Jose-Jesus Fernandez
Subcellular architecture · CINN
Biography
|
PhD in Computer Science in 1992. Accredited as Full Professor (Catedrático de Universidad) since 2008. Visiting researcher at the Laboratory of Molecular Biology – Medical Research Council (Cambridge, United Kingdom) during 2002-2006. Deputy (Adjunto) of the ANEP, responsible for the areas of image processing and high-performance computing during 2009-2013. Andalusia Research Award 2004. Research lines: electron tomography, image processing, high-performance computing, neuroscience. Highlighted results: 3D analysis of the subcellular architecture and molecular organisation of cells and tissues in situ by electron tomography and image processing. |
Profile
| Institution | CINN |
| Position | Científico Titular |
| Home page | https://tiny.cc/neuroarch |
| Contact email | jj.fernandez@csic.es |
| ORCID | 0000-0003-2222-3355 |
BCB Hub
| BCB Committee | Not a member |
| BCB Tools | Tomo3DEM |
| BCB Services | Electron Microscopy Facility at CINN |
Research
Research topics
Computational MethodsResourcesData AnalysisArtificial IntelligenceMachine Learning in BiologyData VisualizationApplications of Computational BiologyModel organismsComputational TechniquesHigh-performance ComputingParallel ComputingImage analysis
View all (2 more)
Deep Learning in BiologyClinical data
Research lines
Projects, networks, transfer & teaching
Funded projects 2
Publications 72 entries
- Myosin-9 is required for lysosome-mediated nonlytic reovirus egress Article · 14 Oct 2025
- The structure of basal body inner junctions from Tetrahymena revealed by electron cryo-tomography Article · 24 Feb 2025
- Denoising in cryoET Book / chapter · 2025
- Evolution of a large periplasmic disk in Campylobacterota flagella enables both efficient motility and autoagglutination Article · Dec 2024
- Markerauto2: A fast and robust fully automatic fiducial marker-based tilt series alignment software for electron tomography Article · Sep 2024
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- Disruption of the mitochondrial network in a mouse model of Huntington's disease visualized by in-tissue multiscale 3D electron microscopy Article · 5 Jun 2024
- Progressive alterations in polysomal architecture and activation of ribosome stalling relief factors in a mouse model of Huntington's disease Article · Jun 2024
- MarkerDetector: A method for robust fiducial marker detection in electron micrographs using wavelet-based template Article · Mar 2024
- Acceleration of 3D feature-enhancing noise filtering in hybrid CPU/GPU systems Article · 20 Feb 2024
- FlowDenoising: Structure-preserving denoising in 3D electron microscopy (3DEM) Article · Jul 2023
- Structure-preserving Gaussian denoising of FIB-SEM volumes Article · Apr 2023
- Computational methods for three-dimensional electron microscopy (3DEM) Article · Oct 2022
- HPC enables efficient 3D membrane segmentation in electron tomography Article · 17 Jun 2022
- Optical flow driven interpolation for isotropic FIB-SEM reconstructions Article · Jun 2022
- Architecture of torovirus replicative organelles Article · 17 Jan 2022
- Electron cryo-tomography structure of axonemal doublet microtubule from Tetrahymena thermophila Article · 30 Dec 2021
- TomoAlign: A novel approach to correcting sample motion and 3D CTF in CryoET Article · Dec 2021
- Electron Tomography to Study the Three-dimensional Structure of the Reovirus Egress Pathway in Mammalian Cells Article · 2021
- A modified lysosomal organelle mediates nonlytic egress of reovirus Article · 1 May 2020
- PolishEM: image enhancement in FIB–SEM Software · 28 Mar 2020
- Consideration of sample motion in cryo-tomography based on alignment residual interpolation Article · Mar 2019
- Electron cryo-tomography provides insight into procentriole architecture and assembly mechanism Article · 11 Feb 2019
- Assembly of Yeast Spindle Pole Body and its Components Revealed by Electron Cryo-Tomography Preprint · 13 Oct 2018
- Cryo-tomography tilt-series alignment with consideration of the beam-induced sample motion Article · Jun 2018
- TomoEED: fast edge-enhancing denoising of tomographic volumes Article · 29 May 2018
- 3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons Article · 1 Jan 2017
- The Structural Architecture of an Infectious Mammalian Prion Using Electron Cryomicroscopy Article · 8 Sep 2016
- Removing Contamination-Induced Reconstruction Artifacts from Cryo-electron Tomograms Article · Feb 2016
- Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy Article · Feb 2016
- Three dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex Article · 1 Jan 2016
- Tuning the cache memory usage in tomographic reconstruction on standard computers with Advanced Vector eXtensions (AVX) Article · Jun 2015
- Tomo3D 2.0 – Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction Article · Feb 2015
- Ring closure activates yeast γTuRC for species-specific microtubule nucleation Article · 19 Jan 2015
- Autofocused 3D Classification of Cryoelectron Subtomograms Article · Oct 2014
- Robust membrane detection based on tensor voting for electron tomography Software · Apr 2014
- A marker-free automatic alignment method based on scale-invariant features Article · Apr 2014
- Reovirus Forms Neo-Organelles for Progeny Particle Assembly within Reorganized Cell Membranes Article · 28 Feb 2014
- Computational methods for materials characterization by electron tomography Article · Jun 2013
- A ridge-based framework for segmentation of 3D electron microscopy datasets Article · Jan 2013
- Evaluation of a Multicore-Optimized Implementation for Tomographic Reconstruction Article · 6 Nov 2012
- Computational methods for electron tomography Article · Oct 2012
- Automatic tuning of the sparse matrix vector product on GPUs based on the ELLR-T approach Article · Aug 2012
- Hybrid computing: CPU+GPU co-processing and its application to tomographic reconstruction Article · Apr 2012
- Three‐dimensional structure of basal body triplet revealed by electron cryo‐tomography Article · 13 Dec 2011
- A differential structure approach to membrane segmentation in electron tomography Article · Sep 2011
- Matrix Implementation of Simultaneous Iterative Reconstruction Technique (SIRT) on GPUs Article · 20 Apr 2011
- Fast Three-Dimensional Noise Reduction for Real-Time Electron Tomography Book / chapter · 2011
- Fast tomographic reconstruction on multicore computers Software · 20 Dec 2010
- A new approach for sparse matrix vector product on NVIDIA GPUs Article · 26 Sep 2010
- Three-dimensional structure of Rubella virus factories Article · Sep 2010
- XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography Article · 27 Aug 2010
- Analytical Performance Prediction for Iterative Reconstruction Techniques in Electron Tomography of Biological Structures Article · 1 Jun 2010
- Vectorization with SIMD extensions speeds up reconstruction in electron tomography Article · Jun 2010
- A matrix approach to tomographic reconstruction and its implementation on GPUs Article · Apr 2010
- Improving the technique of vitreous cryo-sectioning for cryo-electron tomography: Electrostatic charging for section attachment and implementation of an anti-contamination glove box Article · Feb 2010
- Cryo-X-ray tomography of vaccinia virus membranes and inner compartments Article · Nov 2009
- Membrane remodelling during vaccinia virus morphogenesis Article · Jul 2009
- TOMOBFLOW: feature-preserving noise filtering for electron tomography Article · 12 Jun 2009
- Sharpening high resolution information in single particle electron cryomicroscopy Article · Oct 2008
- High performance computing in structural determination by electron cryomicroscopy Article · Oct 2008
- Efficient parallel implementation of iterative reconstruction algorithms for electron tomography Article · May 2008
- EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography Article · 14 Sep 2007
- High performance noise reduction for biomedical multidimensional data Article · Jul 2007
- Three-Dimensional Nanoparticle Distribution and Local Curvature of Heterogeneous Catalysts Revealed by Electron Tomography Article · 30 Jun 2007
- A population global optimization algorithm to solve the image alignment problem in electron crystallography Article · 9 Aug 2006
- CTF determination and correction in electron cryotomography Software · May 2006
- Three-dimensional real-space crystallography of MCM-48 mesoporous silica revealed by scanning transmission electron tomography Article · Feb 2006
- Cryo-electron tomography of vaccinia virus Article · 7 Feb 2005
- Phan3D: design of biological phantoms in 3D electron microscopy Article · 23 Jun 2004
- Floating point arithmetic teaching for computational science Article · Nov 2003
- An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms Article · Oct 2003
- Progressive Image Transmission in Telemicroscopy: A Quantitative Approach for Electron Microscopy Images of Biological Specimens Article · Dec 2002