Publications
Publications in Google Scholars
Publications in peer reviewed journals
-2024-
56. In silico design of DNA sequences for in vivo nucleosome positioning.
Routhier E, Joubert A, Westbrook A, Pierre E, Lancrey A, Cariou M, Boulé JB, Mozziconacci J.
NUCLEIC ACID RESEARCH 2024 Jun 3:gkae468. doi: 10.1093/nar/gkae468. Online ahead of print. PMID: 38828788
Bignaud A, Cockram C, Borde C, Groseille J, Allemand E, Thierry A, Marbouty M, Mozziconacci J, Espéli O, Koszul R.
NSMB 2024 Mar;31(3):489-497. doi: 10.1038/s41594-023-01178-2. Epub 2024 Jan 4. PMID: 38177686
-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 GENOMICS. 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 GENOMICS. 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.
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.
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
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-
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.
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.
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.
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)
-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)
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)