BIOPHYS
Biophysics
Theoretical physics tools applied to systems of biological interest
Network
SELECTED PUBLICATIONS
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L. Giorgetti, R. Galupa, E. P. Nora, T. Piolot, F. Lam, J. Dekker,
G. Tiana and E. Heard,
Predictive polymer modeling reveals coupled uctuations in chromosome
conformation and trascription,
Cell, 157, 950 (2014)
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A. Riba, C. Bosi, M. El Baroudi, L. Ollino, M. Caselle,
A combination of transcriptional and microRNA regulation improves
the stability of the relative concentrations of target genes.
PLoS Comput Biol. 2014 Feb 27;10(2):e1003490
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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.
P.N.A.S. 109: 16173 (2012)
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D. Marinazzo, M. Pellicoro, G. Wu, L. Angelini, J.M. Cortas, S. Stramaglia,
Information Transfer and Criticality in the Ising Model on the Human
Connectome.
PLOS ONE 9:e93616 (2014)
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V. Minicozzi, R. Chiaraluce, V. Consalvi, C. Giordano, C. Narcisi, P. Punzi, G.C. Rossi, S. Morante,
Computational and experimental casus on beta sheet breakers targeting A 1-40 brils,
J. Biol. Chem.(2014)
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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)
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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)
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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)
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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)
Predictive polymer modeling reveals coupled uctuations in chromosome conformation and trascription,
Cell, 157, 950 (2014)
A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes.
PLoS Comput Biol. 2014 Feb 27;10(2):e1003490
Complexity of chromatin folding is captured by the Strings and Binders Switch model.
P.N.A.S. 109: 16173 (2012)
Information Transfer and Criticality in the Ising Model on the Human Connectome.
PLOS ONE 9:e93616 (2014)
Computational and experimental casus on beta sheet breakers targeting A 1-40 brils,
J. Biol. Chem.(2014)
Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture,
Nature Genetics 50, 662 (2018)
Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells,
Nature Struct. Mol. Bio. 24, 515 (2017)
Nonequilibrium Chromosome Looping via Molecular Slip Links,
Phys. Rev. Lett. 108, 158103 (2017)
Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM), a novel ligation-free approach,
Nature 543, 519 (2017)