Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, Kathrin, Byeon, Gun Woo, Kladwang, Wipapat, Wayment-Steele, Hannah K, Kerr, Craig H, Xu, Adele F, Kim, Do Soon, Topkar, Ved V, Choe, Christian, Rothschild, Daphna, Tiu, Gerald C, Wellington-Oguri, Roger, Fujii, Kotaro, Sharma, Eesha, Watkins, Andrew M, Nicol, John J, Romano, Jonathan, Tunguz, Bojan, Diaz, Fernando, Cai, Hui, Guo, Pengbo, Wu, Jiewei, Meng, Fanyu, Shi, Shuai, Participants, Eterna, Dormitzer, Philip R, Solórzano, Alicia, Barna, Maria, Das, Rhiju
Published in Nature communications (22.03.2022)
Published in Nature communications (22.03.2022)
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RNA design rules from a massive open laboratory
Lee, Jeehyung, Kladwang, Wipapat, Lee, Minjae, Cantu, Daniel, Azizyan, Martin, Kim, Hanjoo, Limpaecher, Alex, Yoon, Sungroh, Treuille, Adrien, Das, Rhiju, Participants, EteRNA
Published in Proceedings of the National Academy of Sciences - PNAS (11.02.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (11.02.2014)
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RNA secondary structure packages evaluated and improved by high-throughput experiments
Wayment-Steele, Hannah K, Kladwang, Wipapat, Strom, Alexandra I, Lee, Jeehyung, Treuille, Adrien, Becka, Alex, Das, Rhiju
Published in Nature methods (01.10.2022)
Published in Nature methods (01.10.2022)
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Theoretical basis for stabilizing messenger RNA through secondary structure design
Wayment-Steele, Hannah K, Kim, Do Soon, Choe, Christian A, Nicol, John J, Wellington-Oguri, Roger, Watkins, Andrew M, Parra Sperberg, R Andres, Huang, Po-Ssu, Participants, Eterna, Das, Rhiju
Published in Nucleic acids research (11.10.2021)
Published in Nucleic acids research (11.10.2021)
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Minimization of the E. coli ribosome, aided and optimized by community science
Tangpradabkul, Tiyaporn, Palo, Michael, Townley, Jill, Hsu, Kenneth B, participants, Eterna, Smaga, Sarah, Das, Rhiju, Schepartz, Alanna
Published in Nucleic acids research (09.02.2024)
Published in Nucleic acids research (09.02.2024)
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Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches
Andreasson, Johan O L, Gotrik, Michael R, Wu, Michelle J, Wayment-Steele, Hannah K, Kladwang, Wipapat, Portela, Fernando, Wellington-Oguri, Roger, Das, Rhiju, Greenleaf, William J
Published in Proceedings of the National Academy of Sciences - PNAS (03.05.2022)
Published in Proceedings of the National Academy of Sciences - PNAS (03.05.2022)
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Correction to ‘Theoretical basis for stabilizing messenger RNA through secondary structure design’
Wayment-Steele, Hannah K, Kim, Do Soon, Choe, Christian A, Nicol, John J, Wellington-Oguri, Roger, Watkins, Andrew M, Parra Sperberg, R Andres, Huang, Po-Ssu, Participants, Eterna, Das, Rhiju
Published in Nucleic acids research (08.11.2021)
Published in Nucleic acids research (08.11.2021)
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Community science designed ribosomes with beneficial phenotypes
Krüger, Antje, Watkins, Andrew M, Wellington-Oguri, Roger, Romano, Jonathan, Kofman, Camila, DeFoe, Alysse, Kim, Yejun, Anderson-Lee, Jeff, Fisker, Eli, Townley, Jill, d'Aquino, Anne E, Das, Rhiju, Jewett, Michael C
Published in Nature communications (21.02.2023)
Published in Nature communications (21.02.2023)
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Deep learning models for predicting RNA degradation via dual crowdsourcing
Wayment-Steele, Hannah K, Kladwang, Wipapat, Watkins, Andrew M, Kim, Do Soon, Tunguz, Bojan, Reade, Walter, Demkin, Maggie, Romano, Jonathan, Wellington-Oguri, Roger, Nicol, John J, Gao, Jiayang, Onodera, Kazuki, Fujikawa, Kazuki, Mao, Hanfei, Vandewiele, Gilles, Tinti, Michele, Steenwinckel, Bram, Ito, Takuya, Noumi, Taiga, He, Shujun, Ishi, Keiichiro, Lee, Youhan, Öztürk, Fatih, Chiu, King Yuen, Öztürk, Emin, Amer, Karim, Fares, Mohamed, Das, Rhiju
Published in Nature machine intelligence (01.12.2022)
Published in Nature machine intelligence (01.12.2022)
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Compact RNA sensors for increasingly complex functions of multiple inputs
Choe, Christian, Andreasson, Johan O L, Melaine, Feriel, Kladwang, Wipapat, Wu, Michelle J, Portela, Fernando, Wellington-Oguri, Roger, Nicol, John J, Wayment-Steele, Hannah K, Gotrik, Michael, Participants, Eterna, Khatri, Purvesh, Greenleaf, William J, Das, Rhiju
Published in bioRxiv (16.01.2024)
Published in bioRxiv (16.01.2024)
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Ribonanza: deep learning of RNA structure through dual crowdsourcing
He, Shujun, Huang, Rui, Townley, Jill, Kretsch, Rachael C, Karagianes, Thomas G, Cox, David B T, Blair, Hamish, Penzar, Dmitry, Vyaltsev, Valeriy, Aristova, Elizaveta, Zinkevich, Arsenii, Bakulin, Artemy, Sohn, Hoyeol, Krstevski, Daniel, Fukui, Takaaki, Tatematsu, Fumiya, Uchida, Yusuke, Jang, Donghoon, Lee, Jun Seong, Shieh, Roger, Ma, Tom, Martynov, Eduard, Shugaev, Maxim V, Bukhari, Habib S T, Fujikawa, Kazuki, Onodera, Kazuki, Henkel, Christof, Ron, Shlomo, Romano, Jonathan, Nicol, John J, Nye, Grace P, Wu, Yuan, Choe, Christian, Reade, Walter, Participants, Eterna, Das, Rhiju
Published in bioRxiv (27.02.2024)
Published in bioRxiv (27.02.2024)
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Deep learning models for predicting RNA degradation via dual crowdsourcing
Wayment-Steele, Hannah K, Kladwang, Wipapat, Watkins, Andrew M, Kim, Do Soon, Tunguz, Bojan, Reade, Walter, Demkin, Maggie, Romano, Jonathan, Wellington-Oguri, Roger, Nicol, John J, Gao, Jiayang, Onodera, Kazuki, Fujikawa, Kazuki, Mao, Hanfei, Vandewiele, Gilles, Tinti, Michele, Steenwinckel, Bram, Ito, Takuya, Noumi, Taiga, He, Shujun, Ishi, Keiichiro, Lee, Youhan, Öztürk, Fatih, Chiu, Anthony, Öztürk, Emin, Amer, Karim, Fares, Mohamed, Participants, Eterna, Das, Rhiju
Published in arXiv.org (22.04.2022)
Published in arXiv.org (22.04.2022)
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Journal Article
Predictive models of RNA degradation through dual crowdsourcing
Wayment-Steele, Hannah K., Kladwang, Wipapat, Watkins, Andrew M., Kim, Do Soon, Tunguz, Bojan, Reade, Walter, Demkin, Maggie, Romano, Jonathan, Wellington-Oguri, Roger, Nicol, John J., Gao, Jiayang, Onodera, Kazuki, Fujikawa, Kazuki, Mao, Hanfei, Vandewiele, Gilles, Tinti, Michele, Steenwinckel, Bram, Ito, Takuya, Noumi, Taiga, He, Shujun, Ishi, Keiichiro, Lee, Youhan, Öztürk, Fatih, Chiu, Anthony, Öztürk, Emin, Amer, Karim, Fares, Mohamed, Participants, Eterna, Das, Rhiju
Published in ArXiv.org (14.10.2021)
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Published in ArXiv.org (14.10.2021)
Journal Article
Deep learning models for predicting RNA degradation via dual crowdsourcing
Wayment-Steele, Hannah K, Kladwang, Wipapat, Watkins, Andrew M, Kim, Do Soon, Tunguz, Bojan, Reade, Walter, Demkin, Maggie, Romano, Jonathan, Wellington-Oguri, Roger, Nicol, John J, Gao, Jiayang, Onodera, Kazuki, Fujikawa, Kazuki, Mao, Hanfei, Vandewiele, Gilles, Tinti, Michele, Steenwinckel, Bram, Ito, Takuya, Noumi, Taiga, He, Shujun, Ishi, Keiichiro, Lee, Youhan, Öztürk, Fatih, Chiu, Anthony, Öztürk, Emin, Amer, Karim, Fares, Mohamed, Participants, Eterna, Das, Rhiju
Published in ArXiv.org (14.10.2021)
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Published in ArXiv.org (14.10.2021)
Journal Article
Theoretical basis for stabilizing messenger RNA through secondary structure design
Wayment-Steele, Hannah K, Kim, Do Soon, Choe, Christian A, Nicol, John J, Wellington-Oguri, Roger, Watkins, Andrew M, Sperberg, R Andres Parra, Huang, Po-Ssu, Participants, Eterna, Das, Rhiju
Published in bioRxiv (19.02.2021)
Published in bioRxiv (19.02.2021)
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Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Leppek, Kathrin, Byeon, Gun Woo, Kladwang, Wipapat, Wayment-Steele, Hannah K, Kerr, Craig H, Xu, Adele F, Kim, Do Soon, Topkar, Ved V, Choe, Christian, Rothschild, Daphna, Tiu, Gerald C, Wellington-Oguri, Roger, Fujii, Kotaro, Sharma, Eesha, Watkins, Andrew M, Nicol, John J, Romano, Jonathan, Tunguz, Bojan, Participants, Eterna, Barna, Maria, Das, Rhiju
Published in bioRxiv (30.03.2021)
Published in bioRxiv (30.03.2021)
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Community science designed ribosomes with beneficial phenotypes
Kruger, Antje, Watkins, Andrew M, Wellington-Oguri, Roger, Romano, Jonathan, Kofman, Camila, Defoe, Alysse, Kim, Yejun, Anderson-Lee, Jeff, Fisker, Eli, Townley, Jill, Participants, Eterna, D'aquino, Anne E, Das, Rhiju, Jewett, Michael C
Published in bioRxiv (12.09.2021)
Published in bioRxiv (12.09.2021)
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