Abraham, J. (2020). Passive antibody therapy in COVID-19. Nature Reviews Immunology, 20(7), 401–403. https://doi.org/10.1038/s41577-020-0365-7
Adamson, A. S., & Smith, A. (2018). Machine Learning and Health Care Disparities in Dermatology. JAMA Dermatology, 154(11), 1247. https://doi.org/10.1001/jamadermatol.2018.2348
Afonin, K. A., Dobrovolskaia, M. A., Church, G., & Bathe, M. (2020). Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology. ACS Nano, 14(8), 9221–9227. https://doi.org/10.1021/acsnano.0c04753
Anastassacos, F. (2019). Towards the therapeutic application of DNA origami [Doctoral dissertation]. http://nrs.harvard.edu/urn-3:HUL.InstRepos:42013166
Anastassacos, F. M., Zhao, Z., Zeng, Y., & Shih, W. M. (2020). Glutaraldehyde cross-linking of Oligolysines coating DNA origami greatly reduces susceptibility to nuclease degradation. Journal of the American Chemical Society, 142(7), 3311-3315. https://doi.org/10.1021/jacs.9b11698
Andersen, E. S., Dong, M., Nielsen, M. M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M. M., Sander, B., Stark, H., Oliveira, C. L., Pedersen, J. S., Birkedal, V., Besenbacher, F., Gothelf, K. V., & Kjems, J. (2009). Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459(7243), 73-76. https://doi.org/10.1038/nature07971
Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). The proximal origin of SARS-CoV-2. Nature Medicine, 26(4), 450–452. https://doi.org/10.1038/s41591-020-0820-9
Bujold, K. E., Hsu, J. C. C., & Sleiman, H. F. (2016). Optimized DNA “Nanosuitcases” for Encapsulation and Conditional Release of siRNA. Journal of the American Chemical Society, 138(42), 14030–14038. https://doi.org/10.1021/jacs.6b08369
Burns, J. R., Lamarre, B., Pyne, A. L. B., Noble, J. E., & Ryadnov, M. G. (2018). DNA Origami Inside-Out Viruses. ACS Synthetic Biology, 7(3), 767–773. https://doi.org/10.1021/acssynbio.7b00278
Castro, C. E., Kilchherr, F., Kim, D., Shiao, E. L., Wauer, T., Wortmann, P., Bathe, M., & Dietz, H. (2011). A primer to scaffolded DNA origami. Nature Methods, 8(3), 221-229. https://doi.org/10.1038/nmeth.1570
Engelhardt, F. A. S., Praetorius, F., Wachauf, C. H., Brüggenthies, G., Kohler, F., Kick, B., … Dietz, H. (2019). Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds. ACS Nano, 13(5), 5015–5027. https://doi.org/10.1021/acsnano.9b01025
Galitsky, B. A., Gelfand, I. M., & Kister, A. E. (1998). Predicting amino acid sequences of the antibody human VH chains from its first several residues. Proceedings of the National Academy of Sciences, 95(9), 5193–5198. https://doi.org/10.1073/pnas.95.9.5193
Gerke, S., Minssen, T., & Cohen, G. (2020). Ethical and legal challenges of artificial intelligence-driven healthcare. Artificial Intelligence in Healthcare, 295–336. https://doi.org/10.1016/b978-0-12-818438-7.00012-5
Graves, J., Byerly, J., Priego, E., Makkapati, N., Parish, S. V., Medellin, B., & Berrondo, M. (2020). A Review of Deep Learning Methods for Antibodies. Antibodies, 9(2), 12. https://doi.org/10.3390/antib9020012
Günes, F., Wolfinger, R., & Tan, P.-Y. (2017). Stacked Ensemble Models for Improved Prediction Accuracy. Proceedings of the SAS Global Forum 2017 Conference.
Gustafson, C. E., Kim, C., Weyand, C. M., & Goronzy, J. J. (2020). Influence of immune aging on vaccine responses. Journal of Allergy and Clinical Immunology, 145(5), 1309–1321. https://doi.org/10.1016/j.jaci.2020.03.017
Hahn, J., Chou, L. Y., Sørensen, R. S., Guerra, R. M., & Shih, W. M. (2020). Extrusion of RNA from a DNA-origami-Based Nanofactory. ACS Nano, 14(2), 1550-1559. https://doi.org/10.1021/acsnano.9b06466
Hein, A., Cole, C., & Valafar, H. (2020). An Investigation in Optimal Encoding of Protein Primary Sequence for Structure Prediction by Artificial Neural Networks. ArcXiv.org.
Huo, J., Bas, A. L., Ruza, R. R., Duyvesteyn, H. M. E., Mikolajek, H., Malinauskas, T., … Naismith, J. H. (2020). Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2. Nature Structural & Molecular Biology, 27(9), 846–854. https://doi.org/10.1038/s41594-020-0469-6
Jung, J., Choe, J., Li, L., & Choi, Y. (2000). Regulation of CD27 expression in the course of Germinal center B cell differentiation: The pivotal role of IL-10. European Journal of Immunology, 30(8), 2437-2443. https://doi.org/10.1002/1521-4141(2000)30:8<_x0032_437:_x003a_aid-immu2437>3.0.co;2-m
Kim, D., Kilchherr, F., Dietz, H., & Bathe, M. (2011). Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Research, 40(7), 2862-2868. https://doi.org/10.1093/nar/gkr1173
Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., … Wang, X. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215–220. https://doi.org/10.1038/s41586-020-2180-5
Lashbrook, A. (2018, August 16). AI-Driven Dermatology Could Leave Dark-Skinned Patients Behind. The Atlantic. https://www.theatlantic.com/health/archive/2018/08/machine-learning-dermatology-skin-color/567619/.
Li, X., Deventer, J. A. V., & Hassoun, S. (2020). ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning. PLOS Computational Biology, 16(4). https://doi.org/10.1371/journal.pcbi.1007779
Liu, G., Zeng, H., Mueller, J., Carter, B., Wang, Z., Schilz, J., … Gifford, D. K. (2019). Antibody complementarity determining region design using high-capacity machine learning. Bioinformatics, 36(7), 2126–2133. https://doi.org/10.1093/bioinformatics/btz895
Majikes, J. M., Ferraz, L. C., & LaBean, T. H. (2017). PH-driven actuation of DNA origami via parallel I-motif sequences in solution and on surfaces. Bioconjugate Chemistry, 28(7), 1821-1825. https://doi.org/10.1021/acs.bioconjchem.7b00288
Marovich, M., Mascola, J. R., & Cohen, M. S. (2020). Monoclonal Antibodies for Prevention and Treatment of COVID-19. Jama, 324(2), 131. https://doi.org/10.1001/jama.2020.10245
Nimrod, G., Fischman, S., Austin, M., Herman, A., Keyes, F., Leiderman, O., … Ofran, Y. (2018). Computational Design of Epitope-Specific Functional Antibodies. Cell Reports, 25(8). https://doi.org/10.1016/j.celrep.2018.10.081
Poppleton, E., Bohlin, J., Matthies, M., Sharma, S., Zhang, F., & Šulc, P. (2020). Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation. Nucleic Acids Research, 48(12), e72-e72. https://doi.org/10.1093/nar/gkaa417
Schmidt, M., Safarani, S., Gastinger, J., Jacobs, T., Nicolas, S., & Schülke, A. (2019). On the Performance of Differential Evolution for Hyperparameter Tuning. ArcXiv.org.
Sevy, A. M., Panda, S., Crowe, J. E., Meiler, J., & Vorobeychik, Y. (2018). Integrating linear optimization with structural modeling to increase HIV neutralization breadth. PLOS Computational Biology, 14(2). https://doi.org/10.1371/journal.pcbi.1005999
Singh, J. K. D., Luu, M. T., Abbas, A., & Wickham, S. F. J. (2018). Switchable DNA-origami nanostructures that respond to their environment and their applications. Biophysical Reviews, 10(5), 1283–1293. https://doi.org/10.1007/s12551-018-0462-z
Suma, A., Poppleton, E., Matthies, M., Šulc, P., Romano, F., Louis, A. A., Doye, J. P., Micheletti, C., & Rovigatti, L. (2019). TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami. Journal of Computational Chemistry, 40(29), 2586-2595. https://doi.org/10.1002/jcc.26029
Vayena, E., Blasimme, A., & Cohen, I. G. (2018). Machine learning in medicine: Addressing ethical challenges. PLOS Medicine, 15(11). https://doi.org/10.1371/journal.pmed.1002689
Wagenbauer, K. F., Engelhardt, F. A., Stahl, E., Hechtl, V. K., Stömmer, P., Seebacher, F., Meregalli, L., Ketterer, P., Gerling, T., & Dietz, H. (2017). How we make DNA origami. ChemBioChem, 18(19), 1873-1885. https://doi.org/10.1002/cbic.201700377
Zhang, S., Jiang, H., Xu, M., Hou, J., & Dai, L. (2015). A Fixed-Size Encoding Method for Variable-Length Sequences with its Application to Neural Network Language Models. ArcXiv.org.
Zost, S. J., Gilchuk, P., Chen, R. E., Case, J. B., Reidy, J. X., Trivette, A., … Crowe, J. E. (2020). Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein. Nature
