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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: vilas jl. Biol Imaging. 2023 Jun 29;3:e13. doi: 10.1017/S2633903X23000132. eCollection 2023. Biol Imaging. 2023. PMID: 38510163 Free PMC article.
Using Scipion for stream image processing at Cryo-EM facilities.
Gómez-Blanco J, de la Rosa-Trevín JM, Marabini R, Del Cano L, Jiménez A, Martínez M, Melero R, Majtner T, Maluenda D, Mota J, Rancel Y, Ramírez-Aportela E, Vilas JL, Carroni M, Fleischmann S, Lindahl E, Ashton AW, Basham M, Clare DK, Savage K, Siebert CA, Sharov GG, Sorzano COS, Conesa P, Carazo JM. Gómez-Blanco J, et al. Among authors: vilas jl. J Struct Biol. 2018 Dec;204(3):457-463. doi: 10.1016/j.jsb.2018.10.001. Epub 2018 Oct 5. J Struct Biol. 2018. PMID: 30296492 Free PMC article.
Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion.
Maluenda D, Majtner T, Horvath P, Vilas JL, Jiménez-Moreno A, Mota J, Ramírez-Aportela E, Sánchez-García R, Conesa P, Del Caño L, Rancel Y, Fonseca Y, Martínez M, Sharov G, García CA, Strelak D, Melero R, Marabini R, Carazo JM, Sorzano COS. Maluenda D, et al. Among authors: vilas jl. Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):882-894. doi: 10.1107/S2059798319011860. Epub 2019 Oct 1. Acta Crystallogr D Struct Biol. 2019. PMID: 31588920 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: vilas jl. Molecules. 2021 Oct 15;26(20):6224. doi: 10.3390/molecules26206224. Molecules. 2021. PMID: 34684805 Free PMC article.
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: vilas jl. 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.
ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation.
Jiménez de la Morena J, Conesa P, Fonseca YC, de Isidro-Gómez FP, Herreros D, Fernández-Giménez E, Strelak D, Moebel E, Buchholz TO, Jug F, Martinez-Sanchez A, Harastani M, Jonic S, Conesa JJ, Cuervo A, Losana P, Sánchez I, Iceta M, Del Cano L, Gragera M, Melero R, Sharov G, Castaño-Díez D, Koster A, Piccirillo JG, Vilas JL, Otón J, Marabini R, Sorzano COS, Carazo JM. Jiménez de la Morena J, et al. Among authors: vilas jl. J Struct Biol. 2022 Sep;214(3):107872. doi: 10.1016/j.jsb.2022.107872. Epub 2022 Jun 2. J Struct Biol. 2022. PMID: 35660516 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: vilas jl. Faraday Discuss. 2022 Nov 8;240(0):210-227. doi: 10.1039/d2fd00059h. Faraday Discuss. 2022. PMID: 35861059
Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.
de la Rosa-Trevín JM, 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 JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano CO, Carazo JM. de la Rosa-Trevín JM, et al. Among authors: vilas jl. J Struct Biol. 2016 Jul;195(1):93-9. doi: 10.1016/j.jsb.2016.04.010. Epub 2016 Apr 20. J Struct Biol. 2016. PMID: 27108186
A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.
Sorzano COS, Vargas J, Otón J, de la Rosa-Trevín JM, Vilas JL, Kazemi M, Melero R, Del Caño L, Cuenca J, Conesa P, Gómez-Blanco J, Marabini R, Carazo JM. Sorzano COS, et al. Among authors: vilas jl. Biomed Res Int. 2017;2017:6482567. doi: 10.1155/2017/6482567. Epub 2017 Sep 17. Biomed Res Int. 2017. PMID: 29312997 Free PMC article. Review.
69 results