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1. Full Text Chromosomes Phase Transition to Function
by Nicodemi, Mario and Bianco, Simona
Biophysical journal, ISSN 0006-3495, 08/2020, Volume 119, Issue 4, pp. 724 - 725
Life Sciences & Biomedicine | Biophysics | Science & Technology | Index Medicus
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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 Giaco, 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
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | 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 | Growth conditions | Translocation | Breakpoints | Chromatin | Yeast | DNA damage | Genomes | RNA polymerase | Ribonucleic acid--RNA | Gene expression | DNA-directed RNA polymerase | Loci | Enhancers | Chromosome translocations | Cell cycle | Stem cells | Quality control | DNA methylation | Bioinformatics | Deoxyribonucleic acid--DNA | RNA polymerase II | Index Medicus | Medicin och hälsovetenskap
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3. Full Text Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation
by Conte, Mattia and Fiorillo, Luca and Bianco, Simona and Chiariello, Andrea M and Esposito, Andrea and Nicodemi, Mario
Nature communications, ISSN 2041-1723, 07/2020, Volume 11, Issue 1, pp. 3289 - 3289
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Cohesion | Chromatin | Architecture | Globules | Loci | Physics | Thermodynamics | Molecular modelling | Depletion | Polymer physics | Phase separation | Stochasticity | Cohesin | Polymers | Chromosomes | Folding | Combinatorial analysis | Deoxyribonucleic acid--DNA | Index Medicus
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4. 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
Life Sciences & Biomedicine | Biophysics | Science & Technology | 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 | Eukaryotes | Chromosomes | Deoxyribonucleic acid--DNA | Index Medicus | Binding | Architecture | Deoxyribonucleic acid | Organizations | Switches | Genomes | Nuclei | Biophysical Theory and Modeling
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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, pp. 29775 - 29775
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Chromosomes, Human - chemistry | SOX9 Transcription Factor - metabolism | Chromatin - metabolism | Thermodynamics | Animals | Humans | Mice | SOX9 Transcription Factor - chemistry | Chromosomes, Human - metabolism | Genetic Loci | Chromatin - chemistry | Index Medicus
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6. 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
Internal Medicine | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Animals | Cell Nucleus - genetics | Chromosomes - genetics | Humans | Models, Molecular | Polymers - chemistry | Cell Nucleus - chemistry | Chromosomes - chemistry | Chromosome Structures | Chromosomes | Analysis | Models | Index Medicus
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7. 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 (London), ISSN 0028-0836, 03/2017, Volume 543, Issue 7646, pp. 519 - 524
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | 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 | Index Medicus
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8. 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
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Cell Line | Gene Expression - genetics | Humans | Mice, Inbred C57BL | CCCTC-Binding Factor - genetics | Chromatin Assembly and Disassembly - genetics | Promoter Regions, Genetic - genetics | Animals | Chromosomes - genetics | Receptor, EphA4 - genetics | Polymers - chemistry | Enhancer Elements, Genetic - genetics | Mice | Chromatin - genetics | Chromatin - chemistry | 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 | Index Medicus
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9. 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
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 | Index Medicus
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10. 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
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | 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 | Index Medicus
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