Institute of Mineralogy, Materials Physics, and Cosmochemistry

Sorbonne Université, UMR CNRS 7590, MNHN, IRD

 

 

 

 

 

 

Slavica JONIC

Chargé de Recherche, CNRS (Tenured Associate Scientist, CNRS)

Habilité à Diriger des Recherches (Habilitated to Direct Research)

 

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, F-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

 

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 and a Research Director Habilitation from the Life Sciences Department of the University Pierre and Marie Curie - UPMC in 2015.

 

• Research focus

 

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

 

• Internship proposals

 

Master Proposal 1, Master Proposal 2, Master Proposal 3

 

• Support

 

 CNRS, UPMC, ANR, and European Union

 

• 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)

 

 

 

 

 • Production

 

·        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

·        AIMS Biophysics, Editorial Board Member since 2017 Link

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

Research Topic “Hybrid Biomolecular Modeling” Link

·         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: J Struct Biol, Structure, Bioinformatics, AIMS Biophys, IEEE Trans Comput Imag, IEEE Trans Medical Imag, IET Image Process, IEEE J Sel Topics Sig Process, IEEE Sig Process Lett

·          Conferences proceedings: IEEE Int Conf Image Process – ICIP

 

• 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) since Sep. 2017

 

• Research administration

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

Member of Executive Review Panel since Sep. 2017

·        CNRS GRID2−FR Certification Authority Link

Contact person for IMPMC since 2010

 

 

Slavica Jonic    Modified 13/09/2018