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  1. 1.   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. 2.   Parallel and Population-specific Gene Regulatory Evolution in Cold-Adapted Fly Populations
  2. Huang, Yuheng; Lack,Justin; Hoppel, Grant T.; Pool, John E.
  3. Genetics. 2021, May 14; 218
  1. 3.   Crystal structure of N-{N-[N-acetyl-(S)-leuc-yl]-(S)-leuc-yl}norleucinal (ALLN), an inhibitor of proteasome
  2. Czerwinski, Andrzej; Basava, Channa; Dauter, Miroslawa; Dauter, Zbigniew
  3. Acta crystallographica. Section E, Crystallographic communications. 2015, Mar 01; 71(Pt 3): 254-7.
  1. 4.   Identification of Cis-Acting Elements in the 3 '-Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication
  2. Manzano, M.; Reichert, E. D.; Polo, S.; Falgout, B.; Kasprzak, W.; Shapiro, B. A.; Padmanabhan, R.
  3. Journal of Biological Chemistry. 2011, Jun; 286(25): 22521-22534.
  1. 5.   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. 6.   CyloFold: secondary structure prediction including pseudoknots
  2. Bindewald, E.; Kluth, T.; Shapiro, B. A.
  3. Nucleic Acids Research. 2010, Jul; 38: W368-W372.
  1. 7.   An Intergenic Non-Coding rRNA Correlated with Expression of the rRNA and Frequency of an rRNA Single Nucleotide Polymorphism in Lung Cancer Cells
  2. Shiao, Y. H.; Lupascu, S. T.; Gu, Y. D.; Kasprzak, W.; Hwang, C. J.; Fields, J. R.; Leighty, R. M.; Quinones, O.; Shapiro, B. A.; Alvord, W. G.; Anderson, L. M.
  3. Plos One. 2009, Oct; 4(10): 11.
  1. 8.   The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels
  2. Linnstaedt, S. D.; Kasprzak, W. K.; Shapiro, B. A.; Casey, J. L.
  3. Rna-a Publication of the Rna Society. 2009 15(6): 1177-1187.
  1. 9.   Structural domains within the 3 ' untranslated region of Turnip crinkle virus
  2. McCormack, J. C.; Yuan, X. F.; Yingling, Y. G.; Kasprzak, W.; Zamora, R. E.; Shapiro, B. A.; Simon, A. E.
  3. Journal of Virology. 2008 82(17): 8706-8720.
  1. 10.   Bridging the gap in RNA structure prediction
  2. Shapiro, B. A.; Yingling, Y. G.; Kasprzak, W.; Bindewald, E.
  3. Current Opinion in Structural Biology. 2007, Apr; 17(2): 157-165.
  1. 11.   Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm
  2. Shapiro, B. A.; Kasprzak, W.; Grunewald, C.; Aman, J.
  3. Journal of Molecular Graphics & Modelling. 2006, Dec; 25(4): 514-531.
  1. 12.   A pseudoknot in a preactive form of a viral RNA is part of a structural switch activating minus-strand synthesis
  2. Zhang, J. C.; Zhang, G. H.; Guo, R.; Shapiro, B. A.; Simon, A. E.
  3. Journal of Virology. 2006, Sep; 80(18): 9181-9191.
  1. 13.   Ab initio electronic structure theory as an aid to understanding excited state hydrogen transfer in moderate to large systems
  2. Webb, S. P.
  3. Theoretical Chemistry Accounts. 2006, Aug; 116(1-3): 355-372.
  1. 14.   Structural differentiation of the HIV-1 poly(A) signals
  2. Gee, A. H.; Kasprzak, W.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2006, FEB; 23(4): 417-428.
  1. 15.   A systematic multireference perturbation-theory study of the low-lying states of SiC3
  2. Rintelman, J. M.; Gordon, M. S.; Fletcher, G. D.; Ivanic, J.
  3. Journal of Chemical Physics. 2006, JAN 21; 124(3, Art. No. 034303):
  1. 16.   RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers
  2. Bindewald, E.; Shapiro, B. A.
  3. Rna-a Publication of the Rna Society. 2006 12(3): 342-352.
  1. 17.   A base-specific recognition signal in the 5 ' consensus sequence of rotavirus plus-strand RNAs promotes replication of the double-stranded RNA genome segments
  2. Tortorici, M. A.; Shapiro, R. A.; Patton, J. T.
  3. Rna-a Publication of the Rna Society. 2006, JAN; 12(1): 133-146.
  1. 18.   Both IL-12p70 and IL-23 are synthesized during active Crohn's disease and are down-regulated by treatment with anti-IL-12 p40 monoclonal antibody
  2. Fuss, I. J.; Becker, C.; Yang, Z. Q.; Groden, C.; Hornung, R. L.; Heller, F.; Neurath, M. F.; Strober, W.; Mannon, P. J.
  3. Inflammatory Bowel Diseases. 2006, JAN; 12(1): 9-15.
  1. 19.   Cell cycle sibling rivalry - Cdc2 vs. Cdk2
  2. Kaldis, P.; Aleem, E.
  3. Cell Cycle. 2005, NOV; 4(11): 1491-1494.
  1. 20.   Simian immunodeficiency virus integration preference is similar to that of human immunodeficiency virus type 1
  2. Crise, B.; Li, Y.; Yuan, C. C.; Morcock, D. R.; Whitby, D.; Munroe, D. J.; Arthur, L. O.; Wu, X. L.
  3. Journal of Virology. 2005, OCT; 79(19): 12199-12204.
  1. 21.   Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
  2. Tsai, H. H.; Reches, M.; Tsai, C. J.; Gunasekaran, K.; Gazit, E.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, JUN 7; 102(23): 8174-8179.
  1. 22.   Binding of pregnancy-specific glycoprotein 17 to CD9 on macrophages induces secretion of IL-10, IL-6, PGE(2) and TGF-beta(1)
  2. Ha, C. T.; Waterhouse, R.; Wessells, J.; Wu, J. A.; Dveksler, G. S.
  3. Journal of Leukocyte Biology. 2005, JUN; 77(6): 948-957.
  1. 23.   HPV-16 L1 VLP vaccine elicits a broad-spectrum of cytokine responses in whole blood
  2. Pinto, L. A.; Castle, P. E.; Roden, R. B.; Harro, C. D.; Lowy, D. R.; Schiller, J. T.; Wallace, D.; Williams, M.; Kopp, W.; Frazer, I. H.; Berzofsky, J. A.; Hildesheim, A.
  3. Vaccine. 2005, MAY 20; 23(27): 3555-3564.
  1. 24.   IFN-gamma gene expression is controlled by the architectural transcription factor HMGA1
  2. Chau, K. Y.; Keane-Myers, A. M.; Fedele, M.; Ikeda, Y.; Creusot, R. J.; Menozzi, L.; Cousins, D. J.; Manfioletti, G.; Feigenbaum, L.; Fusco, A.; Ono, S. J.
  3. International Immunology. 2005, MAR; 17(3): 297-306.
  1. 25.   A novel flow cytometric assay for evaluating cell-mediated cytotoxicity
  2. Burkett, M. W.; Weaver, K. A. S.; Strobl, S.; Baseler, M.; Malyguine, A.
  3. Journal of Immunotherapy. 2005, JUL-AUG; 28(4): 396-402.
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