Mohamad Harastani

Publications

Article dans une revue (11)

Template Learning: deep learning with domain randomization for particle picking in cryo-electron tomography Mohamad Harastani,Gurudatt Patra,Charles Kervrann,Mikhail Eltsov Nature Communications, 2025, 16 (8833), pp.1-15. ⟨10.1038/s41467-025-63895-0⟩ Article dans une revue hal-04874266v1
Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM D Herreros,J M Krieger,Y Fonseca,P Conesa,M Harastaniet al. Acta crystallographica Section D : Structural biology [1993-..], 2023, 79, pp.569 - 584. ⟨10.1107/s2059798323004497⟩ Article dans une revue hal-04147629v1
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 International Journal of Molecular Sciences, 2023, 25 (1), pp.20. ⟨10.3390/ijms25010020⟩ Article dans une revue hal-04397719v1
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 Fréchinet al. Journal of Molecular Biology, 2023, pp.167951. ⟨10.1016/j.jmb.2023.167951⟩ Article dans une revue hal-03929029v1
ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation Jorge Jiménez de la Morena,Pablo Conesa,Yunior Cesar Fonseca,Federico Pedro de Isidro-Gómez,David Herreroset al. Journal of Structural Biology, 2022, 214 (3), pp.107872. ⟨10.1016/j.jsb.2022.107872⟩ Article dans une revue hal-03775680v1
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 Journal of Molecular Biology, 2022, 434 (2), pp.167381. ⟨10.1016/j.jmb.2021.167381⟩ Article dans une revue hal-03452809v1
ContinuousFlex: Software package for analyzing continuous conformational variability of macromolecules in cryo electron microscopy and tomography data Mohamad Harastani,Rémi Vuillemot,Ilyes Hamitouche,Nima Barati Moghadam,Slavica Jonic Journal of Structural Biology, 2022, 214 (4), pp.107906. ⟨10.1016/j.jsb.2022.107906⟩ Article dans une revue hal-03821777v1
Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion David Strelak,Amaya Jiménez-Moreno,José L Vilas,Erney Ramírez-Aportela,Ruben Sánchez-Garcíaet al. Molecules, 2021, 26 (20), pp.6224. ⟨10.3390/molecules26206224⟩ Article dans une revue hal-03380603v1
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 Frontiers in Molecular Biosciences, 2021, 8, pp.663121. ⟨10.3389/fmolb.2021.663121⟩ Article dans une revue hal-03217427v1
Hybrid Electron Microscopy Normal Mode Analysis with Scipion Mohamad Harastani,Carlos Oscar S. Sorzano,Slavica Jonic Protein Science, 2020, 29 (1), pp.223-236. ⟨10.1002/pro.3772⟩ Article dans une revue hal-02388487v1
Methamphetamine drug abuse and addiction: Effects on face asymmetry Mohamad Harastani,Amine Benterkia,Farnaz Majid Zadeh,Amine Nait-Ali Computers in Biology and Medicine, 2020, 116, pp.103475 -. ⟨10.1016/j.compbiomed.2019.103475⟩ Article dans une revue hal-03489500v1

Communication dans un congrès (1)

Comparison between HEMNMA-3D and Traditional Classification Techniques for Analyzing Biomolecular Continuous Shape Variability in Cryo Electron Subtomograms Mohamad Harastani,Slavica Jonic 2021 4th International Conference on Bio-Engineering for Smart Technologies (BioSMART), Dec 2021, Paris / Créteil, France. ⟨10.1109/BioSMART54244.2021.9677643⟩ Communication dans un congrès hal-03577374v1

Thèse (1)

Image analysis methods development for in vitro and in situ cryo-electron tomography studies of conformational variability of biomolecular complexes : Case of nucleosome structural and dynamics studies Mohamad Harastani Bioinformatics [q-bio.QM]. Sorbonne Université, 2022. English. ⟨NNT : 2022SORUS283⟩ Thèse tel-03896321v1

Pré-publication, Document de travail (1)

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

Logiciel (1)

Code and test data of ContinuousFlex plugin for analyzing continuous conformational variability of biomolecular complexes in cryo-EM and cryo-ET data Slavica Jonic,Mohamad Harastani 2021, ⟨swh:1:dir:d91ba731dcb03f6a7f9ad943b72b5f31ff5b07e6;origin=https://hal.archives-ouvertes.fr/hal-03501129;visit=swh:1:snp:13f13ae68fa31bf00e6a17af32910f9f724b36f8;anchor=swh:1:rel:94f50ac7155404c91cc35a4a288e1e9089c0dd2f;path=/⟩ Logiciel hal-03501129v1