Institute of Mineralogy, Materials Physics, and Cosmochemistry

Sorbonne University, MNHN, UMR 7590 CNRS

 

 

 

 

 

 

Slavica JONIC

Research Director, CNRS

HDR, Affiliated with Doctoral School EDITE (ED 130)

Group leader, Image analysis methods for studying structure and dynamics of macromolecular complexes

 

ORCID ID: 0000-0001-5112-2743 Link

Loop profile: Link

ResearchGate profile: Link

Google Scholar profile: Link

 

IMPMC - CNRS UMR 7590

Sorbonne Université

Campus Jussieu, CC 115

Tower 23 - Hall 22/23 - 5th floor - Office 5.0.5

4 place Jussieu, 75005 Paris, France

Phone: +33 (0)1 44 27 72 05

Fax: +33 (0)1 44 27 37 85

E-mail: Slavica.Jonic@upmc.fr

Photo_Slavica

 

 

Background Link to CV with Publications

 

Since 1996, her research activities have been taking place at the intersection between informatics, mathematics, physics and biology, with a focus on conception and implementation of algorithms for biomedical signal and image processing.

 

Her first research activities (1996-1999, University of Belgrade, Serbia) were in biomechanics modeling and signal processing for control of walking in paraplegic subjects. They evolved towards multidimensional biomedical data processing during her PhD thesis (1999-2003, Swiss Federal Institute of Technology in Lausanne - EPFL, Switzerland), through development of image processing algorithms for computer-assisted surgery and structural biology. During her postdoc training (2004-2008, University Pierre and Marie Curie, IMPMC-UMR 7590, Paris, France), she specialized in electron-microscopy image processing for three-dimensional reconstruction of biological macromolecular complexes.

 

She obtained a Tenured Associate Scientist position at the French National Centre for Scientific Research – CNRS in 2008, a Research Director Habilitation from the Life Sciences Department of the University Pierre and Marie Curie - UPMC in 2015, and a CNRS Research Director position in 2019. 

 

• Research interests

 

Methodological developments for studying structure and dynamics of biomolecular complexes in vitro and in situ, by combining image processing, molecular dynamics simulation, and deep learning for cryo electron microscopy (cryo-EM), cryo electron tomography (cryo-ET), and X-ray free-electron laser (XFEL) imaging.

 

• Team members

 

Mohamad Harastani, PhD student

Ilyes Hamitouche, PhD student

Rémi Vuillemot, PhD student

Alex Mirzaei, Postdoc

 

• Jobs

 

We are always looking for enthusiastic and creative Master, PhD and Postdoc candidates with an outstanding background in artificial intelligence, computer vision, image processing, data science, or related fields, wishing to work on projects on the frontiers of molecular biosciences and software engineering. Interested candidates should contact Slavica Jonic with a cover letter, CV, and the email addresses of 1-2 references who could be contacted for a recommendation.

 

• Funding

 

ANR, CNRS, Sorbonne University, University of Melbourne, GENCI

 

 

• Highlight: ContinuousFlex

 

ContinuousFlex is a plugin for Scipion 3 (Linux) and includes the latest Scipion protocols for continuous conformational flexibility/heterogeneity analysis of biomolecular complexes from single particle cryo-EM images and cryo-ET subtomograms. The open-source code and the installation instructions can be found at GitHub.

 

 

 

Available protocols:

  • HEMNMA: Hybrid Electron Microscopy Normal Mode Analysis method to interpret heterogeneity of a set of single particle cryo-EM images in terms of continuous macromolecular conformational transitions [1-3]
  • StructMap: Structural Mapping method to interpret heterogeneity of a set of single particle cryo-EM maps in terms of continuous conformational transitions [4]
  • HEMNMA-3D: Extension of HEMNMA to continuous conformational variability analysis of macromolecules from in situ cryo-ET subtomograms [5]

Notes:

  • The plugin additionally provides the test data and automated tests of the protocols in Scipion 3. The following two types of tests of HEMNMA and HEMNMA-3D can be produced by running, in the terminal, "scipion3 tests continuousflex.tests.test_workflow_HEMNMA" and “scipion3 tests continuousflex.tests.test_workflow_HEMNMA3D”, respectively: (1) tests of the entire protocol with the flexible references coming from an atomic structure and from an EM map; and (2) test of the alignment module (test run using 5 MPI threads).
  • HEMNMA additionally provides tools for synthesizing noisy and CTF-affected single particle cryo-EM images with flexible or rigid biomolecular conformations, for several types of conformational distributions, from a given atomic structure or an EM map. One part of the noise is applied on the ideal projections before and the other after the CTF, as described in [6].
  • HEMNMA-3D additionally provides tools for synthesizing noisy, CTF and missing wedge affected cryo-ET tomograms and single particle subtomograms with flexible or rigid biomolecular conformations, for several types of conformational distributions, from a given atomic structure or an EM map. One part of the noise is applied on the ideal projections before and the other after the CTF, as described in [6].
  • ContinuousFlex additionally contains some utility codes, with their corresponding licenses, for subtomogram averaging, missing wedge correction, denoising and data reading. These codes are not used in the methods above and are made optional for data preprocessing and visualization.

Online lectures:

  • Scipion workshop, April 15th, 2021 [Video on YouTube soon]

-      HEMNMA and HEMNMA-3D for in vitro and in situ studies of continuous conformational variability of macromolecular complexes, ContinuousFlex plugin of Scipion

  • One World Cryo-EM seminar series, March 24th, 2021 [List of talks]

-      Combining normal mode analysis, image analysis, and deep learning for in vitro and in situ studies of continuous conformational variability of macromolecular complexes [YouTube video]

 

References:

 

[1]     Jin Q, Sorzano CO, de la Rosa-Trevin JM, Bilbao-Castro JR, Nunez-Ramirez R, Llorca O, Tama F, Jonic S: Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes. Structure 2014, 22:496-506. [Open-access]

[2]    Jonic S: Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images. Curr Opin Struct Biol 2017, 43:114-121. [Link] [Author’s version]

[3]     Harastani M, Sorzano CO, Jonic S: Hybrid Electron Microscopy Normal Mode Analysis with Scipion. Protein Sci 2020, 29:223-36. [Open-access]

[4]    Sanchez Sorzano CO, Alvarez-Cabrera AL, Kazemi M, Carazo JM, Jonic S: StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes. Biophys J 2016, 110:1753-1765. [Open-access]

[5]     Harastani M, Eltsov M, Leforestier A, Jonic S: HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes. Front Mol Biosci 2021,8:663121. [Open-access]

[6]     Jonic S, Sorzano CO, Thevenaz P, El-Bez C, De Carlo S, Unser M: Spline-based image-to-volume registration for three-dimensional electron microscopy. Ultramicroscopy 2005, 103:303-317. [Author’s version]

Continuous conformational variability in cryo-EM and cryo-ET - ContinuousFlex

 

 

Slavica Jonic    Modified 21/05/2021