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In response to pathogens, the adaptive immune system generates specific antibodies that bind and neutralize foreign antigens.
Solving the multiple instance problem with axis-parallel rectangles
Thomas G Dietterich, Richard H Lathrop, and Tomás Lozano-Pérez · 1997
Earlier work this paper cites.
Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells
Sai T Reddy, Xin Ge, Aleksandr E Miklos, Randall A Hughes, Seung Hyun Kang, Kam Hon Hoi, Constantine Chrysostomou, Scott P Hunicke-Smith, Brent L Iverson, Philip W Tucker, et al · 2010
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Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to hiv-1
Xueling Wu, Zhi-Yong Yang, Yuxing Li, Carl-Magnus Hogerkorp, William R Schief, Michael S Seaman, Tongqing Zhou, Stephen D Schmidt, Lan Wu, Ling Xu, et al · 2010
Earlier work this paper cites.
Outer domain of hiv-1 gp120: antigenic optimization, structural malleability, and crystal structure with antibody vrc-pg04
M Gordon Joyce, Masaru Kanekiyo, Ling Xu, Christian Biertümpfel, Jeffrey C Boyington, Stephanie Moquin, Wei Shi, Xueling Wu, Yongping Yang, Zhi-Yong Yang, et al · 2013
Earlier work this paper cites.
Somatic mutations of the immunoglobulin framework are generally required for broad and potent hiv-1 neutralization
Florian Klein, Ron Diskin, Johannes F Scheid, Christian Gaebler, Hugo Mouquet, Ivelin S Georgiev, Marie Pancera, Tongqing Zhou, Reha-Baris Incesu, Brooks Zhongzheng Fu, et al · 2013
Earlier work this paper cites.
Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for hiv-1 neutralization by vrc01-class antibodies
Tongqing Zhou, Jiang Zhu, Xueling Wu, Stephanie Moquin, Baoshan Zhang, Priyamvada Acharya, Ivelin S Georgiev, Han R Altae-Tran, Gwo-Yu Chuang, M Gordon Joyce, et al · 2013
Earlier work this paper cites.
The promise and challenge of high-throughput sequencing of the antibody repertoire
George Georgiou, Gregory C Ippolito, John Beausang, Christian E Busse, Hedda Wardemann, and Stephen R Quake · 2014
Earlier work this paper cites.
Adam: A method for stochastic optimization
Diederik P Kingma and Jimmy Ba · 2014
Earlier work this paper cites.
Structural repertoire of hiv-1-neutralizing antibodies targeting the cd4 supersite in 14 donors
Tongqing Zhou, Rebecca M Lynch, Lei Chen, Priyamvada Acharya, Xueling Wu, Nicole A Doria-Rose, M Gordon Joyce, Daniel Lingwood, Cinque Soto, Robert T Bailer, et al · 2015
Cited alongside, same era.
Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
Cited alongside, same era.
Bert: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova · 2018
Cited alongside, same era.
Attention-based deep multiple instance learning
Maximilian Ilse, Jakub Tomczak, and Max Welling · 2018
Cited alongside, same era.
Observed antibody space: a resource for data mining next-generation sequencing of antibody repertoires
Aleksandr Kovaltsuk, Jinwoo Leem, Sebastian Kelm, James Snowden, Charlotte M Deane, and Konrad Krawczyk · 2018
Cited alongside, same era.
Huggingface’s transformers: State-of-the-art natural language processing
Thomas Wolf, Lysandre Debut, Victor Sanh, Julien Chaumond, Clement Delangue, Anthony Moi, Pierric Cistac, Tim Rault, Rémi Louf, Morgan Funtowicz, et al · 2019
Later among the works it cites.
Ahmed Elnaggar, Michael Heinzinger, Christian Dallago, Ghalia Rihawi, Yu Wang, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Martin Steinegger, et al · 2020
Later among the works it cites.
Single-sequence protein structure prediction using language models from deep learning
Ratul Chowdhury, Nazim Bouatta, Surojit Biswas, Charlotte Rochereau, George M Church, Peter Karl Sorger, and Mohammed N AlQuraishi · 2021
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Evolutionary velocity with protein language models
Brian L Hie, Kevin K Yang, and Peter S Kim · 2021
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Language models enable zero-shot prediction of the effects of mutations on protein function
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Umap: Uniform manifold approximation and projection for dimension reduction
Leland McInnes, John Healy, and James Melville · 2018
Cited alongside, same era.
Clustering huge protein sequence sets in linear time
Martin Steinegger and Johannes Söding · 2018
Cited alongside, same era.
Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu, and Alexander Rives · 2021
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Phenotypic determinism and stochasticity in antibody repertoires of clonally expanded plasma cells
Daniel Neumeier, Alexander Yermanos, Andreas Agrafiotis, Lucia Csepregi, Tasnia Chowdhury, Roy A Ehling, Raphael Kuhn, Raphaël Brisset-Di Roberto, Mariangela Di Tacchio, Renan Antonialli, et al · 2021
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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C Lawrence Zitnick, Jerry Ma, et al · 2021
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