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  1. 1.   Duplicate entries in the Protein Data Bank: how to detect and handle them
  2. Wlodawer,Alexander; Dauter, Zbigniew; Rubach, Pawel; Minor, Wladek; Jaskolski, Mariusz; Jiang, Ziqiu; Jeffcott, William; Anosova, Olga; Kurlin, Vitaliy
  3. Acta Crystallographica. Section D, Structural Biology. 2025, Apr 01;
  1. 2.   Purification of Circular RNAs Using Poly(A) Tailing Followed by RNase R Digestion
  2. Xiao, Mei-Sheng; Wilusz, Jeremy E
  3. Methods in Molecular Biology (Clifton, N.J.). 2024 2765: 3-19.
  1. 3.   Robust regulation of transcription pausing in Escherichia coli by the ubiquitous elongation factor NusG
  2. Yakhnin,Alex; Bubunenko,Mikhail; Mandell, Zachary F; Lubkowska,Lucyna; Husher, Sara; Babitzke, Paul; Kashlev,Mikhail
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Jun 13; 120(24): e2221114120.
  1. 4.   Reply to Wang et al., "Assessment of the Abundance and Potential Function of Human Papillomavirus Type 16 Circular E7 RNA"
  2. Yu,Lulu; Lobanov, Alexei; Zheng,Zhi-Ming
  3. mBio. 2022, May 17; e0075822.
  1. 5.   The mechanism of Raf activation through dimerization
  2. Zhang,Mingzhen; Maloney,Ryan; Jang,Hyunbum; Nussinov,Ruth
  3. Chemical Science. 2021, Dec 08; 12(47): 15609-15619.
  1. 6.   Artificial intelligence in COVID-19 drug repurposing
  2. Zhou, Yadi; Wang, Fei; Tang, Jian; Nussinov,Ruth; Cheng, Feixiong
  3. The Lancet. Digital health. 2020, DEC; 2589-7500:(12): E667-E676.
  1. 7.   Two independent routes of post-translational chemistry in fluorescent protein FusionRed
  2. Muslinkina,Liya; Pletnev, Vladimir Z; Pletneva, Nadya V; Ruchkin, Dmitry A; Kolesov, Danila V; Bogdanov, Alexey M; Kost, Lubov A; Rakitina, Tatiana V; Agapova, Yulia K; Shemyakina, Irina I; Chudakov, Dmitry M; Pletnev, Sergei
  3. International journal of biological macromolecules. 2020, JUL 15; 155: 551-559.
  1. 8.   A Comparative Review of Chemotherapy-Induced Peripheral Neuropathy in In Vivo and In Vitro Models
  2. Eldridge, Sandy; Guo,Liang; Hamre, John
  3. Toxicologic pathology. 2019, Jul 22;
  1. 9.   Genetic background-dependent role of Egr1 for eyelid development.
  2. Oh, Jangsuk; Wang, Yujuan; Chen, Shida; Li, Peng; Du, Ning; Yu, Zu-Xi; Butcher, Donna; Gebregiorgis, Tesfay; Strachan, Erin; Lehmann, Ordan J; Brooks, Brian P; Chan, Chi-Chao; Leonard, Warren J
  3. Proceedings of the National Academy of Sciences of the United States of America. 2017, Aug 04; 114(34): E7131-E7139.
  1. 10.   Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences
  2. Imashimizu, M.; Afek, A.; Takahashi, H.; Lubkowska, Lucyna; Lukatsky, D. B.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2016, Nov 22; 113(47): E7409-E7417.
  1. 11.   SymmRef: A flexible refinement method for symmetric multimers
  2. Mashiach-Farkash, E.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2011, Sep; 79(9): 2607-2623.
  1. 12.   Arginine Methylation by PRMT5 at a Naturally Occurring Mutation Site Is Critical for Liver Metabolic Regulation by Small Heterodimer Partner
  2. Kanamaluru, D.; Xiao, Z.; Fang, S. S.; Choi, S. E.; Kim, D. H.; Veenstra, T. D.; Kemper, J. K.
  3. Molecular and Cellular Biology. 2011, Apr; 31(7): 1540-1550.
  1. 13.   Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection
  2. Batorsky, R.; Kearney, M. F.; Palmer, S. E.; Maldarelli, F.; Rouzine, I. M.; Coffin, J. M.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2011, Apr; 108(14): 5661-5666.
  1. 14.   An integrated suite of fast docking algorithms
  2. Mashiach, E.; Schneidman-Duhovny, D.; Peri, A.; Shavit, Y.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2010, Nov; 78(15): 3197-3204.
  1. 15.   NCAD, a Database Integrating the Intrinsic Conformational Preferences of Non-Coded Amino Acids
  2. Revilla-Lopez, G.; Torras, J.; Curco, D.; Casanovas, J.; Calaza, M. I.; Zanuy, D.; Jimenez, A. I.; Cativiela, C.; Nussinov, R.; Grodzinski, P.; Aleman, C.
  3. Journal of Physical Chemistry B. 2010, Jun; 114(21): 7413-7422.
  1. 16.   Fiber Dock: Flexible induced-fit backbone refinement in molecular docking
  2. Mashiach, E.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2010, May; 78(6): 1503-1519.
  1. 17.   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. 18.   Limb Development Takes a Measured Step Toward Systems Analysis
  2. Mackem, S.; Lewandoski, M.
  3. Science Signaling. 2009, May; 2(71): 4.
  1. 19.   Conformational Preferences of 1-Amino-2-phenylcyclohexanecarboxylic Acid, a Phenylalanine Cyclohexane Analogue
  2. Aleman, C.; Jimenez, A. I.; Cativiela, C.; Nussinov, R.; Casanovas, J.
  3. Journal of Organic Chemistry. 2009 74(20): 7834-7843.
  1. 20.   Mechanism of sequence-specific pausing of bacterial RNA polymerase
  2. Kireeva, M. L.; Kashlev, M.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2009 106(22): 8900-8905.
  1. 21.   Bile acid signaling pathways increase stability of Small Heterodimer Partner (SHP) by inhibiting ubiquitin-proteasomal degradation
  2. Miao, J.; Xiao, Z.; Kanamaluru, D.; Min, G.; Yau, P. M.; Veenstra, T. D.; Ellis, E.; Strom, S.; Suino-Powell, K.; Xu, H. E.; Kemper, J. K.
  3. Genes & Development. 2009 23(8): 986-996.
  1. 22.   LIM homeobox transcription factors integrate signaling events that control three-dimensional limb patterning and growth
  2. Tzchori, I.; Day, T. F.; Carolan, P. J.; Zhao, Y.; Wassif, C. A.; Li, L.; Lewandoski, M.; Gorivodsky, M.; Love, P. E.; Porter, F. D.; Westphal, H.; Yang, Y.
  3. Development. 2009 136(8): 1375-1385.
  1. 23.   Vaccine-Induced Cellular Responses Control Simian Immunodeficiency Virus Replication after Heterologous Challenge
  2. Wilson, N. A.; Keele, B. F.; Reed, J. S.; Piaskowski, S. M.; MacNair, C. E.; Bett, A. J.; Liang, X. P.; Wang, F. B.; Thoryk, E.; Heidecker, G. J.; Citron, M. P.; Huang, L. Y.; Lin, J.; Vitelli, S.; Ahn, C. D.; Kaizu, M.; Maness, N. J.; Reynolds, M. R.
  3. Journal of Virology. 2009 83(13): 6508-6521.
  1. 24.   DNA sequences in gal operon override transcription elongation blocks
  2. Lewis, D.; Komissarova, N.; Le, P.; Kashlev, M.; Adhya, S.
  3. Journal of Molecular Biology. 2008 382(4): 843-858.
  1. 25.   Differential control of the CCAAT/enhancer-binding protein beta (C/EBP beta) products liver-enriched transcriptional activating protein (LAP) and liver- enriched transcriptional inhibitory protein (LIP) and the regulation of gene expression during th
  2. Li, Y.; Bevilacqua, E.; Chiribau, C. B.; Majumder, M.; Wang, C. P.; Croniger, C. M.; Snider, M. D.; Johnson, P. F.; Hatzoglou, M.
  3. Journal of Biological Chemistry. 2008 283(33): 22443-22456.
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