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Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing
Belyaeva, A., Cammarata, L., Radhakrishnan, A., Squires, C., Yang, K. D., Shivashankar, G. V., & Uhler, C. (2021). Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing. Nature Communications, 12(1), 1024 (13 pp.). https://doi.org/10.1038/s41467-021-21056-z
The characteristics of nuclear membrane fluctuations in stem cells
Ghanbarzadeh Nodehi, S., Shivashankar, G. V., Prost, J., & Mohammad-Rafiee, F. (2021). The characteristics of nuclear membrane fluctuations in stem cells. Journal of the Royal Society Interface, 18(176), 20201010 (9 pp.). https://doi.org/10.1098/rsif.2020.1010
Mechanogenomic coupling of lung tissue stiffness, EMT and coronavirus pathogenicity
Uhler, C., & Shivashankar, G. V. (2021). Mechanogenomic coupling of lung tissue stiffness, EMT and coronavirus pathogenicity. Current Opinion in Solid State and Materials Science, 25(1), 100874 (4 pp.). https://doi.org/10.1016/j.cossms.2020.100874
Multi-domain translation between single-cell imaging and sequencing data using autoencoders
Yang, K. D., Belyaeva, A., Venkatachalapathy, S., Damodaran, K., Katcoff, A., Radhakrishnan, A., … Uhler, C. (2021). Multi-domain translation between single-cell imaging and sequencing data using autoencoders. Nature Communications, 12(1), 31 (10 pp.). https://doi.org/10.1038/s41467-020-20249-2
A lipocalin mediates unidirectional heme biomineralization in malaria parasites
Matz, J. M., Drepper, B., Blum, T. B., van Genderen, E., Burrell, A., Martin, P., … Blackman, M. J. (2020). A lipocalin mediates unidirectional heme biomineralization in malaria parasites. Proceedings of the National Academy of Sciences of the United States of America PNAS, 117(28), 16546-16556. https://doi.org/10.1073/pnas.2001153117
Shape-shifting peptide nanomaterials: surface asymmetry enables pH-dependent formation and interconversion of collagen tubes and sheets
Merg, A. D., Touponse, G., van Genderen, E., Blum, T. B., Zuo, X., Bazrafshan, A., … Conticello, V. P. (2020). Shape-shifting peptide nanomaterials: surface asymmetry enables pH-dependent formation and interconversion of collagen tubes and sheets. Journal of the American Chemical Society, 142(47), 19956-19968. https://doi.org/10.1021/jacs.0c08174
Demonstration of the voltage-controlled three-beam interference of high-energy coherent electron beam
Thakkar, P., Guzenko, V., Abrahams, J. P., Tsujino, S., Lu, P. H., & Dunin-Borkowski, R. E. (2020). Demonstration of the voltage-controlled three-beam interference of high-energy coherent electron beam. In 2020 33rd international vacuum nanoelectronics conference (IVNC). 33rd international vacuum nanoelectronics conference (IVNC) July 6-7, 2020 (p. 9203341 (2 pp.). https://doi.org/10.1109/IVNC49440.2020.9203341
Fabrication of low aspect ratio three-element Boersch phase shifters for voltage-controlled three electron beam interference
Thakkar, P., Guzenko, V. A., Lu, P. H., Dunin-Borkowski, R. E., Abrahams, J. P., & Tsujino, S. (2020). Fabrication of low aspect ratio three-element Boersch phase shifters for voltage-controlled three electron beam interference. Journal of Applied Physics, 128(13), 134502 (13 pp.). https://doi.org/10.1063/5.0020383
Functional and structural insights into a novel promiscuous ketoreductase of the lugdunomycin biosynthetic pathway
Xiao, X., Elsayed, S. S., Wu, C., van der Heul, H. U., Metsä-Ketelä, M., Du, C., … van Wezel, G. P. (2020). Functional and structural insights into a novel promiscuous ketoreductase of the lugdunomycin biosynthetic pathway. ACS Chemical Biology, 15(9), 2529-2538. https://doi.org/10.1021/acschembio.0c00564
Sub-pixel electron detection using a convolutional neural network
van Schayck, J. P., van Genderen, E., Maddox, E., Roussel, L., Boulanger, H., Fröjdh, E., … Ravelli, R. B. G. (2020). Sub-pixel electron detection using a convolutional neural network. Ultramicroscopy, 218, 113091 (10 pp.). https://doi.org/10.1016/j.ultramic.2020.113091
The wild-type flagellar filament of the Firmicute <em>Kurthia </em>at 2.8 Å resolution <em>in vivo</em>
Blum, T. B., Filippidou, S., Fatton, M., Junier, P., & Abrahams, J. P. (2019). The wild-type flagellar filament of the Firmicute Kurthia at 2.8 Å resolution in vivo. Scientific Reports, 9(1), 14948 (8 pp.). https://doi.org/10.1038/s41598-019-51440-1
Reducing dynamical electron scattering reveals hydrogen atoms
Clabbers, M. T. B., Gruene, T., van Genderen, E., & Abrahams, J. P. (2019). Reducing dynamical electron scattering reveals hydrogen atoms. Acta Crystallographica Section A: Foundations and Advances, 75(1), 82-93. https://doi.org/10.1107/S2053273318013918
3D electron diffraction: the nanocrystallography revolution
Gemmi, M., Mugnaioli, E., Gorelik, T. E., Kolb, U., Palatinus, L., Boullay, P., … Abrahams, J. P. (2019). 3D electron diffraction: the nanocrystallography revolution. ACS Central Science, 5(8), 1315-1329. https://doi.org/10.1021/acscentsci.9b00394
Inelastic scattering and solvent scattering reduce dynamical diffraction in biological crystals
Latychevskaia, T., & Abrahams, J. P. (2019). Inelastic scattering and solvent scattering reduce dynamical diffraction in biological crystals. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 75, 523-531. https://doi.org/10.1107/S2052520619009661
2D crystal engineering of nanosheets assembled from helical peptide building blocks
Merg, A. D., Touponse, G., van Genderen, E., Zuo, X., Bazrafshan, A., Blum, T., … Conticello, V. P. (2019). 2D crystal engineering of nanosheets assembled from helical peptide building blocks. Angewandte Chemie International Edition, 58(38), 13507-13512. https://doi.org/10.1002/anie.201906214
Seeded heteroepitaxial growth of crystallizable collagen triple helices: engineering multifunctional two-dimensional core-shell nanostructures
Merg, A. D., van Genderen, E., Bazrafshan, A., Su, H., Zuo, X., Touponse, G., … Conticello, V. P. (2019). Seeded heteroepitaxial growth of crystallizable collagen triple helices: engineering multifunctional two-dimensional core-shell nanostructures. Journal of the American Chemical Society, 141(51), 20107-20117. https://doi.org/10.1021/jacs.9b09335
Supramolecular architectures of molecularly thin yet robust free-standing layers
Moradi, M., Opara, N. L., Tulli, L. G., Wäckerlin, C., Dalgarno, S. J., Teat, S. J., … Shahgaldian, P. (2019). Supramolecular architectures of molecularly thin yet robust free-standing layers. Science Advances, 5(2), eaav4489 (7 pp.). https://doi.org/10.1126/sciadv.aav4489
Electron diffraction and three-dimensional crystallography for structural biology
Clabbers, M. T. B., & Abrahams, J. P. (2018). Electron diffraction and three-dimensional crystallography for structural biology. Crystallography Reviews, 24(3), 176-204. https://doi.org/10.1080/0889311X.2018.1446427
Electron diffraction data processing with <em>DIALS</em>
Clabbers, M. T. B., Gruene, T., Parkhurst, J. M., Abrahams, J. P., & Waterman, D. G. (2018). Electron diffraction data processing with DIALS. Acta Crystallographica Section D: Structural Biology, 74(6). https://doi.org/10.1107/S2059798318007726
Electron crystallography with the EIGER detector
Tinti, G., Fröjdh, E., van Genderen, E., Gruene, T., Schmitt, B., de Winter, D. A. M., … Abrahams, J. P. (2018). Electron crystallography with the EIGER detector. IUCrJ, 5(2), 190-199. https://doi.org/10.1107/S2052252518000945