Publications

@article{dekker2026integrated,
  title = {{An integrated view of the structure and function of the human 4D nucleome}},
  author = {Dekker, J. and Oksuz, B. A. and Zhang, Y. and Wang, Y. and Minsk, M. K. and Kuang, S. and Yang, L. and others},
  journal = {Nature},
  year = {2026},
  volume = {649},
  number = {8097},
  pages = {759--776},
  doi = {10.1038/s41586-025-09890-3}
}

@article{markowski2026haplotype,
  title = {{Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes}},
  author = {Markowski, J. and Kukalev, A. and Robens, C. and Thieme, C. J. and Streck, A. and Mao, H. and Parsi, K. M. and Maehr, R. and Pombo, A. and Schwarz, R. F.},
  journal = {bioRxiv},
  year = {2026},
  doi = {10.64898/2026.06.16.732681}
}

@article{klingberg2026stem,
  title = {{Stem cell differentiation disperses transcriptional clusters via a conserved surface-condensate trajectory}},
  author = {Klingberg, T. and Wachter, I. and Pancholi, A. and Akyel, M. and Gohar, Y. and Kumar, P. and others and Fernandes, A. M. and others and Ferrai, C. and Hilbert, L.},
  journal = {Advanced Science},
  year = {2026},
  doi = {10.1002/advs.75924}
}

@article{bruckner2026extrachromosomal,
  title = {{Extrachromosomal DNA micronucleation constrains tumour fitness and improves patient survival}},
  author = {Brückner, L. and Xu, R. and Tang, J. and Gnanasekar, A. and Herrmann, A. and Wong, I. T. L. and others and Kukalev, A. and others and Herzog, S. and others and Pombo, A. and others and Henssen, A. G.},
  journal = {bioRxiv},
  year = {2026},
  doi = {10.1101/2025.04.15.648906}
}

@article{harabula2025specialised,
  title = {{Specialised super-enhancer networks in stem cells and neurons}},
  author = {Harabula, I. and Speakman, L. and Musella, F. and Forillo, L. and Zea-Redondo, L. and Kukalev, A. and Beagrie, R. A. and Morris, K. J. and Fernandes, L. and Irastorza-Azcarate, I. and Fernandes, A. M. and Carvalho, S. and Szabó, D. and Ferrai, C. and Nicodemi, M. and Welch, L. and Pombo, A.},
  journal = {bioRxiv},
  year = {2025},
  doi = {10.1101/2025.08.13.670083}
}

@article{stein2025cryosectioning,
  title = {{Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues}},
  author = {Stein, J. and Ericsson, M. and Nofal, M. and Magni, L. and Aufmkolk, S. and McMillan, R. B. and others},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2025},
  volume = {122},
  number = {32},
  pages = {e2504578122},
  doi = {10.1073/pnas.2504578122}
}

@article{irastorzaazcarate2025extensive,
  title = {{Extensive folding variability between homologous chromosomes in mammalian cells}},
  author = {Irastorza-Azcarate, I. and Kukalev, A. and Kempfer, R. and Thieme, C. J. and Mastrobuoni, G. and others},
  journal = {Molecular Systems Biology},
  year = {2025},
  volume = {21},
  number = {7},
  pages = {735--775},
  doi = {10.1038/s44320-025-00107-3}
}

@article{fontana2025loss,
  title = {{Loss of structural specificity in 3D genome organization upon viral infection is predicted by polymer physics}},
  author = {Fontana, A. and Bianco, S. and Tafuri, F. and Esposito, A. and Abraham, A. and Conte, M. and others and Chiariello, A. M.},
  journal = {Journal of Chemical Physics},
  year = {2025},
  doi = {10.1063/5.0243454}
}

@article{carvalho2024srrm2,
  title = {{SRRM2 splicing factor modulates cell fate in early development}},
  author = {Carvalho, S. and Zea-Redondo, L. and Tang, T. C. C. and Stachel-Braum, P. and Miller, D. and others},
  journal = {Biology Open},
  year = {2024},
  volume = {13},
  number = {4},
  pages = {bio060415},
  url = {https://journals.biologists.com/bio/article/13/4/bio060415/347005/SRRM2-splicing-factor-modulates-cell-fate-in-early}
}

@article{willemin2024epigenetic,
  title = {{Epigenetic regulatory layers in the three-dimensional nucleus}},
  author = {Willemin, A. and Szabó, D. and Pombo, A.},
  journal = {Molecular Cell},
  year = {2024},
  volume = {84},
  number = {3},
  pages = {415--428}
}

@article{szabo2024single,
  title = {{A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons}},
  author = {Szabó, D. and Franke, V. and Bianco, S. and Batiuk, M. Y. and Paul, E. J. and Kukalev, A. and Pfisterer, U. G. and Irastorza-Azcarate, I. and Chiariello, A. M. and Demharter, S. and Zea-Redondo, L. and Lopez-Atalaya, J. P. and Nicodemi, M. and Akalin, A. and Khodosevich, K. and Ungless, M. A. and Winick-Ng, W. and Pombo, A.},
  journal = {bioRxiv},
  year = {2024},
  doi = {10.1101/2024.05.10.593308}
}

@article{bolesani2024transient,
  title = {{Transient stabilization of human cardiovascular progenitor cells from human pluripotent stem cells in vitro reflects stage-specific heart development in vivo}},
  author = {Bolesani, E. and Bornhorst, D. and Iyer, L. I. and Zawada, D. and Friese, N. and Morgan, M. and others and Zweigerdt, R.},
  journal = {Cardiovascular Research},
  year = {2024},
  doi = {10.1093/cvr/cvae118}
}

@article{chiariello2024multiscale,
  title = {{Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells}},
  author = {Chiariello, A. M. and Abraham, A. and Bianco, S. and Esposito, A. and Fontana, A. and Vercellone, F. and Conte, M. and Nicodemi, M.},
  journal = {Nature Communications},
  year = {2024},
  doi = {10.1038/s41467-024-48370-6}
}

@article{thieme2023research,
  title = {{Research briefing}},
  author = {Thieme, C. J. and Pombo, A.},
  journal = {Nature Methods},
  year = {2023},
  volume = {20},
  pages = {993--994}
}

@article{beagrie2023multiplex,
  title = {{Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C}},
  author = {Beagrie, R. A. and Thieme, C. J. and Annunziatella, C. and Baugher, C. and Zhang, Y. and others},
  journal = {Nature Methods},
  year = {2023},
  volume = {20},
  number = {7},
  pages = {1037--1047},
  doi = {10.1038/s41592-023-01903-1}
}

@article{zearedondo2023mechanisms,
  title = {{Mechanisms of enhancer function in neuronal systems in health and disease}},
  author = {Zea-Redondo, L. and Pombo, A.},
  journal = {Current Opinion in Systems Biology},
  year = {2023},
  volume = {32},
  pages = {100443}
}

@article{yanchus2022noncoding,
  title = {{A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation}},
  author = {Yanchus, C. and Drucker, K. L. and Kollmeyer, T. M. and Tsai, R. and Winick-Ng, W. and Liang, M. and others},
  journal = {Science},
  year = {2022},
  volume = {378},
  number = {6615},
  pages = {68--78}
}

@article{mcgarvey2022single,
  title = {{Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos}},
  author = {McGarvey, A. C. and Kopp, W. and Vučićević, D. and Mattonet, K. and Kempfer, R. and Hirsekorn, A. and others},
  journal = {Cell Genomics},
  year = {2022},
  volume = {2},
  number = {1}
}

@article{decastro2022altered,
  title = {{Altered nuclear architecture in blood cells from Huntington’s disease patients}},
  author = {de Castro, I. J. and Toner, B. and Xie, S. Q. and Swingland, J. and Hodges, A. and Tabrizi, S. J. and others},
  journal = {Neurological Sciences},
  year = {2022},
  volume = {43},
  number = {1},
  pages = {379--385}
}

@article{markowski2021gamibhear,
  title = {{GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data}},
  author = {Markowski, J. and Kempfer, R. and Kukalev, A. and Irastorza-Azcarate, I. and Loof, G. and Kehr, B. and others},
  journal = {Bioinformatics},
  year = {2021},
  volume = {37},
  number = {19},
  pages = {3128--3135}
}

@article{winickng2021cell,
  title = {{Cell-type specialization is encoded by specific chromatin topologies}},
  author = {Winick-Ng, W. and Kukalev, A. and Harabula, I. and Zea-Redondo, L. and Szabó, D. and Meijer, M. and others},
  journal = {Nature},
  year = {2021},
  volume = {599},
  number = {7886},
  pages = {684--691},
  doi = {10.1038/s41586-021-04081-2}
}

@article{fiorillo2021comparison,
  title = {{Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin}},
  author = {Fiorillo, L. and Musella, F. and Conte, M. and Kempfer, R. and Chiariello, A. M. and Bianco, S. and others},
  journal = {Nature Methods},
  year = {2021},
  volume = {18},
  number = {5},
  pages = {482--490}
}

@article{harabula2021dynamics,
  title = {{The dynamics of chromatin architecture in brain development and function}},
  author = {Harabula, I. and Pombo, A.},
  journal = {Current Opinion in Genetics & Development},
  year = {2021},
  volume = {67},
  pages = {84--93}
}

@article{rajewsky2020lifetime,
  title = {{LifeTime and improving European healthcare through cell-based interceptive medicine}},
  author = {Rajewsky, N. and Almouzni, G. and Gorski, S. A. and Aerts, S. and Amit, I. and Bertero, M. G. and Bock, C. and others},
  journal = {Nature},
  year = {2020},
  volume = {587},
  number = {7834},
  pages = {377--386}
}

@article{fiorillo2020inference,
  title = {{Inference of chromosome 3D structures from GAM data by a physics computational approach}},
  author = {Fiorillo, L. and Bianco, S. and Chiariello, A. M. and Barbieri, M. and Esposito, A. and others},
  journal = {Methods},
  year = {2020},
  volume = {181},
  pages = {70--79}
}

@article{sparks2020evolving,
  title = {{Evolving methodologies and concepts in 4D nucleome research}},
  author = {Sparks, T. M. and Harabula, I. and Pombo, A.},
  journal = {Current Opinion in Cell Biology},
  year = {2020},
  volume = {64},
  pages = {105--111}
}

@article{kempfer2020methods,
  title = {{Methods for mapping 3D chromosome architecture}},
  author = {Kempfer, R. and Pombo, A.},
  journal = {Nature Reviews Genetics},
  year = {2020},
  volume = {21},
  number = {4},
  pages = {207--226}
}

@article{bickmore2019editorial,
  title = {{Editorial overview: Genome architecture and expression}},
  author = {Bickmore, W. and Pombo, A.},
  journal = {Current Opinion in Genetics and Development},
  year = {2019},
  volume = {55},
  pages = {iii--iv}
}

@article{skourtistathaki2019loops,
  title = {{R-loops enhance polycomb repression at a subset of developmental regulator genes}},
  author = {Skourti-Stathaki, K. and Triglia, E. T. and Warburton, M. and Voigt, P. and Bird, A. and Pombo, A.},
  journal = {Molecular Cell},
  year = {2019},
  volume = {73},
  number = {5},
  pages = {930--945.e4}
}

@article{martirenom2018challenges,
  title = {{Challenges and guidelines toward 4D nucleome data and model standards}},
  author = {Marti-Renom, M. A. and Almouzni, G. and Bickmore, W. A. and Bystricky, K. and Cavalli, G. and others},
  journal = {Nature Genetics},
  year = {2018},
  volume = {50},
  number = {10},
  pages = {1352--1358}
}

@article{bianco2018polymer,
  title = {{Polymer physics predicts the effects of structural variants on chromatin architecture}},
  author = {Bianco, S. and Lupiáñez, D. G. and Chiariello, A. M. and Annunziatella, C. and Kraft, K. and others},
  journal = {Nature Genetics},
  year = {2018},
  volume = {50},
  number = {5},
  pages = {662--667}
}

@article{ferrai2017polymerase,
  title = {{RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation}},
  author = {Ferrai, C. and Triglia, E. T. and Risner-Janiczek, J. R. and Rito, T. and Rackham, O. J. L. and others},
  journal = {Molecular Systems Biology},
  year = {2017},
  volume = {13},
  number = {10},
  pages = {MSB177754}
}

@article{noguchi2017fantom5,
  title = {{FANTOM5 CAGE profiles of human and mouse samples}},
  author = {Noguchi, S. and Arakawa, T. and Fukuda, S. and Furuno, M. and Hasegawa, A. and Hori, F. and others},
  journal = {Scientific Data},
  year = {2017},
  volume = {4},
  number = {1},
  pages = {170112}
}

@article{beagrie2017cell,
  title = {{Cell cycle: Continuous chromatin changes}},
  author = {Beagrie, R. A. and Pombo, A.},
  journal = {Nature},
  year = {2017},
  volume = {547},
  number = {7661},
  pages = {34}
}

@article{kar2017flipping,
  title = {{Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression}},
  author = {Kar, G. and Kim, J. K. and Kolodziejczyk, A. A. and Natarajan, K. N. and Triglia, E. T. and Mifsud, B. and others},
  journal = {Nature Communications},
  year = {2017},
  volume = {8},
  number = {1},
  pages = {36}
}

@article{barbieri2017active,
  title = {{Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells}},
  author = {Barbieri, M. and Xie, S. Q. and Triglia, E. T. and Chiariello, A. M. and Bianco, S. and de Santiago, I. and others},
  journal = {Nature Structural & Molecular Biology},
  year = {2017},
  volume = {24},
  number = {6},
  pages = {515--524}
}

@article{caglio2017keep,
  title = {{Keep them close: PRC2 poises enhancer-promoter interactions at anterior neuronal genes}},
  author = {Caglio, G. and Triglia, E. T. and Pombo, A.},
  journal = {Cell Stem Cell},
  year = {2017},
  volume = {20},
  number = {5},
  pages = {573--575}
}

@article{mattei2017maternal,
  title = {{Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatment}},
  author = {Mattei, D. and Ivanov, A. and Ferrai, C. and Jordan, P. and Guneykaya, D. and Buonfiglioli, A. and others},
  journal = {Translational Psychiatry},
  year = {2017},
  volume = {7},
  number = {5},
  pages = {e1120}
}

@article{beagrie2017complex,
  title = {{Complex multi-enhancer contacts captured by genome architecture mapping}},
  author = {Beagrie, R. A. and Scialdone, A. and Schueler, M. and Kraemer, D. C. A. and Chotalia, M. and Xie, S. Q. and others},
  journal = {Nature},
  year = {2017},
  volume = {543},
  number = {7646},
  pages = {519--524}
}

@article{triglia2017finer,
  title = {{A finer print than TADs: PRC1-mediated domains}},
  author = {Triglia, E. T. and Rito, T. and Pombo, A.},
  journal = {Molecular Cell},
  year = {2017},
  volume = {65},
  number = {3},
  pages = {373--375}
}

@article{beagrie2016examining,
  title = {{Examining topological domain influence on enhancer function}},
  author = {Beagrie, R. A. and Pombo, A.},
  journal = {Developmental Cell},
  year = {2016},
  volume = {39},
  number = {5},
  pages = {523--524}
}

@article{franke2016formation,
  title = {{Formation of new chromatin domains determines pathogenicity of genomic duplications}},
  author = {Franke, M. and Ibrahim, D. M. and Andrey, G. and Schwarzer, W. and Heinrich, V. and Schöpflin, R. and others},
  journal = {Nature},
  year = {2016},
  volume = {538},
  number = {7624},
  pages = {265--269}
}

@article{beagrie2016gene,
  title = {{Gene activation by metazoan enhancers: diverse mechanisms stimulate distinct steps of transcription}},
  author = {Beagrie, R. A. and Pombo, A.},
  journal = {BioEssays},
  year = {2016},
  volume = {38},
  number = {9},
  pages = {881--893}
}

@article{le2016mechanical,
  title = {{Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment}},
  author = {Le, H. Q. and Ghatak, S. and Yeung, C. Y. C. and Tellkamp, F. and Günschmann, C. and Dieterich, C. and others},
  journal = {Nature Cell Biology},
  year = {2016},
  volume = {18},
  number = {8},
  pages = {864--875}
}

@article{dias2015methylation,
  title = {{Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells}},
  author = {Dias, J. D. and Rito, T. and Triglia, E. T. and Kukalev, A. and Ferrai, C. and Chotalia, M. and others},
  journal = {eLife},
  year = {2015},
  volume = {4},
  pages = {e11215}
}

@article{fraser2015hierarchical,
  title = {{Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation}},
  author = {Fraser, J. and Ferrai, C. and Chiariello, A. M. and Schueler, M. and Rito, T. and Laudanno, G. and others},
  journal = {Molecular Systems Biology},
  year = {2015},
  volume = {11},
  number = {12},
  pages = {MSB156492}
}

@article{chiariello2015polymer,
  title = {{Polymer models of the organization of chromosomes in the nucleus of cells}},
  author = {Chiariello, A. M. and Bianco, S. and Piccolo, A. and Annunziatella, C. and Barbieri, M. and Pombo, A. and others},
  journal = {Modern Physics Letters B},
  year = {2015},
  volume = {29},
  number = {09},
  pages = {1530003}
}

@article{pombo2015three,
  title = {{Three-dimensional genome architecture: players and mechanisms}},
  author = {Pombo, A. and Dillon, N.},
  journal = {Nature Reviews Molecular Cell Biology},
  year = {2015},
  volume = {16},
  number = {4},
  pages = {245--257}
}

@article{arner2015transcribed,
  title = {{Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells}},
  author = {Arner, E. and Daub, C. O. and Vitting-Seerup, K. and Andersson, R. and Lilje, B. and Drabløs, F. and others},
  journal = {Science},
  year = {2015},
  volume = {347},
  number = {6225},
  pages = {1010--1014}
}

@article{benitah2014stem,
  title = {{Stem cell epigenetics: looking forward}},
  author = {Benitah, S. A. and Bracken, A. and Dou, Y. and Huangfu, D. and Ivanova, N. and Koseki, H. and others},
  journal = {Cell Stem Cell},
  year = {2014},
  volume = {14},
  number = {6},
  pages = {706--709}
}

@article{nicodemi2014models,
  title = {{Models of chromosome structure}},
  author = {Nicodemi, M. and Pombo, A.},
  journal = {Current Opinion in Cell Biology},
  year = {2014},
  volume = {28},
  pages = {90--95}
}

@article{pombo2014physical,
  title = {{Physical mechanisms behind the large scale features of chromatin organization}},
  author = {Pombo, A. and Nicodemi, M.},
  journal = {Transcription},
  year = {2014},
  volume = {5},
  number = {2},
  pages = {e28447}
}

@article{sabbattini2014h3k9,
  title = {{An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation}},
  author = {Sabbattini, P. and Sjoberg, M. and Nikic, S. and Frangini, A. and Holmqvist, P. H. and Kunowska, N. and others},
  journal = {Molecular Biology of the Cell},
  year = {2014},
  volume = {25},
  number = {6},
  pages = {904--915}
}

@article{barbieri2013polymer,
  title = {{Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus}},
  author = {Barbieri, M. and Scialdone, A. and Gamba, A. and Pombo, A. and Nicodemi, M.},
  journal = {Soft Matter},
  year = {2013},
  volume = {9},
  number = {36},
  pages = {8631--8635}
}

@article{barbieri2013polymer,
  title = {{A polymer model explains the complexity of large-scale chromatin folding}},
  author = {Barbieri, M. and Fraser, J. and Lavitas, L. M. and Chotalia, M. and Dostie, J. and Pombo, A. and others},
  journal = {Nucleus},
  year = {2013},
  volume = {4},
  number = {4},
  pages = {267--273}
}

@article{barbieri2013polymer,
  title = {{Polymer models of chromatin organization}},
  author = {Barbieri, M. and Scialdone, A. and Piccolo, A. and Chiariello, A. M. and di Lanno, C. and Prisco, A. and others},
  journal = {Frontiers in Genetics},
  year = {2013},
  volume = {4},
  pages = {113}
}

@article{barbieri2013model,
  title = {{A model of the large-scale organization of chromatin}},
  author = {Barbieri, M. and Chotalia, M. and Fraser, J. and Lavitas, L. M. and Dostie, J. and Pombo, A. and others},
  journal = {Biochemical Society Transactions},
  year = {2013},
  volume = {41},
  number = {2},
  pages = {508--512}
}

@article{swingland2012mean,
  title = {{Mean expression of the X-chromosome is associated with neuronal density}},
  author = {Swingland, J. T. and Durrenberger, P. F. and Reynolds, R. and Dexter, D. T. and Pombo, A. and others},
  journal = {Frontiers in Neuroscience},
  year = {2012},
  volume = {6},
  pages = {161}
}

@article{barbieri2012complexity,
  title = {{Complexity of chromatin folding is captured by the strings and binders switch model}},
  author = {Barbieri, M. and Chotalia, M. and Fraser, J. and Lavitas, L. M. and Dostie, J. and Pombo, A. and others},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2012},
  volume = {109},
  number = {40},
  pages = {16173--16178}
}

@article{moller2012proteomic,
  title = {{Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease}},
  author = {Möller, A. and Xie, S. Q. and Hosp, F. and Lang, B. and Phatnani, H. P. and James, S. and Ramirez, F. and others},
  journal = {Molecular & Cellular Proteomics},
  year = {2012},
  volume = {11},
  number = {6}
}

@article{brookes2012code,
  title = {{Code breaking: the RNAPII modification code in pluripotency}},
  author = {Brookes, E. and Pombo, A.},
  journal = {Cell Cycle},
  year = {2012},
  volume = {11},
  number = {7},
  pages = {1267--1268}
}

@article{brookes2012polycomb,
  title = {{Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs}},
  author = {Brookes, E. and de Santiago, I. and Hebenstreit, D. and Morris, K. J. and Carroll, T. and Xie, S. Q. and others},
  journal = {Cell Stem Cell},
  year = {2012},
  volume = {10},
  number = {2},
  pages = {157--170}
}

@article{chotalia2011polycomb,
  title = {{Polycomb targets seek closest neighbours}},
  author = {Chotalia, M. and Pombo, A.},
  journal = {PLoS Genetics},
  year = {2011},
  volume = {7},
  number = {3},
  pages = {e1002031}
}

@article{pombo2011nuclear,
  title = {{Nuclear cell biology}},
  author = {Pombo, A. and Starr, D. A.},
  journal = {Molecular Biology of the Cell},
  year = {2011},
  volume = {22},
  number = {6},
  pages = {722--722}
}

@article{alder2010ring1b,
  title = {{Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment}},
  author = {Alder, O. and Lavial, F. and Helness, A. and Brookes, E. and Pinho, S. and Chandrashekran, A. and others},
  journal = {Development},
  year = {2010},
  volume = {137},
  number = {15},
  pages = {2483--2492}
}

@article{kanhere2010short,
  title = {{Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2}},
  author = {Kanhere, A. and Viiri, K. and Araújo, C. C. and Rasaiyaah, J. and Bouwman, R. D. and Whyte, W. A. and others},
  journal = {Molecular Cell},
  year = {2010},
  volume = {38},
  number = {5},
  pages = {675--688}
}

@article{ferrai2010gene,
  title = {{Gene positioning}},
  author = {Ferrai, C. and de Castro, I. J. and Lavitas, L. and Chotalia, M. and Pombo, A.},
  journal = {Cold Spring Harbor Perspectives in Biology},
  year = {2010},
  volume = {2},
  number = {6},
  pages = {a000588}
}

@article{landeira2010jarid2,
  title = {{Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators}},
  author = {Landeira, D. and Sauer, S. and Poot, R. and Dvorkina, M. and Mazzarella, L. and Jørgensen, H. F. and others},
  journal = {Nature Cell Biology},
  year = {2010},
  volume = {12},
  number = {6},
  pages = {618--624}
}

@article{pombo2010nucleus,
  title = {{Nucleus and gene expression: the structure and function conundrum}},
  author = {Pombo, A. and Gilbert, D. M.},
  journal = {Current Opinion in Cell Biology},
  year = {2010},
  volume = {22},
  number = {3},
  pages = {269--270}
}

@article{ferrai2010poised,
  title = {{Poised transcription factories prime silent uPA gene prior to activation}},
  author = {Ferrai, C. and Xie, S. Q. and Luraghi, P. and Munari, D. and Ramirez, F. and Branco, M. R. and Pombo, A. and others},
  journal = {PLoS Biology},
  year = {2010},
  volume = {8},
  number = {1},
  pages = {e1000270}
}

@article{morris2010nuclear,
  title = {{Nuclear architecture in stem cells}},
  author = {Morris, K. J. and Chotalia, M. and Pombo, A.},
  journal = {Advances in Experimental Medicine and Biology},
  year = {2010},
  volume = {695},
  pages = {14--25}
}

@article{baddeley2010measurement,
  title = {{Measurement of replication structures at the nanometer scale using super-resolution light microscopy}},
  author = {Baddeley, D. and Chagin, V. O. and Schermelleh, L. and Martin, S. and Pombo, A. and Carlton, P. M. and others},
  journal = {Nucleic Acids Research},
  year = {2010},
  volume = {38},
  number = {2},
  pages = {e8}
}

@article{hiragamihamada2009molecular,
  title = {{The molecular basis for stability of heterochromatin-mediated silencing in mammals}},
  author = {Hiragami-Hamada, K. and Xie, S. Q. and Saveliev, A. and Uribe-Lewis, S. and Pombo, A. and others},
  journal = {Epigenetics & Chromatin},
  year = {2009},
  volume = {2},
  number = {1},
  pages = {14}
}

@article{brookes2009modifications,
  title = {{Modifications of RNA polymerase II are pivotal in regulating gene expression states}},
  author = {Brookes, E. and Pombo, A.},
  journal = {EMBO Reports},
  year = {2009},
  volume = {10},
  number = {11},
  pages = {1213}
}

@article{ferrai2009chromatin,
  title = {{3D chromatin regulation of Sonic hedgehog in the limb buds}},
  author = {Ferrai, C. and Pombo, A.},
  journal = {Developmental Cell},
  year = {2009},
  volume = {16},
  number = {1},
  pages = {9--11}
}

@article{mayamendoza2009mechanisms,
  title = {{Mechanisms regulating S phase progression in mammalian cells}},
  author = {Maya-Mendoza, A. and Tang, C. W. and Pombo, A. and Jackson, D. A.},
  journal = {Frontiers in Bioscience},
  year = {2009},
  volume = {14},
  number = {11},
  pages = {4199--4213}
}

@article{babu2008eukaryotic,
  title = {{Eukaryotic gene regulation in three dimensions and its impact on genome evolution}},
  author = {Babu, M. M. and Janga, S. C. and de Santiago, I. and Pombo, A.},
  journal = {Current Opinion in Genetics & Development},
  year = {2008},
  volume = {18},
  number = {6},
  pages = {571--582}
}

@article{branco2008changes,
  title = {{Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH}},
  author = {Branco, M. R. and Branco, T. and Ramirez, F. and Pombo, A.},
  journal = {Chromosome Research},
  year = {2008},
  volume = {16},
  number = {3},
  pages = {413--426}
}

@article{noordermeer2008transcription,
  title = {{Transcription and chromatin organization of a housekeeping gene cluster containing an integrated β-globin locus control region}},
  author = {Noordermeer, D. and Branco, M. R. and Splinter, E. and Klous, P. and van IJcken, W. and others},
  journal = {PLoS Genetics},
  year = {2008},
  volume = {4},
  number = {3},
  pages = {e1000016}
}

@article{stock2007ring1,
  title = {{Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells}},
  author = {Stock, J. K. and Giadrossi, S. and Casanova, M. and Brookes, E. and Vidal, M. and Koseki, H. and others},
  journal = {Nature Cell Biology},
  year = {2007},
  volume = {9},
  number = {12},
  pages = {1428--1435}
}

@article{pombo2007functional,
  title = {{Functional organisation of the genome during interphase}},
  author = {Pombo, A. and Branco, M. R.},
  journal = {Current Opinion in Genetics & Development},
  year = {2007},
  volume = {17},
  number = {5},
  pages = {451--455}
}

@article{pombo2007advances,
  title = {{Advances in imaging the interphase nucleus using thin cryosections}},
  author = {Pombo, A.},
  journal = {Histochemistry and Cell Biology},
  year = {2007},
  volume = {128},
  number = {2},
  pages = {97--104}
}

@article{piercy2007desmin,
  title = {{Desmin immunolocalisation in autosomal dominant Emery-Dreifuss muscular dystrophy}},
  author = {Piercy, R. J. and Zhou, H. and Feng, L. and Pombo, A. and Muntoni, F. and Brown, S. C.},
  journal = {Neuromuscular Disorders},
  year = {2007},
  volume = {17},
  number = {4},
  pages = {297--305}
}

@article{branco2007chromosome,
  title = {{Chromosome organization: new facts, new models}},
  author = {Branco, M. R. and Pombo, A.},
  journal = {Trends in Cell Biology},
  year = {2007},
  volume = {17},
  number = {3},
  pages = {127--134}
}

@article{branco2006intermingling,
  title = {{Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations}},
  author = {Branco, M. R. and Pombo, A.},
  journal = {PLoS Biology},
  year = {2006},
  volume = {4},
  number = {5},
  pages = {e138}
}

@article{xie2006splicing,
  title = {{Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on Serine2 residues of the C-terminal domain}},
  author = {Xie, S. Q. and Martin, S. and Guillot, P. V. and Bentley, D. L. and Pombo, A.},
  journal = {Molecular Biology of the Cell},
  year = {2006},
  volume = {17},
  number = {4},
  pages = {1723--1733}
}

@article{xie2006distribution,
  title = {{Distribution of different phosphorylated forms of RNA polymerase II in relation to Cajal and PML bodies in human cells: an ultrastructural study}},
  author = {Xie, S. Q. and Pombo, A.},
  journal = {Histochemistry and Cell Biology},
  year = {2006},
  volume = {125},
  number = {1},
  pages = {21--31}
}

@article{chow2005variant,
  title = {{Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division}},
  author = {Chow, C. M. and Georgiou, A. and Szutorisz, H. and Maia e Silva, A. and Pombo, A. and Barahona, I. and others},
  journal = {EMBO Reports},
  year = {2005},
  volume = {6},
  number = {4},
  pages = {354}
}

@article{ribeiro2005functional,
  title = {{Functional analysis of Vif protein shows less restriction of human immunodeficiency virus type 2 by APOBEC3G}},
  author = {Ribeiro, A. C. and Maia e Silva, A. and Santa-Marta, M. and Pombo, A. and Moniz-Pereira, J. and others},
  journal = {Journal of Virology},
  year = {2005},
  volume = {79},
  number = {2},
  pages = {823--833}
}

@article{kenny2004activation,
  title = {{CD8α is an activation marker for a subset of peripheral CD4 T cells}},
  author = {Kenny, E. and Mason, D. and Saoudi, A. and Pombo, A. and Ramírez, F.},
  journal = {European Journal of Immunology},
  year = {2004},
  volume = {34},
  number = {5},
  pages = {1262--1271}
}

@article{guillot2004fixation,
  title = {{Fixation-induced redistribution of hyperphosphorylated RNA polymerase II in the nucleus of human cells}},
  author = {Guillot, P. V. and Xie, S. Q. and Hollinshead, M. and Pombo, A.},
  journal = {Experimental Cell Research},
  year = {2004},
  volume = {295},
  number = {2},
  pages = {460--468}
}

@article{martin2004measuring,
  title = {{Measuring the size of biological nanostructures with spatially modulated illumination microscopy}},
  author = {Martin, S. and Failla, A. V. and Spori, U. and Cremer, C. and Pombo, A.},
  journal = {Molecular Biology of the Cell},
  year = {2004},
  volume = {15},
  number = {5},
  pages = {2449--2455}
}

@article{boyd2003interaction,
  title = {{Interaction of proteins with promoter elements of the human U2 snRNA genes in vivo}},
  author = {Boyd, D. C. and Pombo, A. and Murphy, S.},
  journal = {Gene},
  year = {2003},
  volume = {315},
  pages = {103--112}
}

@article{martin2003transcription,
  title = {{Transcription factories: quantitative studies of nanostructures in the mammalian nucleus}},
  author = {Martin, S. and Pombo, A.},
  journal = {Chromosome Research},
  year = {2003},
  volume = {11},
  number = {5},
  pages = {461--470}
}

@article{obrien2003genome,
  title = {{Genome function and nuclear architecture: from gene expression to nanoscience}},
  author = {O'Brien, T. P. and Bult, C. J. and Cremer, C. and Grunze, M. and Knowles, B. B. and Langowski, J. and others},
  journal = {Genome Research},
  year = {2003},
  volume = {13},
  number = {6a},
  pages = {1029--1041}
}

@article{politz2003from,
  title = {{From linear genome sequence to three-dimensional organization of the cell nucleus}},
  author = {Politz, J. and van Driel, R. and Sauer, M. and Pombo, A.},
  journal = {Genome Biology},
  year = {2003},
  volume = {4},
  number = {3},
  pages = {310}
}

@article{pombo2003cellular,
  title = {{Cellular genomics: which genes are transcribed, when and where?}},
  author = {Pombo, A.},
  journal = {Trends in Biochemical Sciences},
  year = {2003},
  volume = {28},
  number = {1},
  pages = {6--9}
}

@article{politz2003genomics,
  title = {{Genomics meets nanoscience: probing genes and the cell nucleus at 10−9 meters}},
  author = {Politz, J. and Pombo, A.},
  journal = {Genome Biology},
  year = {2003},
  volume = {3},
  number = {3},
  pages = {reports4007.1}
}