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Computer Science
Spain
2025

D-Index & Metrics

Computer Science

D-Index
61
Citations
15720
World Ranking
3057
National Ranking
38

Research.com Recognitions

  • 2025 - Research.com Computer Science in Spain Leader Award
  • 2022 - Research.com Computer Science in Spain Leader Award

Overview

José María Carazo is affiliated with the Spanish National Research Council in Spain. Their research primarily spans the fields of Biochemistry, Genetics and Molecular Biology, and Materials Science. Within these broad areas, they focus on subfields including Structural Biology, Surfaces, Coatings and Films, Molecular Biology, Materials Chemistry, and Radiation.

Their work engages deeply with several scientific topics, prominently including:

  • Advanced Electron Microscopy Techniques and Applications
  • Electron and X-Ray Spectroscopy Techniques
  • Advanced X-ray Imaging Techniques
  • Enzyme Structure and Function
  • Machine Learning in Materials Science
  • Protein Structure and Dynamics
  • Scientific Computing and Data Management

Several frequent coauthors collaborate with José María Carazo, reflecting ongoing professional partnerships. These include Carlos Óscar S. Sorzano with 71 joint works, Pablo Conesa (28), David Herreros (26), Erney Ramírez-Aportela (22), and Marta Martínez (21).

Publication venues where the scientist has contributed multiple articles are:

  • Faculty Opinions - Post-Publication Peer Review of the Biomedical Literature (20 publications)
  • Journal of Structural Biology (13 publications)
  • Zenodo (CERN European Organization for Nuclear Research) (13 publications)
  • bioRxiv (Cold Spring Harbor Laboratory) (11 publications)
  • Nature Communications (6 publications)

Notable recent papers authored or coauthored by José María Carazo include:

  • DeepEMhancer: a deep learning solution for cryo-EM volume post-processing, 2021, Communications Biology
  • DeepEMhancer: a deep learning solution for cryo-EM volume post-processing, 2020, bioRxiv (Cold Spring Harbor Laboratory)
  • PDBe-KB: collaboratively defining the biological context of structural data, 2021, Nucleic Acids Research
  • Ribosome-associated vesicles: A dynamic subcompartment of the endoplasmic reticulum in secretory cells, 2020, Science Advances
  • Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data, 2020, Progress in Biophysics and Molecular Biology

Best Publications

  • DeepEMhancer: a deep learning solution for cryo-EM volume post-processing.

    Ruben Sanchez-Garcia;Ruben Sanchez-Garcia;Josue Gomez-Blanco;Josue Gomez-Blanco;Ana Cuervo;Jose Maria Carazo

  • GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists

    Pedro Carmona-Saez;Monica Chagoyen;Monica Chagoyen;Francisco Tirado;Jose M Carazo

  • Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

    J.M. de la Rosa-Trevín;A. Quintana;L. del Cano;A. Zaldívar

  • XMIPP: a new generation of an open-source image processing package for electron microscopy

    Carlos Óscar Sánchez Sorzano;Roberto Marabini;Javier Velázquez-Muriel;José Román Bilbao-Castro

  • Nonsmooth nonnegative matrix factorization (nsNMF)

    A. Pascual-Montano;J.M. Carazo;K. Kochi;D. Lehmann

  • GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

    Rubén Nogales-Cadenas;Pedro Carmona-Saez;Miguel Vázquez;Cesar Vicente

  • Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.

    Sjors H W Scheres;Haixiao Gao;Mikel Valle;Gabor T Herman

  • Consistent and elastic registration of histological sections using vector-spline regularization

    Ignacio Arganda-Carreras;Carlos O. S. Sorzano;Roberto Marabini;José María Carazo

  • Image processing for electron microscopy single-particle analysis using XMIPP

    Sjors H. W. Scheres;Rafael Núñez-Ramírez;Carlos Óscar Sánchez Sorzano;José M. Carazo

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

    J.M. de la Rosa-Trevín;J. Otón;R. Marabini;A. Zaldívar

  • Maximum-likelihood Multi-reference Refinement for Electron Microscopy Images

    Sjors H.W. Scheres;Mikel Valle;Rafael Nuñez;Carlos O.S. Sorzano;Carlos O.S. Sorzano

  • Phylogenetic Reconstruction Using an Unsupervised Growing Neural Network That Adopts the Topology of a Phylogenetic Tree

    Joaquín Dopazo;José María Carazo

  • Biclustering of gene expression data by non-smooth non-negative matrix factorization

    Pedro Carmona-Saez;Roberto D. Pascual-Marqui;Francisco Tirado;José María Carazo

  • DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

    Ruben Sanchez Garcia;Josue Gomez-Blanco;Ana Cuervo;Jose Maria Carazo

  • Xmipp: An Image Processing Package for Electron Microscopy

    R. Marabini;I.M. Masegosa;M.C. San Martı́n;S. Marco

  • A clustering approach to multireference alignment of single-particle projections in electron microscopy

    C.O.S. Sorzano;J.R. Bilbao-Castro;Y. Shkolnisky;M. Alcorlo

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

    Jose Luis Vilas;Josué Gómez-Blanco;Pablo Conesa;Roberto Melero

  • 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs).

    Roberto Marabini;Gabor T Herman;José M Carazo

  • Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo.

    Ajasja Ljubetič;Fabio Lapenta;Helena Gradišar;Igor Drobnak

  • Integrated analysis of gene expression by association rules discovery

    Pedro Carmona-Saez;Monica Chagoyen;Andres Rodriguez;Oswaldo Trelles

  • Pattern recognition and classification of images of biological macromolecules using artificial neural networks

    R. Marabini;J.M. Carazo

Frequent Co-Authors

Roberto Marabini
Roberto Marabini Autonomous University of Madrid
Carlos Oscar S. Sorzano
Carlos Oscar S. Sorzano Spanish National Research Council
José Luis Vilas
José Luis Vilas University of the Basque Country
José L. Carrascosa
José L. Carrascosa Spanish National Research Council
Joachim Frank
Joachim Frank Columbia University
Gabor T. Herman
Gabor T. Herman City University of New York
Xiaojiang S. Chen
Xiaojiang S. Chen University of Southern California
María Jesús Martínez
María Jesús Martínez Spanish National Research Council
Roberto D. Pascual-Marqui
Roberto D. Pascual-Marqui University of Zurich
Joaquín Dopazo
Joaquín Dopazo Institute of Biomedicine of Seville

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