Disease variant prediction with deep generative models of evolutionary data
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DOI: 10.1038/s41586-021-04043-8
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- Lasse M. Blaabjerg & Nicolas Jonsson & Wouter Boomsma & Amelie Stein & Kresten Lindorff-Larsen, 2024. "SSEmb: A joint embedding of protein sequence and structure enables robust variant effect predictions," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
- Yaan J. Jang & Qi-Qi Qin & Si-Yu Huang & Arun T. John Peter & Xue-Ming Ding & Benoît Kornmann, 2024. "Accurate prediction of protein function using statistics-informed graph networks," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
- Guoling Li & Xue Dong & Jiamin Luo & Tanglong Yuan & Tong Li & Guoli Zhao & Hainan Zhang & Jingxing Zhou & Zhenhai Zeng & Shuna Cui & Haoqiang Wang & Yin Wang & Yuyang Yu & Yuan Yuan & Erwei Zuo & Chu, 2024. "Engineering TadA ortholog-derived cytosine base editor without motif preference and adenosine activity limitation," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
- Ziyi Zhou & Liang Zhang & Yuanxi Yu & Banghao Wu & Mingchen Li & Liang Hong & Pan Tan, 2024. "Enhancing efficiency of protein language models with minimal wet-lab data through few-shot learning," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Kerr Ding & Michael Chin & Yunlong Zhao & Wei Huang & Binh Khanh Mai & Huanan Wang & Peng Liu & Yang Yang & Yunan Luo, 2024. "Machine learning-guided co-optimization of fitness and diversity facilitates combinatorial library design in enzyme engineering," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Daniel J. Diaz & Chengyue Gong & Jeffrey Ouyang-Zhang & James M. Loy & Jordan Wells & David Yang & Andrew D. Ellington & Alexandros G. Dimakis & Adam R. Klivans, 2024. "Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Henry Webel & Lili Niu & Annelaura Bach Nielsen & Marie Locard-Paulet & Matthias Mann & Lars Juhl Jensen & Simon Rasmussen, 2024. "Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Xuan Xie & Xia Sun & Yuheng Wang & Ben Lehner & Xianghua Li, 2023. "Dominance vs epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Kian Hong Kock & Patrick K. Kimes & Stephen S. Gisselbrecht & Sachi Inukai & Sabrina K. Phanor & James T. Anderson & Gayatri Ramakrishnan & Colin H. Lipper & Dongyuan Song & Jesse V. Kurland & Julia M, 2024. "DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Yinglu Cui & Yanchun Chen & Jinyuan Sun & Tong Zhu & Hua Pang & Chunli Li & Wen-Chao Geng & Bian Wu, 2024. "Computational redesign of a hydrolase for nearly complete PET depolymerization at industrially relevant high-solids loading," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
- Cheyenne Ziegler & Jonathan Martin & Claude Sinner & Faruck Morcos, 2023. "Latent generative landscapes as maps of functional diversity in protein sequence space," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Wenkai Han & Ningning Chen & Xinzhou Xu & Adil Sahil & Juexiao Zhou & Zhongxiao Li & Huawen Zhong & Elva Gao & Ruochi Zhang & Yu Wang & Shiwei Sun & Peter Pak-Hang Cheung & Xin Gao, 2023. "Predicting the antigenic evolution of SARS-COV-2 with deep learning," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Han Meng & Nengxiong Xu & Yunfu Zhu & Gang Mei, 2024. "Generating Stochastic Structural Planes Using Statistical Models and Generative Deep Learning Models: A Comparative Investigation," Mathematics, MDPI, vol. 12(16), pages 1-37, August.
- Nicki Skafte Detlefsen & Søren Hauberg & Wouter Boomsma, 2022. "Learning meaningful representations of protein sequences," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Ertunc Erdil & Anton S. Becker & Moritz Schwyzer & Borja Martinez-Tellez & Jonatan R. Ruiz & Thomas Sartoretti & H. Alberto Vargas & A. Irene Burger & Alin Chirindel & Damian Wild & Nicola Zamboni & B, 2024. "Predicting standardized uptake value of brown adipose tissue from CT scans using convolutional neural networks," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Mofan Feng & Xiaoxi Wei & Xi Zheng & Liangjie Liu & Lin Lin & Manying Xia & Guang He & Yi Shi & Qing Lu, 2024. "Decoding Missense Variants by Incorporating Phase Separation via Machine Learning," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Mischan Vali-Pour & Solip Park & Jose Espinosa-Carrasco & Daniel Ortiz-Martínez & Ben Lehner & Fran Supek, 2022. "The impact of rare germline variants on human somatic mutation processes," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
- Lene Clausen & Vasileios Voutsinos & Matteo Cagiada & Kristoffer E. Johansson & Martin Grønbæk-Thygesen & Snehal Nariya & Rachel L. Powell & Magnus K. N. Have & Vibe H. Oestergaard & Amelie Stein & Do, 2024. "A mutational atlas for Parkin proteostasis," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
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