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Jose Carazo

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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TOP 3
Sorzano C O S; Recarte E; Alcorlo M; Bilbao-Castro J R; San-Martín C; Marabini R; Carazo J M
Automatic particle selection from electron micrographs using machine learning techniques.
Nickell Stephan; Beck Florian; Scheres Sjors H W; Korinek Andreas; Förster Friedrich; Lasker Keren; Mihalache Oana; Sun Na; Nagy István; Sali Andrej; Plitzko Jürgen M; Carazo Jose-Maria; Mann Matthias; Baumeister Wolfgang
Insights into the molecular architecture of the 26S proteasome.
Scheres Sjors H W; Carazo José María
Introducing robustness to maximum-likelihood refinement of electron-microscopy data.

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All Publications

2009: Sorzano C O S; Recarte E; Alcorlo M; Bilbao-Castro J R; San-Martín C; Marabini R; Carazo J M
Automatic particle selection from electron micrographs using machine learning techniques.
Journal of structural biology 2009;167(3):252-60.
2009: Nickell Stephan; Beck Florian; Scheres Sjors H W; Korinek Andreas; Förster Friedrich; Lasker Keren; Mihalache Oana; Sun Na; Nagy István; Sali Andrej; Plitzko Jürgen M; Carazo Jose-Maria; Mann Matthias; Baumeister Wolfgang
Insights into the molecular architecture of the 26S proteasome.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(29):11943-7.
2009: Scheres Sjors H W; Carazo José María
Introducing robustness to maximum-likelihood refinement of electron-microscopy data.
Acta crystallographica. Section D, Biological crystallography 2009;65(Pt 7):672-8.
2009: Nogales-Cadenas Ruben; Carmona-Saez Pedro; Vazquez Miguel; Vicente Cesar; Yang Xiaoyuan; Tirado Francisco; Carazo Jose María; Pascual-Montano Alberto
GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information.
Nucleic acids research 2009;37(Web Server issue):W317-22.
2009: Vazquez Miguel; Carmona-Saez Pedro; Nogales-Cadenas Ruben; Chagoyen Monica; Tirado Francisco; Carazo Jose Maria; Pascual-Montano Alberto
SENT: semantic features in text.
Nucleic acids research 2009;37(Web Server issue):W153-9.
2009: Scheres Sjors H W; Valle Mikel; Grob Patricia; Nogales Eva; Carazo José-María
Maximum likelihood refinement of electron microscopy data with normalization errors.
Journal of structural biology 2009;166(2):234-40.
2009: Iriarte A; Sorzano C O S; Carazo J M; Rubio J L; Marabini R
A theoretical model for EM-ML reconstruction algorithms applied to rotating PET scanners.
Physics in medicine and biology 2009;54(7):1909-34.
2009: Sorzano Carlos Oscar Sanchez; Messaoudi Cédric; Eibauer Matthias; Bilbao-Castro J R; Hegerl R; Nickell S; Marco S; Carazo J M
Marker-free image registration of electron tomography tilt-series.
BMC bioinformatics 2009;10():124.
2009: Sorzano Carlos Oscar S; Otero Abraham; Olmos Estefanía M; Carazo José María
Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra.
BMC structural biology 2009;9():18.
2009: Velázquez-Muriel Javier A; Rueda Manuel; Cuesta Isabel; Pascual-Montano Alberto; Orozco Modesto; Carazo José-María
Comparison of molecular dynamics and superfamily spaces of protein domain deformation.
BMC structural biology 2009;9():6.
2008: Abascal Federico; Carmona-Saez Pedro; Carazo Jose-Maria; Pascual-Montano Alberto
ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data.
Bioinformatics (Oxford, England) 2008;24(9):1208-9.
2008: Chagoyen Monica; Carazo Jose M; Pascual-Montano Alberto
Assessment of protein set coherence using functional annotations.
BMC bioinformatics 2008;9():444.
2008: Scheres Sjors H W; Núñez-Ramírez Rafael; Sorzano Carlos O S; Carazo José María; Marabini Roberto
Image processing for electron microscopy single-particle analysis using XMIPP.
Nature protocols 2008;3(6):977-90.
2007: Sorzano C O S; Jonic S; Núñez-Ramírez R; Boisset N; Carazo J M
Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function.
Journal of structural biology 2007;160(2):249-62.
2007: Scheres Sjors H W; Núñez-Ramírez Rafael; Gómez-Llorente Yacob; San Martín Carmen; Eggermont Paul P B; Carazo José María
Modeling experimental image formation for likelihood-based classification of electron microscopy data.
Structure (London, England : 1993) 2007;15(10):1167-77.
2007: Macías J R; Jiménez-Lozano N; Carazo J M
Integrating electron microscopy information into existing Distributed Annotation Systems.
Journal of structural biology 2007;158(2):205-13.
2007: Velazquez-Muriel Javier A; Carazo José-Mari A
Flexible fitting in 3D-EM with incomplete data on superfamily variability.
Journal of structural biology 2007;158(2):165-81.
2007: Agirrezabala Xabier; Velázquez-Muriel Javier A; Gómez-Puertas Paulino; Scheres Sjors H W; Carazo José M; Carrascosa José L
Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
Structure (London, England : 1993) 2007;15(4):461-72.
2007: Núñez-Ramírez Rafael; Velten Marion; Rivas Germán; Polard Patrice; Carazo José María; Donate Luis Enrique
Loading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase.
Journal of molecular biology 2007;367(3):764-9.
2007: Scheres Sjors H W; Gao Haixiao; Valle Mikel; Herman Gabor T; Eggermont Paul P B; Frank Joachim; Carazo Jose-Maria
Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.
Nature methods 2007;4(1):27-9.
2007: Carmona-Saez Pedro; Chagoyen Monica; Tirado Francisco; Carazo Jose M; Pascual-Montano Alberto
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists.
Genome biology 2007;8(1):R3.
2006: Gil Debora; Carazo Jose Maria; Marabini Roberto
On the nature of 2D crystal unbending.
Journal of structural biology 2006;156(3):546-55.
2006: Velazquez-Muriel Javier-Angel; Valle Mikel; Santamaría-Pang Alberto; Kakadiaris Ioannis A; Carazo José-María
Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.
Structure (London, England : 1993) 2006;14(7):1115-26.
2006: Núñez-Ramírez Rafael; Robledo Yolanda; Mesa Pablo; Ayora Silvia; Alonso Juan Carlos; Carazo José María; Donate Luis Enrique
Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.
Journal of molecular biology 2006;357(4):1063-76.
2006: Valle Mikel; Chen Xiaojiang S; Donate Luis Enrique; Fanning Ellen; Carazo José María
Structural basis for the cooperative assembly of large T antigen on the origin of replication.
Journal of molecular biology 2006;357(4):1295-305.
2006: Pascual-Montano Alberto; Carazo J M; Kochi Kieko; Lehmann Dietrich; Pascual-Marqui Roberto D
Nonsmooth nonnegative matrix factorization (nsNMF).
IEEE transactions on pattern analysis and machine intelligence 2006;28(3):403-15.
2006: Pascual-Montano Alberto; Carmona-Saez Pedro; Chagoyen Monica; Tirado Francisco; Carazo Jose M; Pascual-Marqui Roberto D
bioNMF: a versatile tool for non-negative matrix factorization in biology.
BMC bioinformatics 2006;7():366.
2006: Chagoyen Monica; Carmona-Saez Pedro; Gil Concha; Carazo Jose M; Pascual-Montano Alberto
A literature-based similarity metric for biological processes.
BMC bioinformatics 2006;7():363.
2006: Carmona-Saez Pedro; Pascual-Marqui Roberto D; Tirado F; Carazo Jose M; Pascual-Montano Alberto
Biclustering of gene expression data by Non-smooth Non-negative Matrix Factorization.
BMC bioinformatics 2006;7():78.
2006: Carmona-Saez Pedro; Chagoyen Monica; Rodriguez Andres; Trelles Oswaldo; Carazo Jose M; Pascual-Montano Alberto
Integrated analysis of gene expression by Association Rules Discovery.
BMC bioinformatics 2006;7():54.
2006: Chagoyen Monica; Carmona-Saez Pedro; Shatkay Hagit; Carazo Jose M; Pascual-Montano Alberto
Discovering semantic features in the literature: a foundation for building functional associations.
BMC bioinformatics 2006;7():41.
2005: Gómez-Llorente Yacob; Fletcher Ryan J; Chen Xiaojiang S; Carazo José M; San Martín Carmen
Polymorphism and double hexamer structure in the archaeal minichromosome maintenance (MCM) helicase from Methanobacterium thermoautotrophicum.
The Journal of biological chemistry 2005;280(49):40909-15.
2005: Fletcher Ryan J; Shen Jingping; Gómez-Llorente Yacob; Martín Carmen San; Carazo José M; Chen Xiaojiang S
Double hexamer disruption and biochemical activities of Methanobacterium thermoautotrophicum MCM.
The Journal of biological chemistry 2005;280(51):42405-10.
2005: Scheres Sjors H W; Valle Mikel; Carazo José-María
Fast maximum-likelihood refinement of electron microscopy images.
Bioinformatics (Oxford, England) 2005;21 Suppl 2():ii243-4.
2005: Scheres Sjors H W; Marabini Roberto; Lanzavecchia Salvatore; Cantele Francesca; Rutten Twan; Fuller Stephen D; Carazo José M; Burnett Roger M; San Martín Carmen
Classification of single-projection reconstructions for cryo-electron microscopy data of icosahedral viruses.
Journal of structural biology 2005;151(1):79-91.
2005: Scheres Sjors H W; Valle Mikel; Nuñez Rafael; Sorzano Carlos O S; Marabini Roberto; Herman Gabor T; Carazo Jose-Maria
Maximum-likelihood multi-reference refinement for electron microscopy images.
Journal of molecular biology 2005;348(1):139-49.
2005: Velázquez-Muriel Javier A; Sorzano Carlos O S; Scheres Sjors H W; Carazo José-María
SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps.
Journal of molecular biology 2005;345(4):759-71.
2004: Sorzano C O S; Marabini R; Velázquez-Muriel J; Bilbao-Castro J R; Scheres S H W; Carazo J M; Pascual-Montano A
XMIPP: a new generation of an open-source image processing package for electron microscopy.
Journal of structural biology 2004;148(2):194-204.
2004: Sorzano C O S; de la Fraga L G; Clackdoyle R; Carazo J M
Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy.
Ultramicroscopy 2004;101(2-4):129-38.
2004: Chagoyen M; Kurul M E; De-Alarcón P A; Carazo J M; Gupta A
Designing and executing scientific workflows with a programmable integrator.
Bioinformatics (Oxford, England) 2004;20(13):2092-100.
2004: Sorzano C O S; Jonic S; El-Bez C; Carazo J M; De Carlo S; Thévenaz P; Unser M
A multiresolution approach to orientation assignment in 3D electron microscopy of single particles.
Journal of structural biology 2004;146(3):381-92.
2004: Marabini Roberto; Sorzano Carlos O S; Matej Samuel; Fernández José J; Carazo José M; Herman Gabor T
3-d reconstruction of 2-D crystals in real space.
IEEE transactions on image processing : a publication of the IEEE Signal Processing Society 2004;13(4):549-61.
2004: Sorzano C O S; Marabini R; Herman G T; Censor Y; Carazo J M
Transfer function restoration in 3D electron microscopy via iterative data refinement.
Physics in medicine and biology 2004;49(4):509-22.
2003: Gomez-Lorenzo Maria G; Valle Mikel; Frank Joachim; Gruss Claudia; Sorzano Carlos Oscar S; Chen Xiaojiang S; Donate Luis Enrique; Carazo Jose Maria
Large T antigen on the simian virus 40 origin of replication: a 3D snapshot prior to DNA replication.
The EMBO journal 2003;22(23):6205-13.
2003: Jiménez-Lozano N; Chagoyen M; Cuenca-Alba J; Carazo J M
FEMME database: topologic and geometric information of macromolecules.
Journal of structural biology 2003;144(1-2):104-13.
2003: Velázquez-Muriel J A; Sorzano C O S; Fernández J J; Carazo J M
A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjustment.
Ultramicroscopy 2003;96(1):17-35.
2002: Tagari Mohamed; Newman Richard; Chagoyen Monica; Carazo Jose Maria; Henrick Kim
New electron microscopy database and deposition system.
Trends in biochemical sciences 2002;27(11):589.
2002: De-Alarcón Pedro A; Pascual-Montano Alberto; Gupta Amarnath; Carazo Jose M
Modeling shape and topology of low-resolution density maps of biological macromolecules.
Biophysical journal 2002;83(2):619-32.
2002: Pascual-Montano A; Taylor K A; Winkler H; Pascual-Marqui R D; Carazo J-M
Quantitative self-organizing maps for clustering electron tomograms.
Journal of structural biology 2002;138(1-2):114-22.
2002: Fernández José-Jesús; Lawrence Albert F; Roca Javier; García Inmaculada; Ellisman Mark H; Carazo José-María
High-performance electron tomography of complex biological specimens.
Journal of structural biology 2002;138(1-2):6-20.
2001: Bárcena M; Ruiz T; Donate L E; Brown S E; Dixon N E; Radermacher M; Carazo J M
The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel.
The EMBO journal 2001;20(6):1462-8.
2001: Pascual-Montano A; Donate L E; Valle M; Bárcena M; Pascual-Marqui R D; Carazo J M
A novel neural network technique for analysis and classification of EM single-particle images.
Journal of structural biology 2001;133(2-3):233-45.
2001: Sorzano C O; Marabini R; Boisset N; Rietzel E; Schröder R; Herman G T; Carazo J M
The effect of overabundant projection directions on 3D reconstruction algorithms.
Journal of structural biology 2001;133(2-3):108-18.
2000: Donate L E; Llorca O; Bárcena M; Brown S E; Dixon N E; Carazo J M
pH-controlled quaternary states of hexameric DnaB helicase.
Journal of molecular biology 2000;303(3):383-93.
2000: Pascual A; Bárcena M; Merelo J J; Carazo J M
Mapping and fuzzy classification of macromolecular images using self-organizing neural networks.
Ultramicroscopy 2000;84(1-2):85-99.
2000: Krause S; Barcena M; Pansegrau W; Lurz R; Carazo J M; 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 of the United States of America 2000;97(7):3067-72.
2000: Valle M; Gruss C; Halmer L; Carazo J M; Donate L E
Large T-antigen double hexamers imaged at the simian virus 40 origin of replication.
Molecular and cellular biology 2000;20(1):34-41.
1999: de Alarcón P A; Gupta A; Carazo J M
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 1999;125(2-3):112-22.
1999: Carazo J M; Stelzer E H
The BioImage Database Project: organizing multidimensional biological images in an object-relational database.
Journal of structural biology 1999;125(2-3):97-102.
1999: Valpuesta J M; Fernández J J; Carazo J M; Carrascosa J L
The three-dimensional structure of a DNA translocating machine at 10 A resolution.
Structure (London, England : 1993) 1999;7(3):289-96.
1999: Carazo J M; Stelzer E H; Engel A; Fita I; Henn C; Machtynger J; McNeil P; Shotton D M; Chagoyen M; de Alarcón P A; Fritsch R; Heymann J B; Kalko S; Pittet J J; Rodriguez-Tomé P; Boudier T
Organising multi-dimensional biological image information: the BioImage Database.
Nucleic acids research 1999;27(1):280-3.
1998: Wang H C; Dopazo J; de la Fraga L G; Zhu Y P; Carazo J M
Self-organizing tree-growing network for the classification of protein sequences.
Protein science : a publication of the Protein Society 1998;7(12):2613-22.
1998: Bárcena M; Martín C S; Weise F; Ayora S; Alonso J C; Carazo J M
Polymorphic quaternary organization of the Bacillus subtilis bacteriophage SPP1 replicative helicase (G40 P).
Journal of molecular biology 1998;283(4):809-19.
1998: Trelles O; Andrade M A; Valencia A; Zapata E L; Carazo J M
Computational space reduction and parallelization of a new clustering approach for large groups of sequences.
Bioinformatics (Oxford, England) 1998;14(5):439-51.
1998: San Martin C; Radermacher M; Wolpensinger B; Engel A; Miles C S; Dixon N E; Carazo J M
Three-dimensional reconstructions from cryoelectron microscopy images reveal an intimate complex between helicase DnaB and its loading partner DnaC.
Structure (London, England : 1993) 1998;6(4):501-9.
1998: Marabini R; Herman G T; Carazo J M
3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs).
Ultramicroscopy 1998;72(1-2):53-65.
1998: Trelles O; Ceron C; Wang H C; Dopazo J; Carazo J M
New phylogenetic venues opened by a novel implementation of the DNAml algorithm.
Bioinformatics (Oxford, England) 1998;14(6):544-5.
1998: Wang H C; Dopazo J; Carazo J M
Self-organizing tree growing network for classifying amino acids.
Bioinformatics (Oxford, England) 1998;14(4):376-7.
1997: Marabini R; Rietzel E; Schroeder R; Herman G T; Carazo J M
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 1997;120(3):363-71.
1997: Scherzinger E; Ziegelin G; Bárcena M; Carazo J M; Lurz R; Lanka E
The RepA protein of plasmid RSF1010 is a replicative DNA helicase.
The Journal of biological chemistry 1997;272(48):30228-36.
1997: San Martín M C; Gruss C; Carazo J M
Six molecules of SV40 large T antigen assemble in a propeller-shaped particle around a channel.
Journal of molecular biology 1997;268(1):15-20.
1997: Dopazo J; Carazo J M
Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree.
Journal of molecular evolution 1997;44(2):226-33.
1996: Fernández J J; Carazo J M
Analysis of structural variability within two-dimensional biological crystals by a combination of patch averaging techniques and self organizing maps.
Ultramicroscopy 1996;65(1-2):81-93.
1996: Marabini R; Vaquerizo C; Fernández J J; Carazo J M; Engel A; Frank J
Proposal for a new distributed database of macromolecular and subcellular structures from different areas of microscopy.
Journal of structural biology 1996;116(1):161-5.
1995: Trelles-Salazar O; Zapata E L; Dopazo J; Coulson A F; Carazo J M
An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data.
Computer applications in the biosciences : CABIOS 1995;11(3):301-8.
1995: San Martin M C; Stamford N P; Dammerova N; Dixon N E; Carazo J M
A structural model for the Escherichia coli DnaB helicase based on electron microscopy data.
Journal of structural biology 1995;114(3):167-76.
1994: Trelles-Salazar O; Zapata E L; Carazo J M
On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures.
Computer applications in the biosciences : CABIOS 1994;10(5):509-11.
1994: Marabini R; Carazo J M
Pattern recognition and classification of images of biological macromolecules using artificial neural networks.
Biophysical journal 1994;66(6):1804-14.
1992: Valpuesta J M; Fujisawa H; Marco S; Carazo J M; Carrascosa J L
Three-dimensional structure of T3 connector purified from overexpressing bacteria.
Journal of molecular biology 1992;224(1):103-12.
1992: Carazo J M; Benavides I; Rivera F F; Zapata E L
Detection, classification and 3D reconstruction of biological macromolecules on hypercube computers.
Ultramicroscopy 1992;40(1):13-32.
1991: Carazo J M; Marco S; Abella G; Carrascosa J L; Secilla J P; 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 1991;106(3):211-20.
1990: Carrascosa J L; Abella G; Marco S; Carazo J M
Three-dimensional reconstruction of the sevenfolded form of Bacillus subtilis Gro EL Chaperonin.
Journal of structural biology 1990;104(1-3):2-8.
1990: Carazo J M; Rivera F F; Zapata E L; Radermacher M; Frank J
Fuzzy sets-based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles.
Journal of microscopy 1990;157(Pt 2):187-203.
1989: Carazo J M; 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 1989;55(3):465-77.
1989: Wagenknecht T; Carazo J M; Radermacher M; Frank J
Three-dimensional reconstruction of the ribosome from Escherichia coli.
Biophysical journal 1989;55(3):455-64.
1988: Donate L E; Herranz L; Secilla J P; Carazo J M; Fujisawa H; Carrascosa J L
Bacteriophage T3 connector: three-dimensional structure and comparison with other viral head-tail connecting regions.
Journal of molecular biology 1988;201(1):91-100.
1988: Carazo J M; 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 1988;201(2):393-404.
1988: Frank J; Bretaudiere J P; Carazo J M; Verschoor A; Wagenknecht T
Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli.
Journal of microscopy 1988;150(Pt 2):99-115.
1988: Frank J; Verschoor A; Wagenknecht T; Radermacher M; Carazo J M
A new non-crystallographic image-processing technique reveals the architecture of ribosomes.
Trends in biochemical sciences 1988;13(4):123-7.
1988: Carazo J M; Frank J
Three-dimensional matching of macromolecular structures obtained from electron microscopy: an application to the 70S and 50S E. coli ribosomal particles.
Ultramicroscopy 1988;25(1):13-22.
1986: Carazo J M; Donate L E; Herranz L; Secilla J P; Carrascosa J L
Three-dimensional reconstruction of the connector of bacteriophage phi 29 at 1.8 nm resolution.
Journal of molecular biology 1986;192(4):853-67.

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Jose Carazo

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