Publications

2020

  • Jeannette Reinig*, Frank Ruge*, Martin Howard and Leonie Ringrose (2020) A theoretical model of Polycomb/Trithorax action unites stable epigenetic memory and dynamic regulation. Nature Communications, Published:  https://doi.org/10.1038/s41467-020-18507-4
  • Zambrano 1,2,*, S., Loffreda, A., Carelli, E., Stefanelli, G., Colombo, F., Bertrand, E., Tacchetti, C., Agresti, A., Bianchi, M.E., Molina*, N., and Mazza 2,*, D. (2020) First responders shape a prompt and sharp NF-κB –mediated transcriptional response to TNF-α. iScience September 3 (1 Lead contact, 2 These authors contributed equally, *corresponding authors). doi: https:// doi.org/10.1016/j.isci.2020.101529.
  • Samuel Zambrano 1,2,*, Alessia Loffreda, Elena Carelli, Giacomo Stefanelli, Federica Colombo, Edouard Bertrand, Carlo Tacchetti, Alessandra Agresti, Marco E. Bianchi, Nacho Molina* and Davide Mazza 2,* (2020) First responders shape a prompt and sharp NF-κB–mediated transcriptional response to TNF-α. BioRxiv preprint, version posted June 29. (1 Lead contact, 2 These authors contributed equally, *corresponding authors). doi: https://doi.org/10.1101/2020.06.27.174995.
  • Robert A. Beagrie*, Christoph J. Thieme*, Carlo Annunziatella*, Catherine Baugher, Yingnan Zhang, Markus Schueler, Dorothee CA Kramer, Andrea M. Chiariello, Simona Bianco, Alexander Kukalev, Yichao Li, Rieke Kempfer, Antonio Scialdone, Lonnie R. Welch‡ , Mario Nicodemi‡  and Ana Pombo‡ (2020) Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C. BioRxiv preprint, version posted July 31. (*joint first authors, ‡ joint corresponding authors). doi: https://doi.org/10.1101/2020.07.31.230284.

  • Guido PaciniIlona DunkelNorbert MagesVerena MutzelBernd TimmermannAnnalisa
    Marsico
    and Edda G. Schulz (2020) Integrated analysis of Xist upregulation and gene silencing at the onset of random X-chromosome inactivation at high temporal and allelic resolution. bioRxiv preprint, version posted July 21.
    doi: https://doi.org/10.1101/2020.07.20.211573.
  • Mattia ConteLuca FiorilloSimona BiancoAndrea M. ChiarielloAndrea Esposito and Mario Nicodemi (2020) Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation.
    Nat Commun. Jul 3;11(1):3289.
    doi: 10.1038/s41467-020-17141-4. Pubmed
  • Jack E. FelthamShidong XiStruan C. MurrayMeredith WoutersJulian Urdiain-ArraizaRaphael HeiligCharlotte GeorgeAnna F. TownleyEmile RobertsBenedikt M. KesslerSabrina LiberatoriPhilip D. CharlesAndrew AngelRoman Fischer and Jane Mellor (2020) Transcriptional changes are regulated by metabolic pathway dynamics but decoupled from protein levels. bioRxiv preprint, version posted June 10.
    doi: https://doi.org/10.1101/833921.
  • Simona Bianco, Andrea M. Chiariello, Mattia Conte, Andrea Esposito, Luca Fiorillo, Francesco Musella and Mario Nicodemi (2020) Computational approaches from polymer physics to investigate chromatin folding.
    Curr Opin Cell Biol. Jun;64:10-17. doi: 10.1016/j.ceb.2020.01.002. Pubmed
  • Mattia ConteLuca FiorilloSimona BiancoAndrea M. ChiarielloAndrea Esposito and Mario Nicodemi (2020) Chromatin folding variability across single-cells results from state degeneracy in phase-separation. bioRxiv preprint, version posted May 16.
    doi: https://doi.org/10.1101/2020.05.16.099275. 
  • Verena Mutzel and Edda G. Schulz (2020) Dosage Sensing, Threshold Responses, and Epigenetic Memory: A Systems Biology Perspective on Random X-Chromosome Inactivation. Bioessays. Apr;42(4):e1900163. doi: 10.1002/bies.201900163. Pubmed

  • Luca Fiorillo*, Francesco Musella*, Rieke Kempfer, Andrea M. Chiariello, Simona Bianco, Alexander Kukalev, Ibai Irastorza-Azcarate, Andrea Esposito, Mattia Conte, Antonella Prisco, Ana Pombo and Mario Nicodemi (2020) Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin.
    BioRxiv preprint, version posted April 25. (*these authors contributed equally).
    doi: https://doi.org/10.1101/2020.04.24.059915.

2019

  • Lisa Barros de Andrade E SousaIris JonkersLaurène SyxIlona DunkelJulie ChaumeilChristel PicardBenjamin ForetChong-Jian ChenJohn T Lis*Edith Heard*, Edda G Schulz* and Annalisa Marsico* (2019) Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Genome Res. Jul;29(7):1087-1099. doi: 10.1101/gr.245027.118. Epub 2019 Jun 7.
    (* corresponding authors)
    Pubmed
  • Gaetano Ivan DellinoFernando PalluzziAndrea Maria ChiarielloRossana PiccioniSimona BiancoLaura FuriaGiulia De ContiBritta A. M. BouwmanGiorgio MelloniDavide GuidoLuciano GiacòLucilla LuziDavide CittaroMario FarettaMario NicodemiNicola Crosetto and Pier Giuseppe Pelicci (2019) Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations. Nat Genet. Jun;51(6):1011-1023. doi: 10.1038/s41588-019-0421-z. Epub 2019 May 20. Pubmed
  • Verena MutzelIkuhiro OkamotoIlona DunkelMitinori SaitouLuca GiorgettiEdith Heard and Edda G Schulz (2019) A symmetric toggle switch explains the onset of random X inactivation in different mammals. Nat Struct Mol Biol. May;26(5):350-360.
    doi: 10.1038/s41594-019-0214-1. Epub 2019 Apr 8. Pubmed
  • Kim Sneppen and Leonie Ringrose (2019) Theoretical Analysis of Polycomb-Trithorax Systems Predicts That Poised Chromatin Is Bistable and Not Bivalent. Nat Commun. May 13;10(1):2133.doi: 10.1038/s41467-019-10130-2. Pubmed

2018

  • Thomas BrownFrançoise S. HoweStruan C. MurrayMeredith WoutersPhilipp LorenzEmily SewardScott RataAndrew Angel and  Jane Mellor (2018) Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. Mol Syst Biol. Feb 12;14(2):e8007. doi: 10.15252/msb.20178007. Pubmed