.; Nussinov, R.; Aleman, C.
  3. Journal of Structural Biology. 2007, Nov; 160(2): 177-189.
  1. 25.   Structural basis for viral late-domain binding to Alix
  2. Lee, S.; Joshi, A.; Nagashima, K.; Freed, E. O.; Hurley, J. H.
  3. Nature Structural & Molecular Biology. 2007, Mar; 14(3): 194-199.
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