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Page 1
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: de isidro gomez fp. Molecules. 2021 Oct 15;26(20):6224. doi: 10.3390/molecules26206224. Molecules. 2021. PMID: 34684805 Free PMC 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: de isidro gomez fp. J Vis Exp. 2021 May 29;(171). doi: 10.3791/62261. J Vis Exp. 2021. PMID: 34125107
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: de isidro gomez fp. 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: de isidro gomez fp. 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 in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.
Sorzano COS, Jiménez-Moreno A, Maluenda D, Ramírez-Aportela E, Martínez M, Cuervo A, Melero R, Conesa JJ, Sánchez-García R, Strelak D, Filipovic J, Fernández-Giménez E, de Isidro-Gómez F, Herreros D, Conesa P, Del Caño L, Fonseca Y, de la Morena JJ, Macías JR, Losana P, Marabini R, Carazo JM. Sorzano COS, et al. Methods Mol Biol. 2021;2305:257-289. doi: 10.1007/978-1-0716-1406-8_13. Methods Mol Biol. 2021. PMID: 33950394
Improvements on marker-free images alignment for electron tomography.
Sorzano COS, de Isidro-Gómez F, Fernández-Giménez E, Herreros D, Marco S, Carazo JM, Messaoudi C. Sorzano COS, et al. J Struct Biol X. 2020 Sep 17;4:100037. doi: 10.1016/j.yjsbx.2020.100037. eCollection 2020. J Struct Biol X. 2020. PMID: 33024955 Free PMC article.
Structural analysis of receptors and actin polarity in platelet protrusions.
Sorrentino S, Conesa JJ, Cuervo A, Melero R, Martins B, Fernandez-Gimenez E, de Isidro-Gomez FP, de la Morena J, Studt JD, Sorzano COS, Eibauer M, Carazo JM, Medalia O. Sorrentino S, et al. Among authors: de isidro gomez fp. Proc Natl Acad Sci U S A. 2021 Sep 14;118(37):e2105004118. doi: 10.1073/pnas.2105004118. Proc Natl Acad Sci U S A. 2021. PMID: 34504018 Free PMC article.
Graphite to diamond transition induced by photoelectric absorption of ultraviolet photons.
Gómez de Castro AI, Rheinstädter M, Clancy P, Castilla M, de Isidro F, Larruquert JI, de Lis-Sánchez T, Britten J, Cabero Piris M, de Isidro-Gómez FP. Gómez de Castro AI, et al. Among authors: de isidro gomez fp. Sci Rep. 2021 Jan 28;11(1):2492. doi: 10.1038/s41598-021-81153-3. Sci Rep. 2021. PMID: 33510191 Free PMC article.
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: de isidro gomez fp. Biol Imaging. 2023 Jun 29;3:e13. doi: 10.1017/S2633903X23000132. eCollection 2023. Biol Imaging. 2023. PMID: 38510163 Free PMC article.