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  1. 1.   Multi-scale signaling and tumor evolution in high-grade gliomas
  2. Liu, Jingxian; Cao, Song; Imbach, Kathleen J; Gritsenko, Marina A; Lih, Tung-Shing M; Kyle, Jennifer E; Yaron-Barir, Tomer M; Binder, Zev A; Li, Yize; Strunilin, Ilya; Wang, Yi-Ting; Tsai, Chia-Feng; Ma, Weiping; Chen, Lijun; Clark, Natalie M; Shinkle, Andrew; Naser Al Deen, Nataly; Caravan, Wagma; Houston, Andrew; Simin, Faria Anjum; Wyczalkowski, Matthew A; Wang, Liang-Bo; Storrs, Erik; Chen, Siqi; Illindala, Ritvik; Li, Yuping D; Jayasinghe, Reyka G; Rykunov, Dmitry; Cottingham, Sandra L; Chu, Rosalie K; Weitz, Karl K; Moore, Ronald J; Sagendorf, Tyler; Petyuk, Vladislav A; Nestor, Michael; Bramer, Lisa M; Stratton, Kelly G; Schepmoes, Athena A; Couvillion, Sneha P; Eder, Josie; Kim, Young-Mo; Gao, Yuqian; Fillmore, Thomas L; Zhao, Rui; Monroe, Matthew E; Southard-Smith, Austin N; Li, Yang E; Jui-Hsien Lu, Rita; Johnson, Jared L; Wiznerowicz, Maciej; Hostetter, Galen; Newton, Chelsea J; Ketchum, Karen A; Thangudu, Ratna R; Barnholtz-Sloan, Jill S; Wang, Pei; Fenyö, David; An, Eunkyung; Thiagarajan,Mathangi; Robles, Ana I; Mani, D R; Smith, Richard D; Porta-Pardo, Eduard; Cantley, Lewis C; Iavarone, Antonio; Chen, Feng; Mesri, Mehdi; Nasrallah, MacLean P; Zhang, Hui; Resnick, Adam C; Chheda, Milan G; Rodland, Karin D; Liu, Tao; Ding, Li
  3. Cancer Cell. 2024, Jul 08; 42(7): 1217-1238.e19.
  1. 2.   The Design of a Participatory Peptide Nucleic Acid Duplex Crosslinker to Enhance the Stiffness of Self-Assembled Peptide Gels
  2. Sarkar,Srijani; Anderson,Caleb; Schneider,Joel
  3. Angewandte Chemie (International ed. in English). 2023, Dec 06; e202313507.
  1. 3.   Change in Lipofectamine Carrier as a Tool to Fine-Tune Immunostimulation of Nucleic Acid Nanoparticles
  2. Newton,Hannah; Radwan, Yasmine; Xu,Jie; Clogston,Jeffrey; Dobrovolskaia,Marina; Afonin, Kirill A
  3. Molecules (Basel, Switzerland). 2023, Jun 01; 28(11):
  1. 4.   Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data
  2. Xu, Junlin; Xu, Jielin; Meng, Yajie; Lu, Changcheng; Cai, Lijun; Zeng, Xiangxiang; Nussinov,Ruth; Cheng, Feixiong
  3. Cell Reports Methods. 2023, Jan 23; 3(1): 100382.
  1. 5.   Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
  2. Li, Yize; Lih, Tung-Shing M; Dhanasekaran, Saravana M; Mannan, Rahul; Chen, Lijun; Cieslik, Marcin; Wu, Yige; Lu, Rita Jiu-Hsien; Clark, David J; Kolodziejczak, Iga; Hong, Runyu; Chen, Siqi; Zhao, Yanyan; Chugh, Seema; Caravan, Wagma; Naser Al Deen, Nataly; Hosseini, Noshad; Newton, Chelsea J; Krug, Karsten; Xu, Yuanwei; Cho, Kyung-Cho; Hu, Yingwei; Zhang, Yuping; Kumar-Sinha, Chandan; Ma, Weiping; Calinawan, Anna; Wyczalkowski, Matthew A; Wendl, Michael C; Wang, Yuefan; Guo, Shenghao; Zhang, Cissy; Le, Anne; Dagar, Aniket; Hopkins, Alex; Cho, Hanbyul; Leprevost, Felipe da Veiga; Jing, Xiaojun; Teo, Guo Ci; Liu, Wenke; Reimers, Melissa A; Pachynski, Russell; Lazar, Alexander J; Chinnaiyan, Arul M; Van Tine, Brian A; Zhang, Bing; Rodland, Karin D; Getz, Gad; Mani, D R; Wang, Pei; Chen, Feng; Hostetter, Galen; Thiagarajan,Mathangi; Linehan, W Marston; Fenyö, David; Jewell, Scott D; Omenn, Gilbert S; Mehra, Rohit; Wiznerowicz, Maciej; Robles, Ana I; Mesri, Mehdi; Hiltke, Tara; An, Eunkyung; Rodriguez, Henry; Chan, Daniel W; Ricketts, Christopher J; Nesvizhskii, Alexey I; Zhang, Hui; Ding, Li
  3. Cancer Cell. 2023, Jan 9; 41(1): 139-163.
  1. 6.   Machine Learning Informs RNA-Binding Chemical Space
  2. Yazdani, Kamyar; Jordan, Deondre; Yang,Mo; Fullenkamp,Chris; Schneekloth,Jay; Calabrese,Dave; Boer, Robert E; Hilimire, Thomas A; Allen, Timothy E H; Khan, Rabia T
  3. Angewandte Chemie (International ed. in English). 2022, Dec 30;
  1. 7.   Artificial Immune Cell, AI-cell, a New Tool to Predict Interferon Production by Peripheral Blood Monocytes in Response to Nucleic Acid Nanoparticles
  2. Chandler, Morgan; Jain, Sankalp; Halman, Justin; Hong, Enping; Dobrovolskaia,Marina; Zakharov, Alexey V; Afonin, Kirill A
  3. Small (Weinheim an der Bergstrasse, Germany). 2022, Oct 10; e2204941.
  1. 8.   Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures
  2. Tran, Allison N; Chandler, Morgan; Halman, Justin; Beasock, Damian; Fessler, Adam; McKeough, Riley Q; Lam, Phuong Anh; Furr, Daniel P; Wang, Jian; Cedrone,Edward; Dobrovolskaia,Marina; Dokholyan, Nikolay V; Trammell, Susan R; Afonin, Kirill A
  3. Small (Weinheim an der Bergstrasse, Germany). 2022, Feb 06; e2104814.
  1. 9.   Alpha synuclein, the culprit in Parkinson disease, is required for normal immune function
  2. Alam,Md Masud; Yang,De; Li, Xiao-Qing; Liu, Jia; Back, Timothy Carrel; Trivett, Anna; Karim, Baktiar; Barbut, Denise; Zasloff, Michael; Oppenheim, Joost J
  3. Cell Reports. 2022, Jan 11; 38(2):
  1. 10.   Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities
  2. Chandler, Morgan; Minevich, Brian; Roark, Brandon; Viard,Mathias; Johnson, M Brittany; Rizvi, Mehedi H; Deaton, Thomas A; Kozlov, Seraphim; Panigaj, Martin; Tracy, Joseph B; Yingling, Yaroslava G; Gang, Oleg; Afonin, Kirill A
  3. ACS applied materials & interfaces. 2021, Aug 25; 13(33): 39030-39041.
  1. 11.   PARIS farnesylation prevents neurodegeneration in models of Parkinson's disease
  2. Jo, Areum; Lee, Yunjong; Kam, Tae-In; Kang, Sung-Ung; Neifert, Stewart; Karuppagounder, Senthilkumar S.; Khang, Rin; Kang, Hojin; Park, Hyejin; Chou, Shih-Ching; Oh, Sungtaek; Jiang, Haisong; Swing, Deborah A.; Ham, Sangwoo; Pirooznia, Sheila; Umanah, George K. E.; Mao, Xiaobo; Kumar, Manoj; Ko, Han Seok; Kang, Ho Chul; Lee, Byoung Dae; Lee, Yun-Il; Andrabi, Shaida A.; Park, Chi-Hu; Lee, Ji-Yeong; Kim, Hanna; Kim, Hyein; Kim, Hyojung; Cho, Jin Whan; Paek, Sun Ha; Na, Chan Hyun; Tessarollo,Lino; Dawson, Valina L.; Dawson, Ted M.; Shin, Joo-Ho
  3. Science translational medicine. 2021, Jul 28; 13(604):
  1. 12.   2021: an immunotherapy odyssey and the rise of nucleic acid nanotechnology
  2. Panigaj, Martin; Dobrovolskaia,Marina; Afonin, Kirill A.
  3. NANOMEDICINE. 2021, Jun 24;
  1. 13.   Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
  2. Nguyen, Phuong H.; Ramamoorthy, Ayyalusamy; Sahoo, Bikash R.; Zheng, Jie; Faller, Peter; Straub, John E.; Dominguez, Laura; Shea, Joan-Emma; Dokholyan, Nikolay; De Simone, Alfonso; Ma, Buyong; Nussinov,Ruth; Najafi, Saeed; Ngo, Son Tung; Loquet, Antoine; Chiricotto, Mara; Ganguly, Pritam; McCarty, James; Li, Mai Suan; Hall, Carol; Wang, Yiming; Miller, Yifat; Melchionna, Simone; Habenstein, Birgit; Timr, Stepan; Chen, Jiaxing; Hnath, Brianna; Strodel, Birgit; Kayed, Rakez; Lesne, Sylvain; Wei, Guanghong; Sterpone, Fabio; Doig, Andrew J.; Derreumaux, Philippe
  3. Chemical Reviews. 2021, Feb 24; 121(4): 2545-2647.
  1. 14.   Induction of Cytokines by Nucleic Acid Nanoparticles (NANPs) Depends on the Type of Delivery Carrier
  2. Avila, Yelixza I.; Chandler, Morgan; Cedrone,Edward; Newton,Hannah; Richardson, Melina; Xu,Jie; Clogston,Jeffrey; Liptrott, Neill J.; Afonin, Kirill A.; Dobrovolskaia,Marina
  3. Molecules. 2021, Feb; 26(3):
  1. 15.   The Brighton Collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines
  2. Kim, Denny; Robertson, James S.; Excler, Jean-Louis; Condit, Richard C.; Fast, Patricia E.; Gurwith, Marc; Pavlakis,George; Monath, Thomas P.; Smith, Jonathan; Wood, David; Smith, Emily R.; Chen, Robert T.; Kochhar, Sonali
  3. Vaccine. 2020, JUL 22; 38(34): 5556-5561.
  1. 16.   Modeling ligand docking to RNA in the design of RNA-based nanostructures
  2. Kasprzak,Wojciech; Ahmed, Nour Ali; Shapiro,Bruce
  3. Current opinion in biotechnology. 2020, JUN; 63: 16-25.
  1. 17.   Structural Insights into APOBEC3-Mediated Lentiviral Restriction
  2. Delviks-Frankenberry, Krista A.; Desimmie, Belete A.; Pathak,Vinay
  3. Viruses. 2020, JUN; 12(6):
  1. 18.   A cationic amphiphilic co-polymer as a carrier of nucleic acid nanoparticles (Nanps) for controlled gene silencing, immunostimulation, and biodistribution
  2. Halman, Justin R; Kim, Ki-Taek; Gwak, So-Jung; Pace, Richard; Johnson, Morgan Brittany; Chandler, Morgan R; Rackley, Lauren; Viard,Mathias; Marriott, Ian; Lee, Jeoung Soo; Afonin, Kirill A
  3. Nanomedicine : nanotechnology, biology, and medicine. 2020, Jan; 23: 102094.
  1. 19.   Nucleic acid-induced dimerization of HIV-1 Gag protein
  2. Zhao, Huaying; Datta,Siddhartha; Kim, Sung H.; To, Samuel C.; Chaturvedi, Sumit K.; Rein,Alan; Schuck, Peter
  3. JOURNAL OF BIOLOGICAL CHEMISTRY. 2019, Nov 8; 294(45): 16480-16493.
  1. 20.   RNA2Drawer: Geometrically Strict Drawing of Nucleic Acid Structures with Graphical Structure Editing and Highlighting of Complementary Subsequences
  2. Johnson, Philip Z; Kasprzak,Wojciech; Shapiro,Bruce; Simon, Anne E
  3. RNA biology. 2019, Aug 26; 1-5.
  1. 21.   Parkin interacting substrate zinc finger protein 746 is a pathological mediator in Parkinson's disease
  2. Brahmachari, Saurav; Lee, Saebom; Kim, Sangjune; Yuan, Changqing; Karuppagounder, Senthilkumar S; Ge, Preston; Shi, Rosa; Kim, Esther J; Liu, Alex; Kim, Donghoon; Quintin, Stephan; Jiang, Haisong; Kumar, Manoj; Yun, Seung Pil; Kam, Tae-In; Mao, Xiaobo; Lee, Yunjong; Swing,Debbie; Tessarollo,Lino; Ko, Han Seok; Dawson, Valina L; Dawson, Ted M
  3. Brain : a journal of neurology. 2019, AUG; 142(8): 2380-2401.
  1. 22.   Evidence for ligandable sites in structured RNA throughout the Protein Data Bank
  2. Hewitt, William M.; Calabrese,Dave; Schneekloth,Jay
  3. BIOORGANIC & MEDICINAL CHEMISTRY. 2019, Jun 1; 27(11): 2253-2260.
  1. 23.   A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides
  2. Zakrevsky,Paul; Bindewald,Eckart; Humbertson,Hadley; Viard,Mathias; Dorjsuren, Nomongo; Shapiro,Bruce
  3. Nanomaterials (Basel, Switzerland). 2019, Apr 15; 9(4): pii: E615.
  1. 24.   Toll-Like Receptor-Mediated Recognition of Nucleic Acid Nanoparticles (NANPs) in Human Primary Blood Cells
  2. Hong, Enping; Halman, Justin R; Shah, Ankit; Cedrone,Edward; Truong, Nguyen; Afonin, Kirill A; Dobrovolskaia,Marina
  3. Molecules (Basel, Switzerland). 2019, Mar 2; 24(6): pii: E1094.
  1. 25.   Alpha-synuclein fibrils recruit TBK1 and OPTN to lysosomal damage sites and induce autophagy in microglial cells
  2. Bussi, Claudio; Peralta Ramos, Javier M; Arroyo, Daniela S; Gallea, Jose I; Ronchi, Paolo; Kolovou, Androniki; Wang, Jiming; Florey, Oliver; Celej, Maria S; Schwab, Yannick; Ktistakis, Nicholas T; Iribarren, Pablo
  3. Journal of cell science. 2018, Nov 30; 131(23): pii: jcs.226241.
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