Publications

Rational acquisition of laboratory equipment: an accurate mathematical model to estimate the trade-offs in shared and nonshared equipment.
Sorzano COS, Carazo JM
Acta crystallographica. Section D, Structural biology 82( 6):638 – 645

Insights from aquaporin structures into drug-resistant sleeping sickness.
Matusevicius M, Corey RA, Gragera M, Yamashita K, Sprenger T, Ungogo M, Blaza JN, Castro-Hartmann P, Chirgadze DY, Vedithi SC, Afanasyev P, Melero R, Warshamanage R, Gusach A, Carazo JM, Carrington M, Blundell T, Murshudov GN, Stansfeld PJ, Sansom MSP, De Koning HP, Tate CG, Weyand, S.
ELife. 14:RP107460.

Membrane and vesicle structure detection in cryo-electron tomography based on deep learning.
Morales-Martínez A, Garduño E, Carazo JM, Sorzano COS, Vilas JL.
J Struct Biol. 217(4):108258.

Merging conformational landscapes in a single consensus space with FlexConsensus algorith.
Herreros, D., Perez Mata, C., Sorzano, C.O.S., Carazo, J.M.
Nat Methods. 22(10):2118-2126.

How many (distinguishable) classes can we identify in single-particle analysis?
Lauzirika O, Pernica M, Herreros D, Ramírez-Aportela E, Krieger J, Gragera M, Iceta M, Conesa P, Fonseca Y, Jiménez J, Filipovic J, Carazo JM, Sorzano COS.
Acta Crystallogr D Struct Biol. 81(Pt 10):535-544.

Correction to “Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5′-Untranslated Region of SARS-CoV-2”.
Mertinkus KR, Oxenfarth A, Richter C, Wacker A, Mata CP, Carazo JM, Schlundt A, Schwalbe H.
J Am Chem Soc. 147(8):7158.

Structural analysis of HER2-trastuzumab complex reveals receptor conformational adaptation
Vacca, S., Gragera, M., Buschiazzo, A., Herreros, D., Krieger, J. M., Bonn-Garcia, S., Melero, R., Sorzano, C. O. S., Carazo, J. M., Medalia, O., & Plückthun, A.
Science Advances, 11 (30)

On interrogating electron microscopy images to discover proteins in the cell.
Carazo, J.M.
IUCrJ, 12(2), pp. 139-140

Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Herreros, D., Perez Mata, C., Noddings, C., Irene, D., Krieger, J. M., Agard, D., Tsai, M.-D., Sorzano, C. O. S., & Carazo, J. M.
Nature Communications, 16 (3751)

Automatic detection of alignment errors in cryo-electron tomography.
de Isidro-Gómez, F.P., Vilas, J.L., Carazo, J.M., Sorzano, C.O.S.
Journal of Structural Biology, 217(1)

Merging conformational landscapes in a single consensus space with FlexConsensus algorith.
Herreros, D., Perez Mata, C., Sorzano, C.O.S., Carazo, J.M.
bioRxiv, 2025-01.

Dissecting the Conformational Heterogeneity of Stem-Loop Sibstructures of the Fifth Element in the 5´-Untranslated Region of SARS-CoV-2.
Mertinkus, K. R., Oxenfarth, A., Richter, C., Wacker, A., Mata, C. P., Carazo, J. M., Schlund, A., Schwalbe, H.
Journal of the American Chemical Society, 146(44), 30139-30154.

Fast Global Image Alignment Algorithm for CryoEM through Vector Compression.
Zarrabeitia, O., Ramírez-Aportela, E., Carazo, J.M., Sorzano, C.O.S.
IEEE International Symposium on Biomedical Imaging (ISBI), Athens, Greece, 2024, pp. 1-4,

Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Herreros, D., Perez Mata, C., Noddings, C., Irene, D., Krieger, J. M., Agard, D., Tsai, M.-D., Sorzano, C. O. S., & Carazo, J. M.
bioRxiv

The future of integrated structural biology.
Schwalbe, H., Audergon, P., Haley, N., Alen Amaro, C., Agirre, J., Baldus, M., Banci, L., Baumeister, W., Blackledge, M., Carazo, J. M., Djinovic Carugo, K., Celie, P., Felli, I., Hart, D. J., Hauß, T., Lehtiö, L., Lindorff-Larsen, K., Márquez, J., Matagne, A., Pierattelli, R., Rosato, A., Sobott, F., Sreeramulu, S., Steyaert, J., Sussman, J. L., Trantirek, L., Weiss, M. S., & Wilmanns, M.
Structure.

Scipion flexibility hub and Scipion chem: New frameworks coupling computational biophysics of protein dynamics and virtual screening to cryo-electron microscopy.
Krieger, J.M., Herreros, D., del Hoyo, D., Fonseca, Y., Gragera, M., P. Mata, C., Lomas, A., Ulzurrun, E., Campillo, N.E., Conesa, P., Sorzano, C.O.S., Carazo, J.M.
Biophysical Journal, 123(3), 14a-15a.

Discrimination of etiologically different cholestasis by modeling proteomics datasets.
Guerrero, L., Vindel-Alfageme, J., Hierro, L., Stark, L., Vicent, D., Sorzano, C. Ó., & Corrales, F. J.
International Journal of Molecular Sciences, 25(7), 3684.

A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions.
de Isidro-Gómez, F. P., Vilas, J. L., Losana, P., Carazo, J. M., & Sorzano, C. O. S.
Journal of Structural Biology, 216(1), 108056.

Performance and quality comparison of movie alignment software for Cryogenic Electron Microscopy.
Střelák, D., Marchán, D., Carazo, J. M., & S. Sorzano, C.O.S.
Micromachines, 14(10), 1835.

A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis.
Fernández-Giménez, E., Martínez, M. M., Marabini, R., Strelak, D., Sánchez-García, R., Carazo, J. M., & Sorzano, C. O. S.
Journal of Structural Biology, 215(4), 108024.

Local defocus estimation in single particle analysis in cryo-electron microscopy.
Fernandez-Gimenez, E., Carazo, J. M., & Sorzano, C. O. S.
Journal of Structural Biology, 215(4), 108030.

ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin. 
Cacho-Navas, C., López-Pujante, C., Reglero-Real, N., Colás-Algora, N., Cuervo, A., Conesa, J. J., Barroso, S., De Rivas, G., Ciordia, S., Paradela, A., D’Agostino, G., Manzo, C., Feito, J., Andrés, G., Correas, I., Carazo, J. M., Nourshargh, S., Huch, M., & Millán, J.
eLife.

A survey of the European Open Science Cloud services for expanding the capacity and capabilities of multidisciplinary scientific applications.
Calatrava, A., Asorey, H., Astalos, J., Azevedo, A., Benincasa, F., Blanquer, I., Bobak, M., Brasileiro, F., Codó, L., del Cano, L., Esteban, B., Ferret, M., Handl, J., Kerzenmacher, T., Kozlov, V., Křenek, A., Martins, R., Pavesio, M., Rubio-Montero, A. J., & Sánchez-Ferrero, J.
Computer Science Review, 49, 100571

Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing
Krieger JM; Sorzano COS; Carazo JM
International Journal of Molecular Sciences. 2023; 24(18):14245.

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials.
Herreros D; Lederman RR; Krieger JM; Jimenez-Moreno A; Martinez M; Myska D; Strelak D; Filipovic J; Sorzano COS; Carazo JM
Nature communications. 14(1): 154 – 154

Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.
Herreros D; Krieger JM; Fonseca Y; Conesa P; Harastani M; Vuillemot R; Hamitouche I; Serrano Gutiérrez R; Gragera M; Melero R; Jonic S; Carazo JM; Sorzano COS.
Acta Crystallographica Section D Structural Biology, 79(7), 569-584

ZART: A novel multiresolution reconstruction algorith with motion-blur correction for single particle analysis.
Herreros D; Kiska J; Ramírez-Aportela E; Filipovic K; Carazo JM; Sorzano COS.
Journal of Molecular Biology, 435(9), 168088

A fijivirus major viroplasm protein shows RNA-stimulated ATPase activity by adopting pentameric and hexameric assemblies of dimers.
Llauger G; Melero R; Monti D; Sycz G; Huck-Iriart C; Cerutti ML; Klinke S; Mikkelsen E; Tijman A; Arranz R; Alfonso V; Arellano SM; Goldbaum FA; Sterckx YG; Carazo JM; Kaufman SB; Dans PD; del Vas M; Otero LH.
mBio, 14(2)

Image processing tools for the validation of CryoEM maps.
Sorzano COS; Vilas JL; Ramirez-Aportela E; Krieger J; del Hoyo D; Herreros D; Fernandez-Gimenez E; Marchan D; Gomez F. de Isidro; Macias JR; Sanchez I; del Cano L; Fonseca-Reyna Y; Conesa P; Garcia-Mena A; Burguet J; Condado J; Garcia JM; Martinez M; Munoz-Barrutia A; Marabini R; Vargas J; Carazo, JM.
Faraday Discussions. 240(0): 228 – 228

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.
Ginex T; Marco-Marin C; Wieczor M; Mata CP; Krieger J; Ruiz-Rodriguez P; Lopez-Redondo M; Frances-Gomez C; Melero R; Sanchez-Sorzano CO; Martinez M; Gougeard N; Forcada-Nadal A; Zamora-Caballero S; Gozalbo-Rovira R; Sanz-Frasquet C; Arranz R; Bravo J; Rubio V; Marina A; Geller R; Comas I; Gil C; Coscolla M; Orozco M; Llacer JL; Carazo JM.
PLOS PATHOGENS. 18: e1010631

Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools.
Ramirez-Aportela E; Carazo JM; Sorzano COS.
IUCRJ (9): 632 – 638

Emerging Themes in CryoEM-Single Particle Analysis Image Processing.
Vilas JL; Carazo JM; Sorzano COS.
Chemical Reviews. 122(17): 13915 – 13951

ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation.
de la Morena JJ; Conesa P; Fonseca YC; de Isidro-Gomez FP; Herreros D; Fernandez-Gimenez E; Strelak D; Moebel E; Buchholz TO; Jug F; Martinez-Sanchez A; Harastani M; Jonic S; Conesa JJ; Cuervo A; Losana P; Sanchez I, Iceta M; del Cano L; Gragera M; Melero R; Sharov G; Castano-Diez D; Koster A; Piccirillo JG; Vilas JL; Oton J; Marabini R; Sorzano COS; Carazo JM.
Journal of Structural Biology. 214(3): 107872

BIPSPI plus : Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction.
Sanchez-Garcia R; Macias JR; Sorzano COS; Carazo JM; Segura J.
Journal of Molecular Biology. 434(11): 167556

Cryo-Electron Microscopy: The field of 1,000(+) methods.
Sorzano COS; Carazo JM.
Journal of Structural Biology. 214(3): 107861

Image processing tools for the validation of CryoEM maps.
Sorzano COS; Vilas JL; Ramirez-Aportela E; Krieger J; del Hoyo D; Herreros D; Fernandez-Gimenez E; Marchan D; Macias JR; Sanchez I; del Cano L; Fonseca-Reyna Y; Conesa P; Garcia-Mena A; Burguet J; Garcia Condado J; Mendez Garcia J; Martinez M; Munoz-Barrutia A; Marabini R; Vargas J; Carazo JM.
Faraday Discussions. 240(0): 210 – 227

Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.
Krieger JM; Sorzano COS; Carazo JM; Bahar I.
Acta Crystallographica Section D-Structural Biology. 78: 399 – 409

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy.
Sorzano COS; Jimenez-Moreno A; Maluenda D; Martinez M; Ramirez-Aportela E; Krieger J; Melero R; Cuervo A; Conesa J; Filipovic J; Conesa P; del Cano L; Fonseca YC; Jimenez-de la Morena J; Losana P; Sanchez-Garcia R; Strelak D; Fernandez-Gimenez E; de Isidro-Gomez FP; Herreros D; Vilas JL; Marabini R; Carazo JM.
Acta Crystallographica Section D-Structural Biology. 78: 410 – 423

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials.
Herreros D; Lederman RR; Krieger J; Jimenez-Moreno A; Martinez M; Myska D; Strelak D; Filipovic J; Bahar I; Carazo JM; Sanchez COS.
IUCRJ. 8: 992 – 1005.

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.
Strelak D; Jimenez-Moreno A; Vilas JL; Ramirez-Aportela E; Sanchez-Garcia R; Maluenda D; Vargas J; Herreros D; Fernandez-Gimenez E; de Isidro-Gomez FP; Horacek J; Myska D; Horacek M; Conesa P; Fonseca-Reyna YC; Jimenez J; Martinez M; Harastani M; Jonic S; Filipovic J; Marabini R; Carazo JM; Sorzano COS.
Molecules. 26(20): 6224

Scipion for tomography: An expansion of Scipion software framework towards integration, reproducibility and validation in cryo-electron tomography.
de Isidro Gomez FP; de la Morena JJ; Conesa P; Herreros D; Fernandez-Gimenez E; Fonseca YC; Strelak D; Conesa JJ; Cuervo A; Losana P; Sorzano COS; Carazo JM.
Acta Crystallographica A-Foundation And Advances. 77: A238 – A238

3DBionotes Covid-19 Edition.
Macias JR; Sanchez-Garcia R; Conesa, P; Ramirez-Aportela E; Martinez Gonzalez M; Wert-Carvajal C; Parra-Perez AM; Mora JS; Horrell S; Thorn A; Sorzano, COS; Carazo JM.
Acta Crystallographica A-Foundation And Advances.77: C792 – C792

PDBe-KB: collaboratively defining the biological context of structural.
PDBe-KB Consortium.
Nucleic Acids research. 50(D1): D534 – D542

Improvements on marker-free images alignment for electron tomography
C.O.S.Sorzano, F.de Isidro-Gómez, E.Fernández-Giménez, D.Herreros, S.Marco, J.M.Carazo, C.Messaoudi
Journal of Structural Biology: X.  4: 100037

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.
Roberto Melero, Carlos Oscar S. Sorzano, Brent Foster, José-Luis Vilas, Marta Martínez, Roberto Marabini, Erney Ramírez-Aportela, Ruben Sanchez-Garcia, David Herreros, Laura del Caño, Patricia Losana, Yunior C. Fonseca-Reyna, Pablo Conesa, Daniel Wrapp, Pablo Chacon, Jason S. McLellan, Hemant D. Tagare and Jose-Maria Carazo
IUCrJ. 7(6): 1059-1069

Local resolution estimates of cryoEM reconstructions.
Vilas, J L; Heymann, J B; Tagare, H D; Ramirez-Aportela, E; Carazo, J M; Sorzano, Cos
Current opinion in structural biology. 64:74-78

A benchmark set of highly-efficient CUDA and OpenCL kernels and its dynamic autotuning with Kernel Tuning Toolkit.
FilipPetrovič, DavidStřelák, JanaHozzová, JaroslavOl’ha, Richard Trembecký, Siegfried Benkner, Jiří Filipovičac.
Future Generation Computer Systems. 108: 161-177

FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy
David Střelák, Jiří Filipovič, Amaya Jiménez-Moreno, Jose María Carazo and Carlos Óscar Sánchez Sorzano.
Electronics 2020, 9(6), 1040

Localized reconstruction in scipion expedites the analysis of symmetry mismatches in Cryo-EM data
Vahid Abrishami, Serban L. Ilca, Josue Gomez-Blanco, Ilona Rissanen, José Miguel de la Rosa-Trevín, Vijay S. Reddy, José-Maria Carazo, Juha T. Huiskonen.
Progress in Biophysics and Molecular Biology, 160, 43-52.

MicrographCleaner: a python package for cryo-EM micrograph cleaning using deep learning.
Sanchez-Garcia R, Segura J, Maluenda D, Sorzano COS, Carazo JM.
J Struct Biol. 107498

Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells.
Carter SD, Hampton CM, Langlois R, Melero R, Farino ZJ, Calderon MJ, Li W, Wallace CT, Tran NH, Grassucci RA, Siegmund SE, Pemberton J, Morgenstern TJ, Eisenman L, Aguilar JI, Greenberg NL, Levy ES, Yi E, Mitchell WG, Rice WJ, Wigge C, Pilli J, George EW, Aslanoglou D, Courel M, Freyberg RJ, Javitch JA, Wills ZP, Area-Gomez E, Shiva S, Bartolini F, Volchuk A, Murray SA, Aridor M, Fish KN, Walter P, Balla T, Fass D, Wolf SG, Watkins SC, Carazo JM, Jensen GJ, Frank J, Freyberg Z.
Sci Adv. 6(14):eaay9572

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 YC, Sánchez-García R, Strelak D, Conesa JJ, Fernández-Giménez E, de Isidro F, Sorzano COS, Carazo JM, Marabini R.
J. Chem. Inf. Model.  60(5):2533-2540.

Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening.
Vilas JL, Vargas J, Martinez M, Ramirez-Aportela E, Melero R, Jimenez-Moreno A, Garduño E, Conesa P, Marabini R, Maluenda D, Carazo JM, Sorzano COS.
J Struct Biol. 209(3):107447

Measuring local-directional resolution and local anisotropy in cryo-EM maps.
Vilas JL, Tagare HD, Vargas J, Carazo JM, Sorzano COS.
Nat Commun. 11(1):55

Measurement of local resolution in electron tomography.
Vilas, J L; Oton, J; Messaoudi, C; Melero, R; Conesa, P; Ramirez-Aportela, E; Mota, J; Martinez, M; Jimenez, A; Marabini, R; Carazo, J M; Vargas, J; Sorzano, C O S.
Journal of structural biology: X. 4:100016

Automatic local resolution-based sharpening of cryoEM maps.
Ramirez-Aportela E., Vilas JL, Glukhova, A, Melero, R, Conesa, P, Martínez, M, Manuel, D. Mota, J., Jimenez A, Vargas, J, Marabini R, Sexton PM, Carazo JM, Sorzano COSS.
Bioinformatics. 36(3):765-772

DeepRes: a new deep-learning and aspect-based local resolution method for electron-microscopy maps.
Ramirez-Apotela, E., Mota, J., Conesa, P., Carazo, JM and Sorzano, COSS.
IUCrJ. Volume 6(6)

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion.
Maluenda, D; Majtner, T; Horvath, P; Vilas, J L; Jimenez-Moreno, A; Mota, J; Ramirez-Aportela, E; Sanchez-Garcia, R; Conesa, P; Del Cano, L; Rancel, Y; Fonseca, Y; Martinez, M; Sharov, G; Garcia, C A; Strelak, D; Melero, R; Marabini, R; Carazo, J M; Sorzano, C O S
Acta crystallographica.Volumen:75(10):882-894

A GPU acceleration of 3-D Fourier reconstruction in cryo-EM.
Strelak, D; Sorzano, COS; Carazo, JM ; Filipovic, J.
International Journal of High Performance Computing Applications.33(5): 948-959

Validation of electron microscopy initial models via small angle X-ray scattering curves.
Jimenez, A; Jonic, S ; Majtner, T; Oton, J; Vilas, JL; Maluenda, D; Mota, J; Ramirez-Aportela, E ; Martinez, M; Rancel, Y; Segura, J; Sanchez-Garcia, R; Melero, R; del Cano, L; Conesa, P; Skjaerven, L; Marabini, R; Carazo, JM; Sorzano, COS.
Bioinformatics. 35(14): 2427-2433

BIPSPI: a method for the prediction of partner-specific protein-protein interfaces.
Sanchez-Garcia, R; Sorzano, COS; Carazo, JM; Segura, J
Bioinformatics. 35(3): 470-477

Structural basis for cooperativity of human monoclonal antibodies to meningococcal factor H-binding protein.
Peschiera I, Giuliani M, Giusti F, Melero R, Paccagnini E, Donnarumma D, Pansegrau W, Carazo JM, Sorzano COS, Scarselli M, Masignani V, Liljeroos LJ, Ferlenghi I.
Commun Biol. 2:241

Cryo-Electron Tomography and Proteomics studies of centrosomes from differentiated quiescent thymocytes.
Busselez J, Chichón FJ, Rodríguez MJ, Alpízar A, Gharbi SI, Franch M, Melero R, Paradela A, Carrascosa JL, Carazo JM.
Sci Rep. 9(1):7187

3DBIONOTES v3.0: Crossing molecular and structural biology data with genomic variations.
Segura J, Sanchez-Garcia R, Sorzano COS, Carazo JM.
Bioinformatics. pii: btz118

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.
Sorzano COS, Jiménez A, Mota J, Vilas JL, 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 JM.
Acta Crystallogr F Struct Biol Commun. 75( 1):19-32

Advances in image processing for single-particle analysis by electron cryomicroscopy and challenges ahead.
Vilas JL, Tabassum N, Mota J, Maluenda D, Jiménez-Moreno A, Majtner T, Carazo JM, Acton ST, Sorzano COS.
Curr Opin Struct. 52:127-145

Validation of Electron Microscopy Initial Models via Small Angle X-Ray Scattering Curves.
Jiménez A, Jonic S, Majtner T, Otón J, Vilas JL, Maluenda D, Mota J, Ramírez-Aportela E, Martínez M, Rancel Y, Segura J, Sánchez-García R, Melero R, Del Cano L, Conesa P, Skjaerven L, Marabini R, Carazo JM, Sorzano COS.
Bioinformatics. bty985

Deep Consensus, a deep learning-based approach for particle pruning in cryo-electron microscopy.
Sanchez-Garcia R, Segura J, Maluenda D, Carazo JM, Sorzano COS.
IUCrJ. 5(6):854-865.

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.
J Struct Biol. 204(3):457-463

Map challenge: Analysis using a pair comparison method based on Fourier shell correlation.
Marabini R, Kazemi M, Sorzano COS, Carazo JM.
J Struct Biol. 204(3):527-542.

X-ray structure of full-length human RuvB-Like 2 – mechanistic insights into coupling between ATP binding and mechanical action.
Silva STN, Brito JA, Arranz R, Sorzano CÓS, Ebel C, Doutch J, Tully MD, Carazo JM, Carrascosa JL, Matias PM, Bandeiras TM.
Sci Rep. 8(1):13726

A new algorithm for high-resolution reconstruction of single particles by electron microscopy.
Sorzano COS, Vargas J, de la Rosa-Trevín JM, Jiménez A, Maluenda D, Melero R, Martínez M, Ramírez-Aportela E, Conesa P, Vilas JL, Marabini R, Carazo JM.
J Struct Biol. 204(2):329-337

The first single particle analysis Map Challenge: A summary of the assessments.
Heymann JB, Marabini R, Kazemi M, Sorzano COS, Holmdahl M, Mendez JH, Stagg SM, Jonic S, Palovcak E, Armache JP, Zhao J, Cheng Y, Pintilie G, Chiu W, Patwardhan A, Carazo JM.
J Struct Biol. 204(2):291-300

BIPSPI: a method for the prediction of Partner-Specific Protein-Protein Interfaces.
Sanchez-Garcia R, Sorzano COS, Carazo JM, Segura J.
Bioinformatics. bty647

Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis.
Sacristan C, Ahmad MUD, Keller J, Fermie J, Groenewold V, Tromer E, Fish A, Melero R, Carazo JM, Klumperman J, Musacchio A, Perrakis A, Kops GJ.
Nat Cell Biol. 20(7):800-810

Blind estimation of DED camera gain in Electron Microscopy.
Sorzano COS, Fernández-Giménez E, Peredo-Robinson V, Vargas J, Majtner T, Caffarena G, Otón J, Vilas JL, de la Rosa-Trevín JM, Melero R, Gómez-Blanco J, Cuenca J, Del Cano L, Conesa P, Marabini R, Carazo JM.
J Struct Biol. 203, 90 – 93.

MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.
Josué Gómez-Blanco, Pablo Conesa, Roberto Melero, José Miguel de la Rosa-Trevín, Joaquin Otón, Jesús Cuenca, Roberto Marabini, José María Carazo.
Structure. 26(2): 337-344.

Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo.
Ljubetič A, Lapenta F, Gradišar H, Drobnak I, Aupič J, Strmšek Ž, Lainšček D, Hafner-Bratkovič I, Majerle A, Krivec N, Benčina M, Pisanski T, Veličković TĆ, Round A, Carazo JM, Melero R, Jerala R.
Nat Biotechnol.  35(11):1094-1101.

Scipion web tools: Easy to use cryo-EM image processing over the web.
Conesa Mingo P, Gutierrez J, Quintana A, de la Rosa Trevín JM, Zaldívar-Peraza A, Cuenca Alba J, Kazemi M, Vargas J, Del Cano L, Segura J, Sorzano COS, Carazo JM.
Protein Sci. doi: 10.1002/pro.3315.

Pea PSII-LHCII supercomplexes form pairs by making connections across the stromal gap.
Albanese P, Melero R, Engel BD, Grinzato A, Berto P, Manfredi M, Chiodoni A, Vargas J, Sorzano COS, Marengo E, Saracco G, Zanotti G, Carazo JM, Pagliano C.
Sci Rep. 7(1):10067

Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis.
Vargas J, Melero R, Gómez-Blanco J, Carazo JM, Sorzano COS.
Sci Rep. 7(1):6307

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures.
Cuenca-Alba, Daniel Tabas-Madrid, C.O.S. Sorzano, J.M. Carazo
Bioinformatics. 33(22):3655-3657.

ScipionCloud: An integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds.
Jesús Cuenca-Alba, Laura del Cano, Josué Gómez Blanco, José Miguel de la Rosa Trevín, Pablo Conesa Mingo, Roberto Marabini, Carlos Oscar S. Sorzano, Jose María Carazo.
Journal of Structural Biology. 200(1):20-27

XTEND: Extending the depth of field in soft X-ray tomography
Joaquín Otón, Eva Pereiro José J. Conesa, Francisco J. Chichón, Daniel Luque, Javier M. Rodríguez, Ana J. Perez-Berná, Carlos Oscar S. Sorzano, Joanna Klukowska , Gabor T Herman, Javier Vargas, Roberto Marabini , José L. Carrascosa and José M. Carazo.
Sci Rep. 7: 45808

Electron Microscopy Structural Insights into Cpap Oligomeric Behavior: A Plausible Assembly Process of a Supramolecular Scaffold of the Centrosome
Alvarez-Cabrera, Ana L., Sandra Delgado, David Gil-Carton, Gulnahar B. Mortuza, Guillermo Montoya, Carlos O. S. Sorzano, Tang K. Tang, and Jose M. Carazo.
Frontiers in Molecular Biosciences 4(17)

Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors
Martínez M, Sorzano C.O.S., Pascual-Montano A, Carazo J.M.
PLOS ONE 12(5): e0178316

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.
Journal of Structural Biology. 195(1):93-9

Local analysis of strains and rotations for macromolecular electron microscopy maps
Sorzano COS, Martín-Ramos A, Prieto F, Melero R, Martín-Benito J, Jonic S, Navas-Calvente J, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín JM, Gómez-Blanco J, Vilas JL, Marabini R, Carazo JM
195(1):123-128

Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions
Jonić S, Vargas J, Melero R, Gómez-Blanco J, Carazo JM, Sorzano COS
Journal of Structural Biology. 194(3), 423-433

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes
Sorzano CO1, Alvarez-Cabrera AL, Kazemi M, Carazo JM, Jonić S
Biophysical Journal. 110(8), 1753–1765

3DIANA: 3D Domain Interaction Analysis. A toolbox for quaternary structure modelling.
Segura J, Sanchez-García R, Tabas-Madrid D, Cuenca-Alba J, Sorzano CO, Carazo JM
Biophysical Journal. 110:766-775.

3DBioNotes: A unified, enriched and interactive view of macromolecular information
Tabas-Madrid D, Segura J, Sánchez-Garcia R, Cuenca-Alba J, Sorzano CO, Carazo JM.
J. Structural Biology 194: 231-234

Coarse-graining of Volumes for Modeling of Structure and Dynamics in Electron Microscopy: Algorithm to Automatically Control Accuracy of Approximation.
Jonic S, Sorzano CO.
IEEE J. Selected Topics in Signal Processing, 10: 161-173

A guided tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy
Kervrann C, Sorzano CO, Acton S, Olivo-Marin JC, Unser M.
IEEE J. Special Topics in Signal Processing, 10: 6-30

Particle alignment reliability in single particle electron cryomicroscopy: a general approach.
Vargas J, Otón J, Marabini R, Carazo JM, Sorzano CO.
Nature Scientific Reports 6: 21626

Cryo-soft X-ray tomography as a quantitative three-dimensional tool to model nanoparticle:cell interaction
Chiappi M, Conesa JJ, Pereiro E, Sorzano CO, Rodríguez MJ, Hentzle K, Schneider G, Chichón FJ, Carrascosa JL.
J. Nanobiotechnology 14: 15

Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k
Condezo GN, Marabini R, Ayora S, Carazo JM, Alba R, Chillón M, San Martín C
Journal of Virology. 89(18):9653-64

Struct Map: Multivariate distance analysis of elastically aligned electron microscopy structures for exploring pathways of conformational changes 
Sorzano CO, Álvarez-Cabrera AL, Carazo JM, Jonic S
Nature Scientific Reports, 110(8), 1753-1765.

Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revised.
Sorzano CO, Alcorlo M, de la Rosa-Trevín JM, Melero R, Foche I, Zaldívar-Peraza A, del Cano L, Vargas J, Abrishami J, Otón J, Marabini R, Carazo JM
Nature Scientific Reports.5:14290.

A Statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy
Sorzano CO, Vargas J, de la Rosa-Trevin JM, Oton J, Alvarez-Cabrera AL, Abrishami V, Sesmero E, Marabini R, Carazo JM
Journal of Structural Biology. 189:213-219

Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes
Jin Q, Sorzano CO, de la Rosa-Trevín JM, Bilbao-Castro JR, Núñez-Ramírez R, Llorca O, Tama F, Jonic S
Structure. 2014;2126(14):13-16

Cost-constrained optimal sampling for system identification in pharmacokinetics applications with population priors and nuisance parameters.
Sorzano CO, Perez de la Cruz-Moreno MA, Burguet-Castell J, Montejo C, Aguilar Ros A
Journal of Pharmaceutical Sciences, 104 (6), 2013-2109

Alignment of direct detector device micrographs using a robust optical flow approach.
Abrishami V, Vargas J, Cheng Y, Li X, Marabini R, Sorzano CO, Carazo JM.
Journal of Structural Biology, 189(3):163-76

Fast and accurate conversion of atomic models into electron density maps.
Sorzano CO, Vargas J, Oton J, Abrishami V, de la Rosa-Trevin JM, del Riego S, Fernandez-Alderete A, Martinez Rey C, Marabini R, Carazo JM
AIMS Biophysics, 2: 8-20

Inferring protein-protein domain interactions using neighborhood cohesiveness.
Segura J, Sorzao CO, Cuenca-Alba J, Aloy P, Carazo JM
Bioinformatics. 31(15):2545-52

A competition for undergraduate students: The IEEE Signal Processing Cup, Part 1.
Lam KM, Sorzano CO, Zhang Z, Campisi P
IEEE Signal Processing Magazine. 32(4):123-125

CTF Challenge: Result summary.
Marabini R, Carragher B, Chen S, Chen J, Cheng A, Downing KH, Frank J, Grasucci RA, Heymann JB, Jiang W, Jonic S, Liao H, Ludtke SJ, PatwariS, Piotrowski AL, Quintana A, Sorzano CO, Stahlberg H, Vargas J, Voss NR, Chiu W, Carazo JM
Journal of Structural Biology, 190(3), 348-359.

Fast and accurate conversion of atomic models into electron density maps
Sorzano SO, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín JM, del Riego S, Fernández-Alderete A, Martínez-Rey C, Marabini R, Carazo JM.
AIMS Biophysics. 2(1): 8-20.

Measurement of the modulation transfer function of an X-ray microscope based on multiple Fourier orders analysis of a Siemens star.
Otón J, Sorzano CO, Marabini R, Pereiro E, Carazo JM
Optics Express 23 (8), 9567-9572

Using neighborhood cohesiveness to infer interactions between protein domains.
Segura J, Sorzano CO, Cuenca-Alba J, Aloy P, Carazo JM.
Bioinformatics. 31(15):2545-52.

Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data
Carazo JM, Sorzano CO, Oton J, Marabini R, Vargas J
Archives of Biochemistry and Biophysics. 581: 39-48

A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.
Abrishami V, Bilbao-Castro JR, Vargas J, Marabini R, Carazo JM, Sorzano CO
Ultramicroscopy. 157:79-87

Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited
Sorzano CO, Alcorlo M, de la Rosa-Trevin JM, Melero R, Foche I, Zaldivar-Peraza A, del Cano L, Vargas J, Abrishami V, Oton J, Marabini R, Carazo JM
Scientific Reports. 5:14290

Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes
Jin Q, Sorzano CO, de la Rosa-Trevín JM, Bilbao-Castro JR, Núñez-Ramírez R, Llorca O, Tama F, Jonic S
Structure. 2014;2126(14):13-16

Miro-1 links mitochondria and microtubule dynein motors to control lymphocyte migration and polarity
Morlino G, Barreiro O, Baixauli F, Robles-Valero J, González-Granado, Villa-Bellosta R, Cuenca J, Sorzano COS, Veiga E, Martín-Cófre, Sanchez-Madrid F
Molecular and Cell Biology. 2014;34:1412-1426

3D cryo-electron reconstruction of BmrA, a bacterial multidrug ABC transporter in an inward facing conformation and in a lipidic environment
Fribourg PF, Chami M, Sorzano COS, Gubellini F, Marabini R, Marco S, Jault JM, Levy D
Journal of Molecular Biology. 2014;426:2059-2069

Blind and efficient initial volume determination from single particle electron microscopy
Vargas J, Álvarez-Cabrera AL, Marabini R, Carazo JM, Sorzano COS
Bioinformatics. 2014;30:2891-2898

Comparing scientific performance among equals
Sorzano COS, Vargas J, Caffarena-Ruiz G, Iriarte-Ruiz A
Scientometris, 101, 1731-1745

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol
Sorzano COS, de la Rosa Trevín JM, Tama F, Jonic S
Journal of Structural Biology, 188(2), 134-141

Interchanging geometry information in electron microscopy single particle analysis: mathematical context for the development of a standard
Sorzano COS, Marabini R, Vargas J, Otón J, Cuenca-Alba J, Quintana A, de la Rosa-Trevín JM, Carazo JM
Computational Methods for Three-Dimensional Microscopy Reconstruction. 2014:7-42

Soft X-ray Tomography Imaging for Biological Samples 
Otón J, Sorzano COS, Chichón FJ, Carrascosa JL, Carazo JM, Marabini R
Computational Methods for Three-Dimensional Microscopy Reconstruction. 2014:187-200

The soft x-ray transform
Klukowska J, Herman GT, Otón J, Marabini R, Carazo JM
InverseProblems. 2014;30(12)

Generalization of the Principal Component Analysis algorithm for interferometry
Vargas, J.; Sorzano, C. O. S.; Estrada, J. C.; Carazo J.M.
Optics Communications. 2013;286:130-134

FASTDEF: Fast defocus and astigmatism estimation for high-throughput transmission electron microscopy
Vargas, J; Oton, J; Marabini, R; Jonic, S; de la Rosa Trevin, J.M.; Carazo J.M.; Sorzano C.O
Journal of structural biology. 2013;181:136-148

Fringe pattern denoising by image dimensionality reduction
J. Vargas, C.O.S. Sorzano, J. Antonio Quiroga, J.C. Estrada, J.M. Carazo
Optics and Lasers in Engineering. 2013;51(7):921–928

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy
Roberto Marabini, Jose Ramón Macías, Javier Vargas, Adrián Quintana, Carlos Oscar S. Sorzano and Jose María Carazo
Acta Cryst.. 2013;D69:695–700

Error analysis of the principal component analysis demodulation algorithm
Vargas, J.; Carazo J.M.; Sorzano, C. O. S.
Applied Physics B: Lasers and Optics, 115, 335-364

Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques
Vargas, J.; Abrishami, V; Marabini, R.; de la Rosa-Trevín, J.M.; Zaldivar, A.; Carazo, J.M.; Sorzano, C.O.S.
Journal of Structural Biology. 2013;183(3):342-353

Quadrature Component Analysis for interferometry
Vargas, J.; Sorzano C.O.S
Optics and Lasers in Engineering. 2013;51(5):637-641

Branched1 promotes axillary bud dormancy in response to shade in Arabidopsis
González-Grandío, E.; Poza-Carrión, C.; Sorzano, C.O.S.; Cubas, P.
Plant Cell. 2013;25(3):834-850

High, broad, polyfunctional, and durable T cell immune responses induced in mice
Gómez CE, Perdiguero B, Cepeda MV, Mingorance L, García-Arriaza J, Vandermeeren A, Sorzano CÓ, Esteban M.
Journal of Virology. 2013;87(13):7282-300

Variable internal flexibility characterizes the helical capsid formed by Agrobacterium VirE2 protein on single-stranded DNA.
Bharat TA, Zbaida D, Eisenstein M, Frankenstein Z, Mehlman T, Weiner L, Sorzano CO, Barak Y, Albeck S, Briggs JA, Wolf SG, Elbaum M.
Structure. 2013;21(7):1158-67

3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.
Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vázquez M, Pascual-Montano A, Sorzano CO.
Nucleic Acids Research. 2013;W363-7

Chromothripsis: Breakage-fusion-bridge over and over again
Sorzano C.O., Pascual-Montano A., Sánchez de Diego A., Martínez-A C., van Wely K.H.M.
Cell Cycle. 2013;12(13):2016 – 2023

PI3K p110 is expressed by gp38-CD31 spleen stromal cells
Zotes T., Spada R, Mulens V, Pérez-Yagüe S, Sorzano C.O., Okkenhaug K, Carrera A.C.
PLoS ONE. 2013;8(8):e72960

EFTEM-TomoJ: 3D chemical mapping by EFTEM including SNR improvement by PCA and volume improvement by noise suppression during the ART
Messaoudi C, Aschman N, Cunha M, Oikawa T, Sorzano CO, Marco S.
Microscopy and microanalysis. 2013;19:1669-1677

A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
Abrishami V, Zaldívar-Peraza A, de la Rosa-Trevín JM, Vargas J, Otón J, Marabini R, Shkolnisky Y, Carazo JM, Sorzano CO.
Bioinformatics. 2013;29(19):2460-8

Xmipp 3.0: one step forward in scientific computing for Electron Microscopy
J.M. De la Rosa-Trevín, J. Otón, R. Marabini, A. Zaldívar-Peraza, J. Vargas, J.M. Carazo, C.O.S. Sorzano
Journal of Structural Biology. 2013;184(2):321-8

New vaccinia virus promoter as potential candidate for future vaccines
Di Pilato M., Mejías-Pérez E., Gómez C.E. , Perdiguero B., Sorzano C.O.S., Esteban M.
Journal of General Virology. 2013;September 2013

Structure and non-structure of centrosomal proteins
Dos Santos HG, Abia D, Janowski R, …, Carazo JM, Gonzalez C, Reina J, Valpuesta JM, Vernos I, Zabala JC, Montoya G, Coll M, Bastolla U, Serrano L.
PLoS ONE. 2013;8(5):e62633

Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy.
Sorzano CO, de la Rosa Trevín JM, Otón J, Vega JJ, Cuenca J, Zaldívar-Peraza A, Gómez-Blanco J, Vargas J, Quintana A, Marabini R, Carazo JM
Methods Mol Biol. 2013;950:171-193

Two-step demodulation based on Gram-Schmidt orthonormalization method
J. Vargas, J.A. Quiroga, C.O.S. Sorzano, J.C. Estrada and J.M. Carazo
Optics Letters. 2012;37:443-445

Image formation in cellular X-ray microscopy
J. Otón, C.O.S. Sorzano, E. Pereiro, J. Cuenca, R. Navarro, R. Marabini and J.M. Carazo
J. Structural Biology. 2012;178:29-37

Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of Single Particles in Electron Microscopy. Nanoimaging
C.O.S.Sorzano, J.M.de la Rosa, J.Otón, J.Vega, J.Cuenca, A.Zaldívar-Peraza, J.Gómez-Blanco, J.Vargas, A.Quintana, R.Marabini and J.M.Carazo
(Alioscka Sousa, Michael Kruhlak, Ed). 2012

Epitope insertion at the N-terminal molecular switch of the rabbit hemorrhagic disease virus t=3 capsid protein leads to larger t=4 capsids
Luque, D. and Gonzalez, J. M. and Gomez-Blanco, J. and Marabini, R. and Chichon, J. and Mena, I. and Angulo, I. and Carrascosa, J. L. and Verdaguer, N. and Trus, B. L. and Barcena, J. and Caston, J. R.
J. Virol.. 2012;86:6470–6480

Integrating human and murine anatomical gene expression data for improved comparisons
Jimenez-Lozano, Natalia; Segura, Joan; Ramon Macias, Jose
Bioinformatics. 2012;28:397-402

Shack-Hartmann centroid detection using the spiral phase transform
Vargas, J.; Restrepo, R.; Estrada, J. C.
Applied Optics. 2012;51:7362-7367

Data management challenges in three-dimensional EM
Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, …, Sorzano CO, Sanz-García E, Scheres SH, …, Kleywegt GJ.
Nature Structural Molecular Biology. 2012;19:1203-1207

Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA.
Roberto Melero and Sridharan Rajagopalan and Melisa Lázaro and Andreas C Joerger and Tobias Brandt and Dmitry B Veprintsev and Gorka Lasso and David Gil and Sjors H W Scheres and José María Carazo and Alan R Fersht and Mikel Valle
Proc Natl Acad Sci U S A. 2011;108:557–562

Maximum likelihood based classification of electron tomographic data.
Michael Stölken and Florian Beck and Thomas Haller and Reiner Hegerl and Irina Gutsche and Jose-Maria Carazo and Wolfgang Baumeister and Sjors H W Scheres and Stephan Nickell
J Struct Biol. 2011;173:77–85

Single-Particle Reconstruction Using L2-Gradient Flow
M. Li and G. Xu and C.O.S. Sorzano and F. Sun and C. Bajaj
J. Structural Biology. 2011;176:259-267

Two-step interferometry by a regularized optical flow algorithm
J. Vargas, J.A. Quiroga, C.O.S. Sorzano, J.C. Estrada and J.M. Carazo
Optics Letters. 2011;36:3485-3487

Splines for bioimaging in Optical and Digital Image Processing: Fundamentals and Applications
S. Jonic and C.O.S. Sorzano
(G. Cristóbal, P. Schelkens, H. Thienpont, Ed). 2011:119-134

Non-rigid consistent registration of 2D image sequences
Arganda-Carreras, I. and Sorzano, C. O. and Thevenaz, P. and Munoz-Barrutia, A. and Kybic, J. and Marabini, R. and Carazo, J. M. and Ortiz-de Solorzano, C.
Phys Med Biol. 2010;55:6215–6242

XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography.
J. R. Bilbao-Castro and C. O S Sorzano and I. García and J. J. Fernández
Bioinformatics. 2010;26:2786–2787

tmRNA.SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes.
Kimberley Cheng and Natalia Ivanova and Sjors H W Scheres and Michael Y Pavlov and José María Carazo and Hans Hebert and Måns Ehrenberg and Martin Lindahl
J Struct Biol. 2010;169:342–348

Conformational rearrangements of SV40 large T antigen during early replication events.
Isabel Cuesta and Rafael Núñez-Ramírez and Sjors H W Scheres and Dahai Gai and Xiaojiang S Chen and Ellen Fanning and Jose María Carazo
J Mol Biol. 2010;397:1276–1286

An introduction to maximum-likelihood methods in cryo-EM.
Fred J Sigworth and Peter C Doerschuk and Jose-Maria Carazo and Sjors H W Scheres
Methods Enzymol. 2010;482:263–294

A clustering approach to multireference alignment of single-particle projections in electron microscopy.
C. O S Sorzano and J. R. Bilbao-Castro and Y. Shkolnisky and M. Alcorlo and R. Melero and G. Caffarena-Fernández and M. Li and G. Xu and R. Marabini and J. M. Carazo
J Struct Biol. 2010;171:197–206

Dynamic effects of cofactors and DNA on the oligomeric state of human mitochondrial DNA helicase.
Tawn D Ziebarth and Rocio Gonzalez-Soltero and Magdalena M Makowska-Grzyska and Rafael Núñez-Ramírez and Jose-Maria Carazo and Laurie S Kaguni
J Biol Chem. 2010;285:14639–14647

Structure and uncoating of immature adenovirus
Perez-Berna, A. J. and Marabini, R. and Scheres, S. H. and Menendez-Conejero, R. and Dmitriev, I. P. and Curiel, D. T. and Mangel, W. F. and Flint, S. J. and San Martin, C.
J. Mol. Biol.. 2009;392:547–557

Exploiting desktop supercomputing for three-dimensional electron microscopy reconstructions using ART with blobs.
J. R. Bilbao-Castro and R. Marabini and C. O S Sorzano and I. García and J. M. Carazo and J. J. Fernández
J Struct Biol. 2009;165:19–26

Insights into the molecular architecture of the 26S proteasome.
Stephan Nickell and Florian Beck and Sjors H W Scheres and Andreas Korinek and Friedrich Förster and Keren Lasker and Oana Mihalache and Na Sun and István Nagy and Andrej Sali and Jürgen M Plitzko and Jose-Maria Carazo and Matthias Mann and Wolfgang Baumeister
Proc Natl Acad Sci U S A. 2009;106:11943–11947

CentrosomeDB: a human centrosomal proteins database.
Rubén Nogales-Cadenas and Federico Abascal and Javier Díez-Pérez and José María Carazo and Alberto Pascual-Montano
Nucleic Acids Res. 2009;37:D175–D180

Introducing robustness to maximum-likelihood refinement of electron-microscopy data.
Sjors H W Scheres and José María Carazo
Acta Crystallogr D Biol Crystallogr. 2009;65:672–678

Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization.
Sjors H W Scheres and Roberto Melero and Mikel Valle and Jose-Maria Carazo
Structure. 2009;17:1563–1572

Maximum likelihood refinement of electron microscopy data with normalization errors.
Sjors H W Scheres and Mikel Valle and Patricia Grob and Eva Nogales and José-María Carazo
J Struct Biol. 2009;166:234–240

Marker-free image registration of electron tomography tilt-series.
Carlos Oscar Sanchez Sorzano and Cédric Messaoudi and Matthias Eibauer and J. R. Bilbao-Castro and R. Hegerl and S. Nickell and S. Marco and J. M. Carazo
BMC Bioinformatics. 2009;10:124

Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra.
Carlos Oscar S Sorzano and Abraham Otero and Estefanía M Olmos and José María Carazo
BMC Struct Biol. 2009;9:18

Automatic particle selection from electron micrographs using machine learning techniques.
C. O S Sorzano and E. Recarte and M. Alcorlo and J. R. Bilbao-Castro and C. San-Martín and R. Marabini and J. M. Carazo
J Struct Biol. 2009;167:252–260

Comparison of molecular dynamics and superfamily spaces of protein domain deformation.
Javier A Velázquez-Muriel and Manuel Rueda and Isabel Cuesta and Alberto Pascual-Montano and Modesto Orozco and José-María Carazo
BMC Struct Biol. 2009;9:6

Localization of the N-terminus of minor coat protein IIIa in the adenovirus capsid
San Martín, C. and Glasgow, J.N. and Borovjagin, A. and Beatty, M.S. and Kashentseva, E.A. and Curiel, D.T. and Marabini, R. and Dmitriev, I.P.
J. Mol. Biol.. 2008;383:923–934

An image processing approach to the simulation of atomic models for transmission electron microscopy of biological samples
C.O.S. Sozano and C. Bebeaqua and R. Marabini and M. van Heel and J.M. Carazo
. 2008

An image processing workflow for 3D reconstruction of biological samples improving achieved resolution by electron microscopy and single particle analisys
C.O.S. Sozano and S. Jonic and S. Marco and R. Marabini and N. Boisset and J.M. Carazo
. 2008

Comparison of single-particle analysis and electron tomography approaches: an overview
Jonic, S. and Sorzano, C. O. S. and Boisset, N.
J. Microscopy. 2008;232:562–579

Image processing for electron microscopy single-particle analysis using XMIPP
Scheres, S. H. W. and Núñez-Ramírez, R. and Sorzano, C. O. S. and Carazo, J. M. and Marabini, R.
Nature Protocols. 2008;3:977–990

Volumetric restrictions in 3DEM reconstruction
Sorzano, C. O. S. and Velázquez-Muriel, J. A. and Marabini, R. and Herman, G. T. and Carazo, J. M.
Pattern Recognition. 2008;41:616–626

Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase.
Aaron S Brewster and Ganggang Wang and Xian Yu and William B Greenleaf and José María Carazo and Matthew Tjajadia and Michael G Klein and Xiaojiang S Chen
Proc Natl Acad Sci U S A. 2008;105:20191–20196

Electron tomography of complex biological specimens on the Grid
J.J. Fernández and I. García and J.M. Carazo andR. Marabini
Future Gener. Comp. Sy.. 2007;23:435-446

TomoJ: software for multiple-axis tomography
Messaoudi, C. and Boudier, T. and Sorzano, C. O. S. and Marco, S.
BMC Bioinformatics. 2007;8:288

3D electron microscopy of biological nanomachines: principles and applications
Sorzano,C. O. S. and Jonic, S. and Cottevieille, M. and Larquet, E. and Boisset,N. and Marco, S.
European Biophysics Journal. 2007;36:995–1013

Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
Xabier Agirrezabala and Javier A Velázquez-Muriel and Paulino Gómez-Puertas and Sjors H W Scheres and José M Carazo and José L Carrascosa
Structure. 2007;15:461–472

Integrating electron microscopy information into existing Distributed Annotation Systems.
J. R. Macías and N. Jiménez-Lozano and J. M. Carazo
J Struct Biol. 2007;158:205–213

Loading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase.
Rafael Núñez-Ramírez and Marion Velten and Germán Rivas and Patrice Polard and José María Carazo and Luis Enrique Donate
J Mol Biol. 2007;367:764–769

Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.
Sjors H W Scheres and Haixiao Gao and Mikel Valle and Gabor T Herman and Paul P B Eggermont and Joachim Frank and Jose-Maria Carazo
Nat Methods. 2007;4:27–29

Modeling experimental image formation for likelihood-based classification of electron microscopy data.
Sjors H W Scheres and Rafael Núñez-Ramírez and Yacob Gómez-Llorente and Carmen San Martín and Paul P B Eggermont and José María Carazo
Structure. 2007;15:1167–1177

Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex.
Henning Tidow and Roberto Melero and Efstratios Mylonas and Stefan M V Freund and J. Guenter Grossmann and José María Carazo and Dmitri I Svergun and Mikel Valle and Alan R Fersht
Proc Natl Acad Sci U S A. 2007;104:12324–12329

Flexible fitting in 3D-EM with incomplete data on superfamily variability.
Javier A Velazquez-Muriel and José-Mari A Carazo
J Struct Biol. 2007;158:165–181

Consistent and Elastic Registration of Histological Sections using vector-spline regularization
I. Arganda-Carreras and C.O.S. Sorzano and R. Marabini and J.M. Carazo and C. Ortiz-de-Solorzano and J. Kybic
Lect. Notes Comput. Sc.. 2006;4241:85-95

Optimization Problems in Electron Microscopy of Single Particles
Sorzano, C.O.S. and R. Marabini and Pascual-Montano, A. and Scheres, S.H.W. and Herman, G. T. and Carazo, J.M.
Ann. Oper. Res.. 2006;148:133-165

Improved Bayesian image denoising based on wavelets with applications to Electron Microscopy
Sorzano, C. O. S. and Ortiz, E. and López, M. and Rodrigo, J.
Pattern Recognition. 2006;39:1205–1213

On the nature of 2D crystal unbending.
Debora Gil and Jose Maria Carazo and Roberto Marabini
J Struct Biol. 2006;156:546–555

Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
Rafael Núñez-Ramírez and Yolanda Robledo and Pablo Mesa and Silvia Ayora and Juan Carlos Alonso and José María Carazo and Luis Enrique Donate
J Mol Biol. 2006;357:1063–1076

Structural basis for the cooperative assembly of large T antigen on the origin of replication.
Mikel Valle and Xiaojiang S Chen and Luis Enrique Donate and Ellen Fanning and José María Carazo
J Mol Biol. 2006;357:1295–1305

Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.
Javier-Angel Velazquez-Muriel and Mikel Valle and Alberto Santamaría-Pang and Ioannis A Kakadiaris and José-María Carazo
Structure. 2006;14:1115–1126

On the Suitability of Biological Structure Determination by Electron Microscopy to Grid Computing
J.J. Fernandez and J.R. Bilbao-Castro and R. Marabini, J.M. Carazo and I. Garcia
New Generat. Comput.. 2005;23:101–112

Maximum-likelihood multi-reference refinement for electron microscopy images
Scheres, S.H.W. and Valle, M. and Nuñez, R. and Sorzano, C.O.S. and Marabini, R. and Herman, G.T.and Carazo, J.M.
J. Mol. Biol.. 2005;348:139–149

Biophotonics for life sciences and medicine
Jonic, S. and Thévenaz, P. and Sorzano, C. O. S. and Unser, M.
(Faupel, M. and Smigielski, P. and Brandenburg, A. and Fontaine, J., Ed). 2005:255-274

Multiobjective algorithm parameter optimization using multivariate statistics
Sorzano, C. O. S. and Marabini, R. and Herman, G. T. and Carazo, J. M.
Pattern Recognition. 2005;38:2587–2601

Double hexamer disruption and biochemical activities of Methanobacterium thermoautotrophicum MCM.
Ryan J Fletcher and Jingping Shen and Yacob Gómez-Llorente and Carmen San Martín and José M Carazo and Xiaojiang S Chen
J Biol Chem. 2005;280:42405–42410

Polymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.
Yacob Gómez-Llorente and Ryan J Fletcher and Xiaojiang S Chen and José M Carazo and Carmen San Martín
J Biol Chem. 2005;280:40909–40915

Classification of single-projection reconstructions for cryo-electron microscopy data of icosahedral viruses.
Sjors H W Scheres and Roberto Marabini and Salvatore Lanzavecchia and Francesca Cantele and Twan Rutten and Stephen D Fuller and José M Carazo and Roger M Burnett and Carmen San Martín
J Struct Biol. 2005;151:79–91

Fast maximum-likelihood refinement of electron microscopy images.
Sjors H W Scheres and Mikel Valle and José-María Carazo
Bioinformatics. 2005;21 Suppl 2:ii243–ii244