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Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology.
Conesa P, Fonseca YC, Jiménez de la Morena J, Sharov G, de la Rosa-Trevín JM, Cuervo A, García Mena A, Rodríguez de Francisco B, Del Hoyo D, Herreros D, Marchan D, Strelak D, Fernández-Giménez E, Ramírez-Aportela E, de Isidro-Gómez FP, Sánchez I, Krieger J, Vilas JL, Del Cano L, Gragera M, Iceta M, Martínez M, Losana P, Melero R, Marabini R, Carazo JM, Sorzano COS. Conesa P, et al. Among authors: ramirez aportela e. Biol Imaging. 2023 Jun 29;3:e13. doi: 10.1017/S2633903X23000132. eCollection 2023. Biol Imaging. 2023. PMID: 38510163 Free PMC article.
Image processing tools for the validation of CryoEM maps.
Sorzano COS, Vilas JL, Ramírez-Aportela E, Krieger J, Del Hoyo D, Herreros D, Fernandez-Giménez E, Marchán D, Macías JR, Sánchez I, Del Caño L, Fonseca-Reyna Y, Conesa P, García-Mena A, Burguet J, García Condado J, Méndez García J, Martínez M, Muñoz-Barrutia A, Marabini R, Vargas J, Carazo JM. Sorzano COS, et al. Among authors: ramirez aportela e. Faraday Discuss. 2022 Nov 8;240(0):210-227. doi: 10.1039/d2fd00059h. Faraday Discuss. 2022. PMID: 35861059
On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy.
Sorzano COS, Jiménez-Moreno A, Maluenda D, Martínez M, Ramírez-Aportela E, Krieger J, Melero R, Cuervo A, Conesa J, Filipovic J, Conesa P, Del Caño L, Fonseca YC, Jiménez-de la Morena J, Losana P, Sánchez-García R, Strelak D, Fernández-Giménez E, de Isidro-Gómez FP, Herreros D, Vilas JL, Marabini R, Carazo JM. Sorzano COS, et al. Among authors: ramirez aportela e. Acta Crystallogr D Struct Biol. 2022 Apr 1;78(Pt 4):410-423. doi: 10.1107/S2059798322001978. Epub 2022 Mar 16. Acta Crystallogr D Struct Biol. 2022. PMID: 35362465 Free PMC article.
Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium.
Semchonok DA, Mondal J, Cooper CJ, Schlum K, Li M, Amin M, Sorzano COS, Ramírez-Aportela E, Kastritis PL, Boekema EJ, Guskov A, Bruce BD. Semchonok DA, et al. Among authors: ramirez aportela e. Plant Commun. 2021 Oct 13;3(1):100248. doi: 10.1016/j.xplc.2021.100248. eCollection 2022 Jan 10. Plant Commun. 2021. PMID: 35059628 Free PMC article.
Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.
Strelak D, Jiménez-Moreno A, Vilas JL, Ramírez-Aportela E, Sánchez-García R, Maluenda D, Vargas J, Herreros D, Fernández-Giménez E, de Isidro-Gómez FP, Horacek J, Myska D, Horacek M, Conesa P, Fonseca-Reyna YC, Jiménez J, Martínez M, Harastani M, Jonić S, Filipovic J, Marabini R, Carazo JM, Sorzano COS. Strelak D, et al. Among authors: ramirez aportela e. Molecules. 2021 Oct 15;26(20):6224. doi: 10.3390/molecules26206224. Molecules. 2021. PMID: 34684805 Free PMC article.
Cryo-EM density maps adjustment for subtraction, consensus and sharpening.
Fernández-Giménez E, Martínez M, Sánchez-García R, Marabini R, Ramírez-Aportela E, Conesa P, Carazo JM, Sorzano COS. Fernández-Giménez E, et al. Among authors: ramirez aportela e. J Struct Biol. 2021 Dec;213(4):107780. doi: 10.1016/j.jsb.2021.107780. Epub 2021 Aug 29. J Struct Biol. 2021. PMID: 34469787 Free article.
Cryo-EM and Single-Particle Analysis with Scipion.
Jiménez-Moreno A, Del Caño L, Martínez M, Ramírez-Aportela E, Cuervo A, Melero R, Sánchez-García R, Strelak D, Fernández-Giménez E, de Isidro-Gómez FP, Herreros D, Conesa P, Fonseca Y, Maluenda D, Jiménez de la Morena J, Macías JR, Losana P, Marabini R, Carazo JM, Sorzano COS. Jiménez-Moreno A, et al. Among authors: ramirez aportela e. J Vis Exp. 2021 May 29;(171). doi: 10.3791/62261. J Vis Exp. 2021. PMID: 34125107
3DBionotes COVID-19 edition.
Macias JR, Sanchez-Garcia R, Conesa P, Ramirez-Aportela E, Martinez Gonzalez M, Wert-Carvajal C, Parra-Perez AM, Segura Mora J, Horrell S, Thorn A, Sorzano COS, Carazo JM. Macias JR, et al. Among authors: ramirez aportela e. Bioinformatics. 2021 Nov 18;37(22):4258-4260. doi: 10.1093/bioinformatics/btab397. Bioinformatics. 2021. PMID: 34014278 Free PMC article.
35 results