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Transient stabilization of human cardiovascular progenitor cells from hPSCs in vitro reflects stage-specific heart development in vivo.
Bolesani, E., Bornhorst, D., Iyer, L.I., Zawada, D., Friese, N., Morgan, M., Lange, L., Gonzalez, D., Schrode, N., Leffler, A., Wunder, J., Franke, A., Drakhlis, L., Sebra, R., Schambach, A., Goedel, A., Dubois, N., Dobreva, G., Moretti, A., Zelarayán, L.C., Abdelilah-Seyfried, S. and Zweigerdt, R.
Cardiovascular Research : cvae118. 5 June 2024 (In Press)

Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells.
Chiariello, A.M., Abraham, Alex, Bianco, S., Esposito, A., Fontana, A., Vercellone, F., Conte, M. and Nicodemi, M.
Nature Communications 15 (1): 4014. 13 May 2024

SRRM2 splicing factor modulates cell fate in early development.
Carvalho, S., Zea-Redondo, L., Tang, T.C.C., Stachel-Braum, P., Miller, D., Caldas, P., Kukalev, A., Diecke, S., Grosswendt, S., Grosso, A.R. and Pombo, A.
Biology Open 13 (4): bio060415. April 2024

Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes.
Schindler, M., Osterwalder, M., Harabula, I., Wittler, L., Tzika, A.C., Dechmann, D.K.N., Vingron, M., Visel, A., Haas, S. and Real, F.M.
Development 150 (17): dev201562. 1 September 2023

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
Beagrie, R.A., Thieme, C.J., Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kukalev, A., Kempfer, R., Chiariello, A.M., Bianco, S., Li, Y., Davis, T., Scialdone, A., Welch, L.R., Nicodemi, M. and Pombo, A.
Nature Methods 20 (7): 1037-1047. July 2023

Physics-based polymer models to probe chromosome structure in single molecules.
Conte, M., Chiariello, A.M., Bianco, S., Esposito, A., Abraham, A. and Nicodemi, M.
Methods in Molecular Biology 2655 : 57-66. 2023

A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation.
Yanchus, C., Drucker, K.L., Kollmeyer, T.M., Tsai, R., Winick-Ng, W., Liang, M., Malik, A., Pawling, J., De Lorenzo, S.B., Ali, A., Decker, P.A., Kosel, M.L., Panda, A., Al-Zahrani, K.N., Jiang, L., Browning, J.W.L., Lowden, C., Geuenich, M., Hernandez, J.J., Gosio, J.T., Ahmed, M., Loganathan, S.K., Berman, J., Trcka, D., Michealraj, K.A., Fortin, J., Carson, B., Hollingsworth, E.W., Jacinto, S., Mazrooei, P., Zhou, L., Elia, A., Lupien, M., He, H.H., Murphy, D.J., Wang, L., Abyzov, A., Dennis, J.W., Maass, P.G., Campbell, K., Wilson, M.D., Lachance, D.H., Wrensch, M., Wiencke, J., Mak, T., Pennacchio, L.A., Dickel, D.E., Visel, A., Wrana, J., Taylor, M.D., Zadeh, G., Dirks, P., Eckel-Passow, J.E., Attisano, L., Pombo, A., Ida, C.M., Kvon, E.Z., Jenkins, R.B. and Schramek, D.
Science 378 (6615): 68-78. 7 October 2022

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.
Ringel, A.R., Szabo, Q., Chiariello, A.M., Chudzik, K., Schöpflin, R., Rothe, P., Mattei, A.L., Zehnder, To., Harnett, D., Laupert, V., Bianco, S., Hetzel, S., Glaser, J., Phan, M.H.Q., Schindler, M., Ibrahim, D.M., Paliou, C., Esposito, A., Prada-Medina, C.A., Haas, S.A., Giere, P., Vingron, M., Wittler, L., Meissner, A., Nicodemi, M., Cavalli, G., Bantignies, F., Mundlos, S. and Robson, M.I.
Cell 185 (20): 3689-3704. 29 September 2022

Hmga2 protein loss alters nuclear envelope and 3D chromatin structure.
Divisato, G., Chiariello, A.M., Esposito, A., Zoppoli, P., Zambelli, F., Elia, M.A., Pesole, G., Incarnato, D., Passaro, F., Piscitelli, S., Oliviero, S., Nicodemi, M., Parisi, S. and Russo, T.
BMC Biology 20 (1): 171. 2 August 2022

Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding.
Conte, M., Irani, E., Chiariello, A.M., Abraham, A., Bianco, S., Esposito, A. and Nicodemi, M.
Nature Communications 13 (1): 4070. 13 July 2022

Dynamics of bacteria scanning a porous environment.
Irani, E., Mokhtari, Z. and Zippelius, A.
Physical Review Letters 128 (14): 144501. 5 April 2022

Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states.
Esposito, A., Bianco, S., Chiariello, A.M., Abraham, A., Fiorillo, L., Conte, M., Campanile, R. and Nicodemi, M.
Cell Reports 38 (13): 110601. 29 March 2022

A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome.
Cinque, L., Micale, L., Manara, E., Esposito, A., Palumbo, O., Chiariello, A.M., Bianco, S., Guerri, G., Bertelli, M., Giuffrida, M.G., Bernardini, L., Notarangelo, A., Nicodemi, M. and Castori, M.
Human Genetics 141 (2): 217-227. February 2022

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C., Kopp, W., Vučićević, D., Mattonet, K., Kempfer, R., Hirsekorn, A., Bilić, I., Gil, M., Trinks, A., Merks, A.M., Panáková, D., Pombo, A., Akalin, A., Junker, J.P., Stainier, D.Y.R., Garfield, D., Ohler, U. and Lacadie, S.A.
Cell Genomics 2 (1): 100083. 13 January 2022

Altered nuclear architecture in blood cells from Huntington's disease patients.
de Castro, I.J., Toner, B., Xie, S.Q., Swingland, J., Hodges, A., Tabrizi, S.J., Turkheimer, F., Pombo, A. and Khalil, A.
Neurological Sciences 43 (1): 379-385. January 2022

Efficient computational implementation of polymer physics models to explore chromatin structure.
Conte, M., Esposito, A., Fiorillo, L., Campanile, R., Annunziatella, C., Corrado, A., Chiariello, M.G., Bianco, S. and Chiariello, A.M.
International Journal of Parallel, Emergent and Distributed Systems 37 (1): 91-102. January 2022

A polymer physics model to dissect genome organization in healthy and pathological phenotypes.
Conte, M., Fiorillo, L., Bianco, S., Chiariello, A.M., Esposito, A., Musella, F., Flora, F., Abraham, A. and Nicodemi, M.
Methods in Molecular Biology 2301 : 307-316. 2022

Cell-type specialization is encoded by specific chromatin topologies.
Winick-Ng, W., Kukalev, A., Harabula, I., Zea-Redondo, L., Szabó, D., Meijer, M., Serebreni, L., Zhang, Y., Bianco, S., Chiariello, A.M., Irastorza-Azcarate, I., Thieme, C.J., Sparks, T.M., Carvalho, S., Fiorillo, L., Musella, F., Irani, E., Triglia, E.T., Kolodziejczyk, A.A., Abentung, A., Apostolova, G., Paul, E.J., Franke, V., Kempfer, R., Akalin, A., Teichmann, S.A., Dechant, G., Ungless, M.A., Nicodemi, M., Welch, L., Castelo-Branco, G. and Pombo, A.
Nature 599 (7886): 684-691. 25 November 2021

Dynamic and equilibrium properties of finite-size polymer models of chromosome folding.
Conte, M., Fiorillo, L., Annunziatella, C., Esposito, A., Musella, F., Abraham, A., Bianco, S. and Chiariello, A.M.
Physical Review E 104 (5): 054402. 10 November 2021

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Markowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Kehr, B., Pombo, A., Rahmann, S. and Schwarz, R.F.
Bioinformatics 37 (19): 3128–3135. 1 October 2021

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression.
Franke, M., De la Calle-Mustienes, E., Neto, A., Almuedo-Castillo, M., Irastorza-Azcarate, I., Acemel, R.D., Tena, J.J., Santos-Pereira, J.M. and Gómez-Skarmeta, J.L.
Nature Communications 12 (1): 5415. 13 September 2021

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.
Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A.M., Yu, M., Hu, R., Tastemel, M., Juric, I., Hu, M., Nicodemi, M., Zhuang, X. and Ren, B.
Nature Genetics 53 (7): 1064-1074. July 2021

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J.A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M.C., Chatelain, C., Carninci, P., de Hoon, M.J.L., Wasserman, W.W., Bréhélin, L. and Lecellier, C.H.
Nature Communications 12 (1): 3297. 2 June 2021

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
Fiorillo, L., Musella, F., Conte, M., Kempfer, R., Chiariello, A.M., Bianco, S., Kukalev, A., Irastorza-Azcarate, I., Esposito, A., Abraham, A., Prisco, A., Pombo, A. and Nicodemi, M.
Nature Methods 18 (5): 482-490. May 2021

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.
Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J.D., Conte, M., Gorkin, D., Yu, M., Li, B., Dixon, J.R., Hu, M., Nicodemi, M., Zhao, H. and Ren, B.
Nature Structural & Molecular Biology 28 (2): 152-161. February 2021

Age-related and disease locus-specific mechanisms contribute to early remodelling of chromatin structure in Huntington's disease mice.
Alcalá-Vida, R., Seguin, J., Lotz, C., Molitor, A.M., Irastorza-Azcarate, I., Awada, A., Karasu, N., Bombardier, A., Cosquer, B., Skarmeta, J.L.G., Cassel, J.C., Boutillier, A.L., Sexton, T. and Merienne, K.
Nature Communications 12 (1): 364. 13 January 2021

LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky, N., Almouzni, G., Gorski, S.A., Aerts, S., Amit, I., Bertero, M.G., Bock, C., Bredenoord, A.L., Cavalli, G., Chiocca, S., Clevers, H., De Strooper, B., Eggert, A., Ellenberg, J., Fernández, X.M., Figlerowicz, M., Gasser, S.M., Hubner, N., Kjems, J., Knoblich, J.A., Krabbe, G., Lichter, P., Linnarsson, S., Marine, J.C., Marioni, J., Marti-Renom, M.A., Netea, M.G., Nickel, D., Nollmann, M., Novak, H.R., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J.L., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F.J., Torres-Padilla, M.E., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M. and Voet, T.
Nature 587 (7834): 377-386. 19 November 2020

Inference of chromosome 3D structures from GAM data by a physics computational approach.
Fiorillo, L., Bianco, S., Chiariello, A.M., Barbieri, M., Esposito, A., Annunziatella, C., Conte, M., Corrado, A., Prisco, A., Pombo, A. and Nicodemi, M.
Methods 181-182 : 70-79. 1 October 2020

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation.
Conte, M., Fiorillo, L., Bianco, S., Chiariello, A.M., Esposito, A. and Nicodemi, M.
Nature Communications 11 (1): 3289. 3 July 2020

A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells.
Chiariello, A.M., Bianco, S., Oudelaar, A M., Esposito, A., Annunziatella, C., Fiorillo, L., Conte, M., Corrado, A., Prisco, A., Larke, M.S.C., Telenius, J.M., Sciarretta, R., Musella, F., Buckle, V.J., Higgs, D.R., Hughes, J.R. and Nicodemi, M.
Cell Reports 30 (7): 2125-2135. 18 February 2020

Modeling single-molecule conformations of the HoxD region in mouse embryonic stem and cortical neuronal cells.
Bianco, S., Annunziatella, C., Andrey, G., Chiariello, A.M., Esposito, A., Fiorillo, L., Prisco, A., Conte, M., Campanile, R. and Nicodemi, M.
Cell Reports 28 (6): 1574-1583. 6 August 2019

Discontinuous shear-thinning in adhesive dispersions.
Irani, E., Chaudhuri, P. and Heussinger, C.
Physical Review Fluids 4 (7): 074307. 18 July 2019

Models of polymer physics for the architecture of the cell nucleus.
Esposito, A., Annunziatella, C., Bianco, S., Chiariello, A.M., Fiorillo, L. and Nicodemi, M.
Wiley Interdisciplinary Reviews Systems Biology and Medicine 11 (4): e1444. July 2019

Preformed chromatin topology assists transcriptional robustness of Shh during limb development.
Paliou, C., Guckelberger, P., Schöpflin, R., Heinrich, V., Esposito, A., Chiariello, A.M., Bianco, S., Annunziatella, C., Helmuth, J., Haas, S., Jerković, I., Brieske, N., Wittler, L., Timmermann, B., Nicodemi, M., Vingron, M., Mundlos, S. and Andrey, G.
Proceedings of the National Academy of Sciences of the United States of America 116 (25): 12390-12399. 18 June 2019

Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations.
Dellino, G.I., Palluzzi, F., Chiariello, A.M., Piccioni, R., Bianco, S., Furia, L., De Conti, G., Bouwman, B.A.M., Melloni, G., Guido, D., Giacò, L., Luzi, L., Cittaro, D., Faretta, M., Nicodemi, M., Crosetto, N. and Pelicci, P.G.
Nature Genetics 51 (6): 1011-1023. June 2019

R-loops enhance polycomb repression at a subset of developmental regulator genes.
Skourti-Stathaki, K., Torlai Triglia, E., Warburton, M., Voigt, P., Bird, A. and Pombo, A.
Molecular Cell 73 (5): 930-945. 7 March 2019

Challenges and guidelines toward 4D nucleome data and model standards.
Marti-Renom, M.A., Almouzni, G., Bickmore, W.A., Bystricky, K., Cavalli, G., Fraser, P., Gasser, S.M., Giorgetti, L., Heard, E., Nicodemi, M., Nollmann, M., Orozco, M., Pombo, A. and Torres-Padilla, M.E.
Nature Genetics 50 (10): 1352-1358. October 2018

Molecular Dynamics simulations of the Strings and Binders Switch Model of chromatin.
Annunziatella, C., Chiariello, A.M., Esposito, A., Bianco, S., Fiorillo, L. and Nicodemi, M.
Methods 142 : 81-88. 1 June 2018

Polymer physics predicts the effects of structural variants on chromatin architecture.
Bianco, S., Lupiáñez, D.G., Chiariello, A.M., Annunziatella, C., Kraft, K., Schöpflin, R., Wittler, L., Andrey, G., Vingron, M., Pombo, A., Mundlos, S. and Nicodemi, M.
Nature Genetics 50 (5): 662-667. May 2018

The scaling features of the 3D organization of chromosomes are highlighted by a transformation à la Kadanoff of Hi-C data.
Chiariello, A.M., Bianco, S., Annunziatella, C., Esposito, A. and Nicodemi, M.
EPL 120 (4): 40004. 8 February 2018

Understanding chromatin structure: efficient computational implementation of polymer physics models.
Bianco, S., Annunziatella, C., Esposito, A., Fiorillo, L., Conte, M., Campanile, R. and Chiariello, A.M.
Lecture Notes in Computer Science 11339 : 680-691. 2018

Chaperone-mediated regulation of choline acetyltransferase protein stability and activity by HSC/HSP70, HSP90, and p97/VCP.
Morey, T.M., Winick-Ng, W., Seah, C. and Rylett, R.J.
Frontiers in Molecular Neuroscience 10 : 415. December 2017

Structure of the human chromosome interaction network.
Sarnataro, S., Chiariello, A.M., Esposito, A., Prisco, A. and Nicodemi, M.
PLoS ONE 12 (11): e0188201. 15 November 2017

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.
Wyler, E., Menegatti, J., Franke, V., Kocks, C., Boltengagen, A., Hennig, T., Theil, K., Rutkowski, A., Ferrai, C., Baer, L., Kermas, L., Friedel, C., Rajewsky, N., Akalin, A., Dölken, L., Grässer, F. and Landthaler, M.
Genome Biology 18 (1): 209. 31 October 2017

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.
Ferrai, C., Torlai Triglia, E., Risner-Janiczek, J.R., Rito, T., Rackham, O.J.L., De Santiago, I., Kukalev, A., Nicodemi, M., Akalin, A., Li, M., Ungless, M.A. and Pombo, A.
Molecular Systems Biology 13 (10): 946. 16 October 2017

The 4D nucleome project.
Dekker, J., Belmont, A.S., Guttman, M., Leshyk, V.O., Lis, J.T., Lomvardas, S., Mirny, L.A., O'Shea, C.C., Park, P.J., Ren, B., Politz, J.C.R., Shendure, J. and Zhong, S.
Nature 549 (7671): 219-226. 14 September 2017

FANTOM5 CAGE profiles of human and mouse samples.
Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., Kawashima, T., Kojima, M., Kubosaki, A., Manabe, R.I., Murata, M., Nagao-Sato, S., Nakazato, K., Ninomiya, N., Nishiyori-Sueki, H., Noma, S., Saijyo, E., Saka, A., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R.A., Babina, M., Baillie, J.K., Barnett, T.C., Beckhouse, A.G., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A.J., Clevers, H.C., Davis, C.A., Detmar, M., Dohi, T., Edge, A.S.B., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach-Carson, M.C., Faulkner, G.J., Ferrai, C., Fisher, M.E., Forrester, L.M., Fujita, R., Furusawa, J.I., Geijtenbeek, T.B., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T.J., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P., Hitchens, K.J., Hume, D.A., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y.I., Kempfle, J.S., Kenna, T.J., Kere, J., Khachigian, L.M., Kitamura, T., Klein, S., Klinken, S.P., Knox, A.J., Kojima, S., Koseki, H., Koyasu, S., Lee, W., Lennartsson, A.s, Mackay-Sim, A., Mejhert, N., Mizuno, Y., Morikawa, H., Morimoto, M., Moro, K., Morris, K.J., Motohashi, H., Mummery, C.L., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nozaki, T., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D.A., Passier, R., Patrikakis, M., Pombo, A., Pradhan-Bhatt, S., Qin, X.Y., Rehli, M., Rizzu, P., Roy, S., Sajantila, A., Sakaguchi, S., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schmidl, C., Schneider, C., Schulze-Tanzil, G.G., Schwegmann, A., Sheng, G., Shin, J.W., Sugiyama, D., Sugiyama, T., Summers, K.M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tomoiu, A., Toyoda, H., van de Wetering, M., van den Berg, L.M., Verardo, R., Vijayan, D., Wells, C.A., Winteringham, L.N., Wolvetang, E., Yamaguchi, Y., Yamamoto, M., Yanagi-Mizuochi, C., Yoneda, M., Yonekura, Y., Zhang, P.G., Zucchelli, S., Abugessaisa, I., Arner, E., Harshbarger, J., Kondo, A., Lassmann, T., Lizio, M., Sahin, S., Sengstag, T., Severin, J., Shimoji, H., Suzuki, M., Suzuki, H., Kawai, J., Kondo, N., Itoh, M., Daub, C.O., Kasukawa, T., Kawaji, H., Carninci, P., Forrest, A.R.R. and Hayashizaki, Y.
Scientific Data 4 : 170112. 29 August 2017

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
Kar, G., Kim, J.K., Kolodziejczyk, A.A., Natarajan, K.N., Torlai Triglia, E., Mifsud, B., Elderkin, S., Marioni, J.C., Pombo, A. and Teichmann, S.A.
Nature Communications 8 (1): 36. 26 June 2017

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.
Barbieri, M., Xie, S.Q., Torlai Triglia, E., Chiariello, A.M., Bianco, S., de Santiago, I., Branco, M.R., Rueda, D., Nicodemi, M. and Pombo, A.
Nature Structural & Molecular Biology 24 (6): 515-524. June 2017

Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatment.
Mattei, D., Ivanov, A., Ferrai, C., Jordan, P., Guneykaya, D., Buonfiglioli, A., Schaafsma, W., Przanowski, P., Deuther-Conrad, W., Brust, P., Hesse, S., Patt, M., Sabri, O., Ross, T.L., Eggen, B.J.L., Boddeke, E.W.G.M., Kaminska, B., Beule, D., Pombo, A., Kettenmann, H. and Wolf, S.A.
Translational Psychiatry 7 (5): e1120. 9 May 2017

Complex multi-enhancer contacts captured by genome architecture mapping.
Beagrie, R.A., Scialdone, A., Schueler, M., Kraemer, D.C.A., Chotalia, M., Xie, S.Q., Barbieri, M., de Santiago, I., Lavitas, L.M., Branco, M.R., Fraser, J., Dostie, J., Game, L., Dillon, N., Edwards, P.A.W., Nicodemi, M. and Pombo, A.
Nature 543 (7646): 519-524. 23 March 2017

Formation of new chromatin domains determines pathogenicity of genomic duplications.
Franke, M., Ibrahim, D.M., Andrey, G., Schwarzer, W., Heinrich, V., Schoepflin, R., Kraft, K., Kempfer, R., Jerkovic, I., Chan, W.L., Spielmann, M., Timmermann, B., Wittler, L., Kurth, I., Cambiaso, P., Zuffardi, O., Houge, G., Lambie, L., Brancati, F., Pombo, A., Vingron, M., Spitz, F. and Mundlos, S.
Nature 538 (7624): 265-269. 13 October 2016

Gene activation by metazoan enhancers: diverse mechanisms stimulate distinct steps of transcription.
Beagrie, R.A. and Pombo, A.
BioEssays 38 (9): 881-893. September 2016

Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment.
Le, H.Q., Ghatak, S., Yeung, C.Y.C., Tellkamp, F., Günschmann, C., Dieterich, C., Yeroslaviz, A., Habermann, B., Pombo, A., Niessen, C.M. and Wickström, S.A.
Nature Cell Biology 18 (8): 864-875. August 2016

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.
Fraser, J., Ferrai, C., Chiariello, A.M., Schueler, M., Rito, T., Laudanno, G., Barbieri, M., Moore, B.L., Kraemer, D.C.A., Aitken, S., Xie, S.Q., Morris, K.J., Itoh, M., Kawaji, H., Jaeger, I., Hayashizaki, Y., Carninci, P., Forrest, A.R.R., Semple, C.A., Dostie, J., Pombo, A. and Nicodemi, M.
Molecular Systems Biology 11 (12): 852. 23 December 2015

Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.
Dias, J.D., Rito, T., Torlai Triglia, E., Kukalev, A., Ferrai, C., Chotalia, M., Brookes, E., Kimura, H. and Pombo, A.
eLife 4 : e11215. 19 December 2015

Polymer models of the organization of chromosomes in the nucleus of cells.
Chiariello, A.M., Bianco, S., Piccolo, A., Annunziatella, C., Barbieri, M., Pombo, A. and Nicodemi, M.
Modern Physics Letters B 29 (9): 1530003. 10 April 2015

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
Arner, E., Daub, C.O., Vitting-Seerup, K., Andersson, R., Lilje, B., Drabløs, F., Lennartsson, A., Rönnerblad, M., Hrydziuszko, O., Vitezic, M., Freeman, T.C., Alhendi, A., Arner, P., Axton, R., Baillie, J.K., Beckhouse, A., Bodega, B., Briggs, J., Brombacher, F., Davis, M., Detmar, M., Ehrlund, A., Endoh, M., Eslami, A., Fagiolini, M., Fairbairn, L., Faulkner, G.J., Ferrai, C., Fisher, M.E., Forrester, L., Goldowitz, D., Guler, R., Ha, T., Hara, M., Herlyn, M., Ikawa, T., Kai, C., Kawamoto, H., Khachigian, L., Klinken, P.S., Kojima, S., Koseki, H., Klein, S., Mejhert, N., Miyaguchi, K., Mizuno, Y., Morimoto, M., Morris, K.J., Mummery, C., Nakachi, Y., Ogishima, S., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D., Passier, R., Patrikakis, M., Pombo, A., Qin, X.Y., Roy, S., Sato, H., Savvi, S., Saxena, A., Schwegmann, A., Sugiyama, D., Swoboda, R., Tanaka, H., Tomoiu, A., Winteringham, L.N., Wolvetang, E., Yanagi-Mizuochi, C., Yoneda, M., Zabierowski, S., Zhang, P., Abugessaisa, I., Bertin, N., Diehl, A.D., Fukuda, S., Furuno, M., Harshbarger, J., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Ishizu, Y., Itoh, M., Kawashima, T., Kojima, M., Kondo, N., Lizio, M., Meehan, T.F., Mungall, C.J., Murata, M., Nishiyori-Sueki, H., Sahin, S., Sato-Nagao, S., Severin, J., de Hoon, M.J., Kawai, J., Kasukawa, T., Lassmann, T., Suzuki, H., Kawaji, H., Summers, K.M., Wells, C., Hume, D.A., Forrest, A.R.R., Sandelin, A., Carninci, P. and Hayashizaki, Y.
Science 347 (6225): 1010-1014. 27 February 2015

Models of chromosome structure.
Nicodemi, M. and Pombo, A.
Current Opinion in Cell Biology 28 : 90-95. 1 June 2014

A H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation.
Sabbattini, P., Sjoberg, M., Nikic, S., Frangini, A., Holmqvist, P.H., Kunowska, N., Carroll, T., Brookes, E., Arthur, S.J., Pombo, A. and Dillon, N.
Molecular Biology of the Cell 25 (6): 904-915. March 2014

A polymer model explains the complexity of large-scale chromatin folding.
Barbieri, M., Fraser, J., Lavitas, L.M., Chotalia, M., Dostie, J., Pombo, A. and Nicodemi, M.
Nucleus 4 (4): 267-273. 19 June 2013

A model of the large-scale organization of chromatin.
Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L.M., Dostie, J., Pombo, A. and Nicodemi, M.
Biochemical Society Transactions 41 (2): 508-512. April 2013

Mean expression of the X-chromosome is associated with neuronal density.
Swingland, J.T., Durrenberger, P.F., Reynolds, R., Dexter, D.T., Pombo, A., Deprez, M., Roncaroli, F. and Turkheimer, F.E.
Frontiers in Neuroscience 6 : 161. 12 November 2012

Complexity of chromatin folding is captured by the strings and binders switch model.
Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L.M., Dostie, J., Pombo, A. and Nicodemi, M.
Proceedings of the National Academy of Sciences of the United States of America 109 (40): 16173-16178. 2 October 2012

Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease.
Moeller, A., Xie, S.Q., Hosp, F., Lang, B., Phatnani, H.P., James, S., Ramirez, F., Collin, G.B., Naggert, J.K., Babu, M.M., Greenleaf, A.L., Selbach, M. and Pombo, A.
Molecular & Cellular Proteomics 11 (6): M111.011767. June 2012

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs.
Brookes, E., de Santiago, I., Hebenstreit, D., Morris, K.J., Carroll, T., Xie, S.Q., Stock, J.K., Heidemann, M., Eick, D., Nozaki, N., Kimura, H., Ragoussis, J., Teichmann, S.A. and Pombo, A.
Cell Stem Cell 10 (2): 157-170. 3 February 2012

Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment.
Alder, O., Lavial, F., Helness, A., Brookes, E., Pinho, S., Chandrashekran, A., Arnaud, P., Pombo, A., O'Neill, L. and Azuara, V.
Development 137 (15): 2483-2492. 1 August 2010

Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2.
Kanhere, A., Viiri, K., Araujo, C.C., Rasaiyaah, J., Bouwman, R.D., Whyte, W.A., Pereira, C.F., Brookes, E., Walker, K., Bell, G.W., Pombo, A., Fisher, A.G., Young, R.A. and Jenner, R.G.
Molecular Cell 38 (5): 675-688. 11 June 2010

Gene positioning.
Ferrai, C., de Castro, I.J., Lavitas, L., Chotalia, M. and Pombo, A.
Cold Spring Harbor Perspectives in Biology 2 (6): a000588. June 2010

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.
Landeira, D., Sauer, S., Poot, R., Dvorkina, M., Mazzarella, L., Jorgensen, H.F., Pereira, C.F., Leleu, M., Piccolo, F.M., Spivakov, M., Brookes, E., Pombo, A., Fisher, C., Skarnes, W.C., Snoek, T., Bezstarosti, K., Demmers, J., Klose, R.J., Casanova, M., Tavares, L., Brockdorff, N., Merkenschlager, M. and Fisher, A.G.
Nature Cell Biology 12 (6): 618-624. June 2010

Measurement of replication structures at the nanometer scale using super-resolution light microscopy.
Baddeley, D., Chagin, V.O., Schermelleh, L., Martin, S., Pombo, A., Carlton, P.M., Gahl, A., Domaing, P., Birk, U., Leonhardt, H., Cremer, C. and Cardoso, M.C.
Nucleic Acids Research 38 (2): e8. March 2010

Poised transcription factories prime silent uPA gene prior to activation.
Ferrai, C., Xie, S.Q., Luraghi, P., Munari, D., Ramirez, F., Branco, M.R., Pombo, A. and Crippa, M.P.
PLoS Biology 8 (1): e1000270. 5 January 2010

CryoFISH: fluorescence in situ hybridization on ultrathin cryosections.
Xie, S.Q., Lavitas, L.M. and Pombo, A.
Methods in Molecular Biology 659 : 219-230. 2010

Nuclear architecture in stem cells.
Morris, K.J., Chotalia, M. and Pombo, A.
Advances in Experimental Medicine and Biology 695 : 14-25. 2010

The molecular basis for stability of heterochromatin-mediated silencing in mammals.
Hiragami-Hamada, K., Xie, S.Q., Saveliev, A., Uribe-Lewis, S., Pombo, A. and Festenstein, R.
Epigenetics & Chromatin 2 (1): 14. 4 November 2009

Modifications of RNA polymerase II are pivotal in regulating gene expression states.
Brookes, E. and Pombo, A.
EMBO Reports 10 (11): 1213-1219. November 2009

Mechanisms regulating S phase progression in mammalian cells.
Maya-Mendoza, A., Tang, C.W., Pombo, A. and Jackson, D.A.
Frontiers in Bioscience 14 : 4199-4213. 1 January 2009

Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH.
Branco, M.R., Branco, T., Ramirez, F. and Pombo, A.
Chromosome Research 16 (3): 413-426. May 2008

Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region.
Noordermeer, D., Branco, M.R., Splinter, E., Klous, P., van Ijcken, W., Swagemakers, S., Koutsourakis, M., van der Spek, P., Pombo, A. and de Laat, W.
PLoS Genetics 4 (3): e1000016. 7 March 2008

Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells.
Stock, J.K., Giadrossi, S., Casanova, M., Brookes, E., Vidal, M., Koseki, H., Brockdorff, N., Fisher, A.G. and Pombo, A.
Nature Cell Biology 9 (12): 1428-1435. December 2007

Desmin immunolocalisation in autosomal dominant Emery-Dreifuss muscular dystrophy.
Piercy, R.J., Zhou, H., Feng, L., Pombo, A., Muntoni, F. and Brown, S.C.
Neuromuscular Disorders 17 (4): 297-305. April 2007

Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations.
Branco, M.R. and Pombo, A.
PLoS Biology 4 (5): e138. May 2006

Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain.
Xie, S.Q., Martin, S., Guillot, P.V., Bentley, D.L. and Pombo, A.
Molecular Biology of the Cell 17 (4): 1723-1733. 1 April 2006

Distribution of different phosphorylated forms of RNA polymerase II in relation to Cajal and PML bodies in human cells: an ultrastructural study.
Xie, S.Q. and Pombo, A.
Histochemistry and Cell Biology 125 (1-2): 21-31. January 2006

Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division.
Chow, C.M., Georgiou, A., Szutorisz, H., Maia e Silva, A., Pombo, A., Barahona, I., Dargelos, E., Canzonetta, C. and Dillon, N.
EMBO Reports 6 (4): 354-360. April 2005

Functional analysis of Vif protein shows less restriction of human immunodeficiency virus type 2 by APOBEC3G.
Ribeiro, A.C., Maia e Silva, A., Santa-Marta, M., Pombo, A., Moniz-Pereira, J., Goncalves, J. and Barahona, I.
Journal of Virology 79 (2): 823-833. January 2005

Fixation-induced redistribution of hyperphosphorylated RNA polymerase II in the nucleus of human cells.
Guillot, P.V., Xie, S.Q., Hollinshead, M. and Pombo, A.
Experimental Cell Research 295 (2): 460-468. 1 May 2004

CD8 alpha is an activation marker for a subset of peripheral CD4 T cells.
Kenny, E., Mason, D., Saoudi, A., Pombo, A. and Ramirez, F.
European Journal of Immunology 34 (5): 1262-1271. May 2004

Measuring the size of biological nanostructures with spatially modulated illumination microscopy.
Martin, S., Failla, A.V., Spoeri, U., Cremer, C. and Pombo, A.
Molecular Biology of the Cell 15 (5): 2449-2455. May 2004

Interaction of proteins with promoter elements of the human U2 snRNA genes in vivo.
Boyd, D.C., Pombo, A. and Murphy, S.
Gene 315 (1-2): 103-112. 2 October 2003

Transcription factories: quantitative studies of nanostructures in the mammalian nucleus.
Martin, S. and Pombo, A.
Chromosome Research 11 (5): 461-470. 1 July 2003

Genome function and nuclear architecture: from gene expression to nanoscience.
O'Brien, T.P., Bult, C.J., Cremer, C., Grunze, M., Knowles, B.B., Langowski, J., McNally, J., Pederson, T., Politz, J.C., Pombo, A., Schmahl, G., Spatz, J.P. and van Driel, R.
Genome Research 13 (6A): 1029-1041. June 2003

Cellular genomics: which genes are transcribed, when and where?
Pombo, A.
Trends in Biochemical Sciences 28 (1): 6-9. January 2003

Book Section

Polymer models of the chromosomes in the nucleus of cells.
Chiariello, A.M., Bianco, S., Piccolo, A., Annunziatella, C., Barbieri, M., Pombo, A. and Nicodemi, M.
In: High Performance Scientific Computing Using Distributed Infrastructures. World Scientific Publishing Co., 239-248. ISBN 9789814759700 January 2017

On the nature of chromatin 3D organization.
Nicodemi, M. and Pombo, A.
In: Epigenetics and Systems Biology. Academic Press, 191-201. ISBN 978-012803075-2 2017

Correlative microscopy using Tokuyasu cryosections: applications for immunogold labelling and in situ hybridisation.
Branco, M.R., Xie, S.Q., Martin, S. and Pombo, A.
In: Cell Imaging (Methods Express Series). Methods Express Series . Scion Publishing, Bloxham, 201-217. ISBN 1-904842-26-7 2006

The organization of transcription in the nucleus of mammalian cells.
Guillot, P.V., Martin, S. and Pombo, A.
In: Visions of the Cell Nucleus. American Scientific Publishers, Stevenson Ranch, CA, 95-105. ISBN 1-5883-027-6 2005

Conference or Workshop Item

From linear genome sequence to three-dimensional organization of the cell nucleus.
Politz, J., van Driel, R., Sauer, M. and Pombo, A.
In: Jackson Laboratory 'Advances in nanostructural genomics II' meeting, 3-6 Oct 2002, Bar Harbor, USA. 28 February 2003

Review

Epigenetic regulatory layers in the 3D nucleus.
Willemin, A., Szabo, D. and Pombo, A.
Molecular Cell 84 (3): 415-428. 1 February 2024

Mechanisms of enhancer function in neuronal systems in health and disease.
Zea Redondo, L. and Pombo, A.
Current Opinion in Systems Biology 32-33 : 100443. March 2023

Polymer models of chromatin imaging data in single cells.
Conte, M., Chiariello, A.M., Abraham, A., Bianco, S., Esposito, A., Nicodemi, M., Matteuzzi, T. and Vercellone, F.
Algorithms 15 (9): 330. 16 September 2022

The physics of DNA folding: polymer models and phase-separation.
Esposito, A., Abraham, A., Conte, M., Vercellone, F., Prisco, A., Bianco, S. and Chiariello, A.M.
Polymers 14 (9): 1918. 9 May 2022

Physical mechanisms of chromatin spatial organization.
Chiariello, A.M., Bianco, S., Esposito, A., Fiorillo, L., Conte, M., Irani, E., Musella, F., Abraham, A., Prisco, A. and Nicodemi, M.
FEBS Journal 289 (5): 1180-1190. March 2022

Polymer models are a versatile tool to study chromatin 3D organization.
Esposito, A., Bianco, S., Fiorillo, L., Conte, M., Abraham, A., Musella, F., Nicodemi, M., Prisco, A. and Chiariello, A.M.
Biochemical Society Transactions 49 (4): 1675-1684. August 2021

The dynamics of chromatin architecture in brain development and function.
Harabula, I. and Pombo, A.
Current Opinion in Genetics & Development 67 : 84-93. April 2021

Divergent transcription of the Nkx2-5 locus generates two enhancer RNAs with opposing functions.
Salamon, I., Serio, S., Bianco, S., Pagiatakis, C., Crasto, S., Chiariello, A.M., Conte, M., Cattaneo, P., Fiorillo, L., Felicetta, A., di Pasquale, E., Kunderfranco, P., Nicodemi, M., Papait, R. and Condorelli, G.
iScience 23 (9): 101539. 25 September 2020

Computational approaches from polymer physics to investigate chromatin folding.
Bianco, S., Chiariello, A.M., Conte, M., Esposito, A., Fiorillo, L., Musella, F. and Nicodemi, M.
Current Opinion in Cell Biology 64 : 10-17. June 2020

Evolving methodologies and concepts in 4D nucleome research.
Sparks, T.M., Harabula, I. and Pombo, A.
Current Opinion in Cell Biology 64 : 105-111. June 2020

Methods for mapping 3D chromosome architecture.
Kempfer, R. and Pombo, A.
Nature Reviews Genetics 21 (4): 207-226. April 2020

A polymer physics investigation of the architecture of the murine orthologue of the 7q11.23 human locus.
Chiariello, A.M., Esposito, A., Annunziatella, C., Bianco, S., Fiorillo, L., Prisco, A. and Nicodemi, M.
Frontiers in Neuroscience 11 : 559. 10 October 2017

Three-dimensional genome architecture: players and mechanisms.
Pombo, A. and Dillon, N.
Nature Reviews Molecular Cell Biology 16 (4): 245-257. April 2015

Physical mechanisms behind the large scale features of chromatin organization.
Pombo, A. and Nicodemi, M.
Transcription 5 (2): e28447. April 2014

Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus.
Barbieri, M., Scialdone, A., Gamba, A., Pombo, A. and Nicodemi, M.
Soft Matter 9 (36): 8631-8635. 28 September 2013

Eukaryotic gene regulation in three dimensions and its impact on genome evolution.
Babu, M.M., Janga, S.C., de Santiago, I. and Pombo, A.
Current Opinion in Genetics & Development 18 (6): 571-582. December 2008

Functional organisation of the genome during interphase.
Pombo, A. and Branco, M.R.
Current Opinion in Genetics & Development 17 (5): 451-455. October 2007

Advances in imaging the interphase nucleus using thin cryosections.
Pombo, A.
Histochemistry and Cell Biology 128 (2): 97-104. August 2007

Chromosome organization: new facts, new models.
Branco, M.R. and Pombo, A.
Trends in Cell Biology 17 (3): 127-34. March 2007

Editorial

Genome architecture mapping detects transcriptionally active, multiway chromatin contacts.
Thieme, C.J. and Pombo, A.
Nature Methods 20 (7): 993-994. July 2023

Editorial overview: Genome architecture and expression.
Bickmore, W. and Pombo, A.
Current Opinion in Genetics & Development 55 : iii-iv. April 2019

Cell cycle: continuous chromatin changes.
Beagrie, R.A. and Pombo, A.
Nature 547 (7661): 34-35. 6 July 2017

Keep them close: PRC2 poises enhancer-promoter interactions at anterior neuronal genes.
Caglio, Giulia, Torlai Triglia, E. and Pombo, A.
Cell Stem Cell 20 (5): 573-575. 4 May 2017

A finer print than TADs: PRC1-mediated domains.
Torlai Triglia, E., Rito, Tiago and Pombo, A.
Molecular Cell 65 (3): 373-375. 2 February 2017

Examining topological domain influence on enhancer function.
Beagrie, R.A. and Pombo, A.
Developmental Cell 39 (5): 523-524. 5 December 2016

Stem cell epigenetics: looking forward.
Benitah, S.A., Bracken, A., Dou, Y., Huangfu, D., Ivanova, N., Koseki, H., Laurent, L., Lim, D.A., Meshorer, E., Pombo, A., Sander, M. and Xu, G.L.
Cell Stem Cell 14 (6): 706-709. 5 June 2014

Code breaking: the RNAPII modification code in pluripotency.
Brookes, E. and Pombo, A.
Cell Cycle 11 (7): 1267-1268. 1 April 2012

Nuclear cell biology.
Pombo, A. and Starr, D.A.
Molecular Biology of the Cell 22 (6): 722. 15 March 2011

Polycomb targets seek closest neighbours.
Chotalia, M. and Pombo, A.
PLoS Genetics 7 (3): e1002031. March 2011

Nucleus and gene expression: the structure and function conundrum.
Pombo, A. and Gilbert, D.M.
Current Opinion in Cell Biology 22 (3): 269-270. June 2010

3D chromatin regulation of Sonic hedgehog in the limb buds.
Ferrai, C. and Pombo, A.
Developmental Cell 16 (1): 9-11. 20 January 2009

Comment

Chromosomes phase transition to function.
Nicodemi, M. and Bianco, S.
Biophysical Journal 119 (4): 724-725. 18 August 2020

Polymer models of chromatin organization.
Barbieri, M., Scialdone, A., Piccolo, A., Chiariello, A.M., di Lanno, C., Prisco, A., Pombo, A. and Nicodemi, M.
Frontiers in Genetics 4 : 113. June 2013

Preprint

3D genome topologies distinguish pluripotent epiblast and primitive endoderm cells in the mouse blastocyst.
Loof, G., Szabo, D., Garg, V., Kukalev, A., Zea-Redondo, L., Kempfer, R., Sparks, T.M., Zhang, Yi., Thieme, C.J., Carvalho, S., Weise, A., Balachandran, M., Liehr, T., Welch, L.R., Hadjantonakis, A.K. and Pombo, A.
bioRxiv : 2022.10.19.512781. 20 October 2022

CTCF mediates dosage and sequence-context-dependent transcriptional insulation through formation of local chromatin domains.
Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A.M., Yu, M., Hu, R., Juric, I., Hu, M., Nicodemi, M., Zhuang, X. and Ren, B.
bioRxiv : 2020.07.07.192526. 8 July 2020

Single-cell analysis of the 3D topologies of genomic loci using genome architecture mapping.
Welch, L.R., Baugher, C., Zhang, Y., Davis, T., Marzluff, W.F., Welch, J.D. and Pombo, A.
bioRxiv : 2020.02.10.941047. 13 February 2020

GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data.
Beagrie, R.A. and Schueler, M.
bioRxiv : 114710. 20 March 2017