Institute of Mineralogy, Materials Physics, and Cosmochemistry

Sorbonne Université, UMR CNRS 7590, MNHN, IRD







Slavica JONIC

Directeur de Recherche / Research Director, CNRS

Head of Image analysis methods development for studying structure and dynamics of macromolecular complexes, subgroup of Bioinformatics and biophysics


ORCID ID: 0000-0001-5112-2743 Link

Loop profile: Link

ResearchGate profile: Link

Google Scholar profile: Link



Sorbonne Université

Campus Jussieu, CC 115

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

4 place Jussieu, F-75005 Paris, France

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

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





Background Link to CV


Since 1996, my 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.


My 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 my 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 my postdoc (2004-2008, University Pierre and Marie Curie, IMPMC-UMR 7590, Paris, France), I have specialized in electron-microscopy image processing for three-dimensional reconstruction of biological macromolecular complexes.


I 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 focus


Development of image analysis methods and computational tools for structural and dynamics studies of biological macromolecular complexes


• Jobs


Postdoctoral Fellow



• Support


CNRS, Sorbonne Université/UPMC, GENCI, ANR, European Commission



• Highlights


-       Review of computational methods for analyzing conformational variability of macromolecular complexes from electron microscopy (EM) images [1]


-       Methodology HEMNMA (Hybrid Electron Microscopy Normal Mode Analysis) to interpret heterogeneity of a set of EM images in terms of continuous macromolecular conformational transitions Tutorial on HEMNMA within Scipion [2,3]


-       Methodology StructMap (Structural Mapping) to interpret heterogeneity of a set of EM density maps in terms of continuous macromolecular conformational transitions Tutorial on StructMap within Scipion [4]


-       Web server 3DEM Loupe for Normal Mode Analysis of EM density maps 3DEM Loupe [5]

(note that Normal Mode Analysis of both EM density maps and PDB atomic structures can now also be done with HEMNMA software)


[1]     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] (invited)

[2]     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]

[3]     Sorzano CO, de la Rosa-Trevin JM, Tama F, Jonic S: Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol. J Struct Biol 2014, 188:134-141. [Link]

[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]     Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vazquez M, Pascual-Montano A, Sorzano CO: 3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy. Nucleic Acids Res 2013, 41:W363-367. [Open-access] (the first two authors should be regarded as joint first authors)




• Software download


·      HEMNMA:

                  HEMNMA is currently distributed as part of the ContinuousFlex plugin of Scipion V2.0 Link

-       The code of the plugin can be downloaded and installed as explained at GitHub Link

-       During the plugin installation, NMA basic code will be downloaded and installed from Link



 • Publications and presentations


·      Full articles in:

-       Peer-review journals Link

-       Peer-review conference proceedings Link

·      Books and book chapters Link

·      Conference abstracts in:

-       Peer-review journals Link

-       Non-peer-review conference proceedings Link

·      Presentations

-       Invited Link

-       Other Link


• Organization of conferences and workshops, Teaching at workshops Link


• Teaching at universities, Mentoring, PhD thesis committees Link


• Editorial activities

·      Frontiers in Molecular Biosciences, Editorial Board Member since 2019 Link

      Review Editor for Specialty Section “Biological Modeling and Simulation”

·      AIMS Biophysics, Editorial Board Member since 2017 Link

·      Frontiers in Molecular Biosciences, Research Topic Editor 2016-2017

Research Topic “Hybrid Biomolecular ModelingLink

·       BioMed Research International, Guest Editor 2016

·       Proc. IEEE International Conference on Image Processing (ICIP) 2014, Special Session articles Editor 2014

Special Session “Electron-Microscopy Image-Processing Problems and Applications in Biology” Link


• Manuscript reviewing

·        Journals: Nat Commun, Structure, J Struct Biol, Bioinformatics, Ultramicroscopy, AIMS Biophys, IEEE Trans Comput Imag, IEEE Trans Medical Imag, IEEE Trans Imag Process, IET Image Process, IEEE J Sel Topics Sig Process, IEEE Sig Process Lett, Expert Syst Appl

·        Conferences proceedings: IEEE Int Conf Image Process (ICIP), Int ICT Conf “Telecommunications Forum” (TELFOR)


• Grant reviewing (European grants)

·      CORBEL - Coordinated Research Infrastructures for Life Science Link

Reviewer since Dec. 2016

·      Euro-BioImaging - European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences Link

Reviewer since Nov. 2016

·      iNEXT - Infrastructure for NMR, EM and X−rays for Translational Research Link

- Reviewer Dec. 2015 – Jun. 2017

- EM review moderator (chair): Sep. 2017 – Aug. 2019


• Administration

·      iNEXT - Infrastructure for NMR, EM and X−rays for Translational Research Link

Member of Executive Review Panel from Sep. 2017 to Aug. 2019

·      CNRS GRID2−FR Certification Authority Link

Contact person for IMPMC since 2010

·      IMPMC Unit Council

Elected Member since 2019

·      Seminars planning committee, IMPMC Transverse Axis “Theory, Modeling & Simulation”

Member since 2019



Slavica Jonic    Modified 01/12/2019