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HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.

Autor: Vorontsov, Ilya E, Eliseeva, Irina A, Zinkevich, Arsenii, Nikonov, Mikhail, Abramov, Sergey, Boytsov, Alexandr, Kamenets, Vasily, Kasianova, Alexandra, Kolmykov, Semyon, Yevshin, Ivan S, Favorov, Alexander, Medvedeva, Yulia A, Jolma, Arttu, Kolpakov, Fedor, Makeev, Vsevolod J, Kulakovskiy, Ivan V

Publikováno v: Nucleic Acids Research; 1/5/2024, Vol. 52 Issue D1, pD154-D163, 10p

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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.