Publications

2020

• • 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.  XXXX, XXX, XXX-XXX.
  • 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
  • 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

2019

• • 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.  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. 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. 35(18): 3512–3513
  • 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

2018

• • 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.
    Jose Luis Vilas, 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

2017

• • 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

2016

• • 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

2015

• • 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 (in press).
  • 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 (in press)
  • 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 (in press)
  • 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

2014

• • 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
    Scientometrics. 2014;(in press)
  • 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. 2014;(in press)
  • 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)

2013

• • 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. 2013;in press
  • 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

2012

• • 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
  • Image processing for Ssingle-particle analysis of macromolecular complexes with electron micrographs
    Z. Devaux, C.O.S. Sorzano and S. Jonic
    . 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

2011

• • 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

2010

• • 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

2009

• • 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

2008

• • 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

2007

• • 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

2006

• • 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
  • Algorithms for three-dimensional reconstruction from the imperfect projection data provided by electron microscopy In Electron Tomography
    J.M. Carazo and G.T. Herman and C.O.S. Sorzano and R. Marabini
    (J. Frank, Ed). 2006
  • 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
  • Image Processing and 3-D Reconstruction in Electron Microscopy
    IEEE Signal Processing Magazine. 2006;23:84-94
  • Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell
    Carazo, J. M. and Herman, G. T. and Sorzano, C. O. S. and Marabini, R.
    (Frank, J., Ed). 2006:217–243
  • 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

2005

• 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