Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion
- ️Sorzano, C.O.S.
- ️Tue Oct 01 2019
References
Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C. Ó. S. & Carazo, J. M. (2015). J. Struct. Biol. 189, 163–176. Web of Science CrossRef PubMed Google Scholar
Abrishami, V., Zaldívar-Peraza, A., de la Rosa-Trevín, J. M., Vargas, J., Otón, J., Marabini, R., Shkolnisky, Y., Carazo, J. M. & Sorzano, C. O. S. (2013). Bioinformatics, 29, 2460–2468. Web of Science CrossRef CAS PubMed Google Scholar
Alewijnse, B., Ashton, A. W., Chambers, M. G., Chen, S., Cheng, A., Ebrahim, M., Eng, E. T., Hagen, W. J. H., Koster, A. J., López, C. S., Lukoyanova, N., Ortega, J., Renault, L., Reyntjens, S., Rice, W. J., Scapin, G., Schrijver, R., Siebert, A., Stagg, S. M., Grum-Tokars, V., Wright, E. R., Wu, S., Yu, Z., Zhou, Z. H., Carragher, B. & Potter, C. S. (2017). J. Struct. Biol. 199, 225–236. CrossRef PubMed Google Scholar
Bartesaghi, A., Merk, A., Banerjee, S., Matthies, D., Wu, X., Milne, J. L. S. & Subramaniam, S. (2015). Science, 348, 1147–1151. Web of Science CrossRef CAS PubMed Google Scholar
Biyani, N., Righetto, R. D., McLeod, R., Caujolle-Bert, D., Castano-Diez, D., Goldie, K. N. & Stahlberg, H. (2017). J. Struct. Biol. 198, 124–133. Web of Science CrossRef CAS PubMed Google Scholar
Brilot, A. F., Chen, J. Z., Cheng, A., Pan, J., Harrison, S. C., Potter, C. S., Carragher, B., Henderson, R. & Grigorieff, N. (2012). J. Struct. Biol. 177, 630–637. Web of Science CrossRef CAS PubMed Google Scholar
Campbell, M. G., Cheng, A., Brilot, A. F., Moeller, A., Lyumkis, D., Veesler, D., Pan, J., Harrison, S. C., Potter, C. S., Carragher, B. & Grigorieff, N. (2012). Structure, 20, 1823–1828. Web of Science CrossRef CAS PubMed Google Scholar
Elmlund, D. & Elmlund, H. (2012). J. Struct. Biol. 180, 420–427. CrossRef PubMed Google Scholar
Elmlund, H., Elmlund, D. & Bengio, S. (2013). Structure, 21, 1299–1306. CrossRef CAS PubMed Google Scholar
Frank, J. (2017). Nature Protoc. 12, 209–212. CrossRef CAS Google Scholar
Gómez-Blanco, J., de la Rosa-Trevín, J. M., Marabini, R., Del Cano, L., Jiménez, A., Martínez, M., Melero, R., Majtner, T., Maluenda, D., Mota, J., Rancel, Y., Ramírez-Aportela, E., Vilas, J. L., Carroni, M., Fleischmann, S., Lindahl, E., Ashton, A. W., Basham, M., Clare, D. K., Savage, K., Siebert, C. A., Sharov, G. G., Sorzano, C. O. S., Conesa, P. & Carazo, J. M. (2018). J. Struct. Biol. 204, 457–463. Web of Science PubMed Google Scholar
Grant, T. & Grigorieff, N. (2015). Elife, 4, e06980. Web of Science CrossRef PubMed Google Scholar
Heymann, B. & Belnap, D. (2007). J. Struct. Biol. 157, 3–18. CrossRef PubMed CAS Google Scholar
Hohn, M., Tang, G., Goodyear, G., Baldwin, P. R., Huang, Z., Penczek, P. A., Yang, C., Glaeser, R. M., Adams, P. D. & Ludtke, S. J. (2007). J. Struct. Biol. 157, 47–55. Web of Science CrossRef PubMed CAS Google Scholar
Lander, G. C., Stagg, S. M., Voss, N. R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P. W., Lyumkis, D., Potter, C. S. & Carragher, B. (2009). J. Struct. Biol. 166, 95–102. Web of Science CrossRef PubMed CAS Google Scholar
Rohou, A. & Grigorieff, N. (2015). J. Struct. Biol. 192, 216–221. Web of Science CrossRef PubMed Google Scholar
Rosa-Trevín, J. M. de la, Otón, J., Marabini, R., Zaldívar, A., Vargas, J., Carazo, J. M. & Sorzano, C. O. S. (2013). J. Struct. Biol. 184, 321–328. Web of Science PubMed Google Scholar
Rosa-Trevín, J. M. de la, Quintana, A., del Cano, L., Zaldívar, A., Foche, I., Gutiérrez, J., Gómez-Blanco, J., Burguet-Castell, J., Cuenca-Alba, J., Abrishami, V., Vargas, J., Otón, J., Sharov, G., Vilas, J. L., Navas, J., Conesa, P., Kazemi, M., Marabini, R., Sorzano, C. O. S. & Carazo, J. M. (2016). J. Struct. Biol. 195, 93–99. Web of Science PubMed Google Scholar
Scheres, S. H. W. (2014). J. Struct. Biol. 189, 114–122 CrossRef PubMed Google Scholar
Scheres, S. H. W. (2016). Methods Enzymol. 579, 125–157. Web of Science CrossRef CAS PubMed Google Scholar
Scheres, S. H. W., Valle, M., Nuñez, R., Sorzano, C. O. S., Marabini, R., Herman, G. T. & Carazo, J. M. (2005). J. Mol. Biol. 348, 139–149. Web of Science CrossRef PubMed CAS Google Scholar
Sorzano, C. O. S., Bilbao-Castro, J. R., Shkolnisky, Y., Alcorlo, M., Melero, R., Caffarena-Fernández, G., Li, M., Xu, G., Marabini, R. & Carazo, J. M. (2010). J. Struct. Biol. 171, 197–206. Web of Science CrossRef CAS PubMed Google Scholar
Sorzano, C. O. S., Fernández-Giménez, E., Peredo-Robinson, V., Vargas, J., Majtner, T., Caffarena, G., Otón, J., Vilas, J. L., de la Rosa-Trevín, J. M., Melero, R., Gómez-Blanco, J., Cuenca, J., Del Cano, L., Conesa, P., Marabini, R. & Carazo, J. M. (2018). J. Struct. Biol. 203, 90–93. CrossRef CAS PubMed Google Scholar
Sorzano, C. O. S., Jonic, S., Núñez-Ramírez, R., Boisset, N. & Carazo, J. M. (2007). J. Struct. Biol. 160, 249–262. CrossRef PubMed CAS Google Scholar
Sorzano, C. O. S., Vargas, J., de la Rosa-Trevín, J. M., Otón, J., Álvarez-Cabrera, A. L., Abrishami, V., Sesmero, E., Marabini, R. & Carazo, J. M. (2015). J. Struct. Biol. 189, 213–219. CrossRef CAS PubMed Google Scholar
Sorzano, C. O. S., Vargas, J., de la Rosa-Trevín, J. M., Zaldívar-Peraza, A., Otón, J., Abrishami, V., Foche, I., Marabini, R., Caffarena, G. & Carazo, J. M. (2014). Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO2014, edited by I. Rojas & F. M. Ortuño Guzman, pp. 950–971. Granada: Copicentro Editorial. Google Scholar
Sorzano, C. O. S., Vargas, J., Vilas, J. L., Jiménez-Moreno, A., Mota, J., Majtner, T., Maluenda, D., Martínez, M., Sanchez-García, R., Segura, J., Otón, J., Melero, R., del Cano, L., Conesa, P., Gómez-Blanco, J., Rancel, Y., Marabini, R. & Carazo, J. M. (2018). Appl. Anal. Optim. 2, 299–313. Google Scholar
Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees, I. & Ludtke, S. J. (2007). J. Struct. Biol. 157, 38–46. Web of Science CrossRef PubMed CAS Google Scholar
Tegunov, D. & Cramer, P. (2018). BioRxiv, 338558. Google Scholar
Vargas, J., Abrishami, V., Marabini, R., de la Rosa-Trevín, J. M., Zaldivar, A., Carazo, J. M. & Sorzano, C. O. S. (2013). J. Struct. Biol. 183, 342–353. Web of Science CrossRef CAS PubMed Google Scholar
Vargas, J., Álvarez-Cabrera, A., Marabini, R., Carazo, J. M. & Sorzano, C. O. S. (2014). Bioinformatics, 30, 2891–2898. CrossRef CAS PubMed Google Scholar
Vargas, J., Otón, J., Marabini, R., Jonic, S., de la Rosa-Trevín, J. M., Carazo, J. M. & Sorzano, C. O. S. (2013). J. Struct. Biol. 181, 136–148. CrossRef CAS PubMed Google Scholar
Voss, N. R., Yoshioka, C. K., Radermacher, M., Potter, C. S. & Carragher, B. (2009). J. Struct. Biol. 166, 205–213. Web of Science CrossRef PubMed CAS Google Scholar
Wagner, T., Merino, F., Stabrin, M., Moriya, T., Antoni, C., Apelbaum, A., Hagel, P., Sitsel, O., Raisch, T., Prumbaum, D., Quentin, D., Roderer, D., Tacke, S., Siebolds, B., Schubert, E., Shaikh, T. R., Lill, P., Gatsogiannis, C. & Raunser, S. (2019). Commun. Biol. 2, 218. CrossRef PubMed Google Scholar
Woolford, D., Ericksson, G., Rothnagel, R., Muller, D., Landsberg, M. J., Pantelic, R. S., McDowall, A., Pailthorpe, B., Young, P. R., Hankamer, B. & Banks, J. (2007). J. Struct. Biol. 157, 174–188. CrossRef PubMed CAS Google Scholar
Zhang, K. (2016). J. Struct. Biol. 193, 1–12. Web of Science CrossRef CAS PubMed Google Scholar
Zheng, S. Q., Palovcak, E., Armache, J.-P., Verba, K. A., Cheng, Y. & Agard, D. A. (2017). Nature Methods, 14, 331–332. Web of Science CrossRef CAS PubMed Google Scholar
Zivanov, J., Nakane, T., Forsberg, B. O., Kimanius, D., Hagen, W. J., Lindahl, E. & Scheres, S. H. W. (2018). Elife, 7, e42166. Web of Science CrossRef PubMed Google Scholar
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