Julien Mozziconacci, PhD

Researcher
Multi-scale models of the genome



Theoretical Physics of Condensed matter Lab

Pierre and Marie Curie University, Paris

email: mozziconacci_at_lptmc.jussieu.fr
telephone: +33 1 44 27 45 40

 

 



Research Positions

2009 - present, Lecturer in Physics and Biology

Condensed Matter Theory Lab, Pierre & Marie Curie University, Paris, France

2008 - 2010, Research Associate in Bioinformatics

Computer Lab, Cambridge University, Cambridge, UK

2006 – 2008, Postdoctoral Research in Physics

Condensed Matter Theory Lab, Pierre & Marie Curie University, Paris, France

2004 – 2006, Postdoctoral Research in Molecular Biology

Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany

2001 – 2004, Doctoral Research in Physics

Condensed Matter Theory Lab, Pierre & Marie Curie University, Paris, France



Academic Degrees

2013 H.D.R. in Biology

Condensed Matter Theory Lab, Pierre & Marie Curie University, Paris, France
Models of the genome architecture: from nucleosomes to nuclei.

2004 Ph.D. in Physics

Condensed Matter Theory Lab, Pierre & Marie Curie University, Paris, France
Multi-scale Modeling of Chromatin during the Cell Cycle.
Advisor: Jean-Marc Victor Manuscript in French

2001 M.S. in Physics

Pierre & Marie Curie University, Paris, France
Modeling, Dynamics and Statistics of Complex Systems.


 

Publications

My publications in Google Scholars
My publications in PubMed

Publications in peer reviewed journals

29.The 3D folding of metazoan genomes correlates with the association of similar repetitive elements.
Cournac A, Koszul R and Mozziconacci J,
NUCLEIC ACIS RESEARCH 2015 Nov 24. pii: gkv1292.

28.Generation and Analysis of Chromosomal Contact Maps of Yeast Species.
Cournac A, Marbouty M, Mozziconacci J, Koszul R.
METHODS IN MOLECULAR BIOLOGY 2016;1361:227-45. doi: 10.1007/978-1-4939-3079-1_13.

27. Spatial reorganization of telomeres in long-lived quiescent cells.
Guidi M, Ruault M, Marbouty M, Loïodice I, Cournac A, Billaudeau C, Hocher A, Mozziconacci J, Koszul R, Taddei A.
GENOME BIOLOGY 2015 Sep 23;16(1):206. doi: 10.1186/s13059-015-0766-2.

26. Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging.
Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A, Fiche JB, Mozziconacci J, Murray H, Koszul R, Nollmann
MOLLECULAR CELL 2015 Aug 20;59(4):588-602. doi: 10.1016/j.molcel.2015.07.020.

25. Filling the gap: Micro-C accesses the nucleosomal fiber at 100-1000 bp resolution.
Mozziconacci J, Koszul R.
GENOME BIOLOGY 2015 Aug 21;16(1):169. doi: 10.1186/s13059-015-0744-8.

24. Principles of chromatin organization in yeast: relevance of polymer models to describe nuclear organization and dynamics.
Wang R, Mozziconacci J, Bancaud A, Gadal O.
CURRENT OPINION IN CELL BIOLOGY 2015 May 5;34:54-60. doi: 10.1016/j.ceb.2015.04.004

23.Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. PDF
Marbouty M, Cournac A, Flot JF, Marie-Nelly H, Mozziconacci J, Koszul R.
ELIFE. 2014 Dec 17;3. doi: 10.7554/eLife.03318.

22. The polymorphisms of the chromatin fiber. PDF
Boulé JB, Mozziconacci J, Lavelle C.
J PHYS COND MAT 2014 Dec 1;27(3):033101.

21. 3D genome reconstruction from chromosomal contacts. PDF
Lesne A, Riposo J, Roger P, Cournac A, Mozziconacci J.
NATURE METHODS 2014 Sep 21. doi: 10.1038/nmeth.3104.

20. High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome. PDF
Hajjoul H, Mathon J, Ranchon H, Goiffon I, Mozziconacci J, Albert B, Carrivain P, Victor JM, Gadal O, Bystricky K, Bancaud A.
GENOME RESERACH 2013 Nov;23(11):1829-38

19. Systematic characterization of the conformation and dynamics of budding yeast chromosome XII.
Albert B, Mathon J, Shukla A, Saad H, Normand C, Léger-Silvestre I, Villa D, Kamgoue A, Mozziconacci J, Wong H, Zimmer C, Bhargava P, Bancaud A, Gadal O.
JOURNAL OF CELL BIOLOGY 2013 Jul 22;202(2):201-10.

18. Pulling chromatin apart: Unstacking or Unwrapping? http://www.biomedcentral.com/images/icons/highly-accessed.gif
Victor JM, Zlatanova J, Barbi M, Mozziconacci J.
BMC Biophysics 2012 Nov 27;5(1):21

17.DNA topology in chromosomes: a quantitative survey and its physiological implications. PDF
Barbi M, Mozziconacci J, Wong H, Victor JM.
J. MATH. BIOL. 2012 Nov 20.

16. On the topology of chromatin fibres
Barbi, M; Mozziconacci, J; Victor, JM; et al.
INTERFACE FOCUS 2012 (2): 5, 546-554

15.Electrostatics of DNA compaction in viruses, bacteria and eukaryotes: functional insights and evolutionary perspective PDF
Carrivain, Pascal; Cournac, Axel; Lavelle, Christophe; et al.
SOFT MATTER 2012 (8),36,9285-9301


Journal Cover:Soft Matter, 2012, 8, 9285-9301
14.Normalization of a chromosomal contact map. PDF http://www.biomedcentral.com/images/icons/highly-accessed.gif
Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J.
BMC Genomics. 2012 Aug 30;13(1):436.

13. Nucleosome positioning and nucleosome stacking: two faces of the same coin. PDF
Riposo J, Mozziconacci J.
MOLECULAR BIOSYSTEMS. 2012 Jan 23.PMID:22266567

12.Co-transcriptional architecture in a Y loop in Drosophila melanogaster. PDF
Redhouse JL, Mozziconacci J, White RA.
CHROMOSOMA. 2011 May 10.PMID: 21556802

11.Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide. PDF
Botta M, Haider S, Leung IX, Lio P, Mozziconacci J.
MOLECULAR SYSTEMS BIOLOGY 2010 Nov 2;6:426.PMID: 21045820

10. Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. PDF
Bancaud A, Huet S, Daigle N, Mozziconacci J, Beaudouin J, Ellenberg J.
EMBO J. 2009 Nov 19. PMID: 19927119

9. A molecular model of chromatin organisation and transcription: how a multi-RNA polymerase II machine transcribes and remodels the beta-globin locus during development. PDF
Wong H, Winn PJ, Mozziconacci J.
BIOESSAYS. 2009 Oct 29;31(12):1357-1366. PMID: 19877003

8.Sequence-driven telomeric chromatin structure. PDF
Revaud D, Mozziconacci J, Sabatier L, Desmaze C, Lavelle C.
CELL CYCLE. 2009 Apr 4;8(7)


7. Tubulin dimers oligomerize before their incorporation into microtubules PDF
Mozziconacci J, Sandblad L, Wachsmuth M, Brunner D and Karsenti E.
PLoS ONE 3(11): e3821. doi:10.1371/journal.pone.0003821(2008)

6. An all-atom model of the chromatin fiber containing linker histone reveals a versatile structure tuned by nucleosomal repeat length. PDF
Wong H, Victor JM., Mozziconacci J.
PLoS ONE 2(9): e877. doi:10.1371/journal.pone.0000877 (2007)
Discussed in the May 2008 issue of Chemistry world: "pulling our strings".

5. Nucleosome chiral transition under positive torsional stress in single chromatin fibers. PDF
Bancaud A, Wagner G, Conde E Silva N, Lavelle C, Wong H, Mozziconacci J, Barbi M, Sivolob A, Le Cam E, Mouawad L, Viovy JL, Victor JM, Prunell A.
MOLECULAR CELL 27(1):135-47. (2007)
See the CNRS press release

4. Torsional manipulation of single chromatin fibers reveals a highly flexible structure. PDF
Bancaud A, Cond e Silva N, Barbi M, Allemand JF, Mozziconacci J, Lavelle C, Croquette V, Victor JM,
Prunell A, Viovy JL.
NATURE STRUCTURAL AND MOLECULAR BIOLOGY 13(5):444-50. (2006)
See the CNRS press release

3. A physical model for the condensation and decondensation of eukaryotic chromosomes. PDF
Mozziconacci J, Lavelle C, Barbi M, Lesne A, Victor JM.
FEBS LETTERS 580(2):368-72.(2006).

2. How the chromatin fiber deals with topological constraints. PDF
Barbi M, Mozziconacci J and Victor JM.
PHYSICAL REVIEW E 71 (3 Pt 1):031910 (2005).
Presented in Nature ”News and views” Vol. 429
and in the American Mathematical Society Maths in the Media.
Selected for the April 1, 2005 issue of Virtual Journal of Biological Physics Research.

1. Nucleosome gaping supports a functional structure for the 30 nm chromatin fiber. PDF
Mozziconacci J, Victor JM.
JOURNAL OF STRUCTURAL BIOLOGY 148 72–76 (2003).
 
12 years after our theoretical prediction, gaping was confirmed experimentally !

Conference abstracts

Graphical Modeling of the Beta-Globin Transcription Factory
Wong, H. and Mozziconacci, J.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS Volume: 26 Issue: 6 (2009)

All-atom model of the chromatin fiber : a versatile structure tuned by the repeat length
Mozziconacci J., Wong H. and Victor J.M.
FEBS JOURNAL Volume: 274 Pages: 78 ( 2007)

Chromatin structure and macromolecular confinement.
Bancaud A, Daigle N,Mozziconacci J and Ellenberg J.
BIOPHYSICAL JOURNAL 14 A Suppl (2007)

Chapters in books

Chromatin fiber: 30 years of models
Mozziconacci J. and Lavelle C.
COMPUTATIONAL BIOLOGY: NEW RESEARCH, Nova Science Publishers (2008)

Conferences



Invited contributions

CECAM Workshop GENPHYSCHROM, Lyon, France, June 2015

6th Mechanobiology Conference, Singapore, 2012, selected talk

EMBL Conference: From functional genomics to systems biology, Heidelberg, Germany, 2010, selected talk

EMBL Conference: Chromatin and transcription, Heidelberg, Germany, August 2010, selected talk

FEBS Congress on ”Molecular Machines”. Vienna, Austria, 2007. Contributed poster

Gordon Research Conference on ”Nucleic Acids”. Newport, USA, 2007. Contributed poster,

2nd International PhD Symposium on ”Decoding Nature: Hierarchy of interactions”, Gottingen, Germany, 2005. Selected talk

 

Schools & Workshops

Comparative genomics of vertebrates: concepts and bio-informatics tools. La Londe-Les-Maures, France, 2004.

DNA and chromosomes. Cargese, France, 2004. Contributed poster, “A physical model for the compaction of the mitotic chromosome”

Physics of the cell. Les Houches, France, 2004. Contributed talk, “How does the chromatin fiber deals with topological constraints.”

Understanding Molecular Simulation. Amesterdam, Netherlands, 2002.



Teaching

Teaching in High School : Physics and Chemistry at the Carnot high school in Paris, May and June 2002.

Teaching at the University : Physics (basic physics, history of science and spectral analysis)

My courses in french:


Funding


2015 ANR HiResBac (Partner 150 kE)

2015 IDEX SUPER 3DRNA (Partner 70 kE)

2014 ANR ANDY ANR-13-BSV5-0010 (Partner 100 kE)

2013 Labex CalSim (Partner 100 kE)

2012 INCa PLBIO INCa_5960 (Partner 100 kE)

2011 CONVERGENCE - projet CVG1110 (PI 30 kE)

2010 ANR Pyribio ANR-09-PIRI-0024 (Partner, 100 kE)

2009 EMBO short-term fellowship in 2009 ASTF 277-2009 (PI 20 kE)

 

Awards

 

2013 Winner of the second edition of the Art and Science award from UPMC with the contribution: "comparison between four Hi-C experiments"
MOZZICONACCI_Photo_concours_science troublante

2008 Semi-finalist of the Internatinal Science and Engineering Visualization Challenge in the category informational graphics for the submission of "Graphical modeling of the beta-Globin transcription factory"
http://www.jbsdonline.com/databaseimages/WongWebFigure.jpg

2006 Prix "La Recherche" : J.M. Victor’s group was selected by the jury for great quality and innovative interdisciplinary work.

Referee activity

I have been referee for: Cell, Cell Stem Cell, Nature Methods, Genome Biology, PloS ONE, BMC Genomic, Frontiers in Life Science, BioInformatics, Nucleic Acid Research, Scientific Reports and BMC Bioinformatics.

Supervised Internship

Statistical positionning of nucleosomes and analysis of the effect of various mutants
Valentine Arlot (2014)
 
Carron Leopold (2014)

Modeling nucleosome interactions using classical density functional theory
Florent Bories (2012)

Étude par simulation de la sous diffusion de monomères au sein d'un polymère
Emmanuel Harleaux (2011)

Statistical Mechanics of Nucleosome Positioning in Saccharomyces Cerevisiae
Julien Riposo (2011)



Communication of Science

2015 Spatial reorganization of telomeres in long-lived quiescent cells

2014 3D genome reconstruction from chromosomal contacts.


2014 Participation to the realization of a CNRS fresco et the Montparnasse Metro station.


 
2013 La dynamique des chromosome explorée par la biophysique

2008 An all-atom model of the chromatin fiber containing linker histone reveals a versatile structure tuned by nucleosomal repeat length.
Discussed in the May 2008 issue of Chemistry world: "pulling our strings".

2007 Nucleosome chiral transition under positive torsional stress in single chromatin fibers.
See the CNRS press release

2006 Torsional manipulation of single chromatin fibers reveals a highly flexible structure.
See the CNRS press release

2005 How the chromatin fiber deals with topological constraints.
Presented in Nature ”News and views” Vol. 429
and in the American Mathematical Society Maths in the Media.
Selected for the April 1, 2005 issue of Virtual Journal of Biological Physics Research.

Publicly-available software

SCN (Sequential component Normalization) is a program that aims at normalizing chromosomal contact maps as determined by Hi-C so that the sum of every line and every column is equal (or very close) to one.

There are two options to run SCN the first one uses the Matlab complier runtime environment (MCR), the second one is to run the source code directly on Matlab.


1. Install the MCR for R2014b (8.4) on Linux 64. Download run_SCN and SCN Then execute run_ShRec3D and the program will read the file data.dat in the current folder which contains a contact map and give as an output the file 3Dcoor.xyz which contains the 3D coordinates.
 
2. If you already have Matlab installed, you can direclty use the source code SCN.m

 

ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C.

There are two options to run ShRec3D: the first one uses the Matlab complier runtime environment (MCR), the second one is to run the source code directly on Matlab.

 
1. Install the MCR for R2014b (8.4) on Linux 64. Download run_ShRec3D and ShRec3D. Then execute run_ShRec3D and the program will read the file data.dat in the current folder which contains a contact map and give as an output the file 3Dcoor.xyz which contains the 3D coordinates.
 
2. If you already have Matlab installed, you can direclty use the source code ShRec3D.m
 
Here is an example of data file that can be used:
a real dataset representing the contact map determined for a 30 Mbp regions of a human chromosome
(data from Dixon et al.)