Embedded Files
Journal covers
Journal covers
Selected publications
Neuronal Subcellular Architecture
Neuronal Subcellular Architecture
E Martin-Solana, L Casado-Zueras, TE Torres, GF Goya, MR Fernandez-Fernandez, JJ Fernandez
Acta Neuropathologica Communications 12:88, 2024. [PDF] [Software]
E Martin-Solana, I Diaz-Lopez, Y Mohamedi, I Ventoso, JJ Fernandez, MR Fernandez-Fernandez
Neurobiology of Disease 195:106488, 2024. [PDF] [Software1] [Software2]
Structure-preserving Gaussian denoising of FIB-SEM volumes
V Gonzalez-Ruiz, MR Fernandez-Fernandez, JJ Fernandez
Ultramicroscopy 246:113674, 2023. [PDF] [Software]
Optical flow driven interpolation for isotropic FIB-SEM reconstructions
V Gonzalez-Ruiz, JP Garcia-Ortiz, MR Fernandez-Fernandez, JJ Fernandez
Computer Methods and Programs in Biomedicine 221:106856, 2022. [PDF] [Software]
PolishEM: image enhancement in FIB-SEM
JJ Fernandez, TE Torres, E Martin-Solana, GF Goya, MR Fernandez-Fernandez
Bioinformatics 36:3947-3948, 2020. [PDF] [Software]
Computational Methods for 3DEM
Computational Methods for 3DEM
Structure-preserving Gaussian denoising of FIB-SEM volumes
V Gonzalez-Ruiz, MR Fernandez-Fernandez, JJ Fernandez
Ultramicroscopy 246:113674, 2023. [PDF] [Software]
Optical flow driven interpolation for isotropic FIB-SEM reconstructions
V Gonzalez-Ruiz, JP Garcia-Ortiz, MR Fernandez-Fernandez, JJ Fernandez
Computer Methods and Programs in Biomedicine 221:106856, 2022. [PDF] [Software]
HPC enables efficient 3D membrane segmentation in electron tomography.
JJ Moreno, EM Garzon, JJ Fernandez, A Martinez-Sanchez.
Journal of Supercomputing 78:19097-19113, 2022. [PDF] [Software]
TomoAlign: A novel approach to correcting sample motion and 3D CTF in CryoET
JJ Fernandez, S Li
Journal of Structural Biology 213:107778, 2021. [PDF] [Software]
PolishEM: image enhancement in FIB-SEM
JJ Fernandez, TE Torres, E Martin-Solana, GF Goya, MR Fernandez-Fernandez
Bioinformatics 36:3947-3948, 2020. [PDF] [Software]
Consideration of sample motion in cryo-tomography based on alignment residual interpolation
JJ Fernandez, S Li, DA Agard
Journal of Structural Biology 205:1-6, 2019. [PDF] [Software]
Cryo-tomography Tilt-series Alignment with Consideration of the Beam-induced Sample Motion
JJ Fernandez, S Li, TAM Bharat, DA Agard
Journal of Structural Biology 202:200-209, 2018. [PDF] [Software]
TomoEED: fast edge-enhancing denoising of tomographic volumes.
JJ Moreno, A Martinez-Sanchez, JA Martinez, EM Garzon, JJ Fernandez.
Bioinformatics 34:3776-3778, 2018. [Software]
Removing contamination-induced reconstruction artefacts from cryo electron tomograms
JJ Fernandez, U Laugks, M Schaffer, FJB Bauerlein, M Khoshouei, W Baumeister, V Lucic.
Biophysical Journal 110:850-859, 2016. [Software]
Robust membrane detection based on tensor voting for electron tomography
A Martinez-Sanchez, I Garcia, S. Asano, V Lucic, JJ Fernandez
Journal of Structural Biology 186:49-61, 2014. [PDF] [Software]
A ridge-based framework for segmentation of 3D electron microscopy datasets
A Martinez-Sanchez, I Garcia, JJ Fernandez
Journal of Structural Biology 181:61-70, 2013. [PDF]
Fast tomographic reconstruction on multicore computers.
JI Agulleiro, JJ Fernandez.
Bioinformatics 27:582-583, 2011. [Software]
A differential structure approach to membrane segmentation in electron tomography
A Martinez-Sanchez, I Garcia, JJ Fernandez
Journal of Structural Biology 175:372-383, 2011. [Software]
TOMOBFLOW: Feature-preserving noise filtering for electron tomography
JJ Fernandez
BMC Bioinformatics 2009, 10:178. [Software]
Sharpening high resolution information in single particle electron cryomicroscopy.
JJ Fernandez, D Luque, JR Caston, JL Carrascosa.
Journal of Structural Biology 164:170-175, 2008. [Software]
CTF determination and correction in electron cryotomography.
JJ Fernandez, S Li, RA Crowther.
Ultramicroscopy 106:587-596, 2006. [Software]
Anisotropic nonlinear filtering of cellular structures in cryoelectron tomography.
JJ Fernandez, S Li.
IEEE Computing in Science and Engineering 7(5):54-61, 2005. [Software]
An improved algorithm for anisotropic nonlinear diffusion for denoising cryotomograms.
JJ Fernandez, S Li.
Journal of Structural Biology 144:152-161, 2003. [Software]
Microtubule Organizing Centres
Microtubule Organizing Centres
The structure of basal body inner junctions from Tetrahymena revealed by electron cryo-tomography
S Li, JJ Fernandez, MD Ruehle, RA Howard-Till, AS Fabritius, CG Pearson, DA Agard, ME Winey
EMBO Journal 44:1975-2001, 2025.
Electron Cryo-Tomography Structure of Axonemal Doublet Microtubule from Tetrahymena thermophila
S Li, JJ Fernandez, AS Fabritius, DA Agard, M Winey
Life Science Alliance 5(3): e202101225, 2022.
Electron Cryo-Tomography Provides Insight into Procentriole Architecture and Assembly Mechanism
S Li, JJ Fernandez, WF Marshall, DA Agard
eLife 2019;8:e43434 doi: 10.7554/eLife.43434 [PDF]
Ring closure activates yeast γTuRC for species-specific microtubule nucleation
JM Kollman, CH Greenberg, S Li, M Moritz, A Zelter, KK Fong, JJ Fernandez, A Sali, J Kilmartin, TN Davis, DA Agard
Nature Structural and Molecular Biology 22:132-137, 2015.
Three-dimensional structure of basal body triplet revealed by electron cryo-tomography
S. Li, JJ Fernandez, WF Marshall, DA Agard
EMBO Journal 31:552-562, 2012. [Highlight]
High Performance Computing / Scientific Computing
High Performance Computing / Scientific Computing
HPC enables efficient 3D membrane segmentation in electron tomography.
JJ Moreno, EM Garzon, JJ Fernandez, A Martinez-Sanchez.
Journal of Supercomputing 78:19097-19113, 2022. [PDF] [Software]
TomoEED: fast edge-enhancing denoising of tomographic volumes.
JJ Moreno, A Martinez-Sanchez, JA Martinez, EM Garzon, JJ Fernandez.
Bioinformatics 34:3776-3778, 2018. [Software]
Tomo3D 2.0--exploitation of advanced vector extensions (AVX) for 3D reconstruction.
JI Agulleiro, JJ Fernandez.
Journal of Structural Biology 189:147-152, 2015. [Software]
JI Agulleiro, JJ Fernandez.
Data in Brief 3:116-20, 2015.
Hybrid computing: CPU+GPU co-processing and its application to tomographic reconstruction
JI Agulleiro, F Vazquez, EM Garzon, JJ Fernandez.
Ultramicroscopy 115:109-114, 2012. [Software for developers]
Evaluation of a multicore-optimized implementation for tomographic reconstruction
JI Agulleiro, JJ Fernandez.
PLoS ONE 7(11): e48261, 2012. [PDF] [Software]
Fast tomographic reconstruction on multicore computers.
JI Agulleiro, JJ Fernandez.
Bioinformatics 27:582-583, 2011. [Software]
A new approach for sparse matrix vector product on NVIDIA GPUs.
F Vazquez, JJ Fernandez, EM Garzon.
Concurrency and Computation: Practice and Experience 23:815-826, 2011. [Software]
Vectorization with SIMD extensions speeds up reconstruction in electron tomography
JI Agulleiro, EM Garzon, I Garcia, JJ Fernandez.
Journal of Structural Biology 170:570-575, 2010. [Software]
A matrix approach to tomographic reconstruction and its implementation on GPUs.
F Vazquez, EM Garzon, JJ Fernandez.
Journal of Structural Biology 170:146-151, 2010. [Software]
Efficient parallel implementation of iterative reconstruction algorithms for electron tomography.
JJ Fernandez, D Gordon, R Gordon.
Journal of Parallel and Distributed Computing 68(5):626-640, 2008.
Reviews
Reviews
Computational methods for materials characterization by electron tomography.
JJ Fernandez.
Current Opinion in Solid State and Materials Science 17:93-106, 2013. [PDF]
WZ He, JJ Fernandez.
In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester, UK. 2010.
DOI: 10.1002/9780470015902.a0021877.
High performance computing in structural determination by electron cryomicroscopy.
JJ Fernandez.
Journal of Structural Biology 164:1-6, 2008.
Special Issue on "Computational Methods for 3DEM"
Special Issue on "Computational Methods for 3DEM"
Special Issue on "Computational Methods for Threee-Dimensional Electron Microscopy (3DEM)"
JJ Fernandez and A Martinez-Sanchez (Guest editors)
Computer Methods and Programs in Biomedicine, 2022.
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