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1. Full Text Models of polymer physics for the architecture of the cell nucleus
by Esposito, Andrea and Annunziatella, Carlo and Bianco, Simona and Chiariello, Andrea M and Fiorillo, Luca and Nicodemi, Mario
Wiley Interdisciplinary Reviews: Systems Biology and Medicine, ISSN 1939-5094, 07/2019, Volume 11, Issue 4, pp. e1444 - n/a
The depth and complexity of data now available on chromosome 3D architecture, derived by new technologies such as Hi‐C, have triggered the development of... 
computational biology | chromatin | polymer physics | TOPOLOGY | MEDICINE, RESEARCH & EXPERIMENTAL | COMPLEX | CHROMOSOMAL DOMAINS | PRINCIPLES | PHASE-SEPARATION | ORGANIZATION | 3D GENOME | DYNAMICS | BINDING | Chromatin | Architecture | Computation | Polymer physics | Computer applications | Extrusion | Nuclei (cytology) | New technology | Polymers | Binders | Chromosomes | Physics
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2. Full Text Polymer physics of chromosome large-scale 3D organisation
by Chiariello, Andrea M and Annunziatella, Carlo and Bianco, Simona and Esposito, Andrea and Nicodemi, Mario
Scientific Reports, ISSN 2045-2322, 07/2016, Volume 6, Issue 1, p. 29775
Chromosomes have a complex architecture in the cell nucleus, which serves vital functional purposes, yet its structure and folding mechanisms remain still... 
MOLECULAR-DYNAMICS | INTERPHASE CHROMOSOMES | CHROMATIN DOMAINS | MULTIDISCIPLINARY SCIENCES | MODEL | REGULATORY LANDSCAPE | PRINCIPLES | GENOME ORGANIZATION | Chromosomes, Human - chemistry | SOX9 Transcription Factor - metabolism | Chromatin - metabolism | Thermodynamics | Animals | Humans | Mice | SOX9 Transcription Factor - chemistry | Chromosomes, Human - metabolism | Genetic Loci | Chromatin - chemistry
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3. Full Text Structure of the human chromosome interaction network
by Sarnataro, Sergio and Chiariello, Andrea M and Esposito, Andrea and Prisco, Antonella and Nicodemi, Mario
PLoS ONE, ISSN 1932-6203, 11/2017, Volume 12, Issue 11, p. e0188201
New Hi-C technologies have revealed that chromosomes have a complex network of spatial contacts in the cell nucleus of higher organisms, whose organisation is... 
CELL-NUCLEUS | 3D GENOME | CONTACT MAPS | GENOME ARCHITECTURE | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | DYNAMICS | SEGREGATION | SPATIAL-ORGANIZATION | DOMAINS | GRANULAR MEDIA | Physiological aspects | Research | Human chromosomes | Structure | Territory | Spatial discrimination | Nuclear electric power generation | Homology | Genomes | Gene expression | Nuclei | Physics | Microscopy | Epigenetics | Nuclei (cytology) | Polymers | Chromosomes | Deoxyribonucleic acid--DNA | Electric power distribution | Deoxyribonucleic acid | DNA
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4. Full Text Predicting chromatin architecture from models of polymer physics
by Bianco, Simona and Chiariello, Andrea M and Annunziatella, Carlo and Esposito, Andrea and Nicodemi, Mario
Chromosome Research, ISSN 0967-3849, 3/2017, Volume 25, Issue 1, pp. 25 - 34
We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact... 
Life Sciences | Human Genetics | Brownian motion | Stochastic analysis | Molecular dynamics simulation | Classical statistical mechanics | Random processes | Chromosomes | Fluctuation phenomena | Cell Biology | Animal Genetics and Genomics | Plant Genetics & Genomics | HUMAN-CHROMOSOMES | 3D ORGANIZATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTION | REGIONS | GENETICS & HEREDITY | TOPOLOGICAL DOMAINS | BINDING | GENOME ORGANIZATION | Chromatin - ultrastructure | Chromosomes - ultrastructure | Animals | Epigenomics | Humans | Models, Molecular | Polymers - chemistry | Chromatin | Genetic disorders | Analysis | Genes | Stochastic processes | Molecular dynamics | Models | Polymer industry | Polymers | Gene expression | Simulation | Physics
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5. Full Text Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation
by Fraser, James and Ferrai, Carmelo and Chiariello, Andrea M and Schueler, Markus and Rito, Tiago and Laudanno, Giovanni and Barbieri, Mariano and Moore, Benjamin L and Kraemer, Dorothee CA and Aitken, Stuart and Xie, Sheila Q and Morris, Kelly J and Itoh, Masayoshi and Kawaji, Hideya and Jaeger, Ines and Hayashizaki, Yoshihide and Carninci, Piero and Forrest, Alistair RR and Semple, Colin A and Dostie, Josée and Pombo, Ana and Nicodemi, Mario and FANTOM Consortium and The FANTOM Consortium
Molecular Systems Biology, ISSN 1744-4292, 12/2015, Volume 11, Issue 12, pp. 852 - n/a
Mammalian chromosomes fold into arrays of megabase‐sized topologically associating domains (TADs), which are arranged into compartments spanning multiple... 
polymer modelling | chromosome architecture | chromatin contacts | epigenetics | gene expression | Animals | Epigenesis, Genetic | Cells, Cultured | Gene Expression Regulation | Chromatin Assembly and Disassembly | Mouse Embryonic Stem Cells - cytology | Neurons - cytology | Transcription, Genetic | Cell Differentiation | Chromosomes - chemistry | Mice | Chromatin - chemistry | Chromatin | Genomes | Cellular biology | Gene expression | Chromosomes | Substructures | Trees | Transcription | Neurons | Differentiation (biology) | Innovations | Cell division | Mammals | Structural hierarchy | Datasets | Domains | Stem cells | Packaging | Folding | Deoxyribonucleic acid--DNA
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6. Full Text The scaling features of the 3D organization of chromosomes are highlighted by a transformationà laKadanoff of Hi-C data
by Chiariello, Andrea M and Bianco, Simona and Annunziatella, Carlo and Esposito, Andrea and Nicodemi, Mario
EPL (Europhysics Letters), ISSN 0295-5075, 11/2017, Volume 120, Issue 4, p. 40004
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7. Full Text Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis
by Kragesteen, Bjørt K and Spielmann, Malte and Paliou, Christina and Heinrich, Verena and Schöpflin, Robert and Esposito, Andrea and Annunziatella, Carlo and Bianco, Simona and Chiariello, Andrea M and Jerković, Ivana and Harabula, Izabela and Guckelberger, Philine and Pechstein, Michael and Wittler, Lars and Chan, Wing-Lee and Franke, Martin and Lupiáñez, Darío G and Kraft, Katerina and Timmermann, Bernd and Vingron, Martin and Visel, Axel and Nicodemi, Mario and Mundlos, Stefan and Andrey, Guillaume
Nature Genetics, ISSN 1061-4036, 10/2018, Volume 50, Issue 10, pp. 1463 - 1473
The regulatory specificity of enhancers and their interaction with gene promoters is thought to be controlled by their sequence and the binding of... 
TRANSFORMATION | PELVIC REDUCTION | DETERMINES | GENETICS & HEREDITY | LANDSCAPES | PITX1 | DOMAINS | EXPRESSION | GENOME | HINDLIMB | PRINCIPLES | Paired Box Transcription Factors - genetics | Chromatin - metabolism | Morphogenesis - genetics | Embryo, Mammalian | Forelimb - embryology | Molecular Conformation | Gene Expression Regulation, Developmental - genetics | Paired Box Transcription Factors - physiology | Chromatin Assembly and Disassembly - genetics | Mice, Transgenic | DNA - metabolism | Forelimb - metabolism | DNA - chemistry | Animals | CRISPR-Cas Systems | Hindlimb - embryology | Enhancer Elements, Genetic - physiology | Mice | Nucleic Acid Conformation | Chromatin - genetics | Hindlimb - metabolism | Chromatin - chemistry | Morphogenesis | Chromatin | Research | Health aspects | Extremities (Anatomy) | Transcription factors | Transformation | Genomes | Gene expression | Enhancers | Polymer melts | Animal tissues | Rodents | Stem cells | Pituitary gland | Sensors | Evolution & development | Three dimensional models | Arm | Conformation
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8. Full Text Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin
by Annunziatella, Carlo and Chiariello, Andrea M and Esposito, Andrea and Bianco, Simona and Fiorillo, Luca and Nicodemi, Mario
Methods, ISSN 1046-2023, 06/2018, Volume 142, pp. 81 - 88
In recent years interest has grown on the applications of polymer physics to model chromatin folding in order to try to make sense of the complexity of... 
3D GENOME | GENOME ARCHITECTURE | CHROMOSOMAL DOMAINS | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOCHEMICAL RESEARCH METHODS | SPATIAL-ORGANIZATION | BINDING | PRINCIPLES | Humans | Genetic Loci - genetics | Molecular Dynamics Simulation | Animals | Cell Nucleus - metabolism | Cell Nucleus - genetics | Polymers - chemistry | Mice | Models, Genetic | Genome | Chromatin - genetics | SOX9 Transcription Factor - genetics | Chromatin - chemistry | Case studies | Molecular dynamics | Chromatin | Models | Polymers | Analysis
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9. Full Text Polymer physics predicts the effects of structural variants on chromatin architecture
by Bianco, Simona and Lupiáñez, Darío G and Chiariello, Andrea M and Annunziatella, Carlo and Kraft, Katerina and Schöpflin, Robert and Wittler, Lars and Andrey, Guillaume and Vingron, Martin and Pombo, Ana and Mundlos, Stefan and Nicodemi, Mario
Nature Genetics, ISSN 1061-4036, 05/2018, Volume 50, Issue 5, pp. 662 - 667
Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects... 
ORGANIZATION | MOLECULAR-DYNAMICS | HUMAN GENOME | HI-C | COMPLEXITY | GENETICS & HEREDITY | CHROMOSOME CONFORMATION | GENERATION | DOMAINS | PRINCIPLES | REVEALS | Chromatin | Genes | Genomics | Models | Genomes | Polymer industry | Comparative analysis | Gene expression | Polymers | Annealing | EphA4 protein | Loci | Physics | Limb buds | Domains | Polymer melts | Rewiring | Polymer physics | Predictions | Stem cells | Fibroblasts | Mathematical models | Three dimensional models | Chromosomes | Folding | Conformation
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10. Full Text Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells
by Barbieri, Mariano and Xie, Sheila Q and Torlai Triglia, Elena and Chiariello, Andrea M and Bianco, Simona and De Santiago, Inês and Branco, Miguel R and Rueda, David and Nicodemi, Mario and Pombo, Ana
Nature Structural and Molecular Biology, ISSN 1545-9993, 06/2017, Volume 24, Issue 6, pp. 515 - 524
Gene expression states influence the 3D conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine... 
RNA-POLYMERASE-II | HUMAN NUCLEI | CHROMATIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | CTCF | SPATIAL-ORGANIZATION | CELL BIOLOGY | HUMAN GENOME | BIOPHYSICS | TRANSCRIPTION FACTORIES | HISTONE H1 | IN-VIVO | ES CELLS | Chromatin - metabolism | Promoter Regions, Genetic | In Situ Hybridization, Fluorescence | DNA - metabolism | Genetic Loci | Embryonic Stem Cells - physiology | Transcription Factors - metabolism | Microscopy, Confocal | DNA - chemistry | Animals | Computer Simulation | Fluorescent Antibody Technique | Protein Binding | Mice | Nucleic Acid Conformation | Single-Cell Analysis | Transcription factors | Models | Gene expression | Properties | Protein folding
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11. Full Text Preformed chromatin topology assists transcriptional robustness of Shh during limb development
by Paliou, C and Guckelberger, P and Schopflin, R and Heinrich, V and Esposito, A and Chiariello, AM and Bianco, S and Annunziatella, C and Helmuth, J and Haas, S and Jerkovic, I and Brieske, N and Wittler, L and Timmermann, B and Nicodemi, M and Vingron, M and Mundlos, S and Andrey, G
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, ISSN 0027-8424, 06/2019, Volume 116, Issue 25, pp. 12390 - 12399
Long-range gene regulation involves physical proximity between enhancers and promoters to generate precise patterns of gene expression in space and time.... 
limb | development | READ ALIGNMENT | MULTIDISCIPLINARY SCIENCES | ENHANCER | REGULATORY LANDSCAPES | GENOME | ORGANIZATION | ENCYCLOPEDIA | genetics | gene regulation | DNA ELEMENTS | 3D genome | GENERATION | DOMAINS | EXPRESSION | Chromatin | Genetic aspects | Genetic transcription | Developmental biology | Genes | Genomics | Enhancers | Phenotypes | Clonal deletion | Transcription | Hedgehog protein | Gene regulation | Deletion | Activation | Topology | Gene expression | Binding sites
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12. Full Text Inference of chromosome 3D structures from GAM data by a physics computational approach
by Fiorillo, Luca and Bianco, Simona and Chiariello, Andrea M and Barbieri, Mariano and Esposito, Andrea and Annunziatella, Carlo and Conte, Mattia and Corrado, Alfonso and Prisco, Antonella and Pombo, Ana and Nicodemi, Mario
Methods, ISSN 1046-2023, 10/2019
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13. Full Text The scaling features of the 3D organization of chromosomes are highlighted by a transformation a la Kadanoff of Hi-C data
by Chiariello, Andrea M and Bianco, Simona and Annunziatella, Carlo and Esposito, Andrea and Nicodemi, Mario
EPL, ISSN 0295-5075, 11/2017, Volume 120, Issue 4
Technologies such as Hi-C and GAM have revealed that chromosomes are not randomly folded into the nucleus of cells, but are composed by a sequence of contact... 
ARCHITECTURE | MODELS | PHYSICS, MULTIDISCIPLINARY | DOMAINS | PRINCIPLES | GENOME ORGANIZATION
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14. Full Text Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains
by Oudelaar, A. Marieke and Davies, James O. J and Hanssen, Lars L. P and Telenius, Jelena M and Schwessinger, Ron and Liu, Yu and Brown, Jill M and Downes, Damien J and Chiariello, Andrea M and Bianco, Simona and Nicodemi, Mario and Buckle, Veronica J and Dekker, Job and Higgs, Douglas R and Hughes, Jim R
Nature Genetics, ISSN 1061-4036, 12/2018, Volume 50, Issue 12, pp. 1744 - 1751
The promoters of mammalian genes are commonly regulated by multiple distal enhancers, which physically interact within discrete chromatin domains. How such... 
ORGANIZATION | COMPLEXITY | RESOLUTION | GENETICS & HEREDITY | HYPERSENSITIVE SITES | COHESIN | PHENOTYPIC ROBUSTNESS | IDENTIFICATION | INACTIVE X-CHROMOSOME | GENOME | PRINCIPLES | Chromatin - metabolism | Promoter Regions, Genetic | Mice, Inbred C57BL | Regulatory Sequences, Nucleic Acid | Cells, Cultured | Binding Sites - genetics | Genetic Loci | Linkage Disequilibrium | Transcription Factors - metabolism | Globins - genetics | Animals | Enhancer Elements, Genetic | Gene Expression Regulation, Developmental | Base Sequence | Alleles | Female | Mice | Chromatin - genetics | Chromatin - chemistry | Chromatin | Research | Gene expression | Genetic regulation | Genetic epistasis | Animal genetics | Genes | Analysis | Genomes | Regulatory sequences | Parameter identification | Promoters | Domains | Enhancers | Stem cells | Hubs | Chromosomes | Boundary element method | Binding sites | Conformation
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15. Full Text Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells
by Bianco, Simona and Annunziatella, Carlo and Andrey, Guillaume and Chiariello, Andrea M and Esposito, Andrea and Fiorillo, Luca and Prisco, Antonella and Conte, Mattia and Campanile, Raffaele and Nicodemi, Mario
Cell reports, 08/2019, Volume 28, Issue 6, p. 1574
Complex architectural rearrangements are associated to the control of the HoxD genes in different cell types; yet, how they are implemented in single cells... 
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16. Full Text A polymer physics investigation of the architecture of the murine orthologue of the 7q11.23 human locus
by Chiariello, Andrea M and Esposito, Andrea and Annunziatella, Carlo and Bianco, Simona and Fiorillo, Luca and Prisco, Antonella and Nicodemi, Mario
Frontiers in Neuroscience, ISSN 1662-4548, 10/2017, Volume 11, p. 559
In the last decade, the developments of novel technologies, such as Hi-C or GAM methods, allowed to discover that chromosomes in the nucleus of mammalian cells... 
7q11.23 locus | Chromatin | Neuroscience | Congenital disease | Polymer physics | polymer physics | CHROMOSOMAL DOMAINS | congenital disease | chromatin | SYNDROME REGION | NEUROSCIENCES | PRINCIPLES | ORGANIZATION | CHROMATIN DOMAINS | MODELS | GENOME ARCHITECTURE | DYNAMICS | WILLIAMS-SYNDROME | GRANULAR MEDIA | Embryo cells | Chromosome 7 | Stem cell transplantation | Nervous system | Genomes | Neurodevelopmental disorders | Osteoblasts | Physics | Mammalian cells | Autism | Osteoblastogenesis | Functional morphology | Stem cells | Polymers | Chromosomes | Bone morphogenetic protein 7
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