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• 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 vitro and in situ cryo-ET subtomograms [5]
- TomoFlow: Method for analyzing continuous conformational variability of macromolecules in in vitro and in situ cryogenic subtomograms based on 3D dense optical flow [8]
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). The automated tests of the TomoFlow method are also available.
- 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:
- Instruct Image Processing Center (I2PC) seminar series,
April 15th, 2021 [YouTube]
-
HEMNMA and HEMNMA-3D for
in vitro and in situ studies
of continuous conformational variability of macromolecular
complexes, ContinuousFlex plugin of Scipion
- Combining normal mode analysis,
image analysis, and deep learning for in vitro and in
situ studies of continuous conformational variability of macromolecular
complexes
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]
[7]
Harastani M and Jonic S: Methods for analyzing continuous conformational variability of biomolecules in cryo electron subtomograms: HEMNMA-3D vs. traditional classification. BioRxiv 2021 [Open-access]
[8] Harastani M, Eltsov M, Leforestier A, Jonic S: TomoFlow: Analysis of continuous conformational variability of macromolecules in cryogenic subtomograms based on 3D dense optical flow. J Mol Biol 2021, 167381. [Link] [Author’s version]
[9] Harastani M and Jonic S: Synthetic cryo electron subtomograms containing biomolecular complexes with continuous conformational variability.[Data set] Zenodo. 2021. [Link]
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