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M

Mario Nicodemi

University of Naples Federico II

46H-index
271Paper Count
9.1KCitation Count
Published Papers 53
Publication Date
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Phase separation of ecDNA condensates establishes in-trans contact domains that boost selective MYC regulatory interactions
errNature Communications
IF15.7
err2026-08-05
err0
errOAAI
errMattia Conte; Lana Al Hasani; Tommaso Matteuzzi; Andrea Esposito; Sumanta Kundu; Andrea M. Chiariello; Simona Bianco; Francesca Vercellone; Wenbo Li; Mario Nicodemi
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Physics-Based Modeling of Sparse Single-Cell Hi-C Uncovers Structural and Epigenetic Variability
errInternational Journal of Molecular Sciences
IF4.9
err2026-05-30
err0
errOAAI
errFrancesca Vercellone; Sumanta Kundu; Andrea Esposito; Andrea M. Chiariello; Mattia Conte; Alex Abraham; Andrea Fontana; Florinda Di Pierno; Sougata Guha; Ciro Di Carluccio; Matteo Olimpo; Mario Nicodemi; Francesco Paolo Casale; Simona Bianco
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errSave
Emergent domain segregation in self-interacting polymers explains chromosome 3D conformations in single human cells
errPhysical Review E
IF2.4
err2026-05-01
err0
PREAI
errConte, Mattia; Bianco, Simona; Guha, Sougata; Chiariello, Andrea M.; Esposito, Andrea; Abraham, Alex; Kundu, Sumanta; Vercellone, Francesca; Fontana, Andrea; Di Pierno, Florinda; Di Carluccio, Ciro; Olimpo, Matteo; Nicodemi, Mario
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An integrated view of the structure and function of the human 4D nucleome
errNature
IF48.5
err2025-12-17
err0
errOAAI
errJob Dekker; Betul Akgol Oksuz; Yang Zhang; Ye Wang; Miriam K. Minsk; Shuzhen Kuang; Liyan Yang; Johan H. Gibcus; Nils Krietenstein; Oliver J. Rando; Jie Xu; Derek H. Janssens; Steven Henikoff; Alexander Kukalev; Willemin Andréa; Warren Winick-Ng; Rieke Kempfer; Ana Pombo; Miao Yu; Pradeep Kumar; Liguo Zhang; Andrew S. Belmont; Takayo Sasaki; Tom van Schaik; Laura Brueckner; Daan Peric-Hupkes; Bas van Steensel; Ping Wang; Haoxi Chai; Minji Kim; Yijun Ruan; Ran Zhang; Sofia A. Quinodoz; Prashant Bhat; Mitchell Guttman; Wenxin Zhao; Shu Chien; Yuan Liu; Sergey V. Venev; Dariusz Plewczynski; Ibai Irastorza Azcarate; Dominik Szabó; Christoph J. Thieme; Teresa Szczepińska; Mateusz Chiliński; Kaustav Sengupta; Mattia Conte; Andrea Esposito; Alex Abraham; Ruochi Zhang; Yuchuan Wang; Xingzhao Wen; Qiuyang Wu; Yang Yang; Jie Liu; Lorenzo Boninsegna; Asli Yildirim; Yuxiang Zhan; Andrea Maria Chiariello; Simona Bianco; Lindsay Lee; Ming Hu; Yun Li; R. Jordan Barnett; Ashley L. Cook; Daniel J. Emerson; Claire Marchal; Peiyao Zhao; Peter J. Park; Burak H. Alver; Andrew J. Schroeder; Rahi Navelkar; Clara Bakker; William Ronchetti; Shannon Ehmsen; Alexander D. Veit; Nils Gehlenborg; Ting Wang; Daofeng Li; Xiaotao Wang; Mario Nicodemi; Bing Ren; Sheng Zhong; Jennifer E. Phillips-Cremins; David M. Gilbert; Katherine S. Pollard; Frank Alber; Jian Ma; William S. Noble; Feng Yue
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errSave
Extensive folding variability between homologous chromosomes in mammalian cells
errMOLECULAR SYSTEMS BIOLOGY
IF7.7
err2025-05-06
err0
errOAAI
errIrastorza-Azcarate, Ibai; Kukalev, Alexander; Kempfer, Rieke; Thieme, Christoph J.; Mastrobuoni, Guido; Markowski, Julia; Loof, Gesa; Sparks, Thomas M.; Brookes, Emily; Natarajan, Kedar Nath; Sauer, Stephan; Fisher, Amanda G.; Nicodemi, Mario; Ren, Bing; Schwarz, Roland F.; Kempa, Stefan; Pombo, Ana
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errSave
Loss of structural specificity in 3D genome organization upon viral infection is predicted by polymer physics
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2025-01-02
err1
PREAI
errFontana, Andrea; Bianco, Simona; Tafuri, Fabrizio; Esposito, Andrea; Abraham, Alex; Conte, Mattia; Vercellone, Francesca; Di Pierno, Florinda; Kundu, Sumanta; Guha, Sougata; Di Carluccio, Ciro; Prisco, Antonella; Nicodemi, Mario; Chiariello, Andrea M.
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errSave
Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells
errNATURE COMMUNICATIONS
IF15.7
err2024-05-13
err3
errOAAI
errChiariello, Andrea M.; Abraham, Alex; Bianco, Simona; Esposito, Andrea; Fontana, Andrea; Vercellone, Francesca; Conte, Mattia; Nicodemi, Mario
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errSave
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
errNATURE METHODS
IF32.1
err2023-06-19
err8
errOAAI
errBeagrie, Robert A. A.; Thieme, Christoph J. J.; Annunziatella, Carlo; Baugher, Catherine; Zhang, Yingnan; Schueler, Markus; Kukalev, Alexander; Kempfer, Rieke; Chiariello, Andrea M. M.; Bianco, Simona; Li, Yichao; Davis, Trenton; Scialdone, Antonio; Welch, Lonnie R. R.; Nicodemi, Mario; Pombo, Ana
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errSave
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding
errNATURE COMMUNICATIONS
IF15.7
err2022-07-13
err37
errOAAI
errConte, Mattia; Irani, Ehsan; Chiariello, Andrea M.; Abraham, Alex; Bianco, Simona; Esposito, Andrea; Nicodemi, Mario
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errSave
8-oxodG accumulation within super-enhancers marks fragile CTCF-mediated chromatin loops
errNUCLEIC ACIDS RESEARCH
IF13.1
err2022-03-02
err12
errOAAI
errScala, Giovanni; Gorini, Francesca; Ambrosio, Susanna; Chiariello, Andrea M.; Nicodemi, Mario; Lania, Luigi; Majello, Barbara; Amente, Stefano
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errSave
Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states
errCELL REPORTS
IF6.9
err2022-03-01
err22
errOAAI
errEsposito, Andrea; Bianco, Simona; Chiariello, Andrea M.; Abraham, Alex; Fiorillo, Luca; Conte, Mattia; Campanile, Raffaele; Nicodemi, Mario
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errSave
A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome
errHUMAN GENETICS
IF3.6
err2021-11-25
err3
PREAI
errCinque, Luigia; Micale, Lucia; Manara, Elena; Esposito, Andrea; Palumbo, Orazio; Chiariello, Andrea Maria; Bianco, Simona; Guerri, Giulia; Bertelli, Matteo; Giuffrida, Maria Grazia; Bernardini, Laura; Notarangelo, Angelantonio; Nicodemi, Mario; Castori, Marco
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errSave
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin (vol 18, pg 482, 2021)
errNATURE METHODS
IF32.1
err2021-09-03
err1
errOAAI
errFiorillo, Luca; Musella, Francesco; Conte, Mattia; Kempfer, Rieke; Chiariello, Andrea M.; Bianco, Simona; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Esposito, Andrea; Abraham, Alex; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario
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Physics meets biology: The joining of two forces to further our understanding of cellular function
errMOLECULAR CELL
IF16.6
err2021-08-01
err2
errOAAI
errWang, Michelle D.; Nicodemi, Mario; Dekker, Nynke H.; Gregor, Thomas; Holcman, David; van Oijen, Antoine M.; Manley, Suliana
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errSave
Polymer models are a versatile tool to study chromatin 3D organization
errBIOCHEMICAL SOCIETY TRANSACTIONS
IF4.3
err2021-07-20
err6
PREAI
errEsposito, Andrea; Bianco, Simona; Fiorillo, Luca; Conte, Mattia; Abraham, Alex; Musella, Francesco; Nicodemi, Mario; Prisco, Antonella; Chiariello, Andrea M.
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errSave
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains
errNATURE GENETICS
IF31.8
err2021-05-17
err101
errOAAI
errHuang, Hui; Zhu, Quan; Jussila, Adam; Han, Yuanyuan; Bintu, Bogdan; Kern, Colin; Conte, Mattia; Zhang, Yanxiao; Bianco, Simona; Chiariello, Andrea M.; Yu, Miao; Hu, Rong; Tastemel, Melodi; Juric, Ivan; Hu, Ming; Nicodemi, Mario; Zhuang, Xiaowei; Ren, Bing
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errSave
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin
errNATURE METHODS
IF32.1
err2021-05-07
err36
errOAAI
errFiorillo, Luca; Musella, Francesco; Kempfer, Rieke; Chiariello, Andrea M.; Bianco, Simona; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Esposito, Andrea; Conte, Mattia; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario; Abraham, Alex
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errSave
Physical mechanisms of chromatin spatial organization
errFEBS JOURNAL
IF4.2
err2021-02-22
err13
errOAAI
errChiariello, Andrea M.; Bianco, Simona; Esposito, Andrea; Fiorillo, Luca; Conte, Mattia; Irani, Ehsan; Musella, Francesco; Abraham, Alex; Prisco, Antonella; Nicodemi, Mario
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errSave
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
errNATURE STRUCTURAL & MOLECULAR BIOLOGY
IF10.1
err2021-01-04
err173
errOAAI
errKubo, Naoki; Ishii, Haruhiko; Xiong, Xiong; Bianco, Simona; Meitinger, Franz; Hu, Rong; Hocker, James D.; Conte, Mattia; Gorkin, David; Yu, Miao; Li, Bin; Dixon, Jesse R.; Hu, Ming; Nicodemi, Mario; Zhao, Huimin; Ren, Bing
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errSave
Inference of chromosome 3D structures from GAM data by a physics computational approach
errMETHODS
IF4.3
err2020-10-01
err8
PREAI
errFiorillo, Luca; Bianco, Simona; Chiariello, Andrea M.; Barbieri, Mariano; Esposito, Andrea; Annunziatella, Carlo; Conte, Mattia; Corrado, Alfonso; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario
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Research Directions

No research directions
Co-authors
Cooperation Journals
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Rudolf Jaenisch
H-index: 209 · Papers: 802
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Peter J. Park
H-index: 145 · Papers: 810
S
Sarah A. Teichmann
H-index: 141 · Papers: 677
S
Steven Henikoff
H-index: 141 · Papers: 677
S
Shu Chien
H-index: 133 · Papers: 870
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