You can also see my publications at my Google Scholar profile.
* Corresponding author / bold: Ochi lab team members
2023
Carden, S., Vitiello, E., e Silva, I. R., Holder, J., Quarantotti, V., Kishore, K, Franklin, V. N. R., D'Santos, C., Ochi, T.*, van Breugel, M and Gergely F. Proteomic profiling of centrosomes across multiple cell and tissue types by a new affinity capture method. Developmental Cell 58, 2393-2410.
Khan, H. and Ochi. T.* Plant PAXX has an XLF-like function and stimulates DNA end-joining by the Ku-DNA ligase IV-XRCC4 complex. BioRxiv. [published in The Plant Journal: https://doi.org/10.1111/tpj.16359]
2022
Goff, N. J., Brenière, M., Buehl, C. J., de Melo, A. J., Huskova, H., Ochi, T., Blundell, T. L., Mao, W., Yu, K., Modesti, M. and Meek, K. Catalytically inactive DNA ligase IV promotes DNA repair in living cells. Nucleic Acids Research 50, 11058-11071.
Ochi, T.* Cartwheels create symmetry and asymmetry. Structure 30, 655-657.
2020
Ochi, T.*, Quarantotti, V., Lin, H., Jullien, J., Boselli F., Barnabas, D., Silve, I. R., Johnson, C., McLaughlin, S., Feund, S., Blackford, A., Kimata, Y., Goldstein R. E., Jackson, S. P., Blundell, T. L., Dutcher, S. K., Gergely, F., and Breugel, M. V. CCDC61/VFL3 is a paralog of SAS6 and promotes ciliary functions. Structure 28, 674-689.
2019
Wu, Q., Liang, S., Ochi, T., Chirgadze, D. Y., Huiskonen, J. T. and Blundell, T. L. Understanding the structure and role of DNA-PK in NHEJ: How X-ray diffraction and cryo-EM contribute in complementary ways. Progress in biophysics and molecular biology 147, 26-32.
2018
Wang, J. L., Duboc, C., Wu, Q., Ochi, T., Liang, S., Tsutakawa, S. E., Lees-Miller, S. P., Nadal, M. Tainer, J. A., Blundell, T. L., and Strick, T. R. Dissection of DNA double-strand-break repair using novel single-molecule forceps. Nature Structural & Molecular Biology 25, 482-487.
2017
Liang, S., Esswein, S. R., Ochi, T., Wu, Q., Ascher, D. B., Chirgadze, D., Sibanda, B. L. and Blundell, T. L. Achieving selectivity in space and time with DNA double-strand-break response and repair: molecular stages and scaffolds come with strings attached. Structural Chemistry 28, 161-171.
2016
Chang, H. H. Y., Watanabe, G., Gerodimos, C. A., Ochi, T., Blundell, T. L., Jackson, S. P. and Lieber, M. R. Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency. J. Biol. Chem. 291, 24377-24389.
Wu, Q., Paul, A., Mehmood, S., Su, D., Ochi, T., Robinson, C. V., Wang, B. and Blundell, T. L. Phosphorylated Abraxas promotes dimerization and accumulation of BRCA1 at DNA damage sites. Mol. Cell 61, 1-15.
2015
Ascher, D. B., Jubb, H. C., Pires, D. E. V., Ochi, T., Higueruelo, A. and Blundell, T. L. Protein-Protein Interactions: Structures and Druggability. Multifaceted Roles of Crystallography in Modern Drug Discovery. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer Netherlands, Dordrecht, Ch. 12, 141-163.
Murray, J. E., van der Burg, M., IJspeert, H., Carroll, P., Wu, Q., Ochi, T., Leitch, A., Miller, E. S., Kysela, B., Jawad, A., Bottani, A., Brancati, F., Cappa, M., Cormier-Daire, V., Deshpande, C., Faqeih, E. A., Graham, G., Ranza, E., Blundell, T. L., Jackson, A. P., Stewart, G. S., Bicknell, L. S. Mutations in the NHEJ component XRCC4 cause primordial dwarfism. AJHG 96, 412-424.
Ochi, T., Blackford, A. N., Coates, J., Jhujh, S., Mehmood, S., Tamura, N., Travers, J., Wu, Q., Draviam, V. M., Robinson, C. V., Blundell T. L. and Jackson S. P. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair. Science 347, 185-188.
2014
Ochi, T.*, Wu, Q. and Blundell, T. L. The spatial organization of non-homologous end joining: From Bridging to end joining. DNA Repair 17, 98-109.
2013
Ochi, T.*, Gu, X. and Blundell, T. L. Structure of the catalytic region of DNA ligase IV in complex with an Artemis fragment sheds light on Double-Strand Break Repair. Structure 21, 1-8.
2012
Ochi, T.*, Wu, Q., Chirgadze, D. Y., Grossmann, J. G., Bolanos-Garcia, V. M. and Blundell, T. L. Structural insights into the role of domain flexibility in human DNA ligase IV. Structure 20, 1212-1222.
Bolanos-Garcia, V. M., Wu, Q., Ochi, T., Chirgadze, D. Y., Sibanda, B. L. and Blundell, T. L. Spatial and temporal organization of multi-protein assemblies: achieving sensitive control in information-rich cell-regulatory systems. Phil. Trans. R. Soc. A. 370, 3023-3039.
2011
Wu, Q., Sibanda, B. L., Ochi, T., Bolanos-Garcia, V. M., Blundell, T. L. and Chirgadze, D. Y. Spatial and temporal organisation of multiprotein systems of cell regulation and signalling: What can we learn from NHEJ system of Double-Strand break repair? Macromolecular Crystallography. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer Netherlands, Dordrecht, Ch. 1, 1-31.
Wu, Q., Ochi, T., Matak-Vinkovic, D., Robinson C. V., Chirgadze, D. Y. and Blundell, T. L. Non-homologous end-joining partners in a helical dance: structural studies of XLF-XRCC4 interactions. Biochem. Soc. Trans. 39, 1387-92.
2010
Ochi, T.*, Sibanda, B. L., Wu, Q., Chirgadze, D. Y., Bolanos-Garcia, V. M. and Blundell, T. L. Structural Biology of DNA Repair: Spatial Organisation of the Multicomponent Complexes of Nonhomologous End Joining. Journal of Nucleic Acids, 2010, 1-19.
2009
Ochi, T., Bolanos-Garcia, V. M., Stojanoff, V. and Moreno, A. Perspectives on protein crystallization. Progress in Biophysics and Molecular Biology 101, 56-63.
Surade, S., Ochi, T., Nietlispach, D., Chirgadze, D. and Moreno, A. Investigations into Protein Crystallization in the Presence of a Strong Magnetic Field. Crystal Growth and Design 10, 691-699.