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List of works by Mario Nicodemi

8-oxodG accumulation within super-enhancers marks fragile CTCF-mediated chromatin loops

scientific article published on 01 April 2022

A Polymer Physics Investigation of the Architecture of the Murine Orthologue of the 7q11.23 Human Locus

scientific article

A model of the large-scale organization of chromatin

scientific article published on April 2013

A novel approach to simulate gene-environment interactions in complex diseases

scientific article published on 5 January 2010

A polymer model explains the complexity of large-scale chromatin folding

scientific article published on 19 June 2013

A stochastic model dissects cell states in biological transition processes

scientific article published on 17 January 2014

A thermodynamic switch for chromosome colocalization

scientific article

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.

scientific article published on 24 April 2017

Aggregation of fibrils and plaques in amyloid molecular systems

scientific article published on 12 October 2009

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

scientific article published on 17 May 2021

Challenges and guidelines toward 4D nucleome data and model standards

scientific article published on 27 September 2018

Colocalization of Multiple DNA Loci: A Physical Mechanism ⬇️

scientific article published on November 20, 2012

Complex multi-enhancer contacts captured by genome architecture mapping.

scientific article published on 8 March 2017

Complexity of chromatin folding is captured by the strings and binders switch model

scientific article

Computational approaches from polymer physics to investigate chromatin folding

scientific article published on 08 February 2020

Conformation regulation of the X chromosome inactivation center: a model

scientific article

Creep of superconducting vortices in the limit of vanishing temperature: a fingerprint of off-equilibrium dynamics

scientific article published on 01 May 2001

Critical behavior and axis defining symmetry breaking in Hydra embryonic development

scientific article published on 10 April 2012

Critical clusters and efficient dynamics for frustrated spin models

scientific article published on 01 March 1994

DNA loci cross-talk through thermodynamics

scientific article published on 16 September 2009

Density fluctuations in a model for vibrated granular media

scientific article published on 01 June 1999

Diffusion-based DNA target colocalization by thermodynamic mechanisms ⬇️

scientific article published on 01 November 2010

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

scientific article published on 27 September 2018

Dynamic membrane patterning, signal localization and polarity in living cells.

scientific article published on 07 January 2015

Dynamically induced effective interaction in periodically driven granular mixtures

scientific article published on 19 July 2006

Dynamics and thermodynamics of the spherical frustrated Blume-Emery-Griffiths model

scientific article published on 02 October 2002

Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation

scientific article published on 22 June 2016

Extrusion without a motor: a new take on the loop extrusion model of genome organization. ⬇️

scientific article published on 4 January 2018

Finite driving rate and anisotropy effects in landslide modeling

scientific article published on 21 February 2006

Flow, ordering, and jamming of sheared granular suspensions

scientific article published on 19 February 2008

Glass-glass transition and new dynamical singularity points in an analytically solvable p-spin glasslike model

scientific article published on 15 November 2004

Granular dynamics, jamming, rheology and instabilities

scientific article published on 01 March 2007

Granular packs under vertical tapping: structure evolution, grain motion, and dynamical heterogeneities

scientific article published on 23 February 2007

Granular species segregation under vertical tapping: effects of size, density, friction, and shaking amplitude

scientific article published on 08 February 2006

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.

scientific article published on 23 December 2015

Jamming phase diagram for frictional particles

scientific article published on 28 October 2011

Jamming transition in granular media: a mean-field approximation and numerical simulations

scientific article published on 28 June 2005

Mechanics and dynamics of X-chromosome pairing at X inactivation

scientific article

Models of chromosome structure

scientific article

Models of polymer physics for the architecture of the cell nucleus

scientific article published on 19 December 2018

Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin

scientific article published on 6 March 2018

Nonequilibrium Chromosome Looping via Molecular Slip Links

scientific article published on 26 September 2017

Peak effect in a driven lattice gas model

scientific article published on 11 April 2003

Percolation and cluster Monte Carlo dynamics for spin models

scientific article published on 01 July 1996

Performance of genetic programming to extract the trend in noisy data series

Phenomenology and theory of horizontally oscillated granular mixtures

scientific article published on 21 February 2007

Physical mechanisms behind the large scale features of chromatin organization

scientific article

Polymer Physics of the Large-Scale Structure of Chromatin

scientific article published in January 2016

Polymer models of chromatin organization

scientific article published on 20 June 2013

Polymer models of the hierarchical folding of the Hox-B chromosomal locus

scientific article published on 4 October 2016

Polymer models of the organization of chromosomes in the nucleus of cells

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

scientific article published on 03 July 2020

Polymer physics of chromosome large-scale 3D organisation

scientific article published on 13 July 2016

Polymer physics predicts the effects of structural variants on chromatin architecture

scientific article published on 16 April 2018

Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus

Predicting chromatin architecture from models of polymer physics

scientific article published on 9 January 2017

Preformed chromatin topology assists transcriptional robustness of Shh during limb development

scientific article published on 30 May 2019

Probability distribution of inherent states in models of granular media and glasses

scientific article published on 01 November 2002

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

scientific article published on 04 January 2021

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.

scientific article published on 16 October 2017

Segregation in fluidized versus tapped packs

scientific article published on 02 November 2004

Self-assembly and DNA binding of the blocking factor in x chromosome inactivation

scientific article

Shear instabilities in granular mixtures

scientific article published on 11 May 2005

Shear- and vibration-induced order-disorder transitions in granular media

scientific article published in December 2007

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

scientific article published on 29 October 2018

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation

scientific article published on 12 May 2016

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

scientific article

Size segregation in granular media induced by phase transition

scientific article published on 12 August 2005

Slow relaxation and compaction of granular systems

scientific article

Stochastic transitions and jamming in granular pipe flow

scientific article published on 30 March 2011

Structure of the human chromosome interaction network

scientific article published on 15 November 2017

Symmetry breaking mechanism for epithelial cell polarization.

scientific article

Symmetry-breaking model for X-chromosome inactivation

scientific article published on 7 March 2007

The colocalization transition of homologous chromosomes at meiosis

scientific article published on 17 June 2008

Thermodynamic pathways to genome spatial organization in the cell nucleus

scientific article published on March 2009

Thermodynamics and statistical mechanics of dense granular media

scientific article published on 13 October 2006

Thermodynamics and statistical mechanics of frozen systems in inherent states

scientific article published on 10 December 2002

Universal Fluctuations in Correlated Systems

scientific article

Universality in solar flare and earthquake occurrence

scientific article published on 6 February 2006

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