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Results: 1 to 20 of 142

1.

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 Apr 23. pii: S1047-8477(15)00075-1. doi: 10.1016/j.jsb.2015.04.003. [Epub ahead of print]

PMID:
25913484
2.

Using neighborhood cohesiveness to infer interactions between protein domains.

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

Bioinformatics. 2015 Apr 2. pii: btv188. [Epub ahead of print]

PMID:
25838464
3.

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
4.

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
5.

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.

PMID:
24974203
6.

Xmipp 3.0: an improved software suite for image processing in electron microscopy.

de la Rosa-Trevín JM, Otón J, Marabini R, Zaldívar A, Vargas J, Carazo JM, Sorzano CO.

J Struct Biol. 2013 Nov;184(2):321-8. doi: 10.1016/j.jsb.2013.09.015. Epub 2013 Sep 26.

PMID:
24075951
7.

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 Oct 1;29(19):2460-8. doi: 10.1093/bioinformatics/btt429. Epub 2013 Aug 19.

8.

Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques.

Vargas J, Abrishami V, Marabini R, de la Rosa-Trevín JM, Zaldivar A, Carazo JM, Sorzano CO.

J Struct Biol. 2013 Sep;183(3):342-53. doi: 10.1016/j.jsb.2013.07.015. Epub 2013 Aug 6.

PMID:
23933392
9.

Structure and non-structure of centrosomal proteins.

Dos Santos HG, Abia D, Janowski R, Mortuza G, Bertero MG, Boutin M, Guarín N, Méndez-Giraldez R, Nuñez A, Pedrero JG, Redondo P, Sanz M, Speroni S, Teichert F, Bruix M, Carazo JM, Gonzalez C, Reina J, Valpuesta JM, Vernos I, Zabala JC, Montoya G, Coll M, Bastolla U, Serrano L.

PLoS One. 2013 May 9;8(5):e62633. doi: 10.1371/journal.pone.0062633. Print 2013.

10.

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy.

Marabini R, Macias JR, Vargas J, Quintana A, Sorzano CO, Carazo JM.

Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):695-700. doi: 10.1107/S0907444913007038. Epub 2013 Apr 19.

PMID:
23633578
11.

FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy.

Vargas J, Otón J, Marabini R, Jonic S, de la Rosa-Trevín JM, Carazo JM, Sorzano CO.

J Struct Biol. 2013 Feb;181(2):136-48. doi: 10.1016/j.jsb.2012.12.006. Epub 2012 Dec 20.

PMID:
23261401
12.

Data management challenges in three-dimensional EM.

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, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ.

Nat Struct Mol Biol. 2012 Dec;19(12):1203-7. doi: 10.1038/nsmb.2426. No abstract available.

13.

Shack-Hartmann centroid detection using the spiral phase transform.

Vargas J, Restrepo R, Estrada JC, Sorzano CO, Du YZ, Carazo JM.

Appl Opt. 2012 Oct 20;51(30):7362-7. doi: 10.1364/AO.51.007362.

PMID:
23089793
14.

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;950:171-93. doi: 10.1007/978-1-62703-137-0_11.

PMID:
23086876
15.

Image formation in cellular X-ray microscopy.

Oton J, Sorzano CO, Pereiro E, Cuenca-Alba J, Navarro R, Carazo JM, Marabini R.

J Struct Biol. 2012 Apr;178(1):29-37. doi: 10.1016/j.jsb.2012.01.006. Epub 2012 Feb 15.

PMID:
22343468
16.

Two-step demodulation based on the Gram-Schmidt orthonormalization method.

Vargas J, Quiroga JA, Sorzano CO, Estrada JC, Carazo JM.

Opt Lett. 2012 Feb 1;37(3):443-5. doi: 10.1364/OL.37.000443.

PMID:
22297380
17.

Integrating human and murine anatomical gene expression data for improved comparisons.

Jiménez-Lozano N, Segura J, Macías JR, Vega J, Carazo JM.

Bioinformatics. 2012 Feb 1;28(3):397-402. doi: 10.1093/bioinformatics/btr639. Epub 2011 Nov 20.

18.

Two-step interferometry by a regularized optical flow algorithm.

Vargas J, Quiroga JA, Sorzano CO, Estrada JC, Carazo JM.

Opt Lett. 2011 Sep 1;36(17):3485-7. doi: 10.1364/OL.36.003485.

PMID:
21886252
19.

PRIDEViewer: a novel user-friendly interface to visualize PRIDE XML files.

Medina-Aunon JA, Carazo JM, Albar JP.

Proteomics. 2011 Jan;11(2):334-7. doi: 10.1002/pmic.201000448. Epub 2010 Dec 17.

PMID:
21204261
20.

Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA.

Melero R, Rajagopalan S, Lázaro M, Joerger AC, Brandt T, Veprintsev DB, Lasso G, Gil D, Scheres SH, Carazo JM, Fersht AR, Valle M.

Proc Natl Acad Sci U S A. 2011 Jan 11;108(2):557-62. doi: 10.1073/pnas.1015520107. Epub 2010 Dec 22.

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