Deep learning models for predicting RNA degradation via dual crowdsourcing

Autor: 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

Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited by the intr

Externí odkaz: http://arxiv.org/abs/2110.07531

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Ribonanza: deep learning of RNA structure through dual crowdsourcing.

Autor: He S; Department of Chemical Engineering, Texas A&M University, TX, USA., Huang R; Department of Biochemistry, Stanford CA, USA., Townley J; Eterna Massive Open Laboratory., Kretsch RC; Biophysics Program, Stanford CA, USA., Karagianes TG; Department of Biochemistry, Stanford CA, USA., Cox DBT; Department of Biochemistry, Stanford CA, USA.; Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA., Blair H; Department of Mathematics, Stanford CA, USA., Penzar D; AIRI, Moscow, Russia.; Vavilov Institute of General Genetics, Moscow 119991, Russia.; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia., Vyaltsev V; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation., Aristova E; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation., Zinkevich A; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation., Bakulin A; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation., Sohn H; Department of Chemical Engineering, Texas A&M University, TX, USA.; Department of Biochemistry, Stanford CA, USA.; Eterna Massive Open Laboratory.; Biophysics Program, Stanford CA, USA.; Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA.; Department of Mathematics, Stanford CA, USA.; AIRI, Moscow, Russia.; Vavilov Institute of General Genetics, Moscow 119991, Russia.; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia.; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation.; GO Inc., Tokyo, Japan.; Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea.; DeltaX, Seoul, Republic of Korea.; Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation.; Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA.; Vergesense, CA.; DeNA, Tokyo, Japan.; NVIDIA, Tokyo, Japan.; NVIDIA, Munich.; Howard Hughes Medical Institute.; Department of Bioengineering, Stanford CA, USA.; Kaggle, San Francisco CA, USA., Krstevski D; Department of Chemical Engineering, Texas A&M University, TX, USA.; Department of Biochemistry, Stanford CA, USA.; Eterna Massive Open Laboratory.; Biophysics Program, Stanford CA, USA.; Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA.; Department of Mathematics, Stanford CA, USA.; AIRI, Moscow, Russia.; Vavilov Institute of General Genetics, Moscow 119991, Russia.; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia.; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation.; GO Inc., Tokyo, Japan.; Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea.; DeltaX, Seoul, Republic of Korea.; Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation.; Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA.; Vergesense, CA.; DeNA, Tokyo, Japan.; NVIDIA, Tokyo, Japan.; NVIDIA, Munich.; Howard Hughes Medical Institute.; Department of Bioengineering, Stanford CA, USA.; Kaggle, San Francisco CA, USA., Fukui T; GO Inc., Tokyo, Japan., Tatematsu F; GO Inc., Tokyo, Japan., Uchida Y; GO Inc., Tokyo, Japan., Jang D; Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea., Lee JS; DeltaX, Seoul, Republic of Korea., Shieh R; Department of Chemical Engineering, Texas A&M University, TX, USA.; Department of Biochemistry, Stanford CA, USA.; Eterna Massive Open Laboratory.; Biophysics Program, Stanford CA, USA.; Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA.; Department of Mathematics, Stanford CA, USA.; AIRI, Moscow, Russia.; Vavilov Institute of General Genetics, Moscow 119991, Russia.; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia.; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation.; GO Inc., Tokyo, Japan.; Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea.; DeltaX, Seoul, Republic of Korea.; Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation.; Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA.; Vergesense, CA.; DeNA, Tokyo, Japan.; NVIDIA, Tokyo, Japan.; NVIDIA, Munich.; Howard Hughes Medical Institute.; Department of Bioengineering, Stanford CA, USA.; Kaggle, San Francisco CA, USA., Ma T; Department of Chemical Engineering, Texas A&M University, TX, USA.; Department of Biochemistry, Stanford CA, USA.; Eterna Massive Open Laboratory.; Biophysics Program, Stanford CA, USA.; Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA.; Department of Mathematics, Stanford CA, USA.; AIRI, Moscow, Russia.; Vavilov Institute of General Genetics, Moscow 119991, Russia.; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia.; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation.; GO Inc., Tokyo, Japan.; Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea.; DeltaX, Seoul, Republic of Korea.; Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation.; Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA.; Vergesense, CA.; DeNA, Tokyo, Japan.; NVIDIA, Tokyo, Japan.; NVIDIA, Munich.; Howard Hughes Medical Institute.; Department of Bioengineering, Stanford CA, USA.; Kaggle, San Francisco CA, USA., Martynov E; Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation., Shugaev MV; Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA., Bukhari HST; Vergesense, CA., Fujikawa K; DeNA, Tokyo, Japan., Onodera K; NVIDIA, Tokyo, Japan., Henkel C; NVIDIA, Munich., Ron S; Department of Chemical Engineering, Texas A&M University, TX, USA.; Department of Biochemistry, Stanford CA, USA.; Eterna Massive Open Laboratory.; Biophysics Program, Stanford CA, USA.; Department of Medicine, Division of Hematology, and Department of Biochemistry, Stanford CA, USA.; Department of Mathematics, Stanford CA, USA.; AIRI, Moscow, Russia.; Vavilov Institute of General Genetics, Moscow 119991, Russia.; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia.; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation.; GO Inc., Tokyo, Japan.; Department of Electrical and Computer Engineering, Inha University, Incheon, Republic of Korea.; DeltaX, Seoul, Republic of Korea.; Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Russian Federation.; Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA 22904-4745, USA.; Vergesense, CA.; DeNA, Tokyo, Japan.; NVIDIA, Tokyo, Japan.; NVIDIA, Munich.; Howard Hughes Medical Institute.; Department of Bioengineering, Stanford CA, USA.; Kaggle, San Francisco CA, USA., Romano J; Eterna Massive Open Laboratory.; Howard Hughes Medical Institute., Nicol JJ; Eterna Massive Open Laboratory., Nye GP; Department of Biochemistry, Stanford CA, USA., Wu Y; Department of Biochemistry, Stanford CA, USA.; Howard Hughes Medical Institute., Choe C; Department of Bioengineering, Stanford CA, USA., Reade W; Kaggle, San Francisco CA, USA., Das R; Department of Biochemistry, Stanford CA, USA.; Biophysics Program, Stanford CA, USA.; Howard Hughes Medical Institute.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 11. Date of Electronic Publication: 2024 Jun 11.

Deep learning models for predicting RNA degradation via dual crowdsourcing.

Autor: Wayment-Steele HK; Department of Chemistry, Stanford University, Stanford, California 94305, USA.; Eterna Massive Open Laboratory., Kladwang W; Department of Biochemistry, Stanford University, California 94305, USA.; Eterna Massive Open Laboratory., Watkins AM; Department of Biochemistry, Stanford University, California 94305, USA.; Eterna Massive Open Laboratory., Kim DS; Department of Biochemistry, Stanford University, California 94305, USA.; Eterna Massive Open Laboratory., Tunguz B; Department of Biochemistry, Stanford University, California 94305, USA.; NVIDIA Corporation, Santa Clara, California 95051., Reade W; Kaggle, San Francisco, California 94107., Demkin M; Kaggle, San Francisco, California 94107., Romano J; Department of Biochemistry, Stanford University, California 94305, USA.; Eterna Massive Open Laboratory.; Department of Computer Science and Engineering, State University of New York at Buffalo, Buffalo, New York, 14260, USA., Wellington-Oguri R; Eterna Massive Open Laboratory., Nicol JJ; Eterna Massive Open Laboratory., Gao J; High-flyer AI, Hangzhou, Zhejiang, China, 310000., Onodera K; NVIDIA Corporation, Minato-ku, Tokyo 107-0052, Japan., Fujikawa K; DeNA, Shibuya-ku, Tokyo 150-6140, Japan., Mao H; Yanfu Investments, Shanghai, China, 200000., Vandewiele G; IDLab, Ghent University, Technologiepark-Zwijnaarde, Gent, Belgium, B-9052., Tinti M; College of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom., Steenwinckel B; IDLab, Ghent University, Technologiepark-Zwijnaarde, Gent, Belgium, B-9052., Ito T; Universal Knowledge Inc., Tokyo 150-0013, Japan., Noumi T; Keyence Corporation, 1-3-14, Higashi-Nakajima, Higashi-Yodogawa-ku, Osaka, 533-8555, Japan., He S; Department of Chemical Engineering, Texas A&M University, College Station, TX 77843., Ishi K; Rist Inc, Meguro-ku, Tokyo 153-0063, Japan., Lee Y; Kakao Brain, Seongnam, Gyeonggi-do, Republic of Korea., Öztürk F; H2O, Istanbul, 3400, Turkey., Chiu A; Clover Health, Hong Kong, 999077, PRC., Öztürk E; Afiniti, Istanbul, 3400, Turkey., Amer K; Center for Informatics Science, Nile University, Sheikh Zayed, Giza, Egypt, 12588., Fares M; National Research Centre, Dokki, Cairo, Egypt, 12622., Participants E; Eterna Massive Open Laboratory., Das R; Department of Biochemistry, Stanford University, California 94305, USA.; Eterna Massive Open Laboratory.; Department of Physics, Stanford University, California 94305, USA.

Publikováno v: ArXiv [ArXiv] 2021 Oct 14. Date of Electronic Publication: 2021 Oct 14.