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Items: 1 to 20 of 157

1.

Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ.

Koning RI, Gomez-Blanco J, Akopjana I, Vargas J, Kazaks A, Tars K, Carazo JM, Koster AJ.

Nat Commun. 2016 Aug 26;7:12524. doi: 10.1038/ncomms12524.

PMID:
27561669
2.

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

Sanchez Sorzano CO, Alvarez-Cabrera AL, Kazemi M, Carazo JM, Jonić S.

Biophys J. 2016 Apr 26;110(8):1753-65. doi: 10.1016/j.bpj.2016.03.019.

PMID:
27119636
3.

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
4.

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
5.

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
6.

Intracellular nanoparticles mass quantification by near-edge absorption soft X-ray nanotomography.

Conesa JJ, Otón J, Chiappi M, Carazo JM, Pereiro E, Chichón FJ, Carrascosa JL.

Sci Rep. 2016 Mar 10;6:22354. doi: 10.1038/srep22354.

7.

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.

8.

The Electron Microscopy eXchange (EMX) initiative.

Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB, Carazo JM.

J Struct Biol. 2016 May;194(2):156-63. doi: 10.1016/j.jsb.2016.02.008. Epub 2016 Feb 9.

PMID:
26873784
9.

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.

10.

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.

11.

Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.

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.

Sci Rep. 2015 Sep 22;5:14290. doi: 10.1038/srep14290.

12.

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.

J Virol. 2015 Sep;89(18):9653-64. doi: 10.1128/JVI.01453-15. Epub 2015 Jul 15.

13.

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. 2015 Oct;157:79-87. doi: 10.1016/j.ultramic.2015.05.018. Epub 2015 Jun 12.

PMID:
26094203
14.

Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data.

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

Arch Biochem Biophys. 2015 Sep 1;581:39-48. doi: 10.1016/j.abb.2015.05.003. Epub 2015 May 22. Review.

PMID:
26008761
15.

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.

Opt Express. 2015 Apr 20;23(8):9567-72. doi: 10.1364/OE.23.009567.

PMID:
25968993
16.

CTF Challenge: Result summary.

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, Quintana A, Sorzano CO, Stahlberg H, Vargas J, Voss NR, Chiu W, Carazo JM.

J Struct Biol. 2015 Jun;190(3):348-59. doi: 10.1016/j.jsb.2015.04.003. Epub 2015 Apr 23.

17.

Using neighborhood cohesiveness to infer interactions between protein domains.

Segura J, Sorzano CO, Cuenca-Alba J, Aloy P, Carazo JM.

Bioinformatics. 2015 Aug 1;31(15):2545-52. doi: 10.1093/bioinformatics/btv188. Epub 2015 Apr 2.

18.

Alignment of direct detection device micrographs using a robust Optical Flow approach.

Abrishami V, Vargas J, Li X, Cheng Y, Marabini R, Sorzano CÓ, Carazo JM.

J Struct Biol. 2015 Mar;189(3):163-76. doi: 10.1016/j.jsb.2015.02.001. Epub 2015 Feb 12.

PMID:
25681631
19.

A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.

Sorzano CO, Vargas J, de la Rosa-Trevín JM, Otón J, Álvarez-Cabrera AL, Abrishami V, Sesmero E, Marabini R, Carazo JM.

J Struct Biol. 2015 Mar;189(3):213-9. doi: 10.1016/j.jsb.2015.01.009. Epub 2015 Jan 28.

PMID:
25637660
20.

Efficient initial volume determination from electron microscopy images of single particles.

Vargas J, Álvarez-Cabrera AL, Marabini R, Carazo JM, Sorzano CO.

Bioinformatics. 2014 Oct 15;30(20):2891-8. doi: 10.1093/bioinformatics/btu404. Epub 2014 Jun 27.

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