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  1. 1.   Expression of HIV from a 1-LTR circular DNA in the absence of integration
  2. Gurgo, Corrado; Fenizia, Claudio; McKinnon, Katherine; Hsia,Ru-Ching; Franchini, Genoveffa
  3. Retrovirology. 2025, Mar 17; 22(1): 2.
  1. 2.   Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses
  2. Dremel, Sarah E; Koparde,Vishal; Arbuckle, Jesse H; Hogan, Chad H; Kristie, Thomas M; Krug, Laurie T; Conrad, Nicholas K; Ziegelbauer, Joseph M
  3. The EMBO Journal. 2025, Mar 03;
  1. 3.   Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection
  2. Dremel, Sarah E; Tagawa, Takanobu; Koparde,Vishal; Hernandez-Perez, Carmen; Arbuckle, Jesse H; Kristie, Thomas M; Krug, Laurie T; Ziegelbauer, Joseph M
  3. EMBO Reports. 2024, Mar; 25(3): 1541-1569.
  1. 4.   A virus-induced circular RNA maintains latent infection of Kaposi's sarcoma herpesvirus
  2. Tagawa, Takanobu; Oh, Daniel; Dremel, Sarah; Mahesh, Guruswamy; Koparde,Vishal; Duncan,Gerard; Andresson,Thorkell; Ziegelbauer, Joseph M
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Feb 07; 120(6): e2212864120.
  1. 5.   Human Papillomavirus Type 16 Circular RNA Is Barely Detectable for the Claimed Biological Activity
  2. Yu, Lulu; Zheng, Zhi-Ming
  3. mBio. 2022, Jan 18; 13(1): e0359421.
  1. 6.   Identifying and characterizing virus-encoded circular RNAs
  2. Tagawa, Takanobu; Kopardé, Vishal N; Ziegelbauer, Joseph M
  3. Methods (San Diego, Calif.). 2021, Dec; 196: 129-137.
  1. 7.   Characterizing Expression and Regulation of Gamma-Herpesviral Circular RNAs
  2. Tagawa, Takanobu; Oh, Daniel; Santos, Jerico; Dremel, Sarah; Mahesh, Guruswamy; Uldrick, Thomas S; Yarchoan, Robert; Koparde,Vishal; Ziegelbauer, Joseph M
  3. Frontiers in microbiology. 2021, Jun 30; 12: 670542.
  1. 8.   Proteogenomic Characterization of Endometrial Carcinoma
  2. Dou, Yongchao; Kawaler, Emily A; Cui Zhou, Daniel; Gritsenko, Marina A; Huang, Chen; Blumenberg, Lili; Karpova, Alla; Petyuk, Vladislav A; Savage, Sara R; Satpathy, Shankha; Liu, Wenke; Wu, Yige; Tsai, Chia-Feng; Wen, Bo; Li, Zhi; Cao, Song; Moon, Jamie; Shi, Zhiao; Cornwell, MacIntosh; Wyczalkowski, Matthew A; Chu, Rosalie K; Vasaikar, Suhas; Zhou, Hua; Gao, Qingsong; Moore, Ronald J; Li, Kai; Sethuraman, Sunantha; Monroe, Matthew E; Zhao, Rui; Heiman, David; Krug, Karsten; Clauser, Karl; Kothadia, Ramani; Maruvka, Yosef; Pico, Alexander R; Oliphant, Amanda E; Hoskins, Emily L; Pugh, Samuel L; Beecroft, Sean J I; Adams, David W; Jarman, Jonathan C; Kong, Andy; Chang, Hui-Yin; Reva, Boris; Liao, Yuxing; Rykunov, Dmitry; Colaprico, Antonio; Chen, Xi Steven; Czekanski, Andrzej; Jedryka, Marcin; Matkowski, Rafal; Wiznerowicz, Maciej; Hiltke, Tara; Boja, Emily; Kinsinger, Christopher R; Mesri, Mehdi; Robles, Ana I; Rodriguez, Henry; Mutch, David; Fuh, Katherine; Ellis, Matthew J; DeLair, Deborah; Thiagarajan,Mathangi; Mani, D R; Getz, Gad; Noble, Michael; Nesvizhskii, Alexey I; Wang, Pei; Anderson, Matthew L; Levine, Douglas A; Smith, Richard D; Payne, Samuel H; Ruggles, Kelly V; Rodland, Karin D; Ding, Li; Zhang, Bing; Liu, Tao; Fenyö, David
  3. Cell. 2020, Feb 20; 180(4): 729-748.e26.
  1. 9.   Circular RNAs and RNase L in PKR activation and virus infection
  2. Zheng,Zhi-Ming
  3. CELL AND BIOSCIENCE. 2019, MAY 27; 9(43):
  1. 10.   Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA
  2. Tagawa, Takanobu; Gao, Shaojian; Koparde,Vishal; Gonzalez, Mileidy; Spouge, John L.; Serquina, Anna P.; Lurain, Kathryn; Ramaswami, Ramya; Uldrick, Thomas S.; Yarchoan, Robert; Ziegelbauer, Joseph M.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2018, Dec 11; 115(50): 12805-12810.
  1. 11.   A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution
  2. Shelley, Mee Y.; SeIvan, Myvizhi Esai; Zhao, Jun; Babin, Volodymyr; Liao, Chenyi; Li, Jianing; Shelley, John C.
  3. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2017, Aug; 13(8): 3881-3897.
  1. 12.   Synergistic TRAIL Sensitizers from Barleria alluaudii and Diospyros maritima
  2. Whitson, E. L.; Sun, H.; Thomas, C. L.; Henrich, C. J.; Sayers, T. J.; McMahon, J. B.; Griesinger, C.; McKee, T. C.
  3. Journal of Natural Products. 2012, Mar; 75(3): 394-399.
  1. 13.   A One-Step Miniprep for the Isolation of Plasmid DNA and Lambda Phage Particles
  2. Lezin, G.; Kosaka, Y.; Yost, H. J.; Kuehn, M. R.; Brunelli, L.
  3. Plos One. 2011, Aug; 6(8):
  1. 14.   On the Role of the SP1 Domain in HIV-1 Particle Assembly: a Molecular Switch?
  2. Datta, S. A. K. D. S. A. K.; Temeselew, L. G.; Crist, R. M.; Soheilian, F.; Kamata, A.; Mirro, J.; Harvin, D.; Nagashima, K.; Cachau, R. E.; Rein, A.
  3. Journal of Virology. 2011, May; 85(9): 4111-4121.
  1. 15.   DNA bubble formation in transcription initiation
  2. Tchernaenko, V.; Halvorson, H. R.; Kashlev, M.; Lutter, L. C.
  3. Biochemistry. 2008 47(7): 1871-1884.
  1. 16.   Expression, purification, and characterization of Clostridium botulinum type B light chain
  2. Gilsdorf, J.; Gul, N.; Smith, L. A.
  3. Protein Expression and Purification. 2006, Apr; 46(2): 256-267.
  1. 17.   Isolation and characterization of novel cyclotides from Viola hederaceae - Solution structure and anti-HIV activity of vhl-1, a leaf-specific expressed cyclotide
  2. Chen, B.; Colgrave, M. L.; Daly, N. L.; Rosengren, K. J.; Gustafson, K. R.; Craik, D. J.
  3. Journal of Biological Chemistry. 2005, JUN 10; 280(23): 22395-22405.
  1. 18.   Proteins that bind high-mannose sugars of the HIV envelope
  2. Botos, I.; Wlodawer, A.
  3. Progress in Biophysics and Molecular Biology. 2005, JUN; 88(2): 233-282.
  1. 19.   Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of the cyclic peptide inhibitors of Grb2-SH2 domain: NMR studies for the structural origin
  2. Shi, Y. H.; Song, Y. L.; Lin, D. H.; Tan, J. Z.; Roller, P. P.; Li, Q.; Long, Y. Q.; Song, G. Q.
  3. Biochemical and Biophysical Research Communications. 2005, MAY 20; 330(4): 1254-1261.
  1. 20.   A high-throughput fluorescence-anisotropy screen that identifies small molecule inhibitors of the DNA binding of B-ZIP transcription factors
  2. Rishi, V.; Potter, T.; Laudeman, J.; Reinhart, R.; Silvers, T.; Selby, M.; Stevenson, T.; Krosky, P.; Stephen, A. G.; Acharya, A.; Moll, J.; Oh, W. J.; Scudiero, D.; Shoemaker, R. H.; Vinson, C.
  3. Analytical Biochemistry. 2005, MAY 15; 340(2): 259-271.
  1. 21.   Structure of circulin B and implications for antimicrobial activity of the cyclotides
  2. Koltay, A.; Daly, N. L.; Gustafson, K. R.; Craik, D. J.
  3. International Journal of Peptide Research and Therapeutics. 2005, MAR; 11(1): 99-106.
  1. 22.   Interactions between immunoglobulin-like and catalytic modules in Clostridium thermocellum cellulosomal cellobiohydrolase CbhA
  2. Kataeva, I. A.; Uversky, V. N.; Brewer, J. M.; Schubot, F.; Rose, J. P.; Wang, B. C.; Ljungdahl, L. G.
  3. Protein Engineering Design & Selection. 2004, NOV; 17(11): 759-769.
  1. 23.   The role of the cyclic peptide backbone in the anti-HIV activity of the cyclotide kalata B1
  2. Daly, N. L.; Gustafson, K. R.; Craik, D. J.
  3. Febs Letters. 2004, SEP 10; 574(1-3): 69-72.
  1. 24.   Molecular dynamics simulation of E-coli dihydrofolate reductase and its circular permuted variants: Relative stabilities in experiment and simulations
  2. Hu, Z. J.; Ma, B. Y.; Nussinov, R.; Southerl, W. M.
  3. Abstracts of Papers of the American Chemical Society. 2004, AUG 22; 228(Part 1): 123-COMP, Abstract U519-123-COMP, Abstract U519.
  1. 25.   Solution structure of the cyclotide palicourein: Implications for the development of a pharmaceutical framework
  2. Barry, D. G.; Daly, N. L.; Bokesch, H. R.; Gustafson, K. R.; Craik, D. J.
  3. Structure. 2004 12(1): 85-94.
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