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306 results on '"Nicodemi, M."'

51. Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation (vol 17, 103, 2016)

Author

Proserpio, V, Piccolo, A, Haim-Vilmovsky, L, Kar, G, Lonnberg, T, Svensson, V, Pramanik, J, Natarajan, KN, Zhai, W, Zhang, X, Donati, G, Kayikci, M, Kotar, J, McKenzie, ANJ, Montandon, R, James, KR, Fernandez-Ruiz, D, Heath, WR, Haque, A, Billker, O, Woodhouse, S, Cicuta, P, Nicodemi, M, Teichmann, SA, Proserpio, V, Piccolo, A, Haim-Vilmovsky, L, Kar, G, Lonnberg, T, Svensson, V, Pramanik, J, Natarajan, KN, Zhai, W, Zhang, X, Donati, G, Kayikci, M, Kotar, J, McKenzie, ANJ, Montandon, R, James, KR, Fernandez-Ruiz, D, Heath, WR, Haque, A, Billker, O, Woodhouse, S, Cicuta, P, Nicodemi, M, and Teichmann, SA

Published
2016

53. Comment on 'Universal fluctuations in correlated systems' - Reply

Author

Bramwell ST, Christensen K, Fortin JY, Holdsworth PCW, Jensen HJ, Lise S, Lopez JM, Nicodemi M, Pinton JF, SELLITTO, Mauro, Bramwell, St, Christensen, K, Fortin, Jy, Holdsworth, Pcw, Jensen, Hj, Lise, S, Lopez, Jm, Nicodemi, M, Pinton, Jf, and Sellitto, Mauro

Published
2002

57. A stochastic model dissects cell states in biological transition processes

Author

Armond, JW, Saha, K, Rana, AA, Oates, CJ, Jaenisch, R, Nicodemi, M, Mukherjee, S, Armond, JW, Saha, K, Rana, AA, Oates, CJ, Jaenisch, R, Nicodemi, M, and Mukherjee, S

Abstract

Many biological processes, including differentiation, reprogramming, and disease transformations, involve transitions of cells through distinct states. Direct, unbiased investigation of cell states and their transitions is challenging due to several factors, including limitations of single-cell assays. Here we present a stochastic model of cellular transitions that allows underlying single-cell information, including cell-state-specific parameters and rates governing transitions between states, to be estimated from genome-wide, population-averaged time-course data. The key novelty of our approach lies in specifying latent stochastic models at the single-cell level, and then aggregating these models to give a likelihood that links parameters at the single-cell level to observables at the population level. We apply our approach in the context of reprogramming to pluripotency. This yields new insights, including profiles of two intermediate cell states, that are supported by independent single-cell studies. Our model provides a general conceptual framework for the study of cell transitions, including epigenetic transformations.

Published
2014

58. Single-cell states in the estrogen response of breast cancer cell lines

Author

Casale, FP, Giurato, G, Nassa, G, Armond, JW, Oates, CJ, Corá, D, Gamba, A, Mukherjee, S, Weisz, A, Nicodemi, M, Casale, FP, Giurato, G, Nassa, G, Armond, JW, Oates, CJ, Corá, D, Gamba, A, Mukherjee, S, Weisz, A, and Nicodemi, M

Abstract

Estrogen responsive breast cancer cell lines have been extensively studied to characterize transcriptional patterns in hormone-responsive tumors. Nevertheless, due to current technological limitations, genome-wide studies have typically been limited to population averaged data. Here we obtain, for the first time, a characterization at the single-cell level of the states and expression signatures of a hormone-starved MCF-7 cell system responding to estrogen. To do so, we employ a recently proposed model that allows for dissecting single-cell states from time-course microarray data. We show that within 32 hours following stimulation, MCF-7 cells traverse, most likely, six states, with a faster early response followed by a progressive deceleration. We also derive the genome-wide transcriptional profiles of such single-cell states and their functional characterization. Our results support a scenario where estrogen promotes cell cycle progression by controlling multiple, sequential regulatory steps, whose single-cell events are here identified. © 2014 Casale et al.

Published
2014

59. The Blume-Emery-Griffiths spin glass model

Author

SELLITTO, Mauro, Nicodemi M, Arenzon JJ, Sellitto, Mauro, Nicodemi, M, and Arenzon, Jj

Abstract

The equilibrium properties of the Blume-Emery-Griffiths model with bilinear quenched disorder are studied for the case of attractive as well as repulsive biquadratic interactions. The global phase diagram of the system is calculated in the context of the replica symmetric mean field approximation.

Published
1997

60. Equilibrium properties of the ising frustrated lattice gas

Author

Arenzon JJ, Nicodemi M, SELLITTO, Mauro, Arenzon, Jj, Nicodemi, M, and Sellitto, Mauro

Subjects
Condensed Matter::Strongly Correlated Electrons, Condensed Matter::Disordered Systems and Neural Networks
Abstract

We study the equilibrium properties of an Ising frustrated lattice gas with a mean held replica approach. This model bridges usual Spin Glasses and a version of Frustrated Percolation model, and has proven relevant to describe the glass transition. It shows a rich phase diagram which in a definite limit reduces to the known Sherrington-Kirkpatrick spin glass model.

Published
1996

84. Bramwellet al.Reply

Author

Bramwell, S. T., primary, Christensen, K., additional, Fortin, J.-Y., additional, Holdsworth, P. C. W., additional, Jensen, H. J., additional, Lise, S., additional, López, J. M., additional, Nicodemi, M., additional, Pinton, J.-F., additional, and Sellitto, M., additional

Published
2002
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90. Bramwellet al.Reply

Author

Bramwell, S. T., primary, Christensen, K., additional, Fortin, J.-Y., additional, Holdsworth, P. C. W., additional, Jensen, H. J., additional, Lise, S., additional, López, J. M., additional, Nicodemi, M., additional, Pinton, J.-F., additional, and Sellitto, M., additional

Published
2001
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93. Universal Fluctuations in Correlated Systems

Author

Bramwell, S. T., primary, Christensen, K., additional, Fortin, J.-Y., additional, Holdsworth, P. C. W., additional, Jensen, H. J., additional, Lise, S., additional, López, J. M., additional, Nicodemi, M., additional, Pinton, J.-F., additional, and Sellitto, M., additional

Published
2000
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97. Shear- and vibration-induced order-disorder transitions in granular media.

Author

Ciamarra, M. Pica, Coniglio, A., De Martino, D., and Nicodemi, M.

Subjects
GRANULAR materials, MOLECULAR dynamics, AMPLITUDE modulation, VIBRATION (Mechanics), THERMAL analysis
Abstract

By molecular dynamics simulations we investigate the order-disorder transitions induced in granular media by an applied drive combining vibrations and shear. As the steady state is attained, the pack is found in disordered configurations for comparatively high intensities of the drive; conversely, ordering and packing fractions exceeding the random close packing are found when vibrations and shear are weak. As forcing amplitudes get smaller, we find diverging time scales in the dynamics, as the system enters a jamming region. Under this perspective, our picture supports the intuition that externally applied forcing has, in driven granular media, a role similar to temperature in thermal systems. [ABSTRACT FROM AUTHOR]

Published
2007
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98. Phenomenology and theory of horizontally oscillated granular mixtures.

Author

Ciamarra, M. Pica, Coniglio, A., and Nicodemi, M.

Subjects
GRANULAR materials, THERMAL properties, OSCILLATIONS, PHENOMENOLOGY, PHYSICS
Abstract

We overview the physics of a granular mixture subject to horizontal oscillations, recently investigated via experiments and molecular dynamics simulations. First we discuss the rich phenomenology exhibited by this system, which encompasses both segregation and dynamical instabilities. Then we show that the phenomenology can be explained via an effective interaction approach, by which the driven, non-thermal, granular mixture in mapped into a monodispersed thermal system of particles interacting via an effective potential. After determining the effective interaction we discuss its microscopic origin and investigate how it induces the observed phenomenology. Finally, as much as in thermal fluids, from the effective interaction we derive a Cahn-Hilliard dynamics equation, which appears to capture the essential characteristics of the dynamics of the granular mixture. [ABSTRACT FROM AUTHOR]

Published
2007
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