Rachel J Hagey (Rhiju Das)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 69

Top Venues

bioRxiv : the preprint server for biology

Proceedings of the National Academy of Sciences of the United States of America

Nature communications

Nature machine intelligence

Stanford University School of Medicine

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Stanford University School of Medicine Jun 01 2009

United States

Associate Professor :: Biochemistry

Publications

Rachael C Kretsch, Lily Xu, Ivan N Zheludev, Xueting Zhou, Rui Huang, Grace Nye, Shanshan Li, Kaiming Zhang, Wah Chiu, Rachel J Hagey
Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Christian A Choe, Johan O L Andreasson, Feriel Melaine, Wipapat Kladwang, Michelle J Wu, Fernando Portela, Roger Wellington-Oguri, John J Nicol, Hannah K Wayment-Steele, Michael Gotrik, Eterna Participants, Purvesh Khatri, William J Greenleaf, Rachel J Hagey
Compact RNA sensors for increasingly complex functions of multiple inputs. bioRxiv : the preprint server for biology (2024)
Rachael C Kretsch, Lily Xu, Ivan N Zheludev, Xueting Zhou, Rui Huang, Grace Nye, Shanshan Li, Kaiming Zhang, Wah Chiu, Rachel J Hagey
Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Rachael C Kretsch, Lily Xu, Ivan N Zheludev, Xueting Zhou, Rui Huang, Grace Nye, Shanshan Li, Kaiming Zhang, Wah Chiu, Rachel J Hagey
Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Shujun He, Rui Huang, Jill Townley, Rachael C Kretsch, Thomas G Karagianes, David B T Cox, Hamish Blair, Dmitry Penzar, Valeriy Vyaltsev, Elizaveta Aristova, Arsenii Zinkevich, Artemy Bakulin, Hoyeol Sohn, Daniel Krstevski, Takaaki Fukui, Fumiya Tatematsu, Yusuke Uchida, Donghoon Jang, Jun Seong Lee, Roger Shieh, Tom Ma, Eduard Martynov, Maxim V Shugaev, Habib S T Bukhari, Kazuki Fujikawa, Kazuki Onodera, Christof Henkel, Shlomo Ron, Jonathan Romano, John J Nicol, Grace P Nye, Yuan Wu, Christian A Choe, Walter Reade, null null, Rachel J Hagey
Ribonanza: deep learning of RNA structure through dual crowdsourcing. bioRxiv : the preprint server for biology (2024)
Tiyaporn Tangpradabkul, Michael Z Palo, Jill Townley, Kenneth B Hsu, Eterna Participants, Sarah Smaga, Rachel J Hagey, Alanna Schepartz
Minimization of the E. coli ribosome, aided and optimized by community science. Nucleic acids research (2024)
Shujun He, Rui Huang, Jill Townley, Rachael C Kretsch, Thomas G Karagianes, David B T Cox, Hamish Blair, Dmitry Penzar, Valeriy Vyaltsev, Elizaveta Aristova, Arsenii Zinkevich, Artemy Bakulin, Hoyeol Sohn, Daniel Krstevski, Takaaki Fukui, Fumiya Tatematsu, Yusuke Uchida, Donghoon Jang, Jun Seong Lee, Roger Shieh, Tom Ma, Eduard Martynov, Maxim V Shugaev, Habib S T Bukhari, Kazuki Fujikawa, Kazuki Onodera, Christof Henkel, Shlomo Ron, Jonathan Romano, John J Nicol, Grace P Nye, Yuan Wu, Christian A Choe, Walter Reade, null null, Rachel J Hagey
Ribonanza: deep learning of RNA structure through dual crowdsourcing. bioRxiv : the preprint server for biology (2024)
Shujun He, Rui Huang, Jill Townley, Rachael C Kretsch, Thomas G Karagianes, David B T Cox, Hamish Blair, Dmitry Penzar, Valeriy Vyaltsev, Elizaveta Aristova, Arsenii Zinkevich, Artemy Bakulin, Hoyeol Sohn, Daniel Krstevski, Takaaki Fukui, Fumiya Tatematsu, Yusuke Uchida, Donghoon Jang, Jun Seong Lee, Roger Shieh, Tom Ma, Eduard Martynov, Maxim V Shugaev, Habib S T Bukhari, Kazuki Fujikawa, Kazuki Onodera, Christof Henkel, Shlomo Ron, Jonathan Romano, John J Nicol, Grace P Nye, Yuan Wu, Christian A Choe, Walter Reade, null null, Rachel J Hagey
Ribonanza: deep learning of RNA structure through dual crowdsourcing. bioRxiv : the preprint server for biology (2024)
Christian A Choe, Johan O L Andreasson, Feriel Melaine, Wipapat Kladwang, Michelle J Wu, Fernando Portela, Roger Wellington-Oguri, John J Nicol, Hannah K Wayment-Steele, Michael Gotrik, Eterna Participants, Purvesh Khatri, William J Greenleaf, Rachel J Hagey
Compact RNA sensors for increasingly complex functions of multiple inputs. bioRxiv : the preprint server for biology (2024)
Rachael C Kretsch, Lily Xu, Ivan N Zheludev, Xueting Zhou, Rui Huang, Grace Nye, Shanshan Li, Kaiming Zhang, Wah Chiu, Rachel J Hagey
Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Tiyaporn Tangpradabkul, Michael Z Palo, Jill Townley, Kenneth B Hsu, Eterna Participants, Sarah Smaga, Rachel J Hagey, Alanna Schepartz
Minimization of the E. coli ribosome, aided and optimized by community science. Nucleic acids research 52 (3) (2024)
Shujun He, Rui Huang, Jill Townley, Rachael C Kretsch, Thomas G Karagianes, David B T Cox, Hamish Blair, Dmitry Penzar, Valeriy Vyaltsev, Elizaveta Aristova, Arsenii Zinkevich, Artemy Bakulin, Hoyeol Sohn, Daniel Krstevski, Takaaki Fukui, Fumiya Tatematsu, Yusuke Uchida, Donghoon Jang, Jun Seong Lee, Roger Shieh, Tom Ma, Eduard Martynov, Maxim V Shugaev, Habib S T Bukhari, Kazuki Fujikawa, Kazuki Onodera, Christof Henkel, Shlomo Ron, Jonathan Romano, John J Nicol, Grace P Nye, Yuan Wu, Christian A Choe, Walter Reade, Eterna Participants, Rachel J Hagey
Ribonanza: deep learning of RNA structure through dual crowdsourcing. bioRxiv : the preprint server for biology (2024)
Christian A Choe, Johan O L Andreasson, Feriel Melaine, Wipapat Kladwang, Michelle J Wu, Fernando Portela, Roger Wellington-Oguri, John J Nicol, Hannah K Wayment-Steele, Michael Gotrik, Eterna Participants, Purvesh Khatri, William J Greenleaf, Rachel J Hagey
Compact RNA sensors for increasingly complex functions of multiple inputs. bioRxiv : the preprint server for biology (2024)
Rachael C Kretsch, Lily Xu, Ivan N Zheludev, Xueting Zhou, Rui Huang, Grace Nye, Shanshan Li, Kaiming Zhang, Wah Chiu, Rachel J Hagey
Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Tiyaporn Tangpradabkul, Michael Z Palo, Jill Townley, Kenneth B Hsu, Eterna Participants, Sarah Smaga, Rachel J Hagey, Alanna Schepartz
Minimization of the E. coli ribosome, aided and optimized by community science. Nucleic acids research 52 (3) (2024)
Shujun He, Rui Huang, Jill Townley, Rachael C Kretsch, Thomas G Karagianes, David B T Cox, Hamish Blair, Dmitry Penzar, Valeriy Vyaltsev, Elizaveta Aristova, Arsenii Zinkevich, Artemy Bakulin, Hoyeol Sohn, Daniel Krstevski, Takaaki Fukui, Fumiya Tatematsu, Yusuke Uchida, Donghoon Jang, Jun Seong Lee, Roger Shieh, Tom Ma, Eduard Martynov, Maxim V Shugaev, Habib S T Bukhari, Kazuki Fujikawa, Kazuki Onodera, Christof Henkel, Shlomo Ron, Jonathan Romano, John J Nicol, Grace P Nye, Yuan Wu, Christian A Choe, Walter Reade, null null, Rachel J Hagey
Ribonanza: deep learning of RNA structure through dual crowdsourcing. bioRxiv : the preprint server for biology (2024)
Tiyaporn Tangpradabkul, Michael Z Palo, Jill Townley, Kenneth B Hsu, Eterna Participants, Sarah Smaga, Rachel J Hagey, Alanna Schepartz
Minimization of the E. coli ribosome, aided and optimized by community science. Nucleic acids research 52 (3) (2024)
Rachel J Hagey, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M Keegan, Andriy Kryshtafovych, Daniel J Rigden, Zhichiao Miao, Eric Westhof
Assessment of three-dimensional RNA structure prediction in CASP15. bioRxiv : the preprint server for biology (2023)
Rachel J Hagey, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M Keegan, Andriy Kryshtafovych, Daniel J Rigden, Zhichiao Miao, Eric Westhof
Assessment of three-dimensional RNA structure prediction in CASP15. Proteins (2023)
Rachel J Hagey, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M Keegan, Andriy Kryshtafovych, Daniel J Rigden, Zhichiao Miao, Eric Westhof
Assessment of three-dimensional RNA structure prediction in CASP15. bioRxiv : the preprint server for biology (2023)
Thomas Mulvaney, Rachael C Kretsch, Luc Elliott, Joseph George Beton, Andriy Kryshtafovych, Daniel J Rigden, Rachel J Hagey, Andriy Kryshtafovych
CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps. bioRxiv : the preprint server for biology (2023)
Rachael C Kretsch, Ebbe Sloth Andersen, Janusz M Bujnicki, Wah Chiu, Rachel J Hagey, Bingnan Luo, Benoît Masquida, Ewan K S McRae, Griffin M Schroeder, Zhaoming Su, Joseph E Wedekind, Lily Xu, Kaiming Zhang, Ivan N Zheludev, John Moult, Andriy Kryshtafovych
RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Proteins (2023)
Antje Krüger, Andrew M Watkins, Roger Wellington-Oguri, Jonathan Romano, Camila Kofman, Alysse DeFoe, Yejun Kim, Jeff Anderson-Lee, Eli Fisker, Jill Townley, null null, Anne E d'Aquino, Rachel J Hagey, Michael C Jewett
Community science designed ribosomes with beneficial phenotypes. Nature communications 14 (1) (2023)
Antje Krüger, Andrew M Watkins, Roger Wellington-Oguri, Jonathan Romano, Camila Kofman, Alysse DeFoe, Yejun Kim, Jeff Anderson-Lee, Eli Fisker, Jill Townley, null null, Anne E d'Aquino, Rachel J Hagey, Michael C Jewett
Community science designed ribosomes with beneficial phenotypes. Nature communications 14 (1) (2023)
Antje Krüger, Andrew M Watkins, Roger Wellington-Oguri, Jonathan Romano, Camila Kofman, Alysse DeFoe, Yejun Kim, Jeff Anderson-Lee, Eli Fisker, Jill Townley, null null, Anne E d'Aquino, Rachel J Hagey, Michael C Jewett
Community science designed ribosomes with beneficial phenotypes. Nature communications 14 (1) (2023)
Rachel J Hagey, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M Keegan, Andriy Kryshtafovych, Daniel J Rigden, Zhichiao Miao, Eric Westhof
Assessment of three-dimensional RNA structure prediction in CASP15. bioRxiv : the preprint server for biology (2023)
Rachael C Kretsch, Lily Xu, Ivan N Zheludev, Xueting Zhou, Rui Huang, Grace P Nye, Shanshan Li, Kaiming Zhang, Wah Chiu, Rachel J Hagey
Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. bioRxiv : the preprint server for biology (2023)
Thomas Mulvaney, Rachael C Kretsch, Luc Elliott, Joseph George Beton, Andriy Kryshtafovych, Daniel J Rigden, Rachel J Hagey, Andriy Kryshtafovych
CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps. Proteins 91 (12) (2023)
Andriy Kryshtafovych, Maciej Antczak, Marta Szachniuk, Tomasz Zok, Rachael C Kretsch, Ramya Rangan, Phillip Pham, Rachel J Hagey, Xavier Robin, Gabriel Studer, Janani Durairaj, Jerome Eberhardt, Aaron Sweeney, Maya Topf, Torsten Schwede, Krzysztof Fidelis, John Moult
New prediction categories in CASP15. Proteins (2023)
Hannah K Wayment-Steele, Wipapat Kladwang, Andrew M Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, King Yuen Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, null null, Rachel J Hagey
Deep learning models for predicting RNA degradation via dual crowdsourcing. Nature machine intelligence 4 (12) (2022)
Hannah K Wayment-Steele, Wipapat Kladwang, Andrew M Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, King Yuen Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, null null, Rachel J Hagey
Deep learning models for predicting RNA degradation via dual crowdsourcing. Nature machine intelligence 4 (12) (2022)
Shanshan Li, Michael Z Palo, Grigore Pintilie, Xiaojing Zhang, Zhaoming Su, Kalli Kappel, Wah Chiu, Kaiming Zhang, Rachel J Hagey
Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM. Proceedings of the National Academy of Sciences of the United States of America 119 (37) (2022)
Rachel J Hagey, Menashe Elazar, Edward A Pham, Siqi Tian, Lily Ben-Avi, Claire Bernardin-Souibgui, Matthew F Yee, Fernando R Moreira, Meirav Vilan Rabinovitch, Rita M Meganck, Benjamin Fram, Aimee Beck, Scott A Gibson, Grace Lam, Josephine Devera, Wipapat Kladwang, Khanh Nguyen, Anming Xiong, Steven Schaffert, Talia Avisar, Ping Liu, Arjun Rustagi, Carl J Fichtenbaum, Phillip S Pang, Purvesh Khatri, Chien-Te Kent Tseng, Jeffery K Taubenberger, Catherine A Blish, Brett L Hurst, Timothy P Sheahan, Rachel J Hagey, Jeffrey S Glenn
Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2. Nature medicine 28 (9) (2022)
Do Soon Kim, Andrew Watkins, Erik J Bidstrup, Joongoo Lee, Ved Topkar, Camila Kofman, Kevin J Schwarz, Yan Liu, Grigore Pintilie, Emily Roney, Rachel J Hagey, Michael C Jewett
Three-dimensional structure-guided evolution of a ribosome with tethered subunits. Nature chemical biology 18 (9) (2022)
Hannah K Wayment-Steele, Wipapat Kladwang, Andrew M Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, King Yuen Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, null null, Rachel J Hagey
Deep learning models for predicting RNA degradation via dual crowdsourcing. Nature machine intelligence 4 (12) (2022)
Hannah K Wayment-Steele, Wipapat Kladwang, Alexandra I Strom, Jeehyung Lee, Adrien Treuille, Alexander J Becka, null null, Rachel J Hagey
RNA secondary structure packages evaluated and improved by high-throughput experiments. Nature methods 19 (10) (2022)
Hannah K Wayment-Steele, Wipapat Kladwang, Andrew M Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, King Yuen Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, null null, Rachel J Hagey
Deep learning models for predicting RNA degradation via dual crowdsourcing. Nature machine intelligence 4 (12) (2022)
Kathrin Leppek, Gun Woo Byeon, Wipapat Kladwang, Hannah K Wayment-Steele, Craig H Kerr, Adele Francis Xu, Do Soon Kim, Ved V Topkar, Christian A Choe, Daphna Rothschild, Gerald C Tiu, Roger Wellington-Oguri, Kotaro Fujii, Eesha Sharma, Andrew M Watkins, John J Nicol, Jonathan Romano, Bojan Tunguz, Fernando Diaz, Hui Cai, Pengbo Guo, Jiewei Wu, Fanyu Meng, Shuai Shi, Eterna Participants, Philip R Dormitzer, Alicia Solórzano, Maria Barna, Rachel J Hagey
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. Nature communications 13 (1) (2022)
Johan O L Andreasson, Michael R Gotrik, Michelle J Wu, Hannah K Wayment-Steele, Wipapat Kladwang, Fernando Portela, Roger Wellington-Oguri, null null, Rachel J Hagey, William J Greenleaf
Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. Proceedings of the National Academy of Sciences of the United States of America 119 (18) (2022)
Hannah K Wayment-Steele, Wipapat Kladwang, Andrew M Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, King Yuen Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, null null, Rachel J Hagey
Deep learning models for predicting RNA degradation via dual crowdsourcing. Nature machine intelligence 4 (12) (2022)
George E Ghanim, Adam J Fountain, Anne-Marie M van Roon, Ramya Rangan, Rachel J Hagey, Kathleen Collins, Thi Hoang Duong Nguyen
Structure of human telomerase holoenzyme with bound telomeric DNA. Nature 593 (7859) (2021)
Rachel J Hagey
RNA structure: a renaissance begins? Nature methods 18 (5) (2021)
Rachel J Hagey, Andrew M Watkins
RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams. NAR genomics and bioinformatics 3 (4) (2021)
Rachel J Hagey, Rick Russell
How to Kinetically Dissect an RNA Machine. Biochemistry 60 (46) (2021)
Kaiming Zhang, Ivan N Zheludev, Rachel J Hagey, Raphael Haslecker, Yixuan J Hou, Rachael Kretsch, Grigore D Pintilie, Ramya Rangan, Wipapat Kladwang, Shanshan Li, Marie Teng-Pei Wu, Edward A Pham, Claire Bernardin-Souibgui, Ralph S Baric, Timothy P Sheahan, Victoria D'Souza, Jeffrey S Glenn, Wah Chiu, Rachel J Hagey
Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome. Nature structural & molecular biology 28 (9) (2021)
Julia Koehler Leman, Sergey Lyskov, Steven M Lewis, Jared Adolf-Bryfogle, Rebecca F Alford, Kyle A Barlow, Ziv Ben-Aharon, Daniel P Farrell, Jason S Fell, William A Hansen, Ameya Harmalkar, Jeliazko R Jeliazkov, Georg Kuenze, Justyna Dorota Kryś, Ajasja Ljubetič, Amanda L Loshbaugh, Jack Maguire, Rocco Moretti, Vikram Khipple Mulligan, Morgan L Nance, Phuong T Nguyen, Shane Ó Conchúir, Shourya S Roy Burman, Rituparna Samanta, Shannon T Smith, Frank Teets, Johanna K S Tiemann, Andrew Watkins, Hope Woods, Brahm J Yachnin, Christopher D Bahl, Chris Bailey-Kellogg, Julien S Baker, Rachel J Hagey, Frank DiMaio, Sagar D Khare, Tanja Kortemme, Jason W Labonte, Kresten Lindorff-Larsen, Jens Meiler, William R Schief, Ora Schueler-Furman, Justin B Siegel, Amelie Stein, Vladimir Yarov-Yarovoy, Brian Kuhlman, Andrew Leaver-Fay, Dominik Gront, Jeffrey J Gray, Richard A Bonneau
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature communications 12 (1) (2021)
Raphael J L Townshend, Stephan Eismann, Andrew M Watkins, Ramya Rangan, Masha Karelina, Rachel J Hagey, Ron O Dror
Geometric deep learning of RNA structure. Science (New York, N.Y.) 373 (6558) (2021)
Kathrin Leppek, Gun Woo Byeon, Wipapat Kladwang, Hannah K Wayment-Steele, Craig H Kerr, Adele Francis Xu, Do Soon Kim, Ved V Topkar, Christian Choe, Daphna Rothschild, Gerald C Tiu, Roger Wellington-Oguri, Kotaro Fujii, Eesha Sharma, Andrew M Watkins, John J Nicol, Jonathan Romano, Bojan Tunguz, Eterna Participants, Maria Barna, Rachel J Hagey
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics. bioRxiv : the preprint server for biology (2021)
Zhaoming Su, Kaiming Zhang, Kalli Kappel, Shanshan Li, Michael Z Palo, Grigore D Pintilie, Ramya Rangan, Bingnan Luo, Yuquan Wei, Rachel J Hagey, Wah Chiu
Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution. Nature 596 (7873) (2021)
Xin Liu, Tao Sun, Anna Shcherbina, Qin Li, Inga Jarmoskaite, Kalli Kappel, Gokul Ramaswami, Rachel J Hagey, Anshul Kundaje, Jin Billy Li
Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis. Nature communications 12 (1) (2021)
Kalli Kappel, Kaiming Zhang, Zhaoming Su, Andrew M Watkins, Wipapat Kladwang, Shanshan Li, Grigore D Pintilie, Ved V Topkar, Ramya Rangan, Ivan N Zheludev, Joseph D Yesselman, Wah Chiu, Rachel J Hagey
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nature methods 17 (7) (2020)
Julia Koehler Leman, Brian D Weitzner, Steven M Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Rebecca F Alford, Melanie Aprahamian, Julien S Baker, Kyle A Barlow, Patrick Barth, Benjamin Basanta, Brian J Bender, Kristin Blacklock, Jaume Bonet, Scott E Boyken, Philip G Bradley, Chris Bystroff, Patrick Conway, Seth Cooper, Bruno E Correia, Brian Coventry, Rachel J Hagey, René M De Jong, Frank DiMaio, Lorna Dsilva, Roland L Dunbrack, Alexander S Ford, Brandon Frenz, Darwin Y Fu, Caleb Geniesse, Lukasz Goldschmidt, Ragul Gowthaman, Jeffrey J Gray, Dominik Gront, Sharon Guffy, Scott Horowitz, Po-Ssu Huang, Thomas Huber, Tim M Jacobs, Jeliazko R Jeliazkov, David K Johnson, Kalli Kappel, John Karanicolas, Hamed Khakzad, Karen R Khar, Sagar D Khare, Firas Khatib, Alisa Khramushin, Indigo C King, Robert Kleffner, Brian Koepnick, Tanja Kortemme, Georg Kuenze, Brian Kuhlman, Daisuke Kuroda, Jason W Labonte, Jason K Lai, Gideon Lapidoth, Andrew Leaver-Fay, Steffen Lindert, Thomas Linsky, Nir London, Joseph H Lubin, Sergey Lyskov, Jack Maguire, Lars Malmström, Enrique Marcos, Orly Marcu, Nicholas A Marze, Jens Meiler, Rocco Moretti, Vikram Khipple Mulligan, Santrupti Nerli, Christoffer Norn, Shane Ó'Conchúir, Noah Ollikainen, Sergey Ovchinnikov, Michael S Pacella, Xingjie Pan, Hahnbeom Park, Ryan E Pavlovicz, Manasi Pethe, Brian G Pierce, Kala Bharath Pilla, Barak Raveh, P Douglas Renfrew, Shourya S Roy Burman, Aliza Rubenstein, Marion F Sauer, Andreas Scheck, William R Schief, Ora Schueler-Furman, Yuval Sedan, Alexander M Sevy, Nikolaos G Sgourakis, Lei Shi, Justin B Siegel, Daniel-Adriano Silva, Shannon Smith, Yifan Song, Amelie Stein, Maria Szegedy, Frank D Teets, Summer B Thyme, Ray Yu-Ruei Wang, Andrew Watkins, Lior Zimmerman, Richard A Bonneau
Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature methods 17 (7) (2020)
Zhichiao Miao, Ryszard W Adamiak, Maciej Antczak, Michał J Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang-Chieh Chou, Rachel J Hagey, Nikolay V Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H Mann, Paweł Piątkowski, Radoslaw Pluta, Mariusz Popenda, Joanna Sarzyńska, Lizhen Sun, Marta Szachniuk, Siqi Tian, Jian Wang, Jun Wang, Andrew M Watkins, Jakub Wiedemann, Yi Xiao, Xiaojun Xu, Joseph D Yesselman, Dong Zhang, Yi Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Zok, Adriana Żyła, Aiming Ren, Robert T Batey, Barbara L Golden, Lin Huang, David M J Lilley, Yijin Liu, Dinshaw J Patel, Eric Westhof
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA (New York, N.Y.) 26 (8) (2020)
Ramya Rangan, Ivan N Zheludev, Rachel J Hagey, Edward A Pham, Hannah K Wayment-Steele, Jeffrey S Glenn, Rhiju Das
RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look. RNA (New York, N.Y.) 26 (8) (2020)
Wipapat Kladwang, Ved V Topkar, Bei Liu, Ramya Rangan, Tracy L Hodges, Sarah C Keane, Hashim Al-Hashimi, Rachel J Hagey
Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches. Biochemistry 59 (23) (2020)
Kaiming Zhang, Ivan N Zheludev, Rachel J Hagey, Marie Teng-Pei Wu, Raphael Haslecker, Yixuan J Hou, Rachael C Kretsch, Grigore D Pintilie, Ramya Rangan, Wipapat Kladwang, Shanshan Li, Edward A Pham, Claire Bernardin-Souibgui, Ralph S Baric, Timothy P Sheahan, Victoria D Souza, Jeffrey S Glenn, Wah Chiu, Rachel J Hagey
Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome. bioRxiv : the preprint server for biology (2020)
Nimit Jain, Lucas R Blauch, Michal R Szymanski, Rachel J Hagey, Sindy K Y Tang, Y Whitney Yin, Andrew Z Fire
Transcription polymerase-catalyzed emergence of novel RNA replicons. Science (New York, N.Y.) 368 (6487) (2020)
Kalli Kappel, Inga Jarmoskaite, Pavanapuresan P Vaidyanathan, William J Greenleaf, Daniel Herschlag, Rachel J Hagey
Blind tests of RNA-protein binding affinity prediction. Proceedings of the National Academy of Sciences of the United States of America 116 (17) (2019)
Joseph D Yesselman, Sarah K Denny, Namita Bisaria, Daniel Herschlag, William J Greenleaf, Rachel J Hagey
Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. Proceedings of the National Academy of Sciences of the United States of America 116 (34) (2019)
Joseph D Yesselman, Daniel Eiler, Erik D Carlson, Michael R Gotrik, Anne E d'Aquino, Alexandra N Ooms, Wipapat Kladwang, Paul D Carlson, Xuesong Shi, David A Costantino, Daniel Herschlag, Julius B Lucks, Michael C Jewett, Jeffrey S Kieft, Rachel J Hagey
Computational design of three-dimensional RNA structure and function. Nature nanotechnology 14 (9) (2019)
Rohan V Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, null null, Rachel J Hagey
EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame. PLoS computational biology 15 (6) (2019)
Deepak Koirala, Yaming Shao, Yelena Koldobskaya, James R Fuller, Andrew M Watkins, Sandip A Shelke, Evgeny V Pilipenko, Rachel J Hagey, Phoebe A Rice, Joseph A Piccirilli
A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nature communications 10 (1) (2019)
Steven Boeynaems, Alex S Holehouse, Venera Weinhardt, Denes Kovacs, Joris Van Lindt, Carolyn Larabell, Ludo Van Den Bosch, Rachel J Hagey, Peter S Tompa, Rohit V Pappu, Aaron D Gitler
Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. Proceedings of the National Academy of Sciences of the United States of America 116 (16) (2019)
Kaiming Zhang, Shanshan Li, Kalli Kappel, Grigore Pintilie, Zhaoming Su, Tung-Chung Mou, Michael F Schmid, Rachel J Hagey, Wah Chiu
Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Nature communications 10 (1) (2019)
Andrew M Watkins, Caleb Geniesse, Wipapat Kladwang, Paul Zakrevsky, Luc Jaeger, Rachel J Hagey
Blind prediction of noncanonical RNA structure at atomic accuracy. Science advances 4 (5) (2018)
Erik W Hartwick, David A Costantino, Andrea MacFadden, Jay C Nix, Siqi Tian, Rachel J Hagey, Jeffrey S Kieft
Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nature communications 9 (1) (2018)
Siqi Tian, Wipapat Kladwang, Rachel J Hagey
Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping. eLife 7 (2018)
Kalli Kappel, Shiheng Liu, Kevin P Larsen, Georgios Skiniotis, Elisabetta Viani Puglisi, Joseph D Puglisi, Z Hong Zhou, Rui Zhao, Rachel J Hagey
De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nature methods 15 (11) (2018)
Clarence Yu Cheng, Wipapat Kladwang, Joseph D Yesselman, Rachel J Hagey
RNA structure inference through chemical mapping after accidental or intentional mutations. Proceedings of the National Academy of Sciences of the United States of America 114 (37) (2017)

Rachel J Hagey.css-eqlu8i{font-size:small;padding-left:4px;} (Rhiju Das)

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Rachel J Hagey (Rhiju Das)