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1. Full Text Complexity of chromatin folding is captured by the strings and binders switch model
by Mariano Barbieri and Mita Chotalia and James Fraser and Liron-Mark Lavitas and Josée Dostie and Ana Pombo and Mario Nicodemi
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2012, Volume 109, Issue 40, pp. 16173 - 16178
Chromatin has a complex spatial organization in the cell nucleus that serves vital functional purposes. A variety of chromatin folding conformations has been... 
Chromatin | Architecture | Architectural models | Genomics | Cell lines | Genomes | Fractals | Polymers | Chromosomes | Modeling | Long-range chromatin interactions | Genome architecture | Genome organization | Monte Carlo simulations | Fluorescence in situ hybridization | MULTIDISCIPLINARY SCIENCES | CHROMOSOME TERRITORIES | TRANSCRIPTION | genome architecture | GENOME | PRINCIPLES | fluorescence in situ hybridization | ORGANIZATION | long-range chromatin interactions | NUCLEI | INTERPHASE CHROMOSOMES | genome organization | COLOCALIZATION | SEQUENCE | ARCHITECTURE | Models, Chemical | Gene Expression Regulation - genetics | Computer Simulation | Genome - genetics | In Situ Hybridization, Fluorescence | Monte Carlo Method | Chromatin - chemistry | Chromatin Assembly and Disassembly - physiology | Monte Carlo method | Models | Research | Properties | Protein folding | Biological Sciences
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2. Full Text Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations
by Dellino, Gaetano Ivan and Palluzzi, Fernando and Chiariello, Andrea Maria and Piccioni, Rossana and Bianco, Simona and Furia, Laura and De Conti, Giulia and Bouwman, Britta A M and Melloni, Giorgio and Guido, Davide and Giacò, Luciano and Luzi, Lucilla and Cittaro, Davide and Faretta, Mario and Nicodemi, Mario and Crosetto, Nicola and Pelicci, Pier Giuseppe
Nature genetics, ISSN 1061-4036, 06/2019, Volume 51, Issue 6, pp. 1011 - 1023
It is not clear how spontaneous DNA double-strand breaks (DSBs) form and are processed in normal cells, and whether they predispose to cancer-associated... 
Neoplasms - metabolism | Promoter Regions, Genetic | RNA Splice Sites | Introns | Cells, Cultured | Etoposide - pharmacology | Genetic Loci | RNA Polymerase II - metabolism | DNA Breaks, Double-Stranded | Topoisomerase Inhibitors - pharmacology | Animals | Flow Cytometry | Enhancer Elements, Genetic | Neoplasms - genetics | DNA Repair | Transcription Initiation Site | Fluorescent Antibody Technique | Cell Line, Tumor | Gene Expression Regulation, Neoplastic - drug effects | Genomics - methods | Neoplasms - pathology | Genetic aspects | Translocation (Genetics) | Analysis | Cancer | Chromatin | Yeast | DNA damage | Genomes | DNA-directed RNA polymerase | Cell cycle | DNA methylation | Bioinformatics | Deoxyribonucleic acid--DNA | Growth conditions | Translocation | Breakpoints | Pol II | RNA polymerase | Ribonucleic acid--RNA | Gene expression | Loci | Polymerase | Enhancers | Chromosome translocations | Stem cells | Quality control | RNA polymerase II
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3. Full Text Models of chromosome structure
by Nicodemi, Mario and Pombo, Ana
Current Opinion in Cell Biology, ISSN 0955-0674, 2014, Volume 28, Issue 1, pp. 90 - 95
Understanding the mechanisms that control chromosome folding in the nucleus of eukaryotes and their contribution to gene regulation is a key open issue in... 
Internal Medicine | NUCLEI | TRANSLOCATIONS | GENOME ARCHITECTURE | DNA | TERRITORIES | TRANSCRIPTION | SITES | SWITCH | SPATIAL-ORGANIZATION | PRINCIPLES | CELL BIOLOGY | Animals | Cell Nucleus - genetics | Chromosomes - genetics | Humans | Models, Molecular | Polymers - chemistry | Cell Nucleus - chemistry | Chromosomes - chemistry | Chromosome Structures | Chromosomes | Analysis | Models
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4. Full Text Complex multi-enhancer contacts captured by genome architecture mapping
by Beagrie, Robert A and Scialdone, Antonio and Schueler, Markus and Kraemer, Dorothee C. A and Chotalia, Mita and Xie, Sheila Q and Barbieri, Mariano and De Santiago, Inês and Lavitas, Liron-Mark and Branco, Miguel R and Fraser, James and Dostie, Josée and Game, Laurence and Dillon, Niall and Edwards, Paul A. W and Nicodemi, Mario and Pombo, Ana
Nature, ISSN 0028-0836, 03/2017, Volume 543, Issue 7646, pp. 519 - 524
The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and... 
RNA-POLYMERASE-II | ORGANIZATION | MULTIDISCIPLINARY SCIENCES | EMBRYONIC STEM-CELLS | HI-C DATA | GENES | TRANSCRIPTION ELONGATION | CHROMOSOME CONFORMATION CAPTURE | CHROMATIN INTERACTIONS | DOMAINS | REVEALS | Chromatin - metabolism | Epigenesis, Genetic | Genome - genetics | Male | Mouse Embryonic Stem Cells - cytology | Chromosome Mapping | Sequence Analysis, DNA | Mouse Embryonic Stem Cells - metabolism | Animals | Enhancer Elements, Genetic - genetics | Mice | Models, Genetic | Transcription, Genetic - genetics | Chromatin - genetics | Chromatin - chemistry | Nucleotide sequencing | Genetic transcription | Observations | Methods | DNA sequencing | Datasets | Lasers | Gene loci | Genomes | RNA polymerase | Deoxyribonucleic acid--DNA
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5. 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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6. Unifying concepts in granular media and glasses
by Coniglio, Antonio and Fierro, Annalisa and Herrmann, Hans and Nicodemi, Mario
2004, ISBN 0444516077, viii, 223
Deep connections are emerging in the physics of non-thermal systems,such as granular media, and other "complex systems" such as glass formers, spin glasses,... 
Spin glasses | Granular materials | Glass
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7. Full Text Slow relaxation and compaction of granular systems
by Richard, Patrick and Nicodemi, Mario and Delannay, Renaud and Ribière, Philippe and Bideau, Daniel
Nature Materials, ISSN 1476-1122, 2005, Volume 4, Issue 2, pp. 121 - 128
Granular materials are of substantial importance in many industrial and natural processes, yet their complex behaviours, ranging from mechanical properties of... 
STATISTICAL-MECHANICS | PACKINGS | PHYSICS, CONDENSED MATTER | PHYSICS, APPLIED | MATERIALS SCIENCE, MULTIDISCIPLINARY | CHEMISTRY, PHYSICAL | MODEL | SEGREGATION | GLASSES | MIXTURES | POWDERS | INHERENT STATES | DYNAMICS | MEDIA | Condensed Matter | Materials Science | Statistical Mechanics | Physics | Other
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8. 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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9. 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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10. 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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11. 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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12. Full Text Thermodynamic Pathways to Genome Spatial Organization in the Cell Nucleus
by Nicodemi, Mario and Prisco, Antonella
Biophysical Journal, ISSN 0006-3495, 2009, Volume 96, Issue 6, pp. 2168 - 2177
The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to... 
DNA-BINDING | GLOBIN LOCUS REQUIRES | BIOPHYSICS | INTERPHASE CHROMOSOMES | CHROMATIN | COLOCALIZATION | TRANSCRIPTION | TERRITORIES | GENE-EXPRESSION | HETEROCHROMATIN PROTEIN-1 | MODEL | Thermodynamics | DNA - chemistry | Models, Biological | Computer Simulation | Models, Molecular | Cell Nucleus - chemistry | Chromosomes - chemistry | Genome | Nucleic Acid Conformation | Binding Sites | Monte Carlo Method | Sects | Computer-generated environments | Computer simulation | Analysis | Genes | Genomics | Physiological aspects | Binding proteins | Protein binding | Binding | Architecture | Deoxyribonucleic acid | Organizations | Switches | Genomes | Chromosomes | Nuclei | Biophysical Theory and Modeling
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13. 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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