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Results: 1 to 20 of 138

1.

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

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

Bioinformatics. 2014 Jun 27. pii: btu404. [Epub ahead of print]

PMID:
24974203
[PubMed - as supplied by publisher]
2.

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
[PubMed - indexed for MEDLINE]
3.

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.

PMID:
23958728
[PubMed - indexed for MEDLINE]
4.

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
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
23671615
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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
[PubMed - indexed for MEDLINE]
7.

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
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
23211764
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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
[PubMed - indexed for MEDLINE]
10.

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
[PubMed - indexed for MEDLINE]
11.

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
[PubMed - indexed for MEDLINE]
12.

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
[PubMed - indexed for MEDLINE]
13.

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.

PMID:
22106336
[PubMed - indexed for MEDLINE]
Free Article
14.

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
[PubMed - indexed for MEDLINE]
15.

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
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
21178074
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

An introduction to maximum-likelihood methods in cryo-EM.

Sigworth FJ, Doerschuk PC, Carazo JM, Scheres SH.

Methods Enzymol. 2010;482:263-94. doi: 10.1016/S0076-6879(10)82011-7.

PMID:
20888965
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Non-rigid consistent registration of 2D image sequences.

Arganda-Carreras I, Sorzano CO, Thévenaz P, Muñoz-Barrutia A, Kybic J, Marabini R, Carazo JM, Ortiz-de Solorzano C.

Phys Med Biol. 2010 Oct 21;55(20):6215-42. doi: 10.1088/0031-9155/55/20/012. Epub 2010 Sep 30.

PMID:
20885021
[PubMed - indexed for MEDLINE]
19.

Maximum likelihood based classification of electron tomographic data.

Stölken M, Beck F, Haller T, Hegerl R, Gutsche I, Carazo JM, Baumeister W, Scheres SH, Nickell S.

J Struct Biol. 2011 Jan;173(1):77-85. doi: 10.1016/j.jsb.2010.08.005. Epub 2010 Aug 16.

PMID:
20719249
[PubMed - indexed for MEDLINE]
20.

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures.

Vazquez M, Nogales-Cadenas R, Arroyo J, Botías P, García R, Carazo JM, Tirado F, Pascual-Montano A, Carmona-Saez P.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W228-32. doi: 10.1093/nar/gkq476. Epub 2010 May 31.

PMID:
20513648
[PubMed - indexed for MEDLINE]
Free PMC Article

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