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A.R. Ferré-D′Amaré

National Institutes of Health

65H-index
239Paper Count
1.4WCitation Count
Published Papers 88
Publication Date
The RNA thermometer motif ROSE-G regulates ABC transporter gene expression in bacteria
err2025-12-30
err0
errOAAI
errMadelyn N. Mills; Gabriel Pacheo; Alina Y. Tong; Elisha L. Tong; Michael A. Hannani; Lana Heganovic; Kiana Fleary; Samantha N. Shaffer; Mallika S. Vairavan; Adrian R. Ferré-D’Amaré; Luiz F.M. Passalacqua; Michael M. Abdelsayed
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Structural basis for dual DNA and RNA specificity of the G-quadruplex-resolving DEAH-box helicase DHX36
err2025-08-19
err0
PREAI
errMichael T. Banco; Tapas Paul; Jiansen Jiang; Sua Myong; Adrian R. Ferré-D’Amaré
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Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands
err2025-06-22
err0
errOAAI
errChristopher R. Fullenkamp; Shams Mehdi; Christopher P. Jones; Logan Tenney; Patricio Pichling; Peri R. Prestwood; Adrian R. Ferré-D'Amaré; Pratyush Tiwary; John S. Schneekloth
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Structure-informed design of an ultrabright RNA-activated fluorophore
err2025-05-28
err0
PREAI
errYang, Mo; Prestwood, Peri R.; Passalacqua, Luiz F. M.; Balaratnam, Sumirtha; Fullenkamp, Christopher R.; Arney, J. Winston; Weeks, Kevin M.; Ferre-D'Amare, Adrian
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RNA-Puzzles Round V: blind predictions of 23 RNA structures
err2024-12-02
err0
errOAAI
errBu, Fan; Adam, Yagoub; Adamiak, Ryszard W.; Antczak, Maciej; de Aquino, Belisa Rebeca H.; Badepally, Nagendar Goud; Batey, Robert T.; Baulin, Eugene F.; Boinski, Pawel; Boniecki, Michal J.; Bujnicki, Janusz M.; Carpenter, Kristy A.; Chacon, Jose; Chen, Shi-Jie; Chiu, Wah; Cordero, Pablo; Das, Naba Krishna; Das, Rhiju; Dawson, Wayne K.; Dimaio, Frank; Ding, Feng; Dock-Bregeon, Anne-Catherine; Dokholyan, Nikolay V.; Dror, Ron O.; Dunin-Horkawicz, Stanislaw; Eismann, Stephan; Ennifar, Eric; Esmaeeli, Reza; Farsani, Masoud Amiri; Ferre-D'Amare, Adrian R.; Geniesse, Caleb; Ghanim, George E.; Guzman, Horacio V.; Hood, Iris V.; Huang, Lin; Jain, Dharm Skandh; Jaryani, Farhang; Jin, Lei; Joshi, Astha; Karelina, Masha; Kieft, Jeffrey S.; Kladwang, Wipapat; Kmiecik, Sebastian; Koirala, Deepak; Kollmann, Markus; Kretsch, Rachael C.; Kurcinski, Mateusz; Li, Jun; Li, Shuang; Magnus, Marcin; Masquida, Benoit; Moafinejad, S. Naeim; Mondal, Arup; Mukherjee, Sunandan; Nguyen, Thi Hoang Duong; Nikolaev, Grigory; Nithin, Chandran; Nye, Grace; Pandaranadar Jeyeram, Iswarya P. N.; Perez, Alberto; Pham, Phillip; Piccirilli, Joseph A.; Pilla, Smita Priyadarshini; Pluta, Radoslaw; Poblete, Simon; Ponce-Salvatierra, Almudena; Popenda, Mariusz; Popenda, Lukasz; Pucci, Fabrizio; Rangan, Ramya; Ray, Angana; Ren, Aiming; Sarzynska, Joanna; Sha, Congzhou Mike; Stefaniak, Filip; Su, Zhaoming; Suddala, Krishna C.; Szachniuk, Marta; Townshend, Raphael; Trachman III, Robert J.; Wang, Jian; Wang, Wenkai; Watkins, Andrew; Wirecki, Tomasz K.; Xiao, Yi; Xiong, Peng; Xiong, Yiduo; Yang, Jianyi; Yesselman, Joseph David; Zhang, Jinwei; Zhang, Yi; Zhang, Zhenzhen; Zhou, Yuanzhe; Zok, Tomasz; Zhang, Dong; Zhang, Sicheng; Zyla, Adriana; Westhof, Eric; Miao, Zhichao
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RNA thermometers are widespread upstream of ABC transporter genes in bacteria
err2024-08-01
err1
errOAAI
errTong, Alina Y.; Tong, Elisha L.; Hannani, Michael A.; Shaffer, Samantha N.; Santiago, Danna; Ferre-D Amare, Adrian R.; Passalacqua, Luiz F. M.; Abdelsayed, Michael M.
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Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD
err2024-07-01
err0
errOAAI
errLu, Xiaocen; Passalacqua, Luiz F. M.; Nodwell, Matthew; Kong, Kristen Y. S.; Caballero-Garcia, Guillermo; Dolgosheina, Elena, V; Ferre-D'Amare, Adrian R.; Britton, Robert; Unrau, Peter J.
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Investigating the NRAS 5′ UTR as a target for small molecules
err2023-06-01
err11
errOAAI
errBalaratnam, Sumirtha; Torrey, Zachary R.; Calabrese, David R.; Banco, Michael T.; Yazdani, Kamyar; Liang, Xiao; Fullenkamp, Christopher R.; Seshadri, Srinath; Holewinski, Ronald J.; Andresson, Thorkell; Ferre-D'Amare, Adrian R.; Incarnato, Danny; Schneekloth, John S., Jr.
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Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture
err2023-05-23
err9
errOAAI
errPassalacqua, Luiz F. M.; Starich, Mary R.; Link, Katie A.; Wu, Jiahui; Knutson, Jay R.; Tjandra, Nico; Jaffrey, Samie R.; Ferre-D'Amare, Adrian R.
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Discovery of Small Molecules Targeting the Frameshifting Element RNA in SARS-CoV-2 Viral Genome
err2023-05-11
err12
PREAI
errYang, Mo; Olatunji, Feyisola P.; Rhodes, Curran; Balaratnam, Sumirtha; Dunne-Dombrink, Kara; Seshadri, Srinath; Liang, Xiao; Jones, Christopher P.; Le Grice, Stuart F. J.; Ferre-D'Amare, Adrian R.; Schneekloth, Jr John S.
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The bacterial yjdF riboswitch regulates translation through its tRNA-like fold
err2022-06-01
err4
errOAAI
errTrachman, Robert J., III; Passalacqua, Luiz F. M.; Ferre-D'Amare, Adrian R.
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The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold
err2021-12-22
err19
errOAAI
errTruong, Lynda; Kooshapur, Hamed; Dey, Sourav Kumar; Li, Xing; Tjandra, Nico; Jaffrey, Samie R.; Ferre-D'Amare, Adrian R.
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A Helicase Unwinds Hexanucleotide Repeat RNA G-Quadruplexes and Facilitates Repeat-Associated Non-AUG Translation
err2021-04-15
err42
errOAAI
errLiu, Honghe; Lu, Yu-Ning; Paul, Tapas; Periz, Goran; Banco, Michael T.; Ferre-D'Amare, Adrian R.; Rothstein, Jeffrey D.; Hayes, Lindsey R.; Myong, Sua; Wang, Jiou
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The emerging structural complexity of G-quadruplex RNAs
errRNA
IF5
err2021-01-22
err60
errOAAI
errBanco, Michael T.; Ferre-D'Amare, Adrian R.
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Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET
errRNA
IF5
err2020-12-29
err25
errOAAI
errJeng, Sunny C. Y.; Trachman, Robert J., III; Weissenboeck, Florian; Truong, Lynda; Link, Katie A.; Jepsen, Mette D. E.; Knutson, Jay R.; Andersen, Ebbe S.; Ferre-D'Amare, Adrian R.; Unrau, Peter J.
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Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design
err2020-10-01
err18
errOAAI
errTran, Brandon; Pichling, Patricio; Tenney, Logan; Connelly, Colleen M.; Moon, Michelle H.; Ferre-D'Amare, Adrian R.; Schneekloth, John S., Jr.; Jones, Christopher P.
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Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape
err2020-09-10
err29
errOAAI
errHua, Boyang; Jones, Christopher P.; Mitra, Jaba; Murray, Peter J.; Rosenthal, Rebecca; Ferre-D'Amare, Adrian R.; Ha, Taekjip
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