Biological Theoretical Physics




 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)
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 Com. 11, 3289 (2020).
K. Nass, L. Redecke, M. Perbandt, O. Yefanov, M. Klinge, R. Koopmann, ... & J.M. Lahey-Rudolph, In cell crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors, Nature Com. 11, 1 (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).
J. Redolfi, et al., DamC reveals principles of chromatin folding in vivo without crosslinking and ligation, Nature Str. Mol. Biol. 26 , 471 (2019).
M. Russo, G. Crisafulli, A. Sogari, N. M. Reilly, S. Arena, S. Lamba, A. Bartolini, V. Amodio, A; Magrì, L. Novara, I. Sarotto, Z. D. Nagel, C. G. Piett, A. Amatu, A. Sartore-Bianchi, S. Siena, A. Bertotti, L. Trusolino, M. Corigliano, M. Gherardi, M. Cosentino Lagomarsino, F. Di Nicolantonio, A. Bardelli. Adaptive mutability of colorectal cancers in response to targeted therapies. Science 366 6472, 1473-1480 (2019)
C. Cadart and L. Venkova, P. Recho, M. Cosentino Lagomarsino, M. Piel. The physics of cell-size regulation across timescales. Nature Physics 15, 993-1004 (2019). 
L. Cantini, M. Caselle. Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data. Nature Sci. Rep. 23, 337 (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).
M.J. Akhunzada, F. D’Autilia, B. Chandramouli, N. Bhattacharjee, A. Catte, R. Di Rienzo, F. Cardarelli, G. Brancato, Interplay between lipid lateral diffusion, dye concentration and membrane permeability unveiled by a combined spectroscopic and computational study of a model lipid bilayer, Nature Sci. Rep. 9, 1508 (2019). 
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).
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).
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.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). 
A. De Candia, A. Fierro, A. Coniglio, Scaling and universality in glass transition, Nature Sci. Rep. 11, 1 (2016). 
I. Diez et al., A novel brain partition highlights the modular skeleton shared by structure and function, Nature Sci. Rep. 5, 10532, (2015). 
S. a Beccara, L. Fant, P. Faccioli, Variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent, Phys. Rev. Lett. 114, 098103 (2015). 


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