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  1. 1.   DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking
  2. Balius,Trent; Tan, Y Stanley; Chakrabarti,Mayukh
  3. Journal of Computational Chemistry. 2023, Sep 25;
  1. 2.   Polyethyleneimine/polyethylene glycol-conjugated gold nanoparticles as nanoscale positive/negative controls in nanotoxicology: testing in frog embryo teratogenesis assay-Xenopus and mammalian tissue culture system
  2. Hwang,Rich Yooseok; So,Daeho; Lee,Moonsup; Yoon,Jaeho; Reipa, Vytas; Tona, Alessandro; Yi, Feng; Nelson, Bryant C; LaVan, David A; Hackley, Vincent A; Daar,Ira; Cho, Tae Joon
  3. Nanotoxicology. 2023, Mar 15; 1-22.
  1. 3.   Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
  2. Ingólfsson, Helgi I; Neale, Chris; Carpenter, Timothy S; Shrestha,Rebika; López, Cesar A; Tran, Timothy H; Oppelstrup, Tomas; Bhatia, Harsh; Stanton, Liam G; Zhang, Xiaohua; Sundram, Shiv; Di Natale, Francesco; Agarwal, Animesh; Dharuman, Gautham; Kokkila Schumacher, Sara I L; Turbyville,Tommy; Gulten, Gulcin; Van, Que N; Goswami, Debanjan; Jean-Francois, Frantz; Agamasu, Constance; Chen, De; Hettige, Jeevapani J; Travers, Timothy; Sarkar, Sumantra; Surh, Michael P; Yang, Yue; Moody, Adam; Liu, Shusen; Van Essen, Brian C; Voter, Arthur F; Ramanathan, Arvind; Hengartner, Nicolas W; Simanshu, Dhirendra K; Stephen, Andrew G; Bremer, Peer-Timo; Gnanakaran, S; Glosli, James N; Lightstone, Felice C; McCormick, Frank; Nissley, Dwight V; Streitz, Frederick H
  3. Proceedings of the National Academy of Sciences of the United States of America. 2022, Jan 04; 119(1):
  1. 4.   Performance of the inFLUenza Patient-Reported Outcome Plus (FLU-PRO Plus) Instrument in Patients With Coronavirus Disease 2019
  2. Richard, Stephanie A; Epsi, Nusrat J; Pollett, Simon; Lindholm, David A; Malloy, Allison M W; Maves, Ryan; Utz, Gregory C; Lalani, Tahaniyat; Smith, Alfred G; Mody, Rupal M; Ganesan, Anuradha; Colombo, Rhonda E; Colombo, Christopher J; Chi, Sharon W; Huprikar, Nikhil; Larson, Derek T; Bazan, Samantha; Madar, Cristian; Lanteri, Charlotte; Rozman, Julia S; English, Caroline; Mende, Katrin; Tribble, David R; Agan, Brian K; Burgess, Timothy H; Powers,John
  3. Open Forum Infectious Diseases. 2021, Oct 8; 8(12): ofab517.
  1. 5.   Endpoints for randomized controlled clinical trials for COVID-19 treatments
  2. Dodd, Lori E; Follmann, Dean; Wang,Jing; Koenig, Franz; Korn, Lisa L; Schoergenhofer, Christian; Proschan, Michael; Hunsberger, Sally; Bonnett,Tyler; Makowski, Mat; Belhadi, Drifa; Wang, Yeming; Cao, Bin; Mentre, France; Jaki, Thomas
  3. Clinical trials (London, England). 2020, Jul 16; pii: 1740774520939938.
  1. 6.   Target identification among known drugs by deep learning from heterogeneous networks
  2. Zeng, Xiangxiang; Zhu, Siyi; Lu, Weiqiang; Liu, Zehui; Huang, Jin; Zhou, Yadi; Fang, Jiansong; Huang, Yin; Guo, Huimin; Li, Lang; Trapp, Bruce D.; Nussinov,Ruth; Eng, Charis; Loscalzo, Joseph; Cheng, Feixiong
  3. CHEMICAL SCIENCE. 2020, Feb 21; 11(7): 1775-1797.
  1. 7.   Whole-cell imaging of plasma membrane receptors by 3D lattice light-sheet dSTORM
  2. Wäldchen, Felix; Schlegel, Jan; Götz, Ralph; Luciano,Michael; Schnermann,Martin; Doose, Sören; Sauer, Markus
  3. Nature communications. 2020, Feb 14; 11(1): pii:10.1038/s41467-020-14731-0.
  1. 8.   AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing
  2. Bhattacharya, Tanmoy; Brettin, Thomas; Doroshow, James H.; Evrard,Yvonne; Greenspan, Emily J.; Gryshuk, Amy L.; Hoang, Thuc T.; Lauzon, Carolyn B. Vea; Nissley,Dwight; Penberthy, Lynne; Stahlberg,Eric; Stevens, Rick; Streitz, Fred; Tourassi, Georgia; Xia, Fangfang; Zaki,George
  3. Frontiers in oncology. 2019, Oct 2; 9
  1. 9.   Developments in integrative modeling with dynamical interfaces
  2. Ozdemir, E. Sila; Nussinov,Ruth; Gursoy, Attila; Keskin, Ozlem
  3. CURRENT OPINION IN STRUCTURAL BIOLOGY. 2019, Jun; 56: 11-17.
  1. 10.   Scalable, cGMP-compatible purification of extracellular vesicles carrying bioactive human heterodimeric IL-15/lactadherin complexes
  2. Watson, Dennis; Yung, Bryant C; Bergamaschi, Cristina; Chowdhury, Bhabadeb; Bear, Jenifer; Stellas, Dimitrios; Morales-Kastresana, Aizea; Jones, Jennifer C; Felber, Barbara; Chen, Xiaoyuan; Pavlakis, George
  3. Journal of Extracellular Vesicles. 2018, Feb 28; 7(1): 1442088.
  1. 11.   An overview of enzymatic reagents for the removal of affinity tags
  2. Waugh, D. S.
  3. Protein Expression and Purification. 2011, Dec; 80(2): 283-293.
  1. 12.   Challenges in plasma membrane phosphoproteomics
  2. Orsburn, B. C.; Stockwin, L. H.; Newton, D. L.
  3. Expert Review of Proteomics. 2011, Aug; 8(4): 483-494.
  1. 13.   Purify First: Rapid expression and purification of proteins from XMRV
  2. Gillette, W. K.; Esposito, D.; Taylor, T. E.; Hopkins, R. F.; Bagni, R. K.; Hartley, J. L.
  3. Protein Expression and Purification. 2011, Apr; 76(2): 238-247.
  1. 14.   Symmetry-Based Self-assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers
  2. Buch, I.; Tsai, C. J.; Wolfson, H. J.; Nussinov, R.
  3. Protein and Peptide Letters. 2011, Apr; 18(4): 362-372.
  1. 15.   In vitro assembly of cubic RNA-based scaffolds designed in silico
  2. Afonin, K. A.; Bindewald, E.; Yaghoubian, A. J.; Voss, N.; Jacovetty, E.; Shapiro, B. A.; Jaeger, L.
  3. Nature Nanotechnology. 2010, Sep; 5(9): 676-682.
  1. 16.   Mechanisms of copy number variation and hybrid gene formation in the KIR immune gene complex
  2. Traherne, J. A.; Martin, M.; Ward, R.; Ohashi, M.; Pellett, F.; Gladman, D.; Middleton, D.; Carrington, M.; Trowsdale, J.
  3. Human Molecular Genetics. 2010, Mar; 19(5): 737-751.
  1. 17.   Computational Validation of Protein Nanotubes
  2. Buch, I.; Brooks, B. R.; Wolfson, H. J.; Nussinov, R.
  3. Nano Letters. 2009 9(3): 1096-1102.
  1. 18.   Topological properties of protein interaction networks from a structural perspective
  2. Gursoy, A.; Keskin, O.; Nussinov, R.
  3. Biochemical Society Transactions. 2008 36: 1398-1403.
  1. 19.   Automatic prediction of protein interactions with large scale motion
  2. Schneidman-Duhovny, D.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2007, Dec; 69(4): 764-773.
  1. 20.   Phosphoproteornics for the discovery of kinases as cancer biornarkers and drug targets
  2. Yu, L. R.; Issaq, H. J.; Veenstra, T. D.
  3. Proteomics Clinical Applications. 2007, Sep; 1(9): 1042-1057.
  1. 21.   Recombinant production of anti-HIV protein, griffithsin, by auto-induction in a fermentor culture
  2. Giomarelli, B.; Schumacher, K. M.; Taylor, T. E.; Sowder, R. C.; Hartley, J. L.; McMahon, J. B.; Mori, T.
  3. Protein Expression and Purification. 2006, MAY; 47(1): 194-202.
  1. 22.   Natural products from marine invertebrates and microbes as modulators of antitumor targets
  2. Newman, D. J.; Cragg, G. M.
  3. Current Drug Targets. 2006, MAR; 7(3): 279-304.
  1. 23.   Comprehensive analysis of pathway or functionally related gene expression in the National Cancer Institute's anticancer screen
  2. Huang, R.; Wallqvist, A.; Covell, D. G.
  3. Genomics. 2006, MAR; 87(3): 315-328.
  1. 24.   Transcriptomic response to differentiation induction
  2. Patton, G. W.; Stephens, R.; Sidorov, I. A.; Xiao, X.; Lempicki, R. A.; Dimitrov, D. S.; Shoemaker, R. H.; Tudor, G.
  3. Bmc Bioinformatics. 2006, FEB 17; 7
  1. 25.   Purification and scale-up of a recombinant heavy chain fragment C of botulinum neurotoxin serotype E in Pichia pastoris GS115
  2. Dux, M. P.; Barent, R.; Sinha, J.; Gouthro, M.; Swanson, T.; Barthuli, A.; Inan, M.; Ross, J. T.; Smith, L. A.; Smith, T. J.; Webb, R.; Loveless, B.; Henderson, I.; Meagher, M. M.
  3. Protein Expression and Purification. 2006, Feb; 45(2): 359-367.
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