Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy
de la Rosa-Trevín, J.M., 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.
Published in Journal of structural biology (01.07.2016)
Published in Journal of structural biology (01.07.2016)
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Journal Article
Dysregulated Gut Homeostasis Observed Prior to the Accumulation of the Brain Amyloid-β in Tg2576 Mice
Honarpisheh, Pedram, Reynolds, Caroline R, Blasco Conesa, Maria P, Moruno Manchon, Jose F, Putluri, Nagireddy, Bhattacharjee, Meenakshi B, Urayama, Akihiko, McCullough, Louise D, Ganesh, Bhanu P
Published in International journal of molecular sciences (03.03.2020)
Published in International journal of molecular sciences (03.03.2020)
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Journal Article
Potential caveats of putative microglia-specific markers for assessment of age-related cerebrovascular neuroinflammation
Honarpisheh, Pedram, Lee, Juneyoung, Banerjee, Anik, Blasco-Conesa, Maria P, Honarpisheh, Parisa, d'Aigle, John, Mamun, Abdullah A, Ritzel, Rodney M, Chauhan, Anjali, Ganesh, Bhanu P, McCullough, Louise D
Published in Journal of neuroinflammation (01.12.2020)
Published in Journal of neuroinflammation (01.12.2020)
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Journal Article
Stabilizing histamine release in gut mast cells mitigates peripheral and central inflammation after stroke
Conesa, Maria P Blasco, Blixt, Frank W, Peesh, Pedram, Khan, Romeesa, Korf, Janelle, Lee, Juneyoung, Jagadeesan, Gayathri, Andersohn, Alexander, Das, Tushar K, Tan, Chunfeng, Di Gesu, Claudia, Colpo, Gabriela Delevati, Moruno-Manchón, Jose Félix, McCullough, Louise D, Bryan, Robert, Ganesh, Bhanu P
Published in Journal of neuroinflammation (07.10.2023)
Published in Journal of neuroinflammation (07.10.2023)
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Journal Article
Integration of Cryo-EM Model Building Software in Scipion
Martínez, M, Jiménez-Moreno, A, Maluenda, D, Ramírez-Aportela, E, Melero, R, Cuervo, A, Conesa, P, del Caño, L, Fonseca, Y. C, Sánchez-García, R, Strelak, D, Conesa, J. J, Fernández-Giménez, E, de Isidro, F, Sorzano, C. O. S, Carazo, J. M, Marabini, R
Published in Journal of chemical information and modeling (26.05.2020)
Published in Journal of chemical information and modeling (26.05.2020)
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Journal 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, J.M., Sorzano, C.O.S.
Published in Journal of structural biology (01.12.2021)
Published in Journal of structural biology (01.12.2021)
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Journal Article
Central IRF4/5 Signaling Are Critical for Microglial Activation and Impact on Stroke Outcomes
Ngwa, Conelius, Al Mamun, Abdullah, Qi, Shaohua, Sharmeen, Romana, Conesa, Maria P. Blasco, Ganesh, Bhanu P., Manwani, Bharti, Liu, Fudong
Published in Translational stroke research (01.08.2024)
Published in Translational stroke research (01.08.2024)
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Journal Article
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM
Herreros, D., Krieger, J. M., Fonseca, Y., Conesa, P., Harastani, M., Vuillemot, R., Hamitouche, I., Serrano Gutiérrez, R., Gragera, M., Melero, R., Jonic, S., Carazo, J. M., Sorzano, C. O. S.
Published in Acta crystallographica. Section D, Biological crystallography. (01.07.2023)
Published in Acta crystallographica. Section D, Biological crystallography. (01.07.2023)
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Journal Article
On bias, variance, overfitting, gold standard and consensus in single‐particle analysis by cryo‐electron microscopy
Sorzano, C. O. S., 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, Y. C., Jiménez-de la Morena, J., Losana, P., Sánchez-García, R., Strelak, D., Fernández-Giménez, E., de Isidro-Gómez, F. P., Herreros, D., Vilas, J. L., Marabini, R., Carazo, J. M.
Published in Acta crystallographica. Section D, Biological crystallography. (01.04.2022)
Published in Acta crystallographica. Section D, Biological crystallography. (01.04.2022)
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Journal Article
Peripherally-sourced myeloid antigen presenting cells increase with advanced aging
Honarpisheh, Pedram, Blixt, Frank W., Blasco Conesa, Maria P., Won, William, d'Aigle, John, Munshi, Yashasvee, Hudobenko, Jacob, Furr, J. Weldon, Mobley, Alexis, Lee, Juneyoung, Brannick, Katherine E., Zhu, Liang, Hazen, Amy L., Bryan, Robert M., McCullough, Louise D., Ganesh, Bhanu P.
Published in Brain, behavior, and immunity (01.11.2020)
Published in Brain, behavior, and immunity (01.11.2020)
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Journal Article
A new algorithm for high-resolution reconstruction of single particles by electron microscopy
Sorzano, C.O.S., Vargas, J., de la Rosa-Trevín, J.M., Jiménez, A., Maluenda, D., Melero, R., Martínez, M., Ramírez-Aportela, E., Conesa, P., Vilas, J.L., Marabini, R., Carazo, J.M.
Published in Journal of structural biology (01.11.2018)
Published in Journal of structural biology (01.11.2018)
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Journal Article
Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening
Vilas, J.L., Vargas, J., Martinez, M., Ramirez-Aportela, E., Melero, R., Jimenez-Moreno, A., Garduño, E., Conesa, P., Marabini, R., Maluenda, D., Carazo, J.M., Sorzano, C.O.S.
Published in Journal of structural biology (01.03.2020)
Published in Journal of structural biology (01.03.2020)
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Journal Article
Algorithmic robustness to preferred orientations in single particle analysis by CryoEM
Sorzano, C.O.S., Semchonok, D., Lin, S.-C., Lo, Y.-C., Vilas, J.L., Jiménez-Moreno, A., Gragera, M., Vacca, S., Maluenda, D., Martínez, M., Ramírez-Aportela, E., Melero, R., Cuervo, A., Conesa, J.J., Conesa, P., Losana, P., Caño, L. del, de la Morena, J. Jiménez, Fonseca, Y.C., Sánchez-García, R., Strelak, D., Fernández-Giménez, E., de Isidro, F., Herreros, D., Kastritis, P.L., Marabini, R., Bruce, B.D., Carazo, J.M.
Published in Journal of structural biology (01.03.2021)
Published in Journal of structural biology (01.03.2021)
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Journal Article
Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy
Sorzano, C. O. S., Jiménez, A., Mota, J., Vilas, J. L., Maluenda, D., Martínez, M., Ramírez-Aportela, E., Majtner, T., Segura, J., Sánchez-García, R., Rancel, Y., del Caño, L., Conesa, P., Melero, R., Jonic, S., Vargas, J., Cazals, F., Freyberg, Z., Krieger, J., Bahar, I., Marabini, R., Carazo, J. M.
Published in Acta crystallographica. Section F, Structural biology communications (01.01.2019)
Published in Acta crystallographica. Section F, Structural biology communications (01.01.2019)
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Journal Article
Using Scipion for stream image processing at Cryo-EM facilities
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.
Published in Journal of structural biology (01.12.2018)
Published in Journal of structural biology (01.12.2018)
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Journal Article
Colorectal serrated adenocarcinoma shows a different profile of oncogene mutations, MSI status and DNA repair protein expression compared to conventional and sporadic MSI-H carcinomas
García-Solano, J., Conesa-Zamora, P., Carbonell, P., Trujillo-Santos, J., Torres-Moreno D, D., Pagán-Gómez, I., Rodríguez-Braun, E., Pérez-Guillermo, M.
Published in International journal of cancer (15.10.2012)
Published in International journal of cancer (15.10.2012)
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Journal Article
Flexible workflows for on‐the‐fly electron‐microscopy single‐particle image processing using Scipion
Maluenda, D., Majtner, T., Horvath, P., Vilas, J. L., 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, C.A., Strelak, D., Melero, R., Marabini, R., Carazo, J. M., Sorzano, C. O. S.
Published in Acta crystallographica. Section D, Biological crystallography. (01.10.2019)
Published in Acta crystallographica. Section D, Biological crystallography. (01.10.2019)
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Journal Article
Image processing tools for the validation of CryoEM maps
Sorzano, C. O. S, Vilas, J. L, Ramírez-Aportela, E, Krieger, J, del Hoyo, D, Herreros, D, Fernandez-Giménez, E, Marchán, D, Macías, J. R, 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, J. M
Published in Faraday discussions (08.11.2022)
Published in Faraday discussions (08.11.2022)
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Journal 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, F.P., Herreros, D., Conesa, P., Fonseca, Y., Maluenda, D., Jiménez de la Morena, J., Macías, J.R., Losana, P., Marabini, R., Carazo, J.M., Sorzano, C.O.S.
Published in Journal of visualized experiments (29.05.2021)
Published in Journal of visualized experiments (29.05.2021)
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Journal Article
Blind estimation of DED camera gain in Electron Microscopy
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.
Published in Journal of structural biology (01.08.2018)
Published in Journal of structural biology (01.08.2018)
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Journal Article