| Year |
Citation |
Score |
| 2023 |
Conesa P, Fonseca YC, Jiménez de la Morena J, Sharov G, de la Rosa-Trevín JM, Cuervo A, García Mena A, Rodríguez de Francisco B, Del Hoyo D, Herreros D, Marchan D, Strelak D, Fernández-Giménez E, Ramírez-Aportela E, de Isidro-Gómez FP, ... ... Carazo JM, et al. Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology. Biological Imaging. 3: e13. PMID 38510163 DOI: 10.1017/S2633903X23000132 |
0.345 |
|
| 2023 |
Střelák D, Marchán D, Carazo JM, S Sorzano CO. Performance and Quality Comparison of Movie Alignment Software for Cryogenic Electron Microscopy. Micromachines. 14. PMID 37893272 DOI: 10.3390/mi14101835 |
0.314 |
|
| 2022 |
Ramírez-Aportela E, Carazo JM, Sorzano COS. Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools. Iucrj. 9: 632-638. PMID 36071808 DOI: 10.1107/S2052252522006959 |
0.373 |
|
| 2022 |
Vilas JL, Carazo JM, Sorzano COS. Emerging Themes in CryoEM─Single Particle Analysis Image Processing. Chemical Reviews. PMID 35785962 DOI: 10.1021/acs.chemrev.1c00850 |
0.759 |
|
| 2021 |
Herreros D, Lederman RR, Krieger J, Jiménez-Moreno A, Martínez M, Myška D, Strelak D, Filipovic J, Bahar I, Carazo JM, Sanchez COS. Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials. Iucrj. 8: 992-1005. PMID 34804551 DOI: 10.1107/S2052252521008903 |
0.672 |
|
| 2021 |
Strelak D, Jiménez-Moreno A, Vilas JL, Ramírez-Aportela E, Sánchez-García R, Maluenda D, Vargas J, Herreros D, Fernández-Giménez E, de Isidro-Gómez FP, Horacek J, Myska D, Horacek M, Conesa P, Fonseca-Reyna YC, ... ... Carazo JM, et al. Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion. Molecules (Basel, Switzerland). 26. PMID 34684805 DOI: 10.3390/molecules26206224 |
0.8 |
|
| 2021 |
Sorrentino S, Conesa JJ, Cuervo A, Melero R, Martins B, Fernandez-Gimenez E, de Isidro-Gomez FP, de la Morena J, Studt JD, Sorzano COS, Eibauer M, Carazo JM, Medalia O. Structural analysis of receptors and actin polarity in platelet protrusions. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34504018 DOI: 10.1073/pnas.2105004118 |
0.633 |
|
| 2021 |
Méndez J, Garduño E, Carazo JM, S Sorzano CO. Identification of incorrectly oriented particles in Cryo-EM Single Particle Analysis. Journal of Structural Biology. 107771. PMID 34324977 DOI: 10.1016/j.jsb.2021.107771 |
0.333 |
|
| 2021 |
Lapenta F, Aupič J, Vezzoli M, Strmšek Ž, Da Vela S, Svergun DI, Carazo JM, Melero R, Jerala R. Author Correction: Self-assembly and regulation of protein cages from pre-organised coiled-coil modules. Nature Communications. 12: 1811. PMID 33727540 DOI: 10.1038/s41467-021-21969-9 |
0.599 |
|
| 2021 |
Lapenta F, Aupič J, Vezzoli M, Strmšek Ž, Da Vela S, Svergun DI, Carazo JM, Melero R, Jerala R. Self-assembly and regulation of protein cages from pre-organised coiled-coil modules. Nature Communications. 12: 939. PMID 33574245 DOI: 10.1038/s41467-021-21184-6 |
0.621 |
|
| 2021 |
Ramírez-Aportela E, Maluenda D, Fonseca YC, Conesa P, Marabini R, Heymann JB, Carazo JM, Sorzano COS. FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation. Nature Communications. 12: 42. PMID 33397925 DOI: 10.1038/s41467-020-20295-w |
0.797 |
|
| 2020 |
Vilas JL, Oton J, Messaoudi C, Melero R, Conesa P, Ramirez-Aportela E, Mota J, Martinez M, Jimenez A, Marabini R, Carazo JM, Vargas J, Sorzano COS. Measurement of local resolution in electron tomography. Journal of Structural Biology: X. 4: 100016. PMID 32647820 DOI: 10.1016/j.yjsbx.2019.100016 |
0.804 |
|
| 2020 |
Sanchez-Garcia R, Segura J, Maluenda D, Sorzano COS, Carazo JM. MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning. Journal of Structural Biology. 107498. PMID 32276087 DOI: 10.1016/J.Jsb.2020.107498 |
0.801 |
|
| 2020 |
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, ... ... Carazo JM, et al. Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells. Science Advances. 6: eaay9572. PMID 32270040 DOI: 10.1126/Sciadv.Aay9572 |
0.74 |
|
| 2020 |
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, et al. Integration of Cryo-EM Model Building Software in Scipion. Journal of Chemical Information and Modeling. PMID 31994878 DOI: 10.1021/Acs.Jcim.9B01032 |
0.823 |
|
| 2020 |
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. Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening. Journal of Structural Biology. 107447. PMID 31911170 DOI: 10.1016/J.Jsb.2020.107447 |
0.801 |
|
| 2020 |
Vilas JL, Tagare HD, Vargas J, Carazo JM, Sorzano COS. Measuring local-directional resolution and local anisotropy in cryo-EM maps. Nature Communications. 11: 55. PMID 31896756 DOI: 10.1038/S41467-019-13742-W |
0.733 |
|
| 2020 |
Střelák D, Filipovič J, Jiménez-Moreno A, Carazo JM, Sorzano CÓS. FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy Electronics. 9: 1040. DOI: 10.3390/Electronics9061040 |
0.449 |
|
| 2019 |
Morris C, Andreetto P, Banci L, Bonvin AMJJ, Chojnowski G, Cano LD, Carazo JM, Conesa P, Daenke S, Damaskos G, Giachetti A, Haley NEC, Hekkelman ML, Heuser P, Joosten RP, et al. West-Life: A Virtual Research Environment for structural biology. Journal of Structural Biology: X. 1: 100006. PMID 32647812 DOI: 10.1016/j.yjsbx.2019.100006 |
0.788 |
|
| 2019 |
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. Structural basis for cooperativity of human monoclonal antibodies to meningococcal factor H-binding protein. Communications Biology. 2: 241. PMID 31925134 DOI: 10.1038/s42003-019-0493-4 |
0.621 |
|
| 2019 |
Ramírez-Aportela E, Mota J, Conesa P, Carazo JM, Sorzano COS. : a new deep-learning- and aspect-based local resolution method for electron-microscopy maps. Iucrj. 6: 1054-1063. PMID 31709061 DOI: 10.1107/S2052252519011692 |
0.812 |
|
| 2019 |
Maluenda D, Majtner T, Horvath P, Vilas JL, Jiménez-Moreno A, Mota J, Ramírez-Aportela E, Sánchez-García R, Conesa P, Del Caño L, Rancel Y, Fonseca Y, Martínez M, Sharov G, García CA, ... ... Carazo JM, et al. Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion. Acta Crystallographica. Section D, Structural Biology. 75: 882-894. PMID 31588920 DOI: 10.1107/S2059798319011860 |
0.831 |
|
| 2019 |
Ramírez-Aportela E, Vilas JL, Glukhova A, Melero R, Conesa P, Martínez M, Maluenda D, Mota J, Jiménez A, Vargas J, Marabini R, Sexton PM, Carazo JM, Oscar C, Sorzano S. Automatic local resolution-based sharpening of cryo-EM maps. Bioinformatics (Oxford, England). PMID 31504163 DOI: 10.1093/Bioinformatics/Btz671 |
0.79 |
|
| 2019 |
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. Structural basis for cooperativity of human monoclonal antibodies to meningococcal factor H-binding protein. Communications Biology. 2: 241. PMID 31263785 DOI: 10.1038/s42003-019-0493-4 |
0.621 |
|
| 2019 |
Segura J, Sanchez-Garcia R, Sorzano COS, Carazo JM. 3DBIONOTES v3.0: Crossing molecular and structural biology data with genomic variations. Bioinformatics (Oxford, England). PMID 30768147 DOI: 10.1093/Bioinformatics/Btz118 |
0.779 |
|
| 2019 |
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, ... ... Carazo JM, et al. Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallographica. Section F, Structural Biology Communications. 75: 19-32. PMID 30605122 DOI: 10.1107/S2053230X18015108 |
0.806 |
|
| 2019 |
Střelák D, Sorzano CÓS, Carazo JM, Filipovič J. A GPU acceleration of 3-D Fourier reconstruction in cryo-EM The International Journal of High Performance Computing Applications. 33: 948-959. DOI: 10.1177/1094342019832958 |
0.405 |
|
| 2018 |
Vilas JL, Tabassum N, Mota J, Maluenda D, Jiménez-Moreno A, Majtner T, Carazo JM, Acton ST, Sorzano COS. Advances in image processing for single-particle analysis by electron cryomicroscopy and challenges ahead. Current Opinion in Structural Biology. 52: 127-145. PMID 30509756 DOI: 10.1016/J.Sbi.2018.11.004 |
0.826 |
|
| 2018 |
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, ... ... Carazo JM, et al. Validation of Electron Microscopy Initial Models via Small Angle X-Ray Scattering Curves. Bioinformatics (Oxford, England). PMID 30500892 DOI: 10.1093/Bioinformatics/Bty985 |
0.796 |
|
| 2018 |
Sanchez-Garcia R, Segura J, Maluenda D, Carazo JM, Sorzano COS. , a deep learning-based approach for particle pruning in cryo-electron microscopy. Iucrj. 5: 854-865. PMID 30443369 DOI: 10.1107/S2052252518014392 |
0.809 |
|
| 2018 |
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, ... ... Carazo JM, et al. Using Scipion for Stream Image Processing at Cryo-EM Facilities. Journal of Structural Biology. PMID 30296492 DOI: 10.1016/J.Jsb.2018.10.001 |
0.807 |
|
| 2018 |
Marabini R, Kazemi M, Sorzano COS, Carazo JM. Map Challenge: Analysis using a Pair Comparison Method based on Fourier Shell Correlation. Journal of Structural Biology. PMID 30273658 DOI: 10.1016/J.Jsb.2018.09.009 |
0.767 |
|
| 2018 |
Silva STN, Brito JA, Arranz R, Sorzano CÓS, Ebel C, Doutch J, Tully MD, Carazo JM, Carrascosa JL, Matias PM, Bandeiras TM. X-ray structure of full-length human RuvB-Like 2 - mechanistic insights into coupling between ATP binding and mechanical action. Scientific Reports. 8: 13726. PMID 30213962 DOI: 10.1038/S41598-018-31997-Z |
0.542 |
|
| 2018 |
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. A new algorithm for high-resolution reconstruction of single particles by electron microscopy. Journal of Structural Biology. PMID 30145327 DOI: 10.1016/J.Jsb.2018.08.002 |
0.836 |
|
| 2018 |
Sanchez-Garcia R, Sorzano COS, Carazo JM, Segura J. BIPSPI: a method for the prediction of Partner-Specific Protein-Protein Interfaces. Bioinformatics (Oxford, England). PMID 30020406 DOI: 10.1093/Bioinformatics/Bty647 |
0.772 |
|
| 2018 |
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. Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis. Nature Cell Biology. PMID 29915359 DOI: 10.1038/S41556-018-0130-3 |
0.643 |
|
| 2018 |
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, et al. Blind estimation of DED camera gain in Electron Microscopy. Journal of Structural Biology. PMID 29551714 DOI: 10.1016/J.Jsb.2018.03.007 |
0.825 |
|
| 2018 |
Vilas JL, Gómez-Blanco J, Conesa P, Melero R, Miguel de la Rosa-Trevín J, Otón J, Cuenca J, Marabini R, Carazo JM, Vargas J, Sorzano COS. MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps. Structure (London, England : 1993). 26: 337-344.e4. PMID 29395788 DOI: 10.1016/J.Str.2017.12.018 |
0.806 |
|
| 2018 |
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. Scipion web tools: Easy to use cryo-EM image processing over the web. Protein Science : a Publication of the Protein Society. 27: 269-275. PMID 28971542 DOI: 10.1002/Pro.3315 |
0.808 |
|
| 2018 |
de la Rosa-Trevín JM, Gómez-Blanco J, Conesa P, Rancel Y, del Cano L, Arranz R, Chichón FJ, Martín-Benito J, Carroni M, Fleichman S, Lindahl E, Basham M, Clare DK, Savage K, Siebert CA, ... ... Carazo JM, et al. Using Scipion for stream image processing at cryo-EM facilities Acta Crystallographica Section a Foundations and Advances. 74: a161-a161. DOI: 10.1107/S0108767318098380 |
0.766 |
|
| 2017 |
Sorzano COS, Vargas J, Otón J, de la Rosa-Trevín JM, Vilas JL, Kazemi M, Melero R, Del Caño L, Cuenca J, Conesa P, Gómez-Blanco J, Marabini R, Carazo JM. A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy. Biomed Research International. 2017: 6482567. PMID 29312997 DOI: 10.1155/2017/6482567 |
0.817 |
|
| 2017 |
Sanchez-Garcia R, Sorzano COS, Carazo JM, Segura J. 3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures. Molecules (Basel, Switzerland). 22. PMID 29244774 DOI: 10.3390/Molecules22122230 |
0.787 |
|
| 2017 |
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, et al. Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo. Nature Biotechnology. 35: 1094-1101. PMID 29035374 DOI: 10.1038/Nbt.3994 |
0.667 |
|
| 2017 |
Segura J, Sanchez-Garcia R, Martinez M, Cuenca-Alba J, Tabas-Madrid D, Sorzano COS, Carazo JM. 3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures. Bioinformatics (Oxford, England). 33: 3655-3657. PMID 28961691 DOI: 10.1093/Bioinformatics/Btx483 |
0.796 |
|
| 2017 |
Vargas J, Melero R, Gómez-Blanco J, Carazo JM, Sorzano COS. Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis. Scientific Reports. 7: 6307. PMID 28740215 DOI: 10.1038/S41598-017-06526-Z |
0.741 |
|
| 2017 |
Cuenca-Alba J, Del Cano L, Gómez Blanco J, de la Rosa Trevín JM, Conesa Mingo P, Marabini R, S Sorzano CO, Carazo JM. ScipionCloud: An integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds. Journal of Structural Biology. 200: 20-27. PMID 28658599 DOI: 10.1016/J.Jsb.2017.06.004 |
0.811 |
|
| 2017 |
Martínez M, Sorzano COS, Pascual-Montano A, Carazo JM. Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors. Plos One. 12: e0178316. PMID 28542306 DOI: 10.1371/Journal.Pone.0178316 |
0.736 |
|
| 2017 |
Alvarez-Cabrera AL, Delgado S, Gil-Carton D, Mortuza GB, Montoya G, Sorzano CO, Tang TK, Carazo JM. Electron Microscopy Structural Insights into CPAP Oligomeric Behavior: A Plausible Assembly Process of a Supramolecular Scaffold of the Centrosome. Frontiers in Molecular Biosciences. 4: 17. PMID 28396859 DOI: 10.3389/Fmolb.2017.00017 |
0.819 |
|
| 2017 |
Otón J, Pereiro E, Conesa JJ, Chichón FJ, Luque D, Rodríguez JM, Pérez-Berná AJ, Sorzano CO, Klukowska J, Herman GT, Vargas J, Marabini R, Carrascosa JL, Carazo JM. XTEND: Extending the depth of field in cryo soft X-ray tomography. Scientific Reports. 7: 45808. PMID 28374769 DOI: 10.1038/Srep45808 |
0.802 |
|
| 2017 |
Sorzano CO, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín JM, Gómez-Blanco J, Vilas JL, Marabini R, Carazo JM. A review of resolution measures and related aspects in 3D Electron Microscopy. Progress in Biophysics and Molecular Biology. 124: 1-30. PMID 27666962 DOI: 10.1016/J.Pbiomolbio.2016.09.005 |
0.804 |
|
| 2016 |
Otón J, Pereiro E, Pérez-Berná AJ, Millach L, Sorzano CO, Marabini R, Carazo JM. Characterization of transfer function, resolution and depth of field of a soft X-ray microscope applied to tomography enhancement by Wiener deconvolution. Biomedical Optics Express. 7: 5092-5103. PMID 28018727 DOI: 10.1364/Boe.7.005092 |
0.812 |
|
| 2016 |
Vilas JL, Navas J, Gómez-Blanco J, de la Rosa-Trevín JM, Melero R, Peschiera I, Ferlenghi I, Cuenca J, Marabini R, Carazo JM, Vargas J, Sorzano COS. Fast and automatic identification of particle tilt pairs based on Delaunay triangulation. Journal of Structural Biology. 196: 525-533. PMID 27769763 DOI: 10.1016/J.Jsb.2016.10.007 |
0.828 |
|
| 2016 |
Vargas J, Franken E, Sorzano COS, Gomez-Blanco J, Schoenmakers R, Koster AJ, Carazo JM. Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope. Journal of Structural Biology. 196: 515-524. PMID 27725258 DOI: 10.1016/J.Jsb.2016.10.006 |
0.441 |
|
| 2016 |
Sanchez Sorzano CO, Alvarez-Cabrera AL, Kazemi M, Carazo JM, Jonić S. StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes. Biophysical Journal. 110: 1753-65. PMID 27119636 DOI: 10.1016/J.Bpj.2016.03.019 |
0.81 |
|
| 2016 |
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, ... ... Carazo JM, et al. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy. Journal of Structural Biology. 195: 93-9. PMID 27108186 DOI: 10.1016/J.Jsb.2016.04.010 |
0.809 |
|
| 2016 |
Sorzano CO, 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. Local analysis of strains and rotations for macromolecular electron microscopy maps. Journal of Structural Biology. 195: 123-8. PMID 27102900 DOI: 10.1016/J.Jsb.2016.04.001 |
0.798 |
|
| 2016 |
Jonić S, Vargas J, Melero R, Gómez-Blanco J, Carazo JM, Sorzano CO. Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions. Journal of Structural Biology. 194: 423-33. PMID 27085420 DOI: 10.1016/J.Jsb.2016.04.007 |
0.727 |
|
| 2016 |
Conesa JJ, Otón J, Chiappi M, Carazo JM, Pereiro E, Chichón FJ, Carrascosa JL. Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography. Scientific Reports. 6: 22354. PMID 26960695 DOI: 10.1038/Srep22354 |
0.781 |
|
| 2016 |
Vargas J, Otón J, Marabini R, Carazo JM, Sorzano CO. Particle alignment reliability in single particle electron cryomicroscopy: a general approach. Scientific Reports. 6: 21626. PMID 26899789 DOI: 10.1038/Srep21626 |
0.839 |
|
| 2016 |
Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB, Carazo JM. The Electron Microscopy eXchange (EMX) initiative. Journal of Structural Biology. 194: 156-63. PMID 26873784 DOI: 10.1016/J.Jsb.2016.02.008 |
0.849 |
|
| 2016 |
Tabas-Madrid D, Segura J, Sanchez-Garcia R, Cuenca-Alba J, Sorzano CO, Carazo JM. 3DBIONOTES: A unified, enriched and interactive view of macromolecular information. Journal of Structural Biology. 194: 231-4. PMID 26873783 DOI: 10.1016/J.Jsb.2016.02.007 |
0.804 |
|
| 2016 |
Segura J, Sanchez-Garcia R, Tabas-Madrid D, Cuenca-Alba J, Sorzano CO, Carazo JM. 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling. Biophysical Journal. 110: 766-75. PMID 26772592 DOI: 10.1016/J.Bpj.2015.11.3519 |
0.824 |
|
| 2015 |
Sorzano CO, Alcorlo M, de la Rosa-Trevín JM, Melero R, Foche I, Zaldívar-Peraza A, del Cano L, Vargas J, Abrishami V, Otón J, Marabini R, Carazo JM. Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited. Scientific Reports. 5: 14290. PMID 26390853 DOI: 10.1038/Srep14290 |
0.827 |
|
| 2015 |
Condezo GN, Marabini R, Ayora S, Carazo JM, Alba R, Chillón M, San Martín C. Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k. Journal of Virology. 89: 9653-64. PMID 26178997 DOI: 10.1128/Jvi.01453-15 |
0.8 |
|
| 2015 |
Abrishami V, Bilbao-Castro JR, Vargas J, Marabini R, Carazo JM, Sorzano CO. A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function. Ultramicroscopy. 157: 79-87. PMID 26094203 DOI: 10.1016/J.Ultramic.2015.05.018 |
0.807 |
|
| 2015 |
Carazo JM, Sorzano CO, Otón J, Marabini R, Vargas J. Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data. Archives of Biochemistry and Biophysics. 581: 39-48. PMID 26008761 DOI: 10.1016/J.Abb.2015.05.003 |
0.809 |
|
| 2015 |
Otón J, Sorzano CO, Marabini R, Pereiro E, Carazo JM. Measurement of the modulation transfer function of an X-ray microscope based on multiple Fourier orders analysis of a Siemens star. Optics Express. 23: 9567-72. PMID 25968993 DOI: 10.1364/Oe.23.009567 |
0.802 |
|
| 2015 |
Marabini R, Carragher B, Chen S, Chen J, Cheng A, Downing KH, Frank J, Grassucci RA, Bernard Heymann J, Jiang W, Jonic S, Liao HY, Ludtke SJ, Patwari S, Piotrowski AL, ... ... Carazo JM, et al. CTF Challenge: Result summary. Journal of Structural Biology. 190: 348-59. PMID 25913484 DOI: 10.1016/J.Jsb.2015.04.003 |
0.83 |
|
| 2015 |
Segura J, Sorzano CO, Cuenca-Alba J, Aloy P, Carazo JM. Using neighborhood cohesiveness to infer interactions between protein domains. Bioinformatics (Oxford, England). 31: 2545-52. PMID 25838464 DOI: 10.1093/Bioinformatics/Btv188 |
0.785 |
|
| 2015 |
Abrishami V, Vargas J, Li X, Cheng Y, Marabini R, Sorzano CÓ, Carazo JM. Alignment of direct detection device micrographs using a robust Optical Flow approach. Journal of Structural Biology. 189: 163-76. PMID 25681631 DOI: 10.1016/J.Jsb.2015.02.001 |
0.792 |
|
| 2015 |
Sorzano CO, Vargas J, de la Rosa-Trevín JM, Otón J, Álvarez-Cabrera AL, Abrishami V, Sesmero E, Marabini R, Carazo JM. A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy. Journal of Structural Biology. 189: 213-9. PMID 25637660 DOI: 10.1016/J.Jsb.2015.01.009 |
0.811 |
|
| 2014 |
Vargas J, Álvarez-Cabrera AL, Marabini R, Carazo JM, Sorzano CO. Efficient initial volume determination from electron microscopy images of single particles. Bioinformatics (Oxford, England). 30: 2891-8. PMID 24974203 DOI: 10.1093/Bioinformatics/Btu404 |
0.831 |
|
| 2013 |
de la Rosa-Trevín JM, Otón J, Marabini R, Zaldívar A, Vargas J, Carazo JM, Sorzano CO. Xmipp 3.0: an improved software suite for image processing in electron microscopy. Journal of Structural Biology. 184: 321-8. PMID 24075951 DOI: 10.1016/J.Jsb.2013.09.015 |
0.826 |
|
| 2013 |
Abrishami V, Zaldívar-Peraza A, de la Rosa-Trevín JM, Vargas J, Otón J, Marabini R, Shkolnisky Y, Carazo JM, Sorzano CO. A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs. Bioinformatics (Oxford, England). 29: 2460-8. PMID 23958728 DOI: 10.1093/Bioinformatics/Btt429 |
0.817 |
|
| 2013 |
Vargas J, Abrishami V, Marabini R, de la Rosa-Trevín JM, Zaldivar A, Carazo JM, Sorzano COS. Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques. Journal of Structural Biology. 183: 342-353. PMID 23933392 DOI: 10.1016/J.Jsb.2013.07.015 |
0.805 |
|
| 2013 |
Marabini R, Macias JR, Vargas J, Quintana A, Sorzano CO, Carazo JM. On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy. Acta Crystallographica. Section D, Biological Crystallography. 69: 695-700. PMID 23633578 DOI: 10.1107/S0907444913007038 |
0.785 |
|
| 2013 |
Vargas J, Otón J, Marabini R, Jonic S, de la Rosa-Trevín JM, Carazo JM, Sorzano CO. FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy. Journal of Structural Biology. 181: 136-48. PMID 23261401 DOI: 10.1016/J.Jsb.2012.12.006 |
0.812 |
|
| 2013 |
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. Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy. Methods in Molecular Biology (Clifton, N.J.). 950: 171-93. PMID 23086876 DOI: 10.1007/978-1-62703-137-0_11 |
0.842 |
|
| 2013 |
Vargas J, Sorzano COS, Estrada JC, Carazo JM. Generalization of the Principal Component Analysis algorithm for interferometry Optics Communications. 286: 130-134. DOI: 10.1016/J.Optcom.2012.09.017 |
0.328 |
|
| 2012 |
Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, et al. Data management challenges in three-dimensional EM. Nature Structural & Molecular Biology. 19: 1203-7. PMID 23211764 DOI: 10.1038/Nsmb.2426 |
0.798 |
|
| 2012 |
Oton J, Sorzano CO, Pereiro E, Cuenca-Alba J, Navarro R, Carazo JM, Marabini R. Image formation in cellular X-ray microscopy. Journal of Structural Biology. 178: 29-37. PMID 22343468 DOI: 10.1016/J.Jsb.2012.01.006 |
0.818 |
|
| 2012 |
Jiménez-Lozano N, Segura J, MacÃas JR, Vega J, Carazo JM. Integrating human and murine anatomical gene expression data for improved comparisons. Bioinformatics (Oxford, England). 28: 397-402. PMID 22106336 DOI: 10.1093/Bioinformatics/Btr639 |
0.765 |
|
| 2012 |
Sorzano C, Jonic S, Núñez-Ramírez R, Boisset N, Carazo J. Corrigendum to “Fast, robust and accurate determination of transmission electron microscopy contrast transfer function” [J. Struct. Biol. 160 (2007) 249–262] Journal of Structural Biology. 180: 387. DOI: 10.1016/J.Jsb.2012.05.022 |
0.598 |
|
| 2011 |
Melero R, Rajagopalan S, Lázaro M, Joerger AC, Brandt T, Veprintsev DB, Lasso G, Gil D, Scheres SH, Carazo JM, Fersht AR, Valle M. Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA. Proceedings of the National Academy of Sciences of the United States of America. 108: 557-62. PMID 21178074 DOI: 10.1073/Pnas.1015520107 |
0.775 |
|
| 2010 |
Arganda-Carreras I, Sorzano CO, Thévenaz P, Muñoz-Barrutia A, Kybic J, Marabini R, Carazo JM, Ortiz-de Solorzano C. Non-rigid consistent registration of 2D image sequences. Physics in Medicine and Biology. 55: 6215-42. PMID 20885021 DOI: 10.1088/0031-9155/55/20/012 |
0.771 |
|
| 2010 |
Vazquez M, Nogales-Cadenas R, Arroyo J, Botías P, García R, Carazo JM, Tirado F, Pascual-Montano A, Carmona-Saez P. MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Nucleic Acids Research. 38: W228-32. PMID 20513648 DOI: 10.1093/Nar/Gkq476 |
0.639 |
|
| 2010 |
Sorzano CO, Bilbao-Castro JR, Shkolnisky Y, Alcorlo M, Melero R, Caffarena-Fernández G, Li M, Xu G, Marabini R, Carazo JM. A clustering approach to multireference alignment of single-particle projections in electron microscopy. Journal of Structural Biology. 171: 197-206. PMID 20362059 DOI: 10.1016/J.Jsb.2010.03.011 |
0.81 |
|
| 2010 |
Neves ML, Carazo JM, Pascual-Montano A. Moara: a Java library for extracting and normalizing gene and protein mentions. Bmc Bioinformatics. 11: 157. PMID 20346105 DOI: 10.1186/1471-2105-11-157 |
0.64 |
|
| 2010 |
Cuesta I, Núñez-Ramírez R, Scheres SH, Gai D, Chen XS, Fanning E, Carazo JM. Conformational rearrangements of SV40 large T antigen during early replication events. Journal of Molecular Biology. 397: 1276-86. PMID 20219473 DOI: 10.1016/J.Jmb.2010.02.042 |
0.693 |
|
| 2010 |
Cheng K, Ivanova N, Scheres SH, Pavlov MY, Carazo JM, Hebert H, Ehrenberg M, Lindahl M. tmRNA.SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes. Journal of Structural Biology. 169: 342-8. PMID 19883769 DOI: 10.1016/J.Jsb.2009.10.015 |
0.713 |
|
| 2010 |
Pascual-Montano A, Carazo JM. Efficient functional bioinformatics tools: towards understanding biological processes Embnet.Journal. 16: 31. DOI: 10.14806/Ej.16.1.184 |
0.675 |
|
| 2009 |
Jiménez-Lozano N, Segura J, MacÃas JR, Vega J, Carazo JM. aGEM: an integrative system for analyzing spatial-temporal gene-expression information. Bioinformatics (Oxford, England). 25: 2566-72. PMID 19592395 DOI: 10.1093/Bioinformatics/Btp422 |
0.777 |
|
| 2009 |
Scheres SH, Carazo JM. Introducing robustness to maximum-likelihood refinement of electron-microscopy data. Acta Crystallographica. Section D, Biological Crystallography. 65: 672-8. PMID 19564687 DOI: 10.1107/S0907444909012049 |
0.75 |
|
| 2009 |
Sorzano CO, Recarte E, Alcorlo M, Bilbao-Castro JR, San-Martín C, Marabini R, Carazo JM. Automatic particle selection from electron micrographs using machine learning techniques. Journal of Structural Biology. 167: 252-60. PMID 19555764 DOI: 10.1016/J.Jsb.2009.06.011 |
0.776 |
|
| 2009 |
Nogales-Cadenas R, Carmona-Saez P, Vazquez M, Vicente C, Yang X, Tirado F, Carazo JM, Pascual-Montano A. GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Research. 37: W317-22. PMID 19465387 DOI: 10.1093/Nar/Gkp416 |
0.658 |
|
| 2009 |
Vazquez M, Carmona-Saez P, Nogales-Cadenas R, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A. SENT: semantic features in text. Nucleic Acids Research. 37: W153-9. PMID 19458159 DOI: 10.1093/Nar/Gkp392 |
0.66 |
|
| 2009 |
Sorzano CO, Messaoudi C, Eibauer M, Bilbao-Castro JR, Hegerl R, Nickell S, Marco S, Carazo JM. Marker-free image registration of electron tomography tilt-series. Bmc Bioinformatics. 10: 124. PMID 19397789 DOI: 10.1186/1471-2105-10-124 |
0.455 |
|
| 2009 |
Sorzano CO, Otero A, Olmos EM, Carazo JM. Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra. Bmc Structural Biology. 9: 18. PMID 19321015 DOI: 10.1186/1472-6807-9-18 |
0.354 |
|
| 2009 |
Iriarte A, Sorzano CO, Carazo JM, Rubio JL, Marabini R. A theoretical model for EM-ML reconstruction algorithms applied to rotating PET scanners. Physics in Medicine and Biology. 54: 1909-34. PMID 19265206 DOI: 10.1088/0031-9155/54/7/004 |
0.746 |
|
| 2009 |
Nogales-Cadenas R, Abascal F, Díez-Pérez J, Carazo JM, Pascual-Montano A. CentrosomeDB: a human centrosomal proteins database. Nucleic Acids Research. 37: D175-80. PMID 18971254 DOI: 10.1093/Nar/Gkn815 |
0.661 |
|
| 2009 |
Bilbao-Castro JR, Marabini R, Sorzano CO, García I, Carazo JM, Fernández JJ. Exploiting desktop supercomputing for three-dimensional electron microscopy reconstructions using ART with blobs. Journal of Structural Biology. 165: 19-26. PMID 18940260 DOI: 10.1016/J.Jsb.2008.09.009 |
0.803 |
|
| 2009 |
Gomez-Llorente Y, Fletcher RJ, Chen XS, Carazo JM, San Martín C. Double Hexamer Structure Of The Archaeal Helicase MCM From Methanobacterium Thermoautotrophicum Biophysical Journal. 96: 68a. DOI: 10.1016/J.Bpj.2008.12.252 |
0.763 |
|
| 2008 |
Sorzano CO, Velázquez-Muriel JA, Marabini R, Herman GT, Carazo JM. Volumetric restrictions in single particle 3DEM reconstruction. Pattern Recognition. 41: 616. PMID 20119498 DOI: 10.1016/J.Patcog.2007.06.010 |
0.808 |
|
| 2008 |
Brewster AS, Wang G, Yu X, Greenleaf WB, Carazo JM, Tjajadi M, Klein MG, Chen XS. Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase. Proceedings of the National Academy of Sciences of the United States of America. 105: 20191-6. PMID 19073923 DOI: 10.1073/Pnas.0808037105 |
0.302 |
|
| 2008 |
Chagoyen M, Carazo JM, Pascual-Montano A. Assessment of protein set coherence using functional annotations. Bmc Bioinformatics. 9: 444. PMID 18937846 DOI: 10.1186/1471-2105-9-444 |
0.662 |
|
| 2008 |
Scheres SH, Núñez-Ramírez R, Sorzano CO, Carazo JM, Marabini R. Image processing for electron microscopy single-particle analysis using XMIPP. Nature Protocols. 3: 977-90. PMID 18536645 DOI: 10.1038/Nprot.2008.62 |
0.84 |
|
| 2008 |
Abascal F, Carmona-Saez P, Carazo JM, Pascual-Montano A. ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. Bioinformatics (Oxford, England). 24: 1208-9. PMID 18339638 DOI: 10.1093/Bioinformatics/Btn094 |
0.638 |
|
| 2007 |
Scheres SH, Núñez-Ramírez R, Gómez-Llorente Y, San Martín C, Eggermont PP, Carazo JM. Modeling experimental image formation for likelihood-based classification of electron microscopy data. Structure (London, England : 1993). 15: 1167-77. PMID 17937907 DOI: 10.1016/J.Str.2007.09.003 |
0.83 |
|
| 2007 |
Sorzano CO, Jonic S, Núñez-Ramírez R, Boisset N, Carazo JM. Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function. Journal of Structural Biology. 160: 249-62. PMID 17911028 DOI: 10.1016/J.Jsb.2007.08.013 |
0.709 |
|
| 2007 |
Tidow H, Melero R, Mylonas E, Freund SM, Grossmann JG, Carazo JM, Svergun DI, Valle M, Fersht AR. Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex. Proceedings of the National Academy of Sciences of the United States of America. 104: 12324-9. PMID 17620598 DOI: 10.1073/Pnas.0705069104 |
0.805 |
|
| 2007 |
Agirrezabala X, Velázquez-Muriel JA, Gómez-Puertas P, Scheres SH, Carazo JM, Carrascosa JL. Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold. Structure (London, England : 1993). 15: 461-72. PMID 17437718 DOI: 10.1016/J.Str.2007.03.004 |
0.758 |
|
| 2007 |
Macías JR, Jiménez-Lozano N, Carazo JM. Integrating electron microscopy information into existing Distributed Annotation Systems. Journal of Structural Biology. 158: 205-213. PMID 17400476 DOI: 10.1016/J.Jsb.2007.02.004 |
0.385 |
|
| 2007 |
Núñez-Ramírez R, Velten M, Rivas G, Polard P, Carazo JM, Donate LE. Loading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase. Journal of Molecular Biology. 367: 764-9. PMID 17289076 DOI: 10.1016/J.Jmb.2006.12.075 |
0.321 |
|
| 2007 |
Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A. GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biology. 8: R3. PMID 17204154 DOI: 10.1186/Gb-2007-8-1-R3 |
0.66 |
|
| 2007 |
Fernández J, García I, Carazo J, Marabini R. Electron tomography of complex biological specimens on the Grid Future Generation Computer Systems. 23: 435-446. DOI: 10.1016/J.Future.2006.07.010 |
0.772 |
|
| 2006 |
Gil D, Carazo JM, Marabini R. On the nature of 2D crystal unbending. Journal of Structural Biology. 156: 546-55. PMID 16997575 DOI: 10.1016/J.Jsb.2006.07.012 |
0.766 |
|
| 2006 |
Pascual-Montano A, Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Marqui RD. bioNMF: a versatile tool for non-negative matrix factorization in biology. Bmc Bioinformatics. 7: 366. PMID 16875499 DOI: 10.1186/1471-2105-7-366 |
0.668 |
|
| 2006 |
Chagoyen M, Carmona-Saez P, Gil C, Carazo JM, Pascual-Montano A. A literature-based similarity metric for biological processes. Bmc Bioinformatics. 7: 363. PMID 16872502 DOI: 10.1186/1471-2105-7-363 |
0.653 |
|
| 2006 |
Pascual-Montano A, Carazo JM, Kochi K, Lehmann D, Pascual-Marqui RD. Nonsmooth nonnegative matrix factorization (nsNMF). Ieee Transactions On Pattern Analysis and Machine Intelligence. 28: 403-15. PMID 16526426 DOI: 10.1109/Tpami.2006.60 |
0.666 |
|
| 2006 |
Carmona-Saez P, Pascual-Marqui RD, Tirado F, Carazo JM, Pascual-Montano A. Biclustering of gene expression data by Non-smooth Non-negative Matrix Factorization. Bmc Bioinformatics. 7: 78. PMID 16503973 DOI: 10.1186/1471-2105-7-78 |
0.648 |
|
| 2006 |
Núñez-Ramírez R, Robledo Y, Mesa P, Ayora S, Alonso JC, Carazo JM, Donate LE. Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement. Journal of Molecular Biology. 357: 1063-76. PMID 16490212 DOI: 10.1016/J.Jmb.2006.01.091 |
0.308 |
|
| 2006 |
Valle M, Chen XS, Donate LE, Fanning E, Carazo JM. Structural basis for the cooperative assembly of large T antigen on the origin of replication. Journal of Molecular Biology. 357: 1295-305. PMID 16481006 DOI: 10.1016/J.Jmb.2006.01.021 |
0.757 |
|
| 2006 |
Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A. Integrated analysis of gene expression by Association Rules Discovery. Bmc Bioinformatics. 7: 54. PMID 16464256 DOI: 10.1186/1471-2105-7-54 |
0.652 |
|
| 2006 |
Chagoyen M, Carmona-Saez P, Shatkay H, Carazo JM, Pascual-Montano A. Discovering semantic features in the literature: a foundation for building functional associations. Bmc Bioinformatics. 7: 41. PMID 16438716 DOI: 10.1186/1471-2105-7-41 |
0.667 |
|
| 2006 |
Sorzano COS, Marabini R, Pascual-Montano A, Scheres SHW, Carazo JM. Optimization problems in electron microscopy of single particles Annals of Operations Research. 148: 133-165. DOI: 10.1007/S10479-006-0078-8 |
0.824 |
|
| 2005 |
Gómez-Llorente Y, Fletcher RJ, Chen XS, Carazo JM, San Martín C. Polymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum. The Journal of Biological Chemistry. 280: 40909-15. PMID 16221680 DOI: 10.1074/Jbc.M509760200 |
0.793 |
|
| 2005 |
Fletcher RJ, Shen J, Gómez-Llorente Y, Martín CS, Carazo JM, Chen XS. Double hexamer disruption and biochemical activities of Methanobacterium thermoautotrophicum MCM. The Journal of Biological Chemistry. 280: 42405-10. PMID 16221679 DOI: 10.1074/Jbc.M509773200 |
0.753 |
|
| 2005 |
Scheres SH, Valle M, Carazo JM. Fast maximum-likelihood refinement of electron microscopy images. Bioinformatics (Oxford, England). 21: ii243-4. PMID 16204112 DOI: 10.1093/Bioinformatics/Bti1140 |
0.827 |
|
| 2005 |
Scheres SH, Marabini R, Lanzavecchia S, Cantele F, Rutten T, Fuller SD, Carazo JM, Burnett RM, San Martín C. Classification of single-projection reconstructions for cryo-electron microscopy data of icosahedral viruses. Journal of Structural Biology. 151: 79-91. PMID 15923127 DOI: 10.1016/J.Jsb.2005.04.003 |
0.817 |
|
| 2005 |
Sorzano C, Marabini R, Herman G, Carazo J. Multiobjective algorithm parameter optimization using multivariate statistics in three-dimensional electron microscopy reconstruction Pattern Recognition. 38: 2587-2601. DOI: 10.1016/J.Patcog.2005.03.013 |
0.796 |
|
| 2005 |
Fernandez J, Bilbao-Castro J, Marabini R, Carazo J, Garcia I. On the suitability of Biological structure determination by electron microscopy to Grid Computing New Generation Computing. 23: 101-112. DOI: 10.1007/Bf03037653 |
0.762 |
|
| 2005 |
Rodríguez A, Carazo JM, Trelles O. Mining association rules from biological databases Journal of the American Society For Information Science and Technology. 56: 493-504. DOI: 10.1002/Asi.20138 |
0.323 |
|
| 2004 |
Sorzano CO, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SH, Carazo JM, Pascual-Montano A. XMIPP: a new generation of an open-source image processing package for electron microscopy. Journal of Structural Biology. 148: 194-204. PMID 15477099 DOI: 10.1016/J.Jsb.2004.06.006 |
0.845 |
|
| 2004 |
Sorzano CO, de la Fraga LG, Clackdoyle R, Carazo JM. Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy. Ultramicroscopy. 101: 129-38. PMID 15450658 DOI: 10.1016/J.Ultramic.2004.04.004 |
0.435 |
|
| 2004 |
Marabini R, Sorzano CO, Matej S, Fernández JJ, Carazo JM, Herman GT. 3-d reconstruction of 2-D crystals in real space. Ieee Transactions On Image Processing : a Publication of the Ieee Signal Processing Society. 13: 549-61. PMID 15376589 DOI: 10.1109/Tip.2003.822620 |
0.823 |
|
| 2004 |
Sorzano CO, Jonić S, El-Bez C, Carazo JM, De Carlo S, Thévenaz P, Unser M. A multiresolution approach to orientation assignment in 3D electron microscopy of single particles. Journal of Structural Biology. 146: 381-92. PMID 15099579 DOI: 10.1016/J.Jsb.2004.01.006 |
0.605 |
|
| 2004 |
Chagoyen M, Kurul ME, De-Alarcón PA, Carazo JM, Gupta A. Designing and executing scientific workflows with a programmable integrator. Bioinformatics (Oxford, England). 20: 2092-100. PMID 15059834 DOI: 10.1093/Bioinformatics/Bth209 |
0.308 |
|
| 2004 |
Sorzano CO, Marabini R, Herman GT, Censor Y, Carazo JM. Transfer function restoration in 3D electron microscopy via iterative data refinement. Physics in Medicine and Biology. 49: 509-22. PMID 15005161 DOI: 10.1088/0031-9155/49/4/003 |
0.825 |
|
| 2004 |
Carazo JM. Accessing information on the conformational flexibility of molecular machines. Structure (London, England : 1993). 12: 170-1. PMID 14962375 DOI: 10.1016/J.Str.2004.01.017 |
0.329 |
|
| 2004 |
Bilbao-Castro JR, Marabini R, Carazo JM, Garcia I, Fernandez JJ. THE POTENTIAL OF GRID COMPUTING IN THREE-DIMENSIONAL ELECTRON MICROSCOPY Parallel Processing Letters. 14: 151-162. DOI: 10.1142/S0129626404001805 |
0.777 |
|
| 2004 |
Fernandez J, Bilbao-Castro J, Marabini R, Carazo J, Garcia I. Biological structure determination by EM is well suited to grid computing New Generation Computing. 22: 187-188. DOI: 10.1007/Bf03040957 |
0.749 |
|
| 2003 |
Jiménez-Lozano N, Chagoyen M, Cuenca-Alba J, Carazo JM. FEMME database: topologic and geometric information of macromolecules. Journal of Structural Biology. 144: 104-113. PMID 14643213 DOI: 10.1016/J.Jsb.2003.09.014 |
0.428 |
|
| 2003 |
Gomez-Lorenzo MG, Valle M, Frank J, Gruss C, Sorzano CO, Chen XS, Donate LE, Carazo JM. Large T antigen on the simian virus 40 origin of replication: a 3D snapshot prior to DNA replication. The Embo Journal. 22: 6205-13. PMID 14633980 DOI: 10.1093/Emboj/Cdg612 |
0.776 |
|
| 2003 |
Velázquez-Muriel JA, Sorzano CO, Fernández JJ, Carazo JM. A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjustment. Ultramicroscopy. 96: 17-35. PMID 12623169 DOI: 10.1016/S0304-3991(02)00377-7 |
0.439 |
|
| 2003 |
Carazo J, de Alarcón P, Chagoyen M. Image databases: What are they and what do they bring to microscopy Microscopy and Microanalysis. 9: 1570-1571. DOI: 10.1017/S1431927603447855 |
0.388 |
|
| 2003 |
Fernández J, Bilbao-Castro J, Marabini R, Carazo JM, García I. Grid Computing in structure determination of biological specimens by electron microscope tomography Lecture Notes in Computer Science. 171-181. DOI: 10.1007/978-3-540-24689-3_22 |
0.756 |
|
| 2002 |
Tagari M, Newman R, Chagoyen M, Carazo JM, Henrick K. New electron microscopy database and deposition system. Trends in Biochemical Sciences. 27: 589. PMID 12417136 DOI: 10.1016/S0968-0004(02)02176-X |
0.398 |
|
| 2002 |
De-Alarcón PA, Pascual-Montano A, Gupta A, Carazo JM. Modeling shape and topology of low-resolution density maps of biological macromolecules. Biophysical Journal. 83: 619-32. PMID 12124252 DOI: 10.1016/S0006-3495(02)75196-5 |
0.7 |
|
| 2002 |
Marabini R, Herman GT, Sorzano COS, Carazo JM. Volumetric constraints in 3D tomography applied to electron microscopy Proceedings - International Symposium On Biomedical Imaging. 2002: 641-644. DOI: 10.1109/ISBI.2002.1029339 |
0.814 |
|
| 2001 |
Pascual-Montano A, Donate LE, Valle M, Bárcena M, Pascual-Marqui RD, Carazo JM. A novel neural network technique for analysis and classification of EM single-particle images. Journal of Structural Biology. 133: 233-45. PMID 11472094 DOI: 10.1006/Jsbi.2001.4369 |
0.831 |
|
| 2001 |
Sorzano CO, Marabini R, Boisset N, Rietzel E, Schröder R, Herman GT, Carazo JM. The effect of overabundant projection directions on 3D reconstruction algorithms. Journal of Structural Biology. 133: 108-18. PMID 11472083 DOI: 10.1006/Jsbi.2001.4338 |
0.812 |
|
| 2001 |
Bárcena M, Ruiz T, Donate LE, Brown SE, Dixon NE, Radermacher M, Carazo JM. The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel. The Embo Journal. 20: 1462-8. PMID 11250911 DOI: 10.1093/Emboj/20.6.1462 |
0.331 |
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| 2001 |
Kalko SG, Chagoyen M, Jiménez-Lozano N, Verdaguer N, Fita I, Carazo JM. The need for a shared database infrastructure: combining X-ray crystallography and electron microscopy. European Biophysics Journal : Ebj. 29: 457-62. PMID 11081407 DOI: 10.1007/S002490000089 |
0.423 |
|
| 2001 |
Pascual-Marqui R, Pascual-Montano A, Kochi K, Carazo J. Smoothly distributed fuzzy c-means: a new self-organizing map Pattern Recognition. 34: 2395-2402. DOI: 10.1016/S0031-3203(00)00167-9 |
0.599 |
|
| 2000 |
Donate LE, Llorca O, Bárcena M, Brown SE, Dixon NE, Carazo JM. pH-controlled quaternary states of hexameric DnaB helicase. Journal of Molecular Biology. 303: 383-93. PMID 11031115 DOI: 10.1006/Jmbi.2000.4132 |
0.55 |
|
| 2000 |
Valle M, Gruss C, Halmer L, Carazo JM, Donate LE. Large T-antigen double hexamers imaged at the simian virus 40 origin of replication. Molecular and Cellular Biology. 20: 34-41. PMID 10594006 DOI: 10.1128/Mcb.20.1.34-41.2000 |
0.749 |
|
| 2000 |
Krause S, Barcena M, Pansegrau W, Lurz R, Carazo JM, Lanka E. Sequence-related protein export NTPases encoded by the conjugative transfer region of RP4 and by the cag pathogenicity island of Helicobacter pylori share similar hexameric ring structures Proceedings of the National Academy of Sciences. 97: 3067-3072. DOI: 10.1073/Pnas.97.7.3067 |
0.357 |
|
| 2000 |
Donate LE, Bárcena M, Llorca O, Dixon N, Carazo JM. Quaternary Polymorphism in Helicases and the DnaB.DnaC Complex Microscopy and Microanalysis. 6: 272-273. DOI: 10.1017/S1431927600033857 |
0.535 |
|
| 2000 |
Herman GT, Marabini R, Carazo J, Gardu�o E, Lewitt RM, Matej S. Image processing approaches to biological three-dimensional electron microscopy International Journal of Imaging Systems and Technology. 11: 12-29. DOI: 10.1002/(Sici)1098-1098(2000)11:1<12::Aid-Ima3>3.0.Co;2-N |
0.841 |
|
| 1999 |
Valpuesta JM, Fernández JJ, Carazo JM, Carrascosa JL. The three-dimensional structure of a DNA translocating machine at 10 A resolution. Structure (London, England : 1993). 7: 289-96. PMID 10368298 DOI: 10.1016/S0969-2126(99)80039-2 |
0.545 |
|
| 1999 |
Alarcón PAd, Gupta A, Carazo JM. A framework for querying a database for structural information on 3D images of macromolecules: A web-based query-by-content prototype on the BioImage macromolecular server. Journal of Structural Biology. 125: 112-122. PMID 10222268 DOI: 10.1006/Jsbi.1999.4102 |
0.409 |
|
| 1999 |
Carazo JM, Stelzer EH. The BioImage Database Project: organizing multidimensional biological images in an object-relational database. Journal of Structural Biology. 125: 97-102. PMID 10222266 DOI: 10.1006/Jsbi.1999.4103 |
0.365 |
|
| 1999 |
Carazo JM, Stelzer EH, Engel A, Fita I, Henn C, Machtynger J, McNeil P, Shotton DM, Chagoyen M, de Alarcón PA, Fritsch R, Heymann JB, Kalko S, Pittet JJ, Rodriguez-Tomé P, et al. Organising multi-dimensional biological image information: the BioImage Database. Nucleic Acids Research. 27: 280-3. PMID 9847201 DOI: 10.1093/Nar/27.1.280 |
0.421 |
|
| 1998 |
Bárcena M, Martín CS, Weise F, Ayora S, Alonso JC, Carazo JM. Polymorphic quaternary organization of the Bacillus subtilis bacteriophage SPP1 replicative helicase (G40 P). Journal of Molecular Biology. 283: 809-19. PMID 9790842 DOI: 10.1006/Jmbi.1998.2128 |
0.351 |
|
| 1998 |
San Martin C, Radermacher M, Wolpensinger B, Engel A, Miles CS, Dixon NE, Carazo JM. Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC Structure. 6: 501-509. PMID 9562559 DOI: 10.1016/S0969-2126(98)00051-3 |
0.348 |
|
| 1998 |
Marabini R, Herman GT, Carazo JM. 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs) Ultramicroscopy. 72: 53-65. PMID 9561797 DOI: 10.1016/S0304-3991(97)00127-7 |
0.817 |
|
| 1998 |
Marabini R, Rietzel E, Schroeder R, Herman GT, Carazo JM. Three-dimensional reconstruction from reduced sets of very noisy images acquired following a single-axis tilt schema: application of a new three-dimensional reconstruction algorithm and objective comparison with weighted backprojection. Journal of Structural Biology. 120: 363-71. PMID 9441939 DOI: 10.1006/Jsbi.1997.3923 |
0.827 |
|
| 1998 |
Merelo JJ, Prieto A, Morán F, Marabini R, Carazo JM. Neural Processing Letters. 8: 55-65. DOI: 10.1023/A:1009617113191 |
0.766 |
|
| 1997 |
Scherzinger E, Ziegelin G, Bárcena M, Carazo JM, Lurz R, Lanka E. The RepA protein of plasmid RSF1010 is a replicative DNA helicase. The Journal of Biological Chemistry. 272: 30228-36. PMID 9374507 DOI: 10.1074/Jbc.272.48.30228 |
0.324 |
|
| 1997 |
San Martín MC, Gruss C, Carazo JM. Six molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel. Journal of Molecular Biology. 268: 15-20. PMID 9149137 DOI: 10.1006/Jmbi.1997.0952 |
0.372 |
|
| 1996 |
Marabini R, Masegosa IM, Martı́n MCS, Marco S, Fernández JJ, Fraga LGdl, Vaquerizo C, Carazo JM. Xmipp: An Image Processing Package for Electron Microscopy Journal of Structural Biology. 116: 237-240. PMID 8812978 DOI: 10.1006/Jsbi.1996.0036 |
0.788 |
|
| 1996 |
Marabini R, Vaquerizo C, Fernández JJ, Carazo JM, Engel A, Frank J. Proposal for a new distributed database of macromolecular and subcellular structures from different areas of microscopy. Journal of Structural Biology. 116: 161-5. PMID 8742739 DOI: 10.1006/Jsbi.1996.0026 |
0.81 |
|
| 1996 |
Marco S, Chagoyen M, de la Fraga LG, Carazo JM, Carrascosa JL. A variant to the “random approximation” of the reference-free alignment algorithm Ultramicroscopy. 66: 5-10. DOI: 10.1016/S0304-3991(96)00083-6 |
0.604 |
|
| 1996 |
Marabini R, Carazo J. On a new computationally fast image invariant based on bispectral projections Pattern Recognition Letters. 17: 959-967. DOI: 10.1016/0167-8655(96)00053-0 |
0.765 |
|
| 1995 |
Martin MCS, Stamford NPJ, Dammerova N, Dixon NE, Carazo JM. A structural model for the Escherichia coli DnaB helicase based on electron microscopy data. Journal of Structural Biology. 114: 167-176. PMID 7662485 DOI: 10.1006/Jsbi.1995.1016 |
0.364 |
|
| 1995 |
de la Fraga LG, Dopazo J, Carazo J. Confidence limits for resolution estimation in image averaging by random subsampling Ultramicroscopy. 60: 385-391. DOI: 10.1016/0304-3991(95)00080-1 |
0.372 |
|
| 1994 |
Marabini R, Carazo JM. Pattern recognition and classification of images of biological macromolecules using artificial neural networks. Biophysical Journal. 66: 1804-14. PMID 7915552 DOI: 10.1016/S0006-3495(94)80974-9 |
0.785 |
|
| 1994 |
Marabini R, Carazo J. Practical issues on invariant image averaging using the Bispectrum Signal Processing. 40: 119-128. DOI: 10.1016/0165-1684(94)90063-9 |
0.771 |
|
| 1992 |
Carazo JM, Marco S, Abella G, Carrascosa JL, Secilla JP, Muyal M. Electron microscopy study of GroEL chaperonin: different views of the aggregate appear as a function of cell growth temperature. Journal of Structural Biology. 106: 211-20. PMID 1687110 DOI: 10.1016/1047-8477(91)90071-4 |
0.509 |
|
| 1992 |
Valpuesta JM, Fujisawa H, Marco S, Carazo JM, Carrascosa JL. Three-dimensional structure of T3 connector purified from overexpressing bacteria. Journal of Molecular Biology. 224: 103-12. PMID 1548694 DOI: 10.1016/0022-2836(92)90579-9 |
0.552 |
|
| 1992 |
Carazo JM, Benavides I, Rivera FF, Zapata EL. Detection, classification and 3D reconstruction of biological macromolecules on hypercube computers. Ultramicroscopy. 40: 13-32. PMID 1349774 DOI: 10.1016/0304-3991(92)90232-9 |
0.463 |
|
| 1992 |
Zapata E, Benavides I, Rivera F, Bruguera J, Pena T, Carazo J. Image reconstruction on hypercube computers: Application to electron microscopy Signal Processing. 27: 51-64. DOI: 10.1016/0165-1684(92)90111-9 |
0.384 |
|
| 1991 |
Carrascosa JL, Abella G, Marco S, Carazo JM. Three-dimensional reconstruction of the sevenfolded form of Bacillus subtilis Gro EL Chaperonin. Journal of Structural Biology. 104: 2-8. PMID 1982415 DOI: 10.1016/1047-8477(90)90051-D |
0.589 |
|
| 1990 |
Carazo JM, Rivera FF, Zapata EL, Radermacher M, Frank J. Fuzzy sets-based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles. Journal of Microscopy. 157: 187-203. PMID 2179560 DOI: 10.1111/J.1365-2818.1990.Tb02958.X |
0.621 |
|
| 1990 |
Carrascosa J, Carazo J, Herranz L, Donate L, Secilla J. Study of two related configurations of the neck of bacteriophage Ø29 Computers & Mathematics With Applications. 20: 57-65. DOI: 10.1016/0898-1221(90)90314-A |
0.417 |
|
| 1990 |
Zapata E, Benavides J, Plata O, Rivera F, Carazo J. Image template matching on hypercube SIMD computers Signal Processing. 21: 49-60. DOI: 10.1016/0165-1684(90)90026-U |
0.366 |
|
| 1989 |
Carazo JM, Wagenknecht T, Frank J. Variations of the three-dimensional structure of the Escherichia coli ribosome in the range of overlap views. An application of the methods of multicone and local single-cone three-dimensional reconstruction Biophysical Journal. 55: 465-477. PMID 2649164 DOI: 10.1016/S0006-3495(89)82840-1 |
0.676 |
|
| 1989 |
Wagenknecht T, Carazo JM, Radermacher M, Frank J. Three-dimensional reconstruction of the ribosome from Escherichia coli Biophysical Journal. 55: 455-464. PMID 2649163 DOI: 10.1016/S0006-3495(89)82839-5 |
0.643 |
|
| 1988 |
Carazo JM, Frank J. Three-dimensional matching of macromolecular structures obtained from electron microscopy: an application to the 70S and 50S E. coli ribosomal particles. Ultramicroscopy. 25: 13-22. PMID 3291355 DOI: 10.1016/0304-3991(88)90401-9 |
0.649 |
|
| 1988 |
Bazinet C, Benbasat J, King J, Carazo JM, Carrascosa JL. Purification and organization of the gene 1 portal protein required for phage P22 DNA packaging. Biochemistry. 27: 1849-56. PMID 3288279 DOI: 10.1021/Bi00406A009 |
0.522 |
|
| 1988 |
Donate LE, Herranz L, Secilla JP, Carazo JM, Fujisawa H, Carrascosa JL. Bacteriophage T3 connector: three-dimensional structure and comparison with other viral head-tail connecting regions. Journal of Molecular Biology. 201: 91-100. PMID 3262165 DOI: 10.1016/0022-2836(88)90441-X |
0.526 |
|
| 1988 |
Frank J, Verschoor A, Wagenknecht T, Radermacher M, Carazo JM. A new non-crystallographic image-processing technique reveals the architecture of ribosomes Trends in Biochemical Sciences. 13: 123-127. PMID 3075375 DOI: 10.1016/0968-0004(88)90063-1 |
0.65 |
|
| 1988 |
Carazo JM, Wagenknecht T, Radermacher M, Mandiyan V, Boublik M, Frank J. Three-dimensional structure of 50 S Escherichia coli ribosomal subunits depleted of proteins L7/L12 Journal of Molecular Biology. 201: 393-404. PMID 3047401 DOI: 10.1016/0022-2836(88)90146-5 |
0.612 |
|
| 1988 |
Frank J, Bretaudiere JP, Carazo JM, Verschoor A, Wagenknecht T. Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli Journal of Microscopy. 150. PMID 3045323 DOI: 10.1111/J.1365-2818.1988.Tb04602.X |
0.603 |
|
| 1987 |
Carazo JM, Donate LE, Herranz L, Secilla JP, Carrascosa JL. Three-dimensional reconstruction of the connector of bacteriophage phi 29 at 1.8 nm resolution. Journal of Molecular Biology. 192: 853-67. PMID 3586012 DOI: 10.1016/0022-2836(86)90033-1 |
0.5 |
|
| 1987 |
Carazo JM, Carrascosa JL. Information recovery in missing angular data cases: an approach by the convex projections method in three dimensions Journal of Microscopy. 145: 23-43. DOI: 10.1111/J.1365-2818.1987.Tb01313.X |
0.566 |
|
| 1986 |
Carazo JM, Fujisawa H, Nakasu S, Carrascosa JL. Bacteriophage T3 gene 8 product oligomer structure. Journal of Ultrastructure and Molecular Structure Research. 94: 105-13. PMID 3782924 DOI: 10.1016/0889-1605(86)90056-X |
0.301 |
|
| 1986 |
Jiménez J, Santisteban A, Carazo JM, Carrascosa JL. Computer graphic display method for visualizing three-dimensional biological structures. Science (New York, N.Y.). 232: 1113-5. PMID 3754654 DOI: 10.1126/Science.3754654 |
0.609 |
|
| 1986 |
Carazo JM, Santisteban A, Carrascosa JL. Study of the direct Fourier method for the three-dimensional reconstruction of objects in the case of a missing angular data range Journal of Microscopy. 141: 21-30. DOI: 10.1111/J.1365-2818.1986.Tb02697.X |
0.621 |
|
| 1985 |
Carazo JM, Garcia N, Santisteban A, Carrascosa JL. Structural study of tetragonal-ordered aggregates of phage phi 29 necks. Journal of Ultrastructure Research. 89: 79-88. PMID 6544883 DOI: 10.1016/S0022-5320(84)80025-8 |
0.545 |
|
| 1985 |
Carrascosa JL, Carazo JM, Ibañez C, Santisteban A. Structure of phage phi 29 connector protein assembled in vivo. Virology. 141: 190-200. PMID 3936270 DOI: 10.1016/0042-6822(85)90251-X |
0.57 |
|
| 1984 |
Carrascosa JL, Carazo JM, Carrascosa AL, García N, Santisteban A, Viñuela E. General morphology and capsid fine structure of African swine fever virus particles. Virology. 132: 160-72. PMID 6695498 DOI: 10.1016/0042-6822(84)90100-4 |
0.502 |
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