MARIO NICODEMI

PUBLICATIONS

SELECTED PUBLICATIONS

Papers

Selected peer reviewed scientific publications:

  • A.D. Pourmorady, E.V. Bashkirova, A.M. Chiariello, H. Belagzhal, A. Kodra, R. Duffie, J. Kahiapo, K. Monahan, J. Pulupa, I. Schieren, A. Osterhoudt, J. Dekker, M. Nicodemi and S. Lomvardas, "RNA-mediated symmetry breaking enables singular olfactory receptor choice", Nature 625, 181 (2024)

  • A.M. Chiariello, A. Abraham, S. Bianco, A. Esposito, F. Vercellone, M. Conte, A. Fontana, M. Nicodemi, "Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells", Nature Comm. 15, 4014 (2024)

  • R.A., Beagrie, C.J., Thieme, C., Annunziatella, C. Baugher, Y. Zhang, M. Schueler, A. Kukalev, R. Kempfer, A.M. Chiariello, S. Bianco, Y. Li, T. Davis, A. Scialdone, L.R. Welch, M. Nicodemi and A. Pombo, "Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C", Nature Meth. 20, 1037 (2023)

  • A.R. Ringel, Q. Szabo, A.M. Chiariello, K. Chudzik, R. Schoepflin, P. Rothe, A. L. Mattei, T. Zehnder, D. Harnett, V. Laupert, S. Bianco, S. Hetzel, J. Glaser, M.H.Q. Phan, M. Schindler, D.M. Ibrahim, C. Paliou, A. Esposito, C.A. Prada-Medina, S.A. Haas, P. Giere, M. Vingron, L. Wittler, A. Meissner, M. Nicodemi, G. Cavalli, F. Bantignies, S. Mundlos, M.I. Robson, "Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes", Cell 185, 3689 (2022)

  • M. Conte, E. Irani, A. M. Chiariello, A. Abraham, S. Bianco, A. Esposito, M. Nicodemi, "Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding", Nature Comm. 13, 4070 (2022)

  • W. Winick-Ng, A. Kukalev, I. Harabula, L. Zea-Redondo, D. Szab, M. Meijer, L. Serebreni, Y. Zhang, S. Bianco, A.M. Chiariello, I. Irastorza-Azcarate, C. J. Thieme, T.M. Sparks, S. Carvalho, L. Fiorillo, F. Musella, E. Irani, E. Torlai Triglia, A.A. Kolodziejczyk, A. Abentung, G. Apostolova, E.J. Paul, V. Franke, R. Kempfer, A. Akalin, S.A. Teichmann, G. Dechant, M.A. Ungless, M. Nicodemi, L. Welch, G. Castelo- Branco, A. Pombo, "Cell-type specialization is encoded by specific chromatin topologies", Nature 599, 684 (2021)

  • L. Fiorillo, F. Musella, M. Conte, R. Kempfer, A.M. Chiariello, S. Bianco, A. Kukalev, I. Irastorza-Azcarate, A. Esposito, A. Abraham, A. Prisco, A. Pombo, M. Nicodemi, "Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin", Nature Methods 18, 482 (2021)

  • H. Huang, Q. Zhu, A. Jussila, Y. Han, B. Bintu, C. Kern, M. Conte, Y. Zhang, S. Bianco, A.M. Chiariello, M. Yu, R. Hu, M. Tastemel, I. Juric, M. Hu, M. Nicodemi, X. Zhuang and B. Ren, "CTCF mediates dosage- and sequence- context-dependent transcriptional insulation by forming local chromatin domains", Nature Genetics 53, 1064 (2021)

  • N. Kubo, H. Ishii, X. Xiong, S. Bianco, F. Meitinger, R. Hu, J.D. Hocker, M. Conte, D. Gorkin, M. Yu, B. Li, J.R. Dixon, M. Hu, M. Nicodemi, H. Zhao, B. Ren, "Promoter-proximal CTCF-binding Promotes Long-range-enhancer Dependent Gene Activation", Nature Str. Mol. Bio. 28, 152 (2021)

  • M. Conte, L. Fiorillo, S. Bianco, A. M. Chiariello, A. Esposito, M. Nicodemi, "Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase-separation", Nature Comm. 11, 3289 (2020)

  • G.I. Dellino, F. Palluzzi, R. Piccioni, A.M. Chiariello, S. Bianco, L. Furia, G. De Conti, B. Bouwman, G. Melloni, D. Guido, L. Giaco, L. Luzi, D. Cittaro, M.Faretta, M. Nicodemi, N. Crosetto and P.G. Pelicci, "Release of stalled RNA-Polymerase II at specific loci and chromatin domains favors spontaneous DNA double strand breaks formation and predicts cancer translocations", Nature Genetics 51, 1011 (2019)

  • B.K. Kragesteen, M. Spielmann, C. Paliou, V. Heinrich, R. Schoepflin, A. Esposito, C. Annunziatella, S. Bianco, A.M. Chiariello, I. Jerkovic, I. Harabula, P. Guckelberger, M. Pechstein, L. Wittler, W.-L. Chan, M. Franke, D.G. Lupianez, K. Kraft, B. Timmermann, M. Vingron, A. Visel, M. Nicodemi*, S. Mundlos*, G. Andrey*, "Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis", Nature Genetics 50, 1463 (2018)

  • S. Bianco, D.G. Lupianez, A.M. Chiariello, C. Annunziatella, K. Kraft, R. Schoepflin, L. Wittler, G. Andrey, M. Vingron, A. Pombo, S. Mundlos*, M. Nicodemi*, "Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture", Nature Genetics 50, 662 (2018)

  • A.M. Oudelaar, J.O.J. Davies, L.P. Hanssen, J.M. Telenius, R. Schwessinger, Y. Liu, J.M. Brown, D.J. Downes, A.M. Chiariello, S. Bianco, M. Nicodemi, V.J. Buckle, J. Dekker, D.R. Higgs, J.R. Hughes, "Single- allele chromatin interactions reveal regulatory hubs in dynamic compartmentalized domains", Nature Genetics 50, 1744 (2018)

  • M.A. Marti-Renom, et al. (members of the EU 4DN consortium), "Challenges and guidelines toward 4D nucleome data and model standards", Nature Genetics 50, 1352 (2018)

  • M. Barbieri, S.Q. Xie, E. Torlai Triglia, A.M. Chiariello, S. Bianco, I. de Santiago, M.R. Branco, D. Rueda, M. Nicodemi*, A. Pombo*, "Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells", Nature Struct. Mol. Bio. 24, 515 (2017)

  • C.A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo, "Nonequilibrium Chromosome Looping via Molecular Slip Links", Phys. Rev. Lett. 108, 158103 (2017)

  • R.A. Beagrie, A. Scialdone, M. Schueler, D.C.A. Kraemer, M. Chotalia, S.Q. Xie, M. Barbieri, I. de Santiago, L.-M. Lavitas, M.R. Branco, J. Fraser, J. Dostie, L. Game, N. Dillon, P.A.W. Edwards, M. Nicodemi*, A. Pombo*, "Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM), a novel ligation-free approach", Nature 543, 519 (2017)

  • C. Ferrai, E. Torlai Triglia, J.R. Risner-Janiczek, T. Rito, I. de Santiago, A. Kukalev, O.J.L. Rackham, M. Nicodemi, A. Akalin, M. Li, M.A. Ungless, A. Pombo, "RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation", Molecular Systems Biology 13, 946 (2017)

  • J. Dekker, et al. (members of the NIH 4DN consortium), "The 4D nucleome project", Nature 549, 219 (2017)

  • Andrea M. Chiariello, Carlo Annunziatella, Simona Bianco, Andrea Esposito and Mario Nicodemi, "Polymer physics of chromosome large-scale 3D organisation", Nature Sci. Rep. 6, 29775 (2016)

  • V. Proserpio, A. Piccolo, L. Haim-Vilmovsky, G. Kar, T. Loennberg, V. Svensson, J. Pramanik, K.N. Natarajan, W. Zhai, X. Zhang, G. Donati, M. Kayikci, J. Kotar, A.N.J. McKenzie, R. Montandon, O. Billker, S. Woodhouse, P. Cicuta, M. Nicodemi*, S.A. Teichmann*, "Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation", Genome Biology 17, 103 (2016)

  • J. Fraser, C. Ferrai, A.M. Chiariello, M. Schueler, T. Rito, G. Laudanno, M. Barbieri, B.L. Moore, D.C.A. Kraemer, S. Aitken, S.Q. Xie, K. Morris, M. Itoh, H. Kawaji, I. Jaeger, Y. Hayashizaki, P. Carninci, A.R.R. Forrest, FANTOM, C.A. Semple, J. Dostie, A. Pombo, and M. Nicodemi, "Hierarchical folding of chromosomes is linked to transcriptional changes in cellular differentiation", Molecular Systems Biology 11, 852 (2015)

  • A. Pombo and M. Nicodemi, "Models of chromosome structure", Current Opinion in Cell Biology 28, 90 (2014)

  • J.W. Armond, K. Saha, A.A. Rana, C.J. Oates, R. Jaenisch, M. Nicodemi*, S. Mukherjee*, "A stochastic model dissects cell states in biological transition processes", Nature Scientific Reports 4, 3692 (2014)

  • M. Barbieri, M. Chotalia, J. Fraser, L.-M. Lavitas, J. Dostie, A. Pombo, M. Nicodemi, "Complexity of chromatin folding is captured by the strings and binders switch model", PNAS 109, 16173 (2012)

  • A. Gamba, M. Nicodemi, J. Soriano, A. Ott, "Critical Behavior and Axis Defining Symmetry Breaking in Hydra Embryonic Development", Phys. Rev. Lett. 108, 158103 (2012)

  • M. Nicodemi and A. Prisco, "Thermodynamic pathways to genome spatial organization in the cell nucleus", Biophys.Jou. 96, 2168 (2009)

  • D.S. Grebenkov, M. Pica Ciamarra, M. Nicodemi,  A. Coniglio, "Flow, ordering, and jamming of sheared granular suspensions", Phys. Rev. Lett. 100, 078001 (2008)

  • M. Nicodemi and A. Prisco, "A Symmetry Breaking Model for X Chromosome Inactivation", Phys. Rev. Lett. 98, 108104 (2007)

  • M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, "Thermodynamics and Statistical Mechanics of Dense Granular Media'', Phys. Rev. Lett. 97, 158001 (2006)

  • M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, "Dynamically induced effective interaction in periodically driven granular mixtures'', Phys. Rev. Lett. 97, 038001 (2006)

  • L. de Arcangelis, C. Godano, E. Lippiello, M. Nicodemi, "Universality in solar flare and earthquake occurrence'', Phys. Rev. Lett. 96, 051102 (2006)

  • M. Pica Ciamarra, M.D. De Vizia, A. Fierro, M. Tarzia, A.Coniglio, and M. Nicodemi,"Granular Species Segregation under vertical Tapping: Effects of Size, Density, Friction, and Shaking Amplitude", Phys. Rev. Lett. 96, 58001 (2006)

  • E. Piegari, V. Cataudella, R. Di Maio, L. Milano, and M. Nicodemi, "A cellular automaton for the factor of safety field in landslides modeling'', Geophys. Res. Lett. 33, L01403 (2006)

  • M. Tarzia, A. Fierro, M. Nicodemi, M. Pica Ciamarra, A. Coniglio, "Size segregation in granular media induced by phase transition'', Phys. Rev. Lett. 95, 078001 (2005)

  • M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, "Shear instabilities in granular mixtures'',  Phys. Rev. Lett. 94, 188001 (2005)

  • P. Richard, M. Nicodemi, R. Delannay, P. Ribiere, D. Bideau, "Slow relaxation and compaction of granular systems'', Nature Materials 4, 121 (2005)

  • A. Caiazzo, A. Coniglio, and M. Nicodemi, "Glass glass transition and new dynamical singularity points in an analytically solvable p-spin glass like model", Phys. Rev. Lett. 93, 215701 (2004)

  • M. Tarzia, A. Fierro, M. Nicodemi, A. Coniglio, "Segregation in fluidized versus tapped packs",  Phys. Rev. Lett. 93, 198002 (2004)

  • S.T. Bramwell, K. Christensen, J.-Y. Fortin, P.C.W. Holdsworth, H.J. Jensen, S. Lise, J. Lopez, M. Nicodemi, J.-F.Pinton, M. Sellitto, Phys. Rev. Lett. 89, 208902 (2002)

  • M. Nicodemi and H.J. Jensen, Phys. Rev. Lett. 87, 259702 (2001)

  • S.T. Bramwell, K. Christensen, J.-Y. Fortin, P.C.W. Holdsworth, H.J. Jensen, S. Lise, J. Lopez, M. Nicodemi, J.-F.Pinton, M. Sellitto, Phys. Rev. Lett. 87, 188902 (2001)

  • H.J. Jensen and M. Nicodemi, "Creep of superconducting vortices in the limit of vanishing temperature: A fingerprint of off-equilibrium dynamics'', Phys. Rev. Lett. 86, 4378 (2001)

  • S.T. Bramwell, K. Christensen, J.-Y. Fortin, P.C.W. Holdsworth, H.J. Jensen, S. Lise, J. Lopez, M. Nicodemi, J.-F.Pinton, M. Sellitto, "Universal Fluctuations in Correlated Systems'', Phys. Rev. Lett. 84, 3744 (2000)

  • F. Corberi, M. Nicodemi, M. Piccioni, A. Coniglio, "Off-equilibrium dynamics in a singular diffusion model'', Phys. Rev. Lett. 83, 5054 (1999)

  • M. Nicodemi, "Dynamical response functions in models of vibrated granular media'', Phys. Rev. Lett. 82, 3734 (1999)

  • M. Nicodemi and A. Coniglio,  "Aging in out of equilibrium dynamics of models for granular media", Phys. Rev. Lett. 82, 916 (1999)

  • M. Nicodemi, "Force correlations and arches formation in granular assemblies", Phys. Rev. Lett. 80, 1340 (1998)

  • E. Caglioti, H.J. Herrmann, V. Loreto, M. Nicodemi, "A Tetris-like Model for the Compaction of Dry Granular Media'', Phys. Rev. Lett. 79, 1575 (1997)