Selected publications from collaborations
S Li & DA Agard (MSG-UCSF) - cryoET of MTOCs
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
Kollman JM, Greenberg CH, Li S, Moritz M, Zelter A, Fong KK, Fernandez JJ, Sali A, Kilmartin J, Davis TN, Agard DA.
Nat Struct Mol Biol. 2015 Feb;22(2):132-7.
Three-dimensional structure of basal body triplet revealed by electron cryo-tomography
S. Li, JJ Fernandez, WF Marshall, DA Agard
EMBO Journal 2012, 31:552-562. [PDF] [Highlight]
V Lucic & W Baumeister (Max-Plank Institute for Biochemistry) - Image processing / cryo-FIB milled data
Removing contamination-induced reconstruction artefacts from cryo electron tomograms
JJ Fernandez, U Laugks, M Schaffer, FJB Bauerlein, M Khoshouei, W Baumeister, V Lucic.
Biophys J. 2016, 110(4):850-859. [Software]
Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy
Arnold J, Mahamid J, Lucic V, de Marco A, Fernandez JJ, Laugks T, Mayer T, Hyman AA, Baumeister W, Plitzko JM.
Biophys J. 2016 110(4):860-9.
M Beeby (Imperial College London) - image processing for cryoET of bacterial cells
Cohen EJ, Drobnič T, Ribardo DA, Yoshioka A, Umrekar T, Guo X, Fernandez JJ, Brock E, Wilson L, Nakane D, Hendrixson DR, Beeby M.
Developmental Cell 59:1-16, 2024; doi: https://doi.org/10.1016/j.devcel.2024.09.008
RA Crowther (MRC-LMB) - Computational methods for cryoET
CTF determination and correction in electron cryotomography.
JJ Fernandez, S Li, RA Crowther.
Ultramicroscopy 2006, 106:587-596. [PDF] [Software]
F Zhang (Chinese Academy of Sciences) - Computational methods for cryoET
A marker-free automatic alignment method based on scale-invariant features.
Han R, Zhang F, Wan X, Fernández JJ, Sun F, Liu Z.
J Struct Biol. 2014 Apr;186(1):167-80.
P. Midgley (Dept. Materials Science & Metallurgy, U.Cambridge) - Computational methods for ET in materials science
TJV Yates, JM Thomas, JJ Fernandez, O Terasaki, R Ryoo, PA Midgley.
Chemical Physics Letters 2006, 418:540-543
E.P.W. Ward, T.J.V. Yates, J.J. Fernandez, D.E.W. Vaughan, P.A. Midgley.
Journal of Physical Chemistry C, 2007, 111 (31):11501–11505.
EM Garzón & I García (HPCA group, Univ. Almeria+Malaga) - High performance computing and image processing
HPC enables efficient 3D membrane segmentation in electron tomography.
JJ Moreno, EM Garzon, JJ Fernandez, A Martinez-Sanchez.
Journal of Supercomputing 78:19097-190113, 2022. [Software]
TomoEED: fast edge-enhancing denoising of tomographic volumes.
JJ Moreno, A Martinez-Sanchez, JA Martinez, EM Garzon, JJ Fernandez
Bioinformatics 2018 34:3776-3778. [Software]
Hybrid computing: CPU+GPU co-processing and its application to tomographic reconstruction
JI Agulleiro, F Vazquez, EM Garzon, JJ Fernandez.
Ultramicroscopy 2012, 115:109-114.
A matrix approach to tomographic reconstruction and its implementation on GPUs.
F Vazquez, EM Garzon, JJ Fernandez.
Journal of Structural Biology 2010, 170:146-151.
GF Goya, TE Torres, L Casado (Advanced Microscopy Laboratory) - FIB/SEM of cryofixed samples
PolishEM: image enhancement in FIB-SEM
JJ Fernandez, TE Torres, E Martin-Solana, GF Goya, MR Fernandez-Fernandez
Bioinformatics 2020, 36:3947-3948. [PDF] [Software]
E Martin-Solana, L Casado, TE Torres, P Sola, A Martinez-Sanchez, GF Goya, MR Fernandez-Fernandez, JJ Fernandez.
Microscopy at the Frontiers of Science 2021. [PDF]
E Martin-Solana, L Casado-Zueras, TE Torres, GF Goya, MR Fernandez-Fernandez, JJ Fernandez
Acta Neuropathologica Communications 2024, 12:88. [PDF]
JJ Lucas (CBMSO-CSIC) - Huntington's Disease
Hernández IH, Torres-Peraza J, Santos-Galindo M, Ramos-Morón E, Fernández-Fernández MR, Pérez-Álvarez MJ, Miranda-Vizuete A, Lucas JJ.
Acta Neuropathol. 2017 Dec;134(6):839-850.
Protective neuronal induction of ATF5 in endoplasmic reticulum stress induced by status epilepticus
Torres-Peraza JF, Engel T, Martín-Ibáñez R, Sanz-Rodríguez A, Fernández-Fernández MR, Esgleas M, Canals JM, Henshall DC, Lucas JJ.
Brain. 2013 Apr;136(Pt 4):1161-76.
Impaired ATF6α processing, decreased Rheb and neuronal cell cycle re-entry in Huntington's disease
Fernandez-Fernandez MR, Ferrer I, Lucas JJ.
Neurobiol Dis. 2011 Jan;41(1):23-32.
MA Alonso & G. Andrés (CBMSO-CSIC) - 3D imaging in Ciliogenesis
Novel role for the midbody in primary ciliogenesis by polarized epithelial cells [Highlight]
Bernabé-Rubio M, Andrés G, Casares-Arias J, Fernández-Barrera J, Rangel L, Reglero-Real N, Gershlick DC, Fernández JJ, Millán J, Correas I, Miguez DG, Alonso MA.
J Cell Biol. 2016 Aug 1;214(3):259-73.
J Millan (CBMSO-CSIC) - 3D imaging in Cell Biology of Inflammation
Colas-Algora N, Munoz-Pinillos P, Barroso S, Cacho-Navas C, Caballero A, Cerro-Tello G, de Rivas G, Gonzalez-Fernandez M, Jimenez-Alfaro I, Fresno M, Ribas C, Paradela A, Lopez-Collazo E, Fernandez JJ, Millan J.
BioRxiv. 2024.05.17.594667; doi: https://doi.org/10.1101/2024.05.17.594667
JR Requena (CiMUS-USC) - CryoET of prions
The Structural Architecture of an Infectious Mammalian Prion Using Electron Cryomicroscopy.
Vázquez-Fernández E, Vos MR, Afanasyev P, Cebey L, Sevillano AM, Vidal E, Rosa I, Renault L, Ramos A, Peters PJ, Fernández JJ, van Heel M, Young HS, Requena JR, Wille H.
PLoS Pathog. 2016 Sep 8;12(9):e1005835.
C Risco (CNB-CSIC) - 3D imaging of viral factories
A modified lysosomal organelle mediates nonlytic egress of reovirus
Fernández de Castro I, Tenorio R, Ortega-González P, Knowlton JJ, Zamora PF, Lee CH, Fernández JJ, Dermody TS, Risco C.
J Cell Biol. 2020 Jul 6;219(7):e201910131.
Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex.
Fernández de Castro I, Fernández JJ, Barajas D, Nagy PD, Risco C.
J Cell Sci. 2017 Jan 1;130(1):260-268.
Reovirus forms neo-organelles for progeny particle assembly within reorganized cell membranes.
Fernández de Castro I, Zamora PF, Ooms L, Fernández JJ, Lai CM, Mainou BA, Dermody TS, Risco C.
mBio. 2014 Feb 18;5(1):e00931-13.
C San Martin (CNB-CSIC) - CryoET of adenovirus
Distribution of DNA-condensing protein complexes in the adenovirus core.
Pérez-Berná AJ, Marion S, Chichón FJ, Fernández JJ, Winkler DC, Carrascosa JL, Steven AC, Šiber A, San Martín C.
Nucleic Acids Res. 2015 43(8):4274-83.
D Rodriguez (CNB-CSIC) - Torovirus viral factories
Architecture of torovirus replicative organelles
Avila-Perez G, Rejas MT, Chichon FJ, Guerra M, Fernández JJ, Rodriguez D.
Mol Microbiol 2022 117(4):837-850.