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Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes.
Schindler, M. and Osterwalder, M. and Harabula, I. and Wittler, L. and Tzika, A.C. and Dechmann, D.K.N. and Vingron, M. and Visel, A. and 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. and Thieme, C.J. and Annunziatella, C. and Baugher, C. and Zhang, Y. and Schueler, M. and Kukalev, A. and Kempfer, R. and Chiariello, A.M. and Bianco, S. and Li, Y. and Davis, T. and Scialdone, A. and Welch, L.R. and 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. and Chiariello, A.M. and Bianco, S. and Esposito, A. and 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. and Drucker, K.L. and Kollmeyer, T.M. and Tsai, R. and Winick-Ng, W. and Liang, M. and Malik, A. and Pawling, J. and De Lorenzo, S.B. and Ali, A. and Decker, P.A. and Kosel, M.L. and Panda, A. and Al-Zahrani, K.N. and Jiang, L. and Browning, J.W.L. and Lowden, C. and Geuenich, M. and Hernandez, J.J. and Gosio, J.T. and Ahmed, M. and Loganathan, S.K. and Berman, J. and Trcka, D. and Michealraj, K.A. and Fortin, J. and Carson, B. and Hollingsworth, E.W. and Jacinto, S. and Mazrooei, P. and Zhou, L. and Elia, A. and Lupien, M. and He, H.H. and Murphy, D.J. and Wang, L. and Abyzov, A. and Dennis, J.W. and Maass, P.G. and Campbell, K. and Wilson, M.D. and Lachance, D.H. and Wrensch, M. and Wiencke, J. and Mak, T. and Pennacchio, L.A. and Dickel, D.E. and Visel, A. and Wrana, J. and Taylor, M.D. and Zadeh, G. and Dirks, P. and Eckel-Passow, J.E. and Attisano, L. and Pombo, A. and Ida, C.M. and Kvon, E.Z. and 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. and Szabo, Q. and Chiariello, A.M. and Chudzik, K. and Schöpflin, R. and Rothe, P. and Mattei, A.L. and Zehnder, To. and Harnett, D. and Laupert, V. and Bianco, S. and Hetzel, S. and Glaser, J. and Phan, M.H.Q. and Schindler, M. and Ibrahim, D.M. and Paliou, C. and Esposito, A. and Prada-Medina, C.A. and Haas, S.A. and Giere, P. and Vingron, M. and Wittler, L. and Meissner, A. and Nicodemi, M. and Cavalli, G. and Bantignies, F. and 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. and Chiariello, A.M. and Esposito, A. and Zoppoli, P. and Zambelli, F. and Elia, M.A. and Pesole, G. and Incarnato, D. and Passaro, F. and Piscitelli, S. and Oliviero, S. and Nicodemi, M. and 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. and Irani, E. and Chiariello, A.M. and Abraham, A. and Bianco, S. and Esposito, A. and Nicodemi, M.
Nature Communications 13 (1): 4070. 13 July 2022

Dynamics of bacteria scanning a porous environment.
Irani, E. and 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. and Bianco, S. and Chiariello, A.M. and Abraham, A. and Fiorillo, L. and Conte, M. and 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. and Micale, L. and Manara, E. and Esposito, A. and Palumbo, O. and Chiariello, A.M. and Bianco, S. and Guerri, G. and Bertelli, M. and Giuffrida, M.G. and Bernardini, L. and Notarangelo, A. and 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. and Kopp, W. and Vučićević, D. and Mattonet, K. and Kempfer, R. and Hirsekorn, A. and Bilić, I. and Gil, M. and Trinks, A. and Merks, A.M. and Panáková, D. and Pombo, A. and Akalin, A. and Junker, J.P. and Stainier, D.Y.R. and Garfield, D. and 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. and Toner, B. and Xie, S.Q. and Swingland, J. and Hodges, A. and Tabrizi, S.J. and Turkheimer, F. and 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. and Esposito, A. and Fiorillo, L. and Campanile, R. and Annunziatella, C. and Corrado, A. and Chiariello, M.G. and 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. and Fiorillo, L. and Bianco, S. and Chiariello, A.M. and Esposito, A. and Musella, F. and Flora, F. and 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. and Kukalev, A. and Harabula, I. and Zea-Redondo, L. and Szabó, D. and Meijer, M. and Serebreni, L. and Zhang, Y. and Bianco, S. and Chiariello, A.M. and Irastorza-Azcarate, I. and Thieme, C.J. and Sparks, T.M. and Carvalho, S. and Fiorillo, L. and Musella, F. and Irani, E. and Triglia, E.T. and Kolodziejczyk, A.A. and Abentung, A. and Apostolova, G. and Paul, E.J. and Franke, V. and Kempfer, R. and Akalin, A. and Teichmann, S.A. and Dechant, G. and Ungless, M.A. and Nicodemi, M. and Welch, L. and 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. and Fiorillo, L. and Annunziatella, C. and Esposito, A. and Musella, F. and Abraham, A. and 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. and Kempfer, R. and Kukalev, A. and Irastorza-Azcarate, I. and Loof, G. and Kehr, B. and Pombo, A. and 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. and De la Calle-Mustienes, E. and Neto, A. and Almuedo-Castillo, M. and Irastorza-Azcarate, I. and Acemel, R.D. and Tena, J.J. and 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. and Zhu, Q. and Jussila, A. and Han, Y. and Bintu, B. and Kern, C. and Conte, M. and Zhang, Y. and Bianco, S. and Chiariello, A.M. and Yu, M. and Hu, R. and Tastemel, M. and Juric, I. and Hu, M. and Nicodemi, M. and 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. and Saraswat, M. and Bessière, C. and Menichelli, C. and Ramilowski, J.A. and Severin, J. and Hayashizaki, Y. and Itoh, M. and Tagami, M. and Murata, M. and Kojima-Ishiyama, M. and Noma, S. and Noguchi, S. and Kasukawa, T. and Hasegawa, A. and Suzuki, H. and Nishiyori-Sueki, H. and Frith, M.C. and Chatelain, C. and Carninci, P. and de Hoon, M.J.L. and Wasserman, W.W. and 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. and Musella, F. and Conte, M. and Kempfer, R. and Chiariello, A.M. and Bianco, S. and Kukalev, A. and Irastorza-Azcarate, I. and Esposito, A. and Abraham, A. and Prisco, A. and 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. and Ishii, H. and Xiong, X. and Bianco, S. and Meitinger, F. and Hu, R. and Hocker, J.D. and Conte, M. and Gorkin, D. and Yu, M. and Li, B. and Dixon, J.R. and Hu, M. and Nicodemi, M. and 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. and Seguin, J. and Lotz, C. and Molitor, A.M. and Irastorza-Azcarate, I. and Awada, A. and Karasu, N. and Bombardier, A. and Cosquer, B. and Skarmeta, J.L.G. and Cassel, J.C. and Boutillier, A.L. and 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. and Almouzni, G. and Gorski, S.A. and Aerts, S. and Amit, I. and Bertero, M.G. and Bock, C. and Bredenoord, A.L. and Cavalli, G. and Chiocca, S. and Clevers, H. and De Strooper, B. and Eggert, A. and Ellenberg, J. and Fernández, X.M. and Figlerowicz, M. and Gasser, S.M. and Hubner, N. and Kjems, J. and Knoblich, J.A. and Krabbe, G. and Lichter, P. and Linnarsson, S. and Marine, J.C. and Marioni, J. and Marti-Renom, M.A. and Netea, M.G. and Nickel, D. and Nollmann, M. and Novak, H.R. and Parkinson, H. and Piccolo, S. and Pinheiro, I. and Pombo, A. and Popp, C. and Reik, W. and Roman-Roman, S. and Rosenstiel, P. and Schultze, J.L. and Stegle, O. and Tanay, A. and Testa, G. and Thanos, D. and Theis, F.J. and Torres-Padilla, M.E. and Valencia, A. and Vallot, C. and van Oudenaarden, A. and 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. and Bianco, S. and Chiariello, A.M. and Barbieri, M. and Esposito, A. and Annunziatella, C. and Conte, M. and Corrado, A. and Prisco, A. and 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. and Fiorillo, L. and Bianco, S. and Chiariello, A.M. and 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. and Bianco, S. and Oudelaar, A M. and Esposito, A. and Annunziatella, C. and Fiorillo, L. and Conte, M. and Corrado, A. and Prisco, A. and Larke, M.S.C. and Telenius, J.M. and Sciarretta, R. and Musella, F. and Buckle, V.J. and Higgs, D.R. and 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. and Annunziatella, C. and Andrey, G. and Chiariello, A.M. and Esposito, A. and Fiorillo, L. and Prisco, A. and Conte, M. and Campanile, R. and Nicodemi, M.
Cell Reports 28 (6): 1574-1583. 6 August 2019

Discontinuous shear-thinning in adhesive dispersions.
Irani, E. and 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. and Annunziatella, C. and Bianco, S. and Chiariello, A.M. and 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. and Guckelberger, P. and Schöpflin, R. and Heinrich, V. and Esposito, A. and Chiariello, A.M. and Bianco, S. and Annunziatella, C. and Helmuth, J. and Haas, S. and Jerković, I. and Brieske, N. and Wittler, L. and Timmermann, B. and Nicodemi, M. and Vingron, M. and 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. and Palluzzi, F. and Chiariello, A.M. and Piccioni, R. and Bianco, S. and Furia, L. and De Conti, G. and Bouwman, B.A.M. and Melloni, G. and Guido, D. and Giacò, L. and Luzi, L. and Cittaro, D. and Faretta, M. and Nicodemi, M. and 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. and Torlai Triglia, E. and Warburton, M. and Voigt, P. and 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. and Almouzni, G. and Bickmore, W.A. and Bystricky, K. and Cavalli, G. and Fraser, P. and Gasser, S.M. and Giorgetti, L. and Heard, E. and Nicodemi, M. and Nollmann, M. and Orozco, M. and 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. and Chiariello, A.M. and Esposito, A. and Bianco, S. and 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. and Lupiáñez, D.G. and Chiariello, A.M. and Annunziatella, C. and Kraft, K. and Schöpflin, R. and Wittler, L. and Andrey, G. and Vingron, M. and Pombo, A. and 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. and Bianco, S. and Annunziatella, C. and Esposito, A. and Nicodemi, M.
EPL 120 (4): 40004. 8 February 2018

Understanding chromatin structure: efficient computational implementation of polymer physics models.
Bianco, S. and Annunziatella, C. and Esposito, A. and Fiorillo, L. and Conte, M. and 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. and Winick-Ng, W. and Seah, C. and Rylett, R.J.
Frontiers in Molecular Neuroscience 10 : 415. December 2017

Structure of the human chromosome interaction network.
Sarnataro, S. and Chiariello, A.M. and Esposito, A. and 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. and Menegatti, J. and Franke, V. and Kocks, C. and Boltengagen, A. and Hennig, T. and Theil, K. and Rutkowski, A. and Ferrai, C. and Baer, L. and Kermas, L. and Friedel, C. and Rajewsky, N. and Akalin, A. and Dölken, L. and 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. and Torlai Triglia, E. and Risner-Janiczek, J.R. and Rito, T. and Rackham, O.J.L. and De Santiago, I. and Kukalev, A. and Nicodemi, M. and Akalin, A. and Li, M. and Ungless, M.A. and Pombo, A.
Molecular Systems Biology 13 (10): 946. 16 October 2017

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

FANTOM5 CAGE profiles of human and mouse samples.
Noguchi, S. and Arakawa, T. and Fukuda, S. and Furuno, M. and Hasegawa, A. and Hori, F. and Ishikawa-Kato, S. and Kaida, K. and Kaiho, A. and Kanamori-Katayama, M. and Kawashima, T. and Kojima, M. and Kubosaki, A. and Manabe, R.I. and Murata, M. and Nagao-Sato, S. and Nakazato, K. and Ninomiya, N. and Nishiyori-Sueki, H. and Noma, S. and Saijyo, E. and Saka, A. and Sakai, M. and Simon, C. and Suzuki, N. and Tagami, M. and Watanabe, S. and Yoshida, S. and Arner, P. and Axton, R.A. and Babina, M. and Baillie, J.K. and Barnett, T.C. and Beckhouse, A.G. and Blumenthal, A. and Bodega, B. and Bonetti, A. and Briggs, J. and Brombacher, F. and Carlisle, A.J. and Clevers, H.C. and Davis, C.A. and Detmar, M. and Dohi, T. and Edge, A.S.B. and Edinger, M. and Ehrlund, A. and Ekwall, K. and Endoh, M. and Enomoto, H. and Eslami, A. and Fagiolini, M. and Fairbairn, L. and Farach-Carson, M.C. and Faulkner, G.J. and Ferrai, C. and Fisher, M.E. and Forrester, L.M. and Fujita, R. and Furusawa, J.I. and Geijtenbeek, T.B. and Gingeras, T. and Goldowitz, D. and Guhl, S. and Guler, R. and Gustincich, S. and Ha, T.J. and Hamaguchi, M. and Hara, M. and Hasegawa, Y. and Herlyn, M. and Heutink, P. and Hitchens, K.J. and Hume, D.A. and Ikawa, T. and Ishizu, Y. and Kai, C. and Kawamoto, H. and Kawamura, Y.I. and Kempfle, J.S. and Kenna, T.J. and Kere, J. and Khachigian, L.M. and Kitamura, T. and Klein, S. and Klinken, S.P. and Knox, A.J. and Kojima, S. and Koseki, H. and Koyasu, S. and Lee, W. and Lennartsson, A.s and Mackay-Sim, A. and Mejhert, N. and Mizuno, Y. and Morikawa, H. and Morimoto, M. and Moro, K. and Morris, K.J. and Motohashi, H. and Mummery, C.L. and Nakachi, Y. and Nakahara, F. and Nakamura, T. and Nakamura, Y. and Nozaki, T. and Ogishima, S. and Ohkura, N. and Ohno, H. and Ohshima, M. and Okada-Hatakeyama, M. and Okazaki, Y. and Orlando, V. and Ovchinnikov, D.A. and Passier, R. and Patrikakis, M. and Pombo, A. and Pradhan-Bhatt, S. and Qin, X.Y. and Rehli, M. and Rizzu, P. and Roy, S. and Sajantila, A. and Sakaguchi, S. and Sato, H. and Satoh, H. and Savvi, S. and Saxena, A. and Schmidl, C. and Schneider, C. and Schulze-Tanzil, G.G. and Schwegmann, A. and Sheng, G. and Shin, J.W. and Sugiyama, D. and Sugiyama, T. and Summers, K.M. and Takahashi, N. and Takai, J. and Tanaka, H. and Tatsukawa, H. and Tomoiu, A. and Toyoda, H. and van de Wetering, M. and van den Berg, L.M. and Verardo, R. and Vijayan, D. and Wells, C.A. and Winteringham, L.N. and Wolvetang, E. and Yamaguchi, Y. and Yamamoto, M. and Yanagi-Mizuochi, C. and Yoneda, M. and Yonekura, Y. and Zhang, P.G. and Zucchelli, S. and Abugessaisa, I. and Arner, E. and Harshbarger, J. and Kondo, A. and Lassmann, T. and Lizio, M. and Sahin, S. and Sengstag, T. and Severin, J. and Shimoji, H. and Suzuki, M. and Suzuki, H. and Kawai, J. and Kondo, N. and Itoh, M. and Daub, C.O. and Kasukawa, T. and Kawaji, H. and Carninci, P. and 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. and Kim, J.K. and Kolodziejczyk, A.A. and Natarajan, K.N. and Torlai Triglia, E. and Mifsud, B. and Elderkin, S. and Marioni, J.C. and 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. and Xie, S.Q. and Torlai Triglia, E. and Chiariello, A.M. and Bianco, S. and de Santiago, I. and Branco, M.R. and Rueda, D. and 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. and Ivanov, A. and Ferrai, C. and Jordan, P. and Guneykaya, D. and Buonfiglioli, A. and Schaafsma, W. and Przanowski, P. and Deuther-Conrad, W. and Brust, P. and Hesse, S. and Patt, M. and Sabri, O. and Ross, T.L. and Eggen, B.J.L. and Boddeke, E.W.G.M. and Kaminska, B. and Beule, D. and Pombo, A. and 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. and Scialdone, A. and Schueler, M. and Kraemer, D.C.A. and Chotalia, M. and Xie, S.Q. and Barbieri, M. and de Santiago, I. and Lavitas, L.M. and Branco, M.R. and Fraser, J. and Dostie, J. and Game, L. and Dillon, N. and Edwards, P.A.W. and 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. and Ibrahim, D.M. and Andrey, G. and Schwarzer, W. and Heinrich, V. and Schoepflin, R. and Kraft, K. and Kempfer, R. and Jerkovic, I. and Chan, W.L. and Spielmann, M. and Timmermann, B. and Wittler, L. and Kurth, I. and Cambiaso, P. and Zuffardi, O. and Houge, G. and Lambie, L. and Brancati, F. and Pombo, A. and Vingron, M. and 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. and Ghatak, S. and Yeung, C.Y.C. and Tellkamp, F. and Günschmann, C. and Dieterich, C. and Yeroslaviz, A. and Habermann, B. and Pombo, A. and 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. and Ferrai, C. and Chiariello, A.M. and Schueler, M. and Rito, T. and Laudanno, G. and Barbieri, M. and Moore, B.L. and Kraemer, D.C.A. and Aitken, S. and Xie, S.Q. and Morris, K.J. and Itoh, M. and Kawaji, H. and Jaeger, I. and Hayashizaki, Y. and Carninci, P. and Forrest, A.R.R. and Semple, C.A. and Dostie, J. and 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. and Rito, T. and Torlai Triglia, E. and Kukalev, A. and Ferrai, C. and Chotalia, M. and Brookes, E. and 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. and Bianco, S. and Piccolo, A. and Annunziatella, C. and Barbieri, M. and 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. and Daub, C.O. and Vitting-Seerup, K. and Andersson, R. and Lilje, B. and Drabløs, F. and Lennartsson, A. and Rönnerblad, M. and Hrydziuszko, O. and Vitezic, M. and Freeman, T.C. and Alhendi, A. and Arner, P. and Axton, R. and Baillie, J.K. and Beckhouse, A. and Bodega, B. and Briggs, J. and Brombacher, F. and Davis, M. and Detmar, M. and Ehrlund, A. and Endoh, M. and Eslami, A. and Fagiolini, M. and Fairbairn, L. and Faulkner, G.J. and Ferrai, C. and Fisher, M.E. and Forrester, L. and Goldowitz, D. and Guler, R. and Ha, T. and Hara, M. and Herlyn, M. and Ikawa, T. and Kai, C. and Kawamoto, H. and Khachigian, L. and Klinken, P.S. and Kojima, S. and Koseki, H. and Klein, S. and Mejhert, N. and Miyaguchi, K. and Mizuno, Y. and Morimoto, M. and Morris, K.J. and Mummery, C. and Nakachi, Y. and Ogishima, S. and Okada-Hatakeyama, M. and Okazaki, Y. and Orlando, V. and Ovchinnikov, D. and Passier, R. and Patrikakis, M. and Pombo, A. and Qin, X.Y. and Roy, S. and Sato, H. and Savvi, S. and Saxena, A. and Schwegmann, A. and Sugiyama, D. and Swoboda, R. and Tanaka, H. and Tomoiu, A. and Winteringham, L.N. and Wolvetang, E. and Yanagi-Mizuochi, C. and Yoneda, M. and Zabierowski, S. and Zhang, P. and Abugessaisa, I. and Bertin, N. and Diehl, A.D. and Fukuda, S. and Furuno, M. and Harshbarger, J. and Hasegawa, A. and Hori, F. and Ishikawa-Kato, S. and Ishizu, Y. and Itoh, M. and Kawashima, T. and Kojima, M. and Kondo, N. and Lizio, M. and Meehan, T.F. and Mungall, C.J. and Murata, M. and Nishiyori-Sueki, H. and Sahin, S. and Sato-Nagao, S. and Severin, J. and de Hoon, M.J. and Kawai, J. and Kasukawa, T. and Lassmann, T. and Suzuki, H. and Kawaji, H. and Summers, K.M. and Wells, C. and Hume, D.A. and Forrest, A.R.R. and Sandelin, A. and 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. and Sjoberg, M. and Nikic, S. and Frangini, A. and Holmqvist, P.H. and Kunowska, N. and Carroll, T. and Brookes, E. and Arthur, S.J. and 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. and Fraser, J. and Lavitas, L.M. and Chotalia, M. and Dostie, J. and Pombo, A. and Nicodemi, M.
Nucleus 4 (4): 267-273. 19 June 2013

A model of the large-scale organization of chromatin.
Barbieri, M. and Chotalia, M. and Fraser, J. and Lavitas, L.M. and Dostie, J. and 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. and Durrenberger, P.F. and Reynolds, R. and Dexter, D.T. and Pombo, A. and Deprez, M. and 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. and Chotalia, M. and Fraser, J. and Lavitas, L.M. and Dostie, J. and 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. and Xie, S.Q. and Hosp, F. and Lang, B. and Phatnani, H.P. and James, S. and Ramirez, F. and Collin, G.B. and Naggert, J.K. and Babu, M.M. and Greenleaf, A.L. and 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. and de Santiago, I. and Hebenstreit, D. and Morris, K.J. and Carroll, T. and Xie, S.Q. and Stock, J.K. and Heidemann, M. and Eick, D. and Nozaki, N. and Kimura, H. and Ragoussis, J. and 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. and Lavial, F. and Helness, A. and Brookes, E. and Pinho, S. and Chandrashekran, A. and Arnaud, P. and Pombo, A. and 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. and Viiri, K. and Araujo, C.C. and Rasaiyaah, J. and Bouwman, R.D. and Whyte, W.A. and Pereira, C.F. and Brookes, E. and Walker, K. and Bell, G.W. and Pombo, A. and Fisher, A.G. and Young, R.A. and Jenner, R.G.
Molecular Cell 38 (5): 675-688. 11 June 2010

Gene positioning.
Ferrai, C. and de Castro, I.J. and Lavitas, L. and 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. and Sauer, S. and Poot, R. and Dvorkina, M. and Mazzarella, L. and Jorgensen, H.F. and Pereira, C.F. and Leleu, M. and Piccolo, F.M. and Spivakov, M. and Brookes, E. and Pombo, A. and Fisher, C. and Skarnes, W.C. and Snoek, T. and Bezstarosti, K. and Demmers, J. and Klose, R.J. and Casanova, M. and Tavares, L. and Brockdorff, N. and 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. and Chagin, V.O. and Schermelleh, L. and Martin, S. and Pombo, A. and Carlton, P.M. and Gahl, A. and Domaing, P. and Birk, U. and Leonhardt, H. and 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. and Xie, S.Q. and Luraghi, P. and Munari, D. and Ramirez, F. and Branco, M.R. and 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. and Lavitas, L.M. and Pombo, A.
Methods in Molecular Biology 659 : 219-230. 2010

Nuclear architecture in stem cells.
Morris, K.J. and 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. and Xie, S.Q. and Saveliev, A. and Uribe-Lewis, S. and 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. and Tang, C.W. and 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. and Branco, T. and 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. and Branco, M.R. and Splinter, E. and Klous, P. and van Ijcken, W. and Swagemakers, S. and Koutsourakis, M. and van der Spek, P. and 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. and Giadrossi, S. and Casanova, M. and Brookes, E. and Vidal, M. and Koseki, H. and Brockdorff, N. and 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. and Zhou, H. and Feng, L. and Pombo, A. and 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. and Martin, S. and Guillot, P.V. and 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. and Georgiou, A. and Szutorisz, H. and Maia e Silva, A. and Pombo, A. and Barahona, I. and Dargelos, E. and 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. and Maia e Silva, A. and Santa-Marta, M. and Pombo, A. and Moniz-Pereira, J. and 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. and Xie, S.Q. and 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. and Mason, D. and Saoudi, A. and 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. and Failla, A.V. and Spoeri, U. and 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. and 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. and Bult, C.J. and Cremer, C. and Grunze, M. and Knowles, B.B. and Langowski, J. and McNally, J. and Pederson, T. and Politz, J.C. and Pombo, A. and Schmahl, G. and 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. and Bianco, S. and Piccolo, A. and Annunziatella, C. and Barbieri, M. and 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. and Xie, S.Q. and 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. and 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. and van Driel, R. and 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. and 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. and Chiariello, A.M. and Abraham, A. and Bianco, S. and Esposito, A. and Nicodemi, M. and Matteuzzi, T. and Vercellone, F.
Algorithms 15 (9): 330. 16 September 2022

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

Physical mechanisms of chromatin spatial organization.
Chiariello, A.M. and Bianco, S. and Esposito, A. and Fiorillo, L. and Conte, M. and Irani, E. and Musella, F. and Abraham, A. and 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. and Bianco, S. and Fiorillo, L. and Conte, M. and Abraham, A. and Musella, F. and Nicodemi, M. and 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. and Serio, S. and Bianco, S. and Pagiatakis, C. and Crasto, S. and Chiariello, A.M. and Conte, M. and Cattaneo, P. and Fiorillo, L. and Felicetta, A. and di Pasquale, E. and Kunderfranco, P. and Nicodemi, M. and Papait, R. and Condorelli, G.
iScience 23 (9): 101539. 25 September 2020

Computational approaches from polymer physics to investigate chromatin folding.
Bianco, S. and Chiariello, A.M. and Conte, M. and Esposito, A. and Fiorillo, L. and 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. and 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. and Esposito, A. and Annunziatella, C. and Bianco, S. and Fiorillo, L. and 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. and Scialdone, A. and Gamba, A. and 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. and Janga, S.C. and 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 and 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. and 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. and Bracken, A. and Dou, Y. and Huangfu, D. and Ivanova, N. and Koseki, H. and Laurent, L. and Lim, D.A. and Meshorer, E. and Pombo, A. and 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. and Scialdone, A. and Piccolo, A. and Chiariello, A.M. and di Lanno, C. and Prisco, A. and Pombo, A. and Nicodemi, M.
Frontiers in Genetics 4 : 113. June 2013

Preprint

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies.
Winick-Ng, W. and Kukalev, A. and Harabula, I. and Zea Redondo, L. and Meijer, M. and Serebreni, L. and Bianco, S. and Szabo, D. and Chiariello, A.M. and Irastorza-Azcarate, I. and Fiorillo, L. and Musella, F. and Thieme, C. and Irani, E. and Torlai Triglia, E. and Kolodziejczyk, A.A. and Abentung, A. and Apostolova, G, and Paul, E.J. and Franke, V. and Kempfer, R. and Akalin, A. and Teichmann, S. and Dechant, G. and Ungless, M.A. and Nicodemi, M. and Castelo-Branco, G. and Pombo, A.
bioRxiv : 2020.04.02.020990. 12 May 2021

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C.
Beagrie, R.A. and Thieme, C.J. and Annunziatella, C. and Baugher, C. and Zhang, Y. and Schueler, M. and Kramer, D.C.A. and Chiariello, A.M. and Bianco, S. and Kukalev, A. and Li, Y. and Kempfer, R. and Scialdone, A. and Welch, L.R. and Nicodemi, M. and Pombo, A.
bioRxiv : 2020.07.31.230284. 31 July 2020

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

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos.
McGarvey, A.C. and Kopp, W. and Vučićević, D. and Kempfer, R. and Mattonet, K. and Hirsekorn, A. and Bilić, I. and Trinks, A. and Merks, A.M. and Panáková, D. and Pombo, A. and Akalin, A. and Junker, J.P. and Stainier, D.Y.R. and Garfield, D. and Ohler, U. and Lacadie, S.A.
bioRxiv : 2020.06.26.173377. 26 June 2020

Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin.
Fiorillo, L. and Musella, F. and Kempfer, R. and Chiariello, A.M. and Bianco, S. and Kukalev, A. and Irastorza-Azcarate, I. and Esposito, A. and Conte, M. and Prisco, A. and Pombo, A. and Nicodemi, M.
bioRxiv : 2020.04.24.059915. 25 April 2020

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

GAMIBHEAR: whole-genome haplotype reconstruction from genome architecture mapping data.
Markowski, J. and Kempfer, R. and Kukalev, A. and Irastorza-Azcarate, I. and Loof, G. and Pombo, A. and Schwarz, R.F.
bioRxiv : 2020.01.30.927061. 31 January 2020

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

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
Kar, G. and Kim, J.K. and Kolodziejczyk, A.A. and Natarajan, K.N. and Torlai Triglia, E. and Mifsud, B. and Elderkin, S. and Marioni, J.C. and Pombo, A. and Teichmann, S.A.
bioRxiv : 117267. 16 March 2017

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.
Barbieri, M. and Xie, S.Q. and Torlai Triglia, E. and de Santiago, I. and Branco, M.R. and Rueda, D. and Nicodemi, M. and Pombo, A.
bioRxiv : 111773. 28 February 2017