2023 Submitted [Preprint on BioRxiv]
MDTOMO: Continuous conformational variability analysis in cryo electron subtomogram data using flexible fitting based on Molecular Dynamics simulations
Vuillemot R, Rouiller I, and Jonic, S
2023 J Mol Biol 435:167951 [Author's version]
[Journal]
MDSPACE: Extracting continuous conformational landscapes from cryo-EM single particle datasets using 3D-to-2D flexible fitting based on Molecular Dynamics simulation
Vuillemot R, Mirzaei A, Harastani M, Hamitouche I, Fréchin L, Klaholz BP, Miyashita O, Tama F, Rouiller I, and Jonic, S
2022 J Struct Biol 214: 107906 [Author's version]
[Journal]
ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data
Harastani M, Vuillemot R, Hamitouche I, Barati Moghadam N,I and Jonic, S
2022 Front Mol Biosci 9:965645 [Author's version]
[Journal]
DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images
Hamitouche I and Jonic, S
2022 BMC Mol and Cell Biol 23: 39 [Author's version]
[Journal]
In silico prediction, characterization, docking studies and molecular dynamics simulation of human p97 in complex with p37 cofactor
Mirzadeh A, Kobakhidze G, Vuillemot R, Jonic, S., and Rouiller, I
2022 J Struct Biol 214: 10787 [Author's version]
[Journal]
ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation
Jiménez de la Morena, J. P. Conesa, Y.C. Fonseca, F.P. de Isidro-Gómez, D. Herreros, E. Fernández-Giménez, D. Strelak, E. Moebel, T.O. Buchholz, F. Jug, A. Martinez-Sanchez, M. Harastani, S. Jonic, J.J. Conesa, A. Cuervo, P. Losana, I. Sánchez, M. Iceta, L. del Cano, M. Gragera, R. Melero, G. Sharov, D. Castaño-Díez, A. Koster, J.G. Piccirillo, J.L. Vilas, J. Otón, R. Marabini, C.O.S. Sorzano, and J.M. Carazo
2022 J Mol Biol 434:167483 [Author's version]
[Journal]
NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacement
Vuillemot R, Miyashita O, Tama F, Rouiller I, and Jonic, S.
2021 J Mol Biol 434:167381 [Author's version]
[Journal]
TomoFlow: Analysis of continuous conformational variability of macromolecules in cryogenic subtomograms based on 3D dense optical flow
Harastani, M., Eltsov M, Leforestier A, and Jonic, S.
2021 Molecules 26: 6224 [Open-access]
Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion
Strelak, D.; Jiménez-Moreno, A.; Vilas, J.L.; Ramírez-Aportela, E.; Sánchez-García, R.; Maluenda, D.; Vargas, J.; Herreros, D.; Fernández-Giménez, E.; de Isidro-Gómez, F.P.; Horacek, J.; Myska, D.; Horacek, M.; Conesa, P.;
Fonseca-Reyna, Y.C.; Jiménez, J.; Martínez, M.; Harastani, M.; ., Jonic, S., Filipovic, J.; Marabini, R.; Carazo, J.M.; Sorzano, C.O.S.
2021 Frontiers Mol Biosci 8:663121 [Open-access]
HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes
Harastani, M., Eltsov M, Leforestier A, and Jonic, S.
2020 Protein Science 29:223−236 [Open-access]
Hybrid Electron Microscopy Normal Mode Analysis with Scipion
Harastani, M.,Sorzano,
C.O.S, and Jonic, S.
2020 Cellular and Molecular Life Sciences
77: 859-874 [Link]
PEBP1/RKIP behavior: a mirror of actin-membrane organization
Schoentgen, F. and Jonic, S.
2020 International Journal of Molecular Sciences 21, 9204 [Open-access]
Insulin Modulates the Bioenergetic
and Thermogenic Capacity of Rat Brown Adipocytes In Vivo by Modulating Mitochondrial Mosaicism
Golic, I., Kalezic,
A., Jankovic, A., Jonic, S., Korac, B.,
and Korac, A.
2019 Bioinformatics 35: 2427–2433 [Open-access]
Validation of Electron Microscopy Initial Models via Small Angle X-Ray Scattering Curves
Jimenez,
A., Jonic, S., Majtner, T.,
Oton, J, Vilas, J.L., Maluenda,
D., Mota, J., Ramirez-Aportela,
E., Martinez, M., Rancel, Y., Segura, J.,
Sanchez-Garcia, R., Melero, R., del Cano, L., Conesa, P., Skjaerven, L., Marabini, R., Carazo, J.M., and Sorzano,
C.O.S.
2019 Acta Cryst Sect F 75: 19-32 [Link]
Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy
Sorzano, C.O.S., Jimenez, A., de la Mota, J., Vilas, J.L., Maluenda,
D., Martinez, M., Ramirez-Aportela, E., Majtner, T.,
Segura, J., Sanchez-Garcia, R., Rancel, Y., del
Cano, L., Conesa, P., Jonic, S., Vargas, J., Cazals, F.,
Freyberg, Z., Krieger, J., Bahar, I., Marabini, R., and Carazo, J.M.
2018 Front Mol Biosci
5: Article 98 [Open-access]
Editorial: Hybrid Biomolecular Modeling
Jonic, S., Miyashita, O., and Callebaut, I.
2018 IET Image Process 12: 2264-2274 [Open-access]
Poisson image denoising by piecewise principal component analysis and its application in single-particle X-ray diffraction imaging
Jin,
Q., Miyashita, O., Tama, F., Yang, J., and Jonic, S.
2018 J Struct Biol 204:291-300
[Link]
(invited)
The First Single Particle Analysis Map Challenge: A Summary of the Assessments
Heymann, J.B., Marabini,
R., Kazemi, M., Sorzano,
C.O.S., Holmdahl, M., Mendez, J.H., Stagg, S.M., Jonic, S., Palovcak,
E., Armache, J.-P., Zhao, J., Cheng, Y., Pintilie, G., Chiu, W., Patwardhan,
A., and Carazo, J.M.
2018 J Struct Biol 204:344-350 [Link] [Author’s version]
A methodology using Gaussian-based density map approximation to assess sets of cryo-electron microscopy density maps.
Jonic, S.
2018 J Synch Radiat 25: 1010-1021 [Link]
Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution
Nakano,
M., Miyashita, O., Jonic, S., Tokuhisa,
A., and Tama, F.
2017 J Synch Radiat 24: 727-737 [Link]
Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL
Nakano, M., Miyashita, O., Jonic, S.,
Song, C., Nam, D., Joti, Y. and Tama, F.
2017 Curr Opin Struct Biol 43:114–121 [Link] [Author’s version] (invited)
Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images
Jonic, S.
2016 BioMed Res Int vol. 2016, Article ID 7060348, 11 pages [Open-access] (invited)
Versatility of approximating single-particle electron-microscopy density maps using pseudoatoms and approximation-accuracy control
Jonic, S. and Sorzano, C.O.S.
2016 Comput Struct Biotech J 14:385-390 [Open-access] (invited)
Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes
Jonic, S.
2016 J Struct Biol 195:123–128 [Link]
Local analysis of strains and rotations for macromolecular electron microscopy maps
Sorzano, C.O.S., Martín-Ramos,
A. , Prieto, F., Melero,
R., Martín-Benito, J., Jonic, S., Navas-Calvente,
J., Vargas, J., Otón, J., Abrishami,
V. , de la Rosa-Trevín, J.M., Gómez-Blanco,
J., Vilas, J.L., Marabini, R., and Carazo, J.M.
2016 J Struct Biol 194:423-433 [Link]
Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions
Jonic, S., Vargas, J., Melero, R., Gómez-Blanco, J.,
Carazo, J.M., and Sorzano, C. O. S.
2016 Biophys J 110:1753-1765 [Open-access]
StructMap:
Elastic distance analysis of electron microscopy maps for studying
conformational changes
Sanchez Sorzano, C. O., Alvarez-Cabrera, A. L., Kazemi, M., Carazo, J. M., and Jonic, S.
2016 J Struct Biol 194:325-336 [Link]
Hybrid Approach for
Structural Modeling of Biological Systems from X-ray Free Electron Laser
Diffraction Patterns
Tokuhisa, A.,
Jonic, S., Tama, F., and Miyashita, O.
2016 Arch Biol Sci, 68:767-772 [Link]
Methods for studying
the localization of mitochondrial complexes III and IV by immunofluorescent and immunogold
microscopy
Golic, I.,
Aleksic, M., Lazarevic,
A., Bogdanovic, M., Jonic, S., and Korac,
A.
2016 IEEE J Sel Top Signal Process 10:161-173 [Open-access]
Coarse-graining of
volumes for modeling of structure and dynamics in electron microscopy:
Algorithm to automatically control accuracy of approximation
Jonic, S. and Sorzano,
C.O.S.
2015 J Struct Biol 190:348-59 [Link]
CTF Challenge: Result
Summary
Marabini, R., Carragher, B., Chen, S., Chen, J., Cheng, A., Downing,
K.H., Frank, J., Grassucci, R.A., Heymann, J.B., Jiang, W., Jonic, S., Liao, H.Y., Ludtke, S.J., Patwari, S., Piotrowski, A.L., Quintana, A., Sorzano,
C.O.S., Stahlberg, H., Vargas, J., Voss, N.R., Chiu, W., and Carazo, J.M.
2015 Cell Mol Life Sci 72:1377-1403 [Open-access]
Full-open and closed CFTR
channels, with lateral tunnels from the cytoplasm and an alternative
position of the F508 region, as revealed by molecular dynamics
Mornon, J.-P., Hoffmann,
B., Jonic, S., Lehn, P., and Callebaut, I.
2014 J Struct Biol 188:134-141 [Link] [Author’s
version]
Hybrid Electron Microscopy
Normal Mode Analysis graphical interface and protocol
Sorzano, C.O., de la Rosa-Trevin, J.M., Tama, F., and Jonic, S
2014 J Health Inf Dev Count 8:73-92 [Open-access]
A dynamic personal medical
record improvement: pilot study for diabetes self-management in Serbia
Petrovic, D., Popovic, M.D., Vuckovic, A.,
and Jonic, S.
2014
Structure 22:496-506 [Open-access]
Iterative
Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying
Structural Dynamics of Large Macromolecular Complexes
Q.
Jin, C.O.S. Sorzano, J.M.
de la Rosa-Trevín, J.R. Bilbao-Castro,
R. Núñez-Ramírez, O. Llorca,
F. Tama, and S. Jonic
2013
Nucleic Acids Res 41:W363-7 [Open-access]
3DEM
Loupe: analysis of macromolecular dynamics using structures from electron
microscopy
R.
Nogales-Cadenas, S. Jonic,
F.
Tama, A.A. Arteni, D. Tabas-Madrid, M. Vázquez, A. Pascual-Montano, and C.O.S. Sorzano
(the first two authors should be regarded as joint
first authors)
2013
J Struct Biol
181:136–148 [Link]
FASTDEF:
Fast defocus and astigmatism estimation for Transmission Electron
Microscopy
J.
Vargas, J. Otón, R. Marabini,
S. Jonic,
J.M. de la Rosa−Trevín, J.M. Carazo, and
C.O.S. Sorzano
2012 Meth Cell Biol 112:295-310 [Link] (invited)
Processing of Transmission
Electron Microscopy Images for Single-Particle Analysis of Macromolecular
Complexes
Devaux, Z., Sorzano, C.O.S., Jonic, S.
2009 Structure 17:1117-1127 [Open-access]
The structure of phosphorylase
kinase holoenzyme at
9.9 Å resolution and location of the catalytic subunit and the substrate
glycogen phosphorylase
C. Vénien-Bryan, S.
Jonic, V. Skamnaki,
N. Brown, N. Bischler,
N. G.
Oikonomakos, N. Boisset,
and L. N. Johnson
2009 Curr Opin Pharmacol 9:636-642
[Link] (invited)
Protein structure determination by
electron cryo-microscopy
S. Jonic and C. Vénien-Bryan
2008
Bioch Biophys Acta (BBA) -
Molecular Basis of Disease 1782:664-670 [Open-access]
3D mapping of glycogenosis-causing
mutations in the large regulatory alpha subunit of phosphorylase
kinase
C. Carriere,
S. Jonic, J.P. Mornon,
and I. Callebaut
2008 J Microsc 232:562-579 [Link]
Comparison of single-particle analysis
and electron tomography approaches: an overview
S. Jonic, C.O.S. Sorzano, and N. Boisset
2008 J Biol
Chem 283:8237-8249 [Open-access]
The subnanometer resolution structure of the glutamate synthase 1.2 MDa hexamer by cryo-electron
microscopy and its oligomerization behavior in
solution: functional implications
M. Cottevieille, E. Larquet, S. Jonic, M. V. Petoukhov, G.
Caprini, S. Paravisi, D.I. Svergun,
M.A. Vanoni, and N. Boisset
2007 Langmuir 23:9523-9526 [Link]
Radiation-induced synthesis and Cryo-TEM characterization of silver nanoshells
on linoleate spherical micelles
J. Attia, S. Rémita, S. Jonic, E. Lacaze, M-C. Fauré, E. Larquet, and M. Goldmann
2007 J Struct
Biol 160:249–262 [Link]
Fast, robust and accurate
determination of transmission electron microscopy contrast transfer
function
C.O.S. Sorzano,
S. Jonic, R. Nuñez,
N. Boisset, and J.M. Carazo
2007 Eur Biophys J
36:995-1013 [Link]
3D Electron Microscopy of Biological
Nanomachines: Principles and Applications
C.O.S. Sorzano,
S. Jonic,
M. Cottevieille, E. Larquet,
N. Boisset, and S. Marco
2007 J
Struct Biol 157:156–167 [Link]
A novel
method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas
S. Jonic,
C.O.S. Sorzano, M. Cottevieille,
E. Larquet, and N. Boisset
2006 Int J
Biomed Imag 2006:1-12 [Open-access]
An optimized spline-based
registration of a 3D CT to a set of C-arm images
S. Jonic, P. Thévenaz, G. Zheng, L.-P.
Nolte, and M. Unser
2005 J
Struct Biol
149:243-255 [Open-access]
Spectral signal-to-noise
ratio and resolution assessment of 3D reconstructions
M.
Unser, C.O.S. Sorzano, P. Thévenaz,
S. Jonic, C.
El-Bez, S. De Carlo, J. Conway, and B.L. Trus
2005 Ultramicroscopy
103:303-17 [Link]
Spline-based image-to-volume registration for
three-dimensional electron microscopy
S. Jonic, C.O.S. Sorzano,
P. Thévenaz, C. El-Bez,
S. De Carlo, and M. Unser
2004 J
Struct Biol 146:381-392
(cover) [Link]
A multiresolution
approach to orientation assignment in 3-D electron microscopy of single
particles
C.O.S.
Sorzano, S. Jonic, C.
El-Bez, J.M. Carazo, S. De Carlo, P. Thévenaz, and M. Unser
2000 J Aut
Control 10:1-22
Control
of near-ballistic walking in paraplegics
D.B. Popovic, J.J. Struijk, and S. Jonic
1999 Med Eng Phys 21:329-341 [Link]
Automatic synthesis of synergies for
control of reaching-hierarchical clustering
M. Jovovic, S.
Jonic, and D. Popovic
1999 IEEE
Trans Biomed Eng 46:300-310 [Link] [Author’s version]
Three
machine learning techniques for automatic determination of rules to control
locomotion
S. Jonic, T. Jankovic, V. Gajic, and D. Popovic
1999 IEEE
Trans Rehab Eng 7:69-79 [Link][Author’s version]
Optimal
control of walking with functional electrical stimulation: A computer
simulation study
D. Popovic, R.B. Stein, M.N. Oguztöreli,
M. Lebiedowska, and S. Jonic
1998
Facta Universitatis,
Series: Electronics and Energetics 11:1-24 [Open-access]
Identification of rules for a
rule-based control of walking
S. Jonic and
D. Popovic
