Publications

Publications in Google Scholars 

Publications in peer reviewed journals

-2023-

54. Design, construction, and functional characterization of a tRNA neochromosome in yeast.

Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MDC, Zhao Y, Ballerini A, Blount BA, Cai J, Ogunlana L, Liu W, Jönsson K, Abramczyk D, Garcia-Ruiz E, Turowski TW, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Y. Cell. 2023 Nov 22;186(24):5237-5253.e22. doi: 10.1016/j.cell.2023.10.015. Epub 2023 Nov 8. PMID: 37944512 Free article.

53. Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function.

Luo J, Vale-Silva LA, Raghavan AR, Mercy G, Heldrich J, Sun X, Li MK, Zhang W, Agmon N, Yang K, Cai J, Stracquadanio G, Thierry A, Zhao Y, Coelho C, McCulloch LH, Lauer S; Build-A-Genome Class; Kaback DB, Bader JS, Mitchell LA, Mozziconacci J, Koszul R, Hochwagen A, Boeke JD. Cell Genom. 2023 Nov 9;3(11):100439. doi: 10.1016/j.xgen.2023.100439. eCollection 2023 Nov 8. PMID: 38020967

-2022-

52. Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts.

Lazar-Stefanita L, Luo J, Montagne R, Thierry A, Sun X, Mercy G, Mozziconacci J, Koszul R, Boeke JD. Cell Genom. 2022 Aug 10;2(8):None. doi: 10.1016/j.xgen.2022.100163. PMID: 35983101 

51. Genomics enters the deep learning era.

Routhier E, Mozziconacci J. PeerJ. 2022 Jun 24;10:e13613. doi: 10.7717/peerj.13613. eCollection 2022. 

50. Nucleosome Positioning on Large Tandem DNA Repeats of the '601' Sequence Engineered in Saccharomyces cerevisiae.

Lancrey A, Joubert A, Duvernois-Berthet E, Routhier E, Raj S, Thierry A, Sigarteu M, Ponger L, Croquette V, Mozziconacci J, Boulé JB. 

J Mol Biol. 2022 Feb 18;434(7):167497. doi: 10.1016/j.jmb.2022.167497. 

49. Contribution of 3D genome topological domains to genetic risk of cancers: a genome-wide computational study.

Jablonski KP, Carron L, Mozziconacci J, Forné T, Hütt MT, Lesne A. 

Hum Genomics. 2022 Jan 11;16(1):2. doi: 10.1186/s40246-022-00375-2. 

48. The 3D Organization of Chromatin Colors in Mammalian Nuclei.

Carron L, Morlot JB, Lesne A, Mozziconacci J. 

METHODS IN MOLECULAR BIOLOGY 2022;2301:317-336. doi: 10.1007/978-1-0716-1390-0_17.

-2021-

47. Improving distance measures between genomic tracks with mutual proximity.

Haschka T, Morlot JB, Carron L, Mozziconacci J. 

BRIEFINGS IN BIOINFORMATICS 2021 Nov 5;22(6):bbab266. doi: 10.1093/bib/bbab266

46. Epigenetic rewriting at centromeric DNA repeats leads to increased chromatin accessibility and chromosomal instability.

Decombe S, Loll F, Caccianini L, Affannoukoué K, Izeddin I, Mozziconacci J, Escudé C, Lopes J. 

EPIGENETICS CHROMATIN. 2021 Jul 28;14(1):35. doi: 10.1186/s13072-021-00410-x.

45. MNHN-Tree-Tools: A toolbox for tree inference using multi-scale clustering of a set of sequences.

Haschka T, Ponger L, Escudé C, Mozziconacci J. 

BIOINFORMATICS. 2021 Jun 8:btab430. doi: 10.1093/bioinformatics/btab430.

-2020-

44. Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics.

Routhier E, Pierre E, Khodabandelou G, Mozziconacci J. 

GENOME RESEARCH 2020 Dec 18;31(2):317-26. doi: 10.1101/gr.264416.120.

43. Keras_Dna: A Wrapper For Fast Implementation Of Deep Learning Models In Genomics.

Routhier E, Kamruddin AB, Mozziconacci J. 

BIOINFORMATICS. 2020 Nov 2:btaa929. doi: 10.1093/bioinformatics/btaa929. Online ahead of print. PMID: 33135730

42. Genome annotation across species using deep convolutional neural networks.

Khodabandelou G, Routhier E, Mozziconacci J. 

PeerJ Computer Science. 2020 6:e278 https://doi.org/10.7717/peerj-cs.278

-2019-

41. The 3D genome shapes the regulatory code of developmental genes.

Mozziconacci J, Merle M, Lesne A.

J Mol Biol. 2019 Nov 2. pii: S0022-2836(19)30613-8. doi: 10.1016/j.jmb.2019.10.017.

40. Turing-like patterns in an asymmetric dynamic Ising model.

Merle M, Messio L, Mozziconacci J.

Phys Rev E. 2019 Oct;100(4-1):042111. doi: 10.1103/PhysRevE.100.042111.

39. Boost-HiC: Computational enhancement of long-range contacts in chromosomal contact maps.

Carron L, Morlot JB, Matthys V, Lesne A, Mozziconacci J.

BIOINFORMATICS. 2019 Jan 4. doi: 10.1093/bioinformatics/bty1059.

-2018-

38. High-salt-recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies.

Baudement MO, Cournac A, Court F, Seveno M, Parrinello H, Reynes C, Sabatier R, Bouschet T, Yi Z, Sallis S, Tancelin M, Rebouissou C, Cathala G, Lesne A, Mozziconacci J*, Journot L*, Forné T*.

GENOME RESEARCH. 2018 Nov;28(11):1733-1746. doi: 10.1101/gr.237073.118. 

37. Kinetic Signature of Cooperativity in the Irreversible Collapse of a Polymer.

Scolari VF, Mercy G, Koszul R, Lesne A, Mozziconacci J.

PHYSICAL REVIEW LETTERS. 2018 Aug 3;121(5):057801. doi: 10.1103/PhysRevLett.121.057801.

36.Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi-C.

Muller H, Scolari VF, Agier N, Piazza A, Thierry A, Mercy G, Descorps-Declere S, Lazar-Stefanita L, Espeli O, Llorente B, Fischer G, Mozziconacci J*, Koszul R*.

MOLECULAR SYSTEMS BIOLOGY 2018 Jul 16;14(7):e8293. doi: 10.15252/msb.20188293.

35. Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins.

Lioy VS, Cournac A, Marbouty M, Duigou S, Mozziconacci J, Espéli O, Boccard F, Koszul R.

CELL 2018 Jan 10. pii: S0092-8674(17)31507-6. doi: 10.1016/j.cell.2017.12.027.

-2017-

34. P-Body Purification Reveals the Condensation of Repressed mRNA Regulons.

Hubstenberger A, Courel M, Bénard M, Souquere S, Ernoult-Lange M, Chouaib R, Yi Z, Morlot JB, Munier A, Fradet M, Daunesse M, Bertrand E, Pierron G, Mozziconacci J, Kress M, Weil D.

MOLLECULAR CELL 2017 Sep 27. pii: S1097-2765(17)30651-2. doi: 10.1016/j.molcel.2017.09.003.

33. Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle.

Lazar-Stefanita L, Scolari VF, Mercy G, Muller H, Guérin TM, Thierry A, Mozziconacci J*, Koszul R*.

EMBO J. 2017 Jul 20. pii: e201797342. doi: 10.15252/embj.201797342.

32.3D organization of synthetic and scrambled chromosomes.

Mercy G*, Mozziconacci J*, Scolari VF, Yang K, Zhao G, Thierry A, Luo Y, Mitchell LA, Shen M, Shen Y, Walker R, Zhang W, Wu Y, Xie ZX, Luo Z, Cai Y, Dai J, Yang H, Yuan YJ, Boeke JD, Bader JS, Muller H, Koszul R.

SCIENCE  2017 Mar 10;355(6329). pii: eaaf4597. doi: 10.1126/science.aaf4597.

-2016-

31. The physics of epigenetics

R Cortini, M Barbi, B Caré, C Lavelle, A Lesne, J Mozziconacci, JM Victor

REVIEW OF MODERN PHYSICS  2016 88, 025002

30. Network concepts for analyzing 3D genome structure from chromosomal contact maps

JB Morlot, J Mozziconacci, A Lesne

EPJ Nonlinear Biomedical Physics 2016 4 (1), 1-15

29.The 3D folding of metazoan genomes correlates with the association of similar repetitive elements.

Cournac A, Koszul R and Mozziconacci J,

NUCLEIC ACID RESEARCH  2016 Jan 8;44(1):245-55. doi: 10.1093/nar/gkv1292015

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.

-2015-

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

-2014-

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.

-2013-

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.

-2012-

18. Pulling chromatin apart: Unstacking or Unwrapping? 

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

14.Normalization of a chromosomal contact map. PDF 

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

-2011-

12.Co-transcriptional architecture in a Y loop in Drosophila melanogaster. PDF

Redhouse JL, Mozziconacci J, White RA.

CHROMOSOMA. 2011 May 10.PMID: 21556802

-2010-

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

-2009-

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)

-2008-

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)

-2007-

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

-2006-

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).

-2005-

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.

-2003-

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 !

Chapters in books

Chromatin fiber: 30 years of models

Mozziconacci J. and Lavelle C.

COMPUTATIONAL BIOLOGY: NEW RESEARCH, Nova Science Publishers (2008)