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Items: 1 to 50 of 138

1.
2.

3DBIONOTES v3.0: Crossing molecular and structural biology data with genomic variations.

Segura J, Sanchez-Garcia R, Sorzano COS, Carazo JM.

Bioinformatics. 2019 Feb 15. pii: btz118. doi: 10.1093/bioinformatics/btz118. [Epub ahead of print]

PMID:
30768147
3.

Potent Anti-hepatitis C Virus (HCV) T Cell Immune Responses Induced in Mice Vaccinated with DNA-Launched RNA Replicons and Modified Vaccinia Virus Ankara-HCV.

Marín MQ, Pérez P, Ljungberg K, Sorzano CÓS, Gómez CE, Liljeström P, Esteban M, García-Arriaza J.

J Virol. 2019 Mar 21;93(7). pii: e00055-19. doi: 10.1128/JVI.00055-19. Print 2019 Apr 1.

PMID:
30674625
4.

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. 2019 Jan 1;75(Pt 1):19-32. doi: 10.1107/S2053230X18015108. Epub 2019 Jan 1.

PMID:
30605122
5.

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 Biol. 2018 Oct;52:127-145. doi: 10.1016/j.sbi.2018.11.004. Epub 2018 Nov 30. Review.

PMID:
30509756
6.

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. 2018 Nov 30. doi: 10.1093/bioinformatics/bty985. [Epub ahead of print]

PMID:
30500892
7.

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. 2018 Oct 30;5(Pt 6):854-865. doi: 10.1107/S2052252518014392. eCollection 2018 Nov 1.

8.

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. 2018 Dec;204(3):457-463. doi: 10.1016/j.jsb.2018.10.001. Epub 2018 Oct 5.

9.

Map challenge: Analysis using a pair comparison method based on Fourier shell correlation.

Marabini R, Kazemi M, Sorzano COS, Carazo JM.

J Struct Biol. 2018 Dec;204(3):527-542. doi: 10.1016/j.jsb.2018.09.009. Epub 2018 Sep 28.

PMID:
30273658
10.

Fast multiscale reconstruction for Cryo-EM.

Donati L, Nilchian M, Sorzano COS, Unser M.

J Struct Biol. 2018 Dec;204(3):543-554. doi: 10.1016/j.jsb.2018.09.008. Epub 2018 Sep 24.

11.

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. 2018 Sep 13;8(1):13726. doi: 10.1038/s41598-018-31997-z.

12.

Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function.

Martínez-Muñoz L, Rodríguez-Frade JM, Barroso R, Sorzano CÓS, Torreño-Pina JA, Santiago CA, Manzo C, Lucas P, García-Cuesta EM, Gutierrez E, Barrio L, Vargas J, Cascio G, Carrasco YR, Sánchez-Madrid F, García-Parajo MF, Mellado M.

Mol Cell. 2018 Sep 6;71(5):873. doi: 10.1016/j.molcel.2018.08.012. No abstract available.

PMID:
30193101
13.

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. 2018 Nov;204(2):329-337. doi: 10.1016/j.jsb.2018.08.002. Epub 2018 Aug 24.

PMID:
30145327
14.

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. 2018 Nov;204(2):291-300. doi: 10.1016/j.jsb.2018.08.010. Epub 2018 Aug 13.

PMID:
30114512
15.

Potent HIV-1-Specific CD8 T Cell Responses Induced in Mice after Priming with a Multiepitopic DNA-TMEP and Boosting with the HIV Vaccine MVA-B.

Perdiguero B, Raman SC, Sánchez-Corzo C, Sorzano COS, Valverde JR, Esteban M, Gómez CE.

Viruses. 2018 Aug 13;10(8). pii: E424. doi: 10.3390/v10080424.

16.

Removal of the C6 Vaccinia Virus Interferon-β Inhibitor in the Hepatitis C Vaccine Candidate MVA-HCV Elicited in Mice High Immunogenicity in Spite of Reduced Host Gene Expression.

Marín MQ, Pérez P, Gómez CE, Sorzano CÓS, Esteban M, García-Arriaza J.

Viruses. 2018 Aug 8;10(8). pii: E414. doi: 10.3390/v10080414.

17.

BIPSPI: a method for the prediction of partner-specific protein-protein interfaces.

Sanchez-Garcia R, Sorzano COS, Carazo JM, Segura J.

Bioinformatics. 2019 Feb 1;35(3):470-477. doi: 10.1093/bioinformatics/bty647.

18.

Reconstruction From Multiple Particles for 3D Isotropic Resolution in Fluorescence Microscopy.

Fortun D, Guichard P, Hamel V, Sorzano COS, Banterle N, Gonczy P, Unser M.

IEEE Trans Med Imaging. 2018 May;37(5):1235-1246. doi: 10.1109/TMI.2018.2795464.

PMID:
29727286
19.

Correction: Safety and vaccine-induced HIV-1 immune responses in healthy volunteers following a late MVA-B boost 4 years after the last immunization.

Guardo AC, Gómez CE, Díaz-Brito V, Pich J, Arnaiz JA, Perdiguero B, García-Arriaza J, González N, Sorzano COS, Jiménez L, Jiménez JL, Muñoz-Fernández MÁ, Gatell JM, Alcamí J, Esteban M, de Quirós JCLB, García F, Plana M; RISVAC02boost study.

PLoS One. 2018 Apr 10;13(4):e0195915. doi: 10.1371/journal.pone.0195915. eCollection 2018.

20.

Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function.

Martínez-Muñoz L, Rodríguez-Frade JM, Barroso R, Sorzano CÓS, Torreño-Pina JA, Santiago CA, Manzo C, Lucas P, García-Cuesta EM, Gutierrez E, Barrio L, Vargas J, Cascio G, Carrasco YR, Sánchez-Madrid F, García-Parajo MF, Mellado M.

Mol Cell. 2018 Apr 5;70(1):106-119.e10. doi: 10.1016/j.molcel.2018.02.034. Erratum in: Mol Cell. 2018 Sep 6;71(5):873.

PMID:
29625032
21.

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. 2018 Aug;203(2):90-93. doi: 10.1016/j.jsb.2018.03.007. Epub 2018 Mar 15.

PMID:
29551714
22.

MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.

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.

Structure. 2018 Feb 6;26(2):337-344.e4. doi: 10.1016/j.str.2017.12.018. Epub 2018 Jan 27.

23.

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.

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.

Biomed Res Int. 2017;2017:6482567. doi: 10.1155/2017/6482567. Epub 2017 Sep 17. Review.

24.

Immune Modulation of NYVAC-Based HIV Vaccines by Combined Deletion of Viral Genes that Act on Several Signalling Pathways.

Gómez CE, Perdiguero B, Sánchez-Corzo C, Sorzano COS, Esteban M.

Viruses. 2017 Dec 27;10(1). pii: E7. doi: 10.3390/v10010007.

25.

3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures.

Sanchez-Garcia R, Sorzano COS, Carazo JM, Segura J.

Molecules. 2017 Dec 15;22(12). pii: E2230. doi: 10.3390/molecules22122230.

26.

Safety and vaccine-induced HIV-1 immune responses in healthy volunteers following a late MVA-B boost 4 years after the last immunization.

Guardo AC, Gómez CE, Díaz-Brito V, Pich J, Arnaiz JA, Perdiguero B, García-Arriaza J, González N, Sorzano COS, Jiménez L, Jiménez JL, Muñoz-Fernández MÁ, Gatell JM, Alcamí J, Esteban M, López Bernaldo de Quirós JC, García F, Plana M; RISVAC02boost study.

PLoS One. 2017 Oct 24;12(10):e0186602. doi: 10.1371/journal.pone.0186602. eCollection 2017. Erratum in: PLoS One. 2018 Apr 10;13(4):e0195915.

27.

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. 2018 Jan;27(1):269-275. doi: 10.1002/pro.3315. Epub 2017 Nov 6.

28.

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures.

Segura J, Sanchez-Garcia R, Martinez M, Cuenca-Alba J, Tabas-Madrid D, Sorzano COS, Carazo JM.

Bioinformatics. 2017 Nov 15;33(22):3655-3657. doi: 10.1093/bioinformatics/btx483.

29.

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 CÓS, Marengo E, Saracco G, Zanotti G, Carazo JM, Pagliano C.

Sci Rep. 2017 Aug 30;7(1):10067. doi: 10.1038/s41598-017-10700-8.

30.

Identification of Chlamydomonas Central Core Centriolar Proteins Reveals a Role for Human WDR90 in Ciliogenesis.

Hamel V, Steib E, Hamelin R, Armand F, Borgers S, Flückiger I, Busso C, Olieric N, Sorzano COS, Steinmetz MO, Guichard P, Gönczy P.

Curr Biol. 2017 Aug 21;27(16):2486-2498.e6. doi: 10.1016/j.cub.2017.07.011. Epub 2017 Aug 3.

31.

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. 2017 Jul 24;7(1):6307. doi: 10.1038/s41598-017-06526-z.

32.

Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors.

Martínez M, Sorzano COS, Pascual-Montano A, Carazo JM.

PLoS One. 2017 May 24;12(5):e0178316. doi: 10.1371/journal.pone.0178316. eCollection 2017.

33.

Distinct Roles of Vaccinia Virus NF-κB Inhibitor Proteins A52, B15, and K7 in the Immune Response.

Di Pilato M, Mejías-Pérez E, Sorzano COS, Esteban M.

J Virol. 2017 Jun 9;91(13). pii: e00575-17. doi: 10.1128/JVI.00575-17. Print 2017 Jul 1.

34.

Electron Microscopy Structural Insights into CPAP Oligomeric Behavior: A Plausible Assembly Process of a Supramolecular Scaffold of the Centrosome.

Alvarez-Cabrera AL, Delgado S, Gil-Carton D, Mortuza GB, Montoya G, Sorzano CO, Tang TK, Carazo JM.

Front Mol Biosci. 2017 Mar 27;4:17. doi: 10.3389/fmolb.2017.00017. eCollection 2017.

35.

XTEND: Extending the depth of field in cryo soft X-ray tomography.

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.

Sci Rep. 2017 Apr 4;7:45808. doi: 10.1038/srep45808.

36.

A Prime/Boost PfCS14KM/MVA-sPfCSM Vaccination Protocol Generates Robust CD8+ T Cell and Antibody Responses to Plasmodium falciparum Circumsporozoite Protein and Protects Mice against Malaria.

Vijayan A, Mejías-Pérez E, Espinosa DA, Raman SC, Sorzano COS, Zavala F, Esteban M.

Clin Vaccine Immunol. 2017 May 5;24(5). pii: e00494-16. doi: 10.1128/CVI.00494-16. Print 2017 May.

37.

Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control.

Jonić S, Sorzano CO.

Biomed Res Int. 2016;2016:7060348. doi: 10.1155/2016/7060348. Epub 2016 Dec 21. Review.

38.

Characterization of transfer function, resolution and depth of field of a soft X-ray microscope applied to tomography enhancement by Wiener deconvolution.

Otón J, Pereiro E, Pérez-Berná AJ, Millach L, Sorzano CO, Marabini R, Carazo JM.

Biomed Opt Express. 2016 Nov 14;7(12):5092-5103. doi: 10.1364/BOE.7.005092. eCollection 2016 Dec 1.

39.

Fast and automatic identification of particle tilt pairs based on Delaunay triangulation.

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.

J Struct Biol. 2016 Dec;196(3):525-533. doi: 10.1016/j.jsb.2016.10.007. Epub 2016 Oct 18.

PMID:
27769763
40.

Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope.

Vargas J, Franken E, Sorzano COS, Gomez-Blanco J, Schoenmakers R, Koster AJ, Carazo JM.

J Struct Biol. 2016 Dec;196(3):515-524. doi: 10.1016/j.jsb.2016.10.006. Epub 2016 Oct 8.

PMID:
27725258
41.

A review of resolution measures and related aspects in 3D Electron Microscopy.

Sorzano CO, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín JM, Gómez-Blanco J, Vilas JL, Marabini R, Carazo JM.

Prog Biophys Mol Biol. 2017 Mar;124:1-30. doi: 10.1016/j.pbiomolbio.2016.09.005. Epub 2016 Sep 22. Review.

PMID:
27666962
42.

Clathrin regulates lymphocyte migration by driving actin accumulation at the cellular leading edge.

Ramírez-Santiago G, Robles-Valero J, Morlino G, Cruz-Adalia A, Pérez-Martínez M, Zaldivar A, Torres-Torresano M, Chichón FJ, Sorrentino A, Pereiro E, Carrascosa JL, Megías D, Sorzano CO, Sánchez-Madrid F, Veiga E.

Eur J Immunol. 2016 Oct;46(10):2376-2387. doi: 10.1002/eji.201646291. Epub 2016 Aug 25.

43.

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.

J Struct Biol. 2016 Jul;195(1):93-9. doi: 10.1016/j.jsb.2016.04.010. Epub 2016 Apr 20.

PMID:
27108186
44.

Local analysis of strains and rotations for macromolecular electron microscopy maps.

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.

J Struct Biol. 2016 Jul;195(1):123-8. doi: 10.1016/j.jsb.2016.04.001. Epub 2016 Apr 19.

PMID:
27102900
45.

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 CO.

J Struct Biol. 2016 Jun;194(3):423-33. doi: 10.1016/j.jsb.2016.04.007. Epub 2016 Apr 13.

PMID:
27085420
46.

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, Henzler K, Schneider G, Chichón FJ, Carrascosa JL.

J Nanobiotechnology. 2016 Mar 3;14:15. doi: 10.1186/s12951-016-0170-4.

47.

Particle alignment reliability in single particle electron cryomicroscopy: a general approach.

Vargas J, Otón J, Marabini R, Carazo JM, Sorzano CO.

Sci Rep. 2016 Feb 22;6:21626. doi: 10.1038/srep21626.

48.

3DBIONOTES: A unified, enriched and interactive view of macromolecular information.

Tabas-Madrid D, Segura J, Sanchez-Garcia R, Cuenca-Alba J, Sorzano CO, Carazo JM.

J Struct Biol. 2016 May;194(2):231-4. doi: 10.1016/j.jsb.2016.02.007. Epub 2016 Feb 10.

49.

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.

Segura J, Sanchez-Garcia R, Tabas-Madrid D, Cuenca-Alba J, Sorzano CO, Carazo JM.

Biophys J. 2016 Feb 23;110(4):766-75. doi: 10.1016/j.bpj.2015.11.3519. Epub 2016 Jan 7.

50.

System models for PET statistical iterative reconstruction: A review.

Iriarte A, Marabini R, Matej S, Sorzano CO, Lewitt RM.

Comput Med Imaging Graph. 2016 Mar;48:30-48. doi: 10.1016/j.compmedimag.2015.12.003. Epub 2015 Dec 19. Review.

PMID:
26748039

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