Hybrid methods for analyzing conformational variability in cryo-EM and cryo-ET data
Slavica Jonic
Doctoral. CNRS Thematic School AlgoSB (Algorithms in Structural Bioinformatics), Cargese, France, November 20-24, 2023, France. 2023
Cours
hal-04310867v1
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Hybrid Electron Microscopy Normal Mode Analysis with Scipion
Mohamad Harastani
,
Carlos Oscar S. Sorzano
,
Slavica Jonic
Article dans une revue
hal-02388487v1
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In silico prediction, characterization, docking studies and molecular dynamics simulation of human p97 in complex with p37 cofactor
Abolfazl Mirzadeh
,
George Kobakhidze
,
Rémi Vuillemot
,
Slavica Jonic
,
Isabelle Rouiller
Article dans une revue
hal-03775673v1
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Methods for analyzing continuous conformational variability of biomolecules in cryo electron subtomograms: HEMNMA-3D vs. traditional classification
Mohamad Harastani
,
Slavica Jonic
2021
Pré-publication, Document de travail
hal-03378493v1
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Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol
Carlos Oscar S. Sorzano
,
José Miguel de La Rosa-Trevín
,
Florence Tama
,
Slavica Jonić
Article dans une revue
hal-01148382v1
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Splines in biomedical image processing
Slavica Jonic
,
Carlos Oscar S. Sorzano
G. Cristobal; P. Schelkens; H. Thienpont.
Optical and Digital Image Processing-Fundamentals and Applications , Wiley-VCH Verlag GmbH & Co. KGaA, 2011,
⟨10.1002/9783527635245⟩
Chapitre d'ouvrage
hal-01149076v1
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Processing of Transmission Electron Microscopy Images for Single-Particle Analysis of Macromolecular Complexes
Zaelle Devaux
,
Carlos Oscar S. Sorzano
,
Slavica Jonic
Article dans une revue
hal-01430532v1
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Methods for studying the localization of mitochondrial complexes III and IV by immunofluorescent and immunogold microscopy
Igor Golić
,
Marija Aleksić
,
Anita Lazarević
,
Maja Bogdanović
,
Slavica Jonić
,
et al.
Article dans une revue
hal-01429731v1
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The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution - Functional implications
Magali Cottevieille
,
Eric Larquet
,
Slavica Jonic
,
Maxim V. Petoukhov
,
Gianluca Caprini
,
et al.
Article dans une revue
hal-00326457v1
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Cryo-electron microscopy analysis of structurally heterogeneous macromolecular complexes
Slavica Jonić
Article dans une revue
hal-01383194v1
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MDSPACE: Extracting continuous conformational landscapes from cryo-EM single particle datasets using 3D-to-2D flexible fitting based on Molecular Dynamics simulation
Rémi Vuillemot
,
Alex Mirzaei
,
Mohamad Harastani
,
Ilyes Hamitouche
,
Léo Fréchin
,
et al.
Article dans une revue
hal-03929029v1
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TomoFlow: Analysis of continuous conformational variability of macromolecules in cryogenic subtomograms based on 3D dense optical flow
Mohamad Harastani
,
Mikhail Eltsov
,
Amélie Leforestier
,
Slavica Jonic
Article dans une revue
hal-03452809v1
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Insulin Modulates the Bioenergetic and Thermogenic Capacity of Rat Brown Adipocytes In Vivo by Modulating Mitochondrial Mosaicism
Igor Golic
,
Andjelika Kalezic
,
Aleksandra Jankovic
,
Slavica Jonic
,
Bato Korac
,
et al.
International Journal of Molecular Sciences , 2020, 21 (23), pp.9204
Article dans une revue
hal-03028101v1
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3D mapping of glycogenosis-causing mutations in the large regulatory alpha subunit of phosphorylase kinase
Cathelène Carrière
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Slavica Jonic
,
Jean-Paul Mornon
,
Isabelle Callebaut
Article dans une revue
hal-00501593v1
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Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes
Qiyu Jin
,
Carlos Oscar S. Sorzano
,
José Miguel de La Rosa-Trevín
,
José Román Bilbao-Castro
,
Rafael Nunez-Ramirez
,
et al.
Article dans une revue
hal-01430531v1
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MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based on molecular dynamics simulations
Rémi Vuillemot
,
Isabelle Rouiller
,
Slavica Jonić
Article dans une revue
hal-04147646v1
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NMMD: Efficient cryo-EM flexible fitting based on simultaneous Normal Mode and Molecular Dynamics atomic displacements
Rémi Vuillemot
,
Osamu Miyashita
,
Florence Tama
,
Isabelle Rouiller
,
Slavica Jonic
Article dans une revue
hal-03577246v1
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Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns
Atsushi Tokuhisa
,
Slavica Jonic
,
Florence Tama
,
Osamu Miyashita
Article dans une revue
hal-01430528v1
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Macromolecular Dynamics by Hybrid Electron Microscopy Normal Mode Analysis
Qiyu Jin
,
Carlos Oscar S. Sorzano
,
Jose Miguel de La Rosa-Trevín
,
Florence Tama
,
Slavica Jonić
Communication dans un congrès
hal-01431467v1
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Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion
David Strelak
,
Amaya Jiménez-Moreno
,
José L Vilas
,
Erney Ramírez-Aportela
,
Ruben Sánchez-García
,
et al.
Article dans une revue
hal-03380603v1
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Glutamate synthase: self-regulation and oligomeric structure
Maria A. Vanoni
,
Bruno Curti
,
Laura Dossena
,
Gianluca Caprini
,
Stefano Paravisi
,
et al.
16th international symposium on flavins and flavoproteins , Jun 2008, Jaca, Spain
Communication dans un congrès
hal-01431483v1
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MDSPACE and MDTOMO Software for Extracting Continuous Conformational Landscapes from Datasets of Single Particle Images and Subtomograms Based on Molecular Dynamics Simulations: Latest Developments in ContinuousFlex Software Package
Rémi Vuillemot
,
Mohamad Harastani
,
Ilyes Hamitouche
,
Slavica Jonic
Article dans une revue
hal-04397719v1
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Coarse-Graining of Volumes for Modeling of Structure and Dynamics in Electron Microscopy: Algorithm to Automatically Control Accuracy of Approximation
Slavica Jonić
,
Carlos Óscar Sánchez Sorzano
Article dans une revue
hal-01430529v1
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Comparison between HEMNMA-3D and Traditional Classification Techniques for Analyzing Biomolecular Continuous Shape Variability in Cryo Electron Subtomograms
Mohamad Harastani
,
Slavica Jonic
Communication dans un congrès
hal-03577374v1
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Combined Bayesian and Normal Mode Flexible Fitting with Hamiltonian Monte Carlo Sampling for Cryo Electron Microscopy
Rémi Vuillemot
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Slavica Jonic
Communication dans un congrès
hal-03266628v1
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HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes
Mohamad Harastani
,
Mikhail Eltsov
,
Amélie Leforestier
,
Slavica Jonic
Article dans une revue
hal-03217427v1
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CTF Challenge: Result summary
Roberto Marabini
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Bridget Carragher
,
Shaoxia Chen
,
James Chen
,
Anchi Cheng
,
et al.
Article dans une revue
hal-01431465v1
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Radiation-Induced Synthesis and Cryo-TEM Characterization of Silver Nanoshells on Linoleate Spherical Micelles
Judith Attia
,
S. Remita
,
Slavica Jonic
,
Emmanuelle Lacaze
,
Marie-Claude Fauré
,
et al.
Article dans une revue
istex
hal-00378373v1
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StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes
Carlos oscar Sanchez sorzano
,
Ana lucia Alvarez-Cabrera
,
Mohsen Kazemi
,
Jose maría Carazo
,
Slavica Jonić
Article dans une revue
hal-01311676v1
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Elastic image registration to fully explore macromolecular dynamics by electron microscopy
Qiyu Jin
,
Carlos Oscar Sanchez Sorzano
,
Isabelle Callebaut
,
Florence Tama
,
Slavica Jonic
Communication dans un congrès
hal-01431471v1
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