Riboformer: a deep learning framework for predicting context-dependent translation dynamics
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DOI: 10.1038/s41467-024-46241-8
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- Patrick B. F. O’Connor & Dmitry E. Andreev & Pavel V. Baranov, 2016. "Comparative survey of the relative impact of mRNA features on local ribosome profiling read density," Nature Communications, Nature, vol. 7(1), pages 1-12, December.
- Gene-Wei Li & Eugene Oh & Jonathan S. Weissman, 2012. "The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria," Nature, Nature, vol. 484(7395), pages 538-541, April.
- Kevin C. Stein & Fabián Morales-Polanco & Joris Lienden & T. Kelly Rainbolt & Judith Frydman, 2022. "Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis," Nature, Nature, vol. 601(7894), pages 637-642, January.
- Yaara Finkel & Orel Mizrahi & Aharon Nachshon & Shira Weingarten-Gabbay & David Morgenstern & Yfat Yahalom-Ronen & Hadas Tamir & Hagit Achdout & Dana Stein & Ofir Israeli & Adi Beth-Din & Sharon Melam, 2021. "The coding capacity of SARS-CoV-2," Nature, Nature, vol. 589(7840), pages 125-130, January.
- Amin Espah Borujeni & Jing Zhang & Hamid Doosthosseini & Alec A. K. Nielsen & Christopher A. Voigt, 2020. "Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage," Nature Communications, Nature, vol. 11(1), pages 1-18, December.
- Mian Zhou & Jinhu Guo & Joonseok Cha & Michael Chae & She Chen & Jose M. Barral & Matthew S. Sachs & Yi Liu, 2013. "Non-optimal codon usage affects expression, structure and function of clock protein FRQ," Nature, Nature, vol. 495(7439), pages 111-115, March.
- Kazuki Saito & Hanna Kratzat & Annabelle Campbell & Robert Buschauer & A. Maxwell Burroughs & Otto Berninghausen & L. Aravind & Rachel Green & Roland Beckmann & Allen R. Buskirk, 2022. "Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria," Nature, Nature, vol. 603(7901), pages 503-508, March.
- Michael VanInsberghe & Jeroen Berg & Amanda Andersson-Rolf & Hans Clevers & Alexander Oudenaarden, 2021. "Single-cell Ribo-seq reveals cell cycle-dependent translational pausing," Nature, Nature, vol. 597(7877), pages 561-565, September.
- Silvi Rouskin & Meghan Zubradt & Stefan Washietl & Manolis Kellis & Jonathan S. Weissman, 2014. "Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo," Nature, Nature, vol. 505(7485), pages 701-705, January.
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