2026
Stem cell differentiation disperses transcriptional clusters via a conserved surface-condensate trajectory.
Klingberg, Tim, Wachter, Irina, Pancholi, Agnieszka, Akyel, Matthias, Gohar, Yomna, Kumar, Priya, Fernandes, Ana Miguel, Bao, Yuzhi, Schmidt-Heydt, Alica, Piepers, Marcel, Günthel, Alicia, Sobucki, Marcel, Kämmer, Elisa, Eroğlu-Kayıkçı, Süheyla, Allgeier, Stephan 
ORCID: https://orcid.org/0000-0002-1218-448X, Erhardt, Sylvia ORCID: https://orcid.org/0000-0003-3169-241X, Zaburdaev, Vasily ORCID: https://orcid.org/0000-0001-8234-3442, Ferrai, Carmelo ORCID: https://orcid.org/0000-0002-8088-2757 and Hilbert, Lennart ORCID: https://orcid.org/0000-0003-4478-5607
Advanced Science
: e75924.
9 June 2026
(In Press)
Extrachromosomal DNA micronucleation constrains tumour fitness and improves patient survival.
Brückner, L. ORCID: https://orcid.org/0000-0002-6155-2277, Xu, R. ORCID: https://orcid.org/0000-0002-5618-246X, Tang, J., Gnanasekar, A., Herrmann, A., Wong, I.T.L., Zhang, S., Tu, F., Pilon, M., Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Pardon, K., Sidorova, O. ORCID: https://orcid.org/0009-0004-1459-1662, Atta, J., Yu, Q. ORCID: https://orcid.org/0000-0002-2151-9624, Montouri, G., Pradella, D., Ilić, M., Suina, K., Novais-Cruz, M., Kaltenbach, S., Treue, D., Giurgiu-Kraljič, M. ORCID: https://orcid.org/0000-0001-5007-7442, Herzog, S., Hollinger, A.S., Wittstruck, N., Fernandez, M., Wolozyn, N., Becker, F., Louma, V.R., Yan, X., Schmargon, R. ORCID: https://orcid.org/0009-0009-3535-7185, Dörr, J. ORCID: https://orcid.org/0000-0002-4927-6548, Gamlin, D., Lehmann, A., Gürgen, D. ORCID: https://orcid.org/0000-0001-9241-6537, Richter, M. ORCID: https://orcid.org/0000-0002-5339-0781, Dubois, F. ORCID: https://orcid.org/0000-0002-7654-6208, Simeoni, F., Pennycook, B.R., Hamilton, A., Lindemann, R.K., Dawes, C., Balmus, G., Hero, B., Fischer, M., Bafna, V., Verhaak, R., Wahl, G., Liu, Y., Koche, R.P., Papathanasiou, S., Medema, R., Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Ventura, A., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Huang, W., Scheer, M., Werner, B., Chang, H.Y., Mischel, P.S. and Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X
bioRxiv
: 2025.04.15.648906.
19 February 2026
An integrated view of the structure and function of the human 4D nucleome.
Dekker, Job, Oksuz, Betul Akgol, Zhang, Yang, Wang, Ye, Minsk, Miriam K., Kuang, Shuzhen, Yang, Liyan, Gibcus, Johan H., Krietenstein, Nils, Rando, Oliver J., Xu, Jie, Janssens, Derek H., Henikoff, Steven, Kukalev, Alexander ORCID: https://orcid.org/0000-0001-5847-3773, Willemin, Andréa ORCID: https://orcid.org/0000-0002-4370-6914, Winick-Ng, Warren ORCID: https://orcid.org/0000-0002-8716-5558, Kempfer, Rieke ORCID: https://orcid.org/0000-0002-8588-8576, Pombo, Ana ORCID: https://orcid.org/0000-0002-7493-6288, Yu, Miao, Kumar, Pradeep, Zhang, Liguo, Belmont, Andrew S., Sasaki, Takayo, van Schaik, Tom, Brueckner, Laura, Peric-Hupkes, Daan, van Steensel, Bas, Wang, Ping, Chai, Haoxi, Kim, Minji, Ruan, Yijun, Zhang, Ran, Quinodoz, Sofia A., Bhat, Prashant, Guttman, Mitchell, Zhao, Wenxin, Chien, Shu, Liu, Yuan, Venev, Sergey V., Plewczynski, Dariusz, Irastorza Azcarate, Ibai ORCID: https://orcid.org/0000-0001-5245-2322, Szabó, Dominik ORCID: https://orcid.org/0000-0001-8109-5088, Thieme, Christoph J. ORCID: https://orcid.org/0000-0002-1566-0971, Szczepińska, Teresa ORCID: https://orcid.org/0000-0001-9749-1253, Chiliński, Mateusz, Sengupta, Kaustav, Conte, Mattia ORCID: https://orcid.org/0000-0002-6670-9800, Esposito, Andrea ORCID: https://orcid.org/0000-0002-5903-8439, Abraham, Alex, Zhang, Ruochi, Wang, Yuchuan, Wen, Xingzhao, Wu, Qiuyang, Yang, Yang, Liu, Jie, Boninsegna, Lorenzo, Yildirim, Asli, Zhan, Yuxiang, Chiariello, Andrea Maria ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, Simona ORCID: https://orcid.org/0000-0001-5819-060X, Lee, Lindsay, Hu, Ming, Li, Yun, Barnett, R. Jordan, Cook, Ashley L., Emerson, Daniel J., Marchal, Claire, Zhao, Peiyao, Park, Peter J., Alver, Burak H., Schroeder, Andrew J., Navelkar, Rahi, Bakker, Clara, Ronchetti, William, Ehmsen, Shannon, Veit, Alexander D., Gehlenborg, Nils, Wang, Ting, Li, Daofeng, Wang, Xiaotao, Nicodemi, Mario ORCID: https://orcid.org/0000-0002-8416-6416, Ren, Bing, Zhong, Sheng, Phillips-Cremins, Jennifer E., Gilbert, David M., Pollard, Katherine S., Alber, Frank, Ma, Jian, Noble, William S. and Yue, Feng
Nature 649
(8097): 759-776.
15 January 2026
2025
Extended supplementary data for manuscript: Gene regulatory mechanisms of cellular memory of a single cocaine exposure in VTA dopaminergic neurons.
Zea-Redondo, Luna ORCID: https://orcid.org/0000-0001-9064-9126, Franke, Vedran ORCID: https://orcid.org/0000-0003-3606-6792, Paul, Eleanor J., Kukalev, Alexander ORCID: https://orcid.org/0000-0001-5847-3773, Arguedas Jimenez, Laura ORCID: https://orcid.org/0009-0004-2240-7781, Braeuning, Caroline ORCID: https://orcid.org/0009-0007-1439-9920, Marin, Oscar, Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117, Ungless, Mark A., Winick-Ng, Warren ORCID: https://orcid.org/0000-0002-8716-5558 and Pombo, Ana ORCID: https://orcid.org/0000-0002-7493-6288
[Dataset]
4 September 2025
Specialised super-enhancer networks in stem cells and neurons.
Harabula, Izabela ORCID: https://orcid.org/0000-0002-9094-0519, Speakman, Liam ORCID: https://orcid.org/0009-0003-8950-6146, Musella, Francesco ORCID: https://orcid.org/0000-0002-2174-5840, Forillo, Luca ORCID: https://orcid.org/0000-0003-2967-0123, Zea-Redondo, Luna ORCID: https://orcid.org/0000-0001-9064-9126, Kukalev, Alexander ORCID: https://orcid.org/0000-0001-5847-3773, Beagrie, Robert A. ORCID: https://orcid.org/0000-0003-1076-5595, Morris, Kelly J., Fernandes, Lucas ORCID: https://orcid.org/0009-0004-6471-8713, Irastorza-Azcarate, Ibai ORCID: https://orcid.org/0000-0001-5245-2322, Fernandes, Ana M., Carvalho, Silvia ORCID: https://orcid.org/0000-0001-6436-205X, Szabó, Dominik ORCID: https://orcid.org/0000-0001-8109-5088, Ferrai, Carmelo ORCID: https://orcid.org/0000-0002-8088-2757, Nicodemi, Mario ORCID: https://orcid.org/0000-0002-8416-6416, Welch, Lonnie ORCID: https://orcid.org/0000-0001-6419-9416 and Pombo, Ana ORCID: https://orcid.org/0000-0002-7493-6288
bioRxiv
: 2025.08.13.670083.
13 August 2025
Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues.
Stein, Johannes, Ericsson, Maria, Nofal, Michel, Magni, Lorenzo, Aufmkolk, Sarah, McMillan, Ryan B., Breimann, Laura ORCID: https://orcid.org/0000-0001-7702-5749, Herlihy, Conor P., Lee, S. Dean, Willemin, Andréa ORCID: https://orcid.org/0000-0002-4370-6914, Wohlmann, Jens, Arguedas-Jimenez, Laura ORCID: https://orcid.org/0009-0004-2240-7781, Yin, Peng, Pombo, Ana ORCID: https://orcid.org/0000-0002-7493-6288, Church, George M. and Wu, Chao-Ting
Proceedings of the National Academy of Sciences of the United States of America 122
(32): e2504578122.
12 August 2025
Extensive folding variability between homologous chromosomes in mammalian cells.
Irastorza-Azcarate, I. ORCID: https://orcid.org/0000-0001-5245-2322, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971, Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Markowski, J. ORCID: https://orcid.org/0000-0002-0573-7832, Loof, G. ORCID: https://orcid.org/0000-0003-3967-6115, Sparks, T.M. ORCID: https://orcid.org/0000-0002-9455-8309, Brookes, E. ORCID: https://orcid.org/0000-0003-2175-4349, Natarajan, K.N. ORCID: https://orcid.org/0000-0002-9264-1280, Sauer, S., Fisher, A.G. ORCID: https://orcid.org/0000-0003-3010-3644, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Ren, B., Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Molecular Systems Biology 21
(7): 735-775.
2 July 2025
Loss of structural specificity in 3D genome organization upon viral infection is predicted by polymer physics.
Fontana, A. ORCID: https://orcid.org/0009-0004-1996-4800, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Tafuri, F., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Abraham, A., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Vercellone, F., Di Pierno, F. ORCID: https://orcid.org/0009-0009-1042-082X, Kundu, S. ORCID: https://orcid.org/0000-0003-2099-1270, Guha, S. ORCID: https://orcid.org/0000-0003-4376-0731, Di Carluccio, C., Prisco, A., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416 and Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167
Journal of Chemical Physics 162
(1): 014903.
7 January 2025
Extended supplementary data for manuscript: Specialised super-enhancer networks in stem cells and neurons.
Harabulă, Izabela ORCID: https://orcid.org/0000-0002-9094-0519, Speakman, Liam ORCID: https://orcid.org/0009-0003-8950-6146, Musella, Francesco ORCID: https://orcid.org/0000-0002-2174-5840, Fiorillo, Luca ORCID: https://orcid.org/0000-0003-2967-0123, Zea-Redondo, Luna ORCID: https://orcid.org/0000-0001-9064-9126, Kukalev, Alexander ORCID: https://orcid.org/0000-0001-5847-3773, Beagrie, Robert A. ORCID: https://orcid.org/0000-0003-1076-5595, Morris, Kelly J., Fernandes, Lucas ORCID: https://orcid.org/0009-0004-6471-8713, Irastorza-Azcarate, Ibai ORCID: https://orcid.org/0000-0001-5245-2322, Fernandes, Ana M., Carvalho, Silvia ORCID: https://orcid.org/0000-0001-6436-205X, Szabó, Dominik ORCID: https://orcid.org/0000-0001-8109-5088, Ferrai, Carmelo ORCID: https://orcid.org/0000-0002-8088-2757, Nicodemi, Mario ORCID: https://orcid.org/0000-0002-8416-6416, Welch, Lonnie and Pombo, Ana ORCID: https://orcid.org/0000-0002-7493-6288
[Dataset]
2025
2024
Transient stabilization of human cardiovascular progenitor cells from human pluripotent stem cells in vitro reflects stage-specific heart development in vivo.
Bolesani, E. ORCID: https://orcid.org/0000-0002-4237-2705, 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. ORCID: https://orcid.org/0000-0002-4814-9416, Moretti, A., Zelarayán, L.C. ORCID: https://orcid.org/0000-0002-9001-0346, Abdelilah-Seyfried, S. ORCID: https://orcid.org/0000-0003-3183-3841 and Zweigerdt, R.
Cardiovascular Research 120
(11): 1295-1311.
July 2024
Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells.
Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Abraham, Alex ORCID: https://orcid.org/0000-0003-3533-6543, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Fontana, A. ORCID: https://orcid.org/0009-0004-1996-4800, Vercellone, F. ORCID: https://orcid.org/0000-0003-3933-8458, Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800 and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Nature Communications 15
(1): 4014.
13 May 2024
A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.
Szabó, D. ORCID: https://orcid.org/0000-0001-8109-5088, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Batiuk, M.Y. ORCID: https://orcid.org/0000-0001-6681-4048, Paul, E.J. ORCID: https://orcid.org/0000-0003-1183-9285, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Pfisterer, U.G. ORCID: https://orcid.org/0000-0002-4613-6427, Irastorza-Azcarate, I. ORCID: https://orcid.org/0000-0001-5245-2322, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Demharter, S. ORCID: https://orcid.org/0000-0001-7352-3994, Zea-Redondo, L. ORCID: https://orcid.org/0000-0001-9064-9126, Lopez-Atalaya, J.P. ORCID: https://orcid.org/0000-0001-6064-7584, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Khodosevich, K. ORCID: https://orcid.org/0000-0001-7232-5558, Ungless, M.A. ORCID: https://orcid.org/0000-0002-1730-3353, Winick-Ng, W. ORCID: https://orcid.org/0000-0002-8716-5558 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
bioRxiv
: 2024.05.10.593308.
12 May 2024
SRRM2 splicing factor modulates cell fate in early development.
Carvalho, S. ORCID: https://orcid.org/0000-0001-6436-205X, Zea-Redondo, L. ORCID: https://orcid.org/0000-0001-9064-9126, Tang, T.C.C., Stachel-Braum, P., Miller, D. ORCID: https://orcid.org/0000-0001-9852-677X, Caldas, P., Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Diecke, S. ORCID: https://orcid.org/0000-0002-5219-5992, Grosswendt, S. ORCID: https://orcid.org/0000-0001-7722-2937, Grosso, A.R. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Biology Open 13
(4): bio060415.
April 2024
Epigenetic regulatory layers in the 3D nucleus.
Willemin, A. ORCID: https://orcid.org/0000-0002-4370-6914, Szabo, D. ORCID: https://orcid.org/0000-0001-8109-5088 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Molecular Cell 84
(3): 415-428.
1 February 2024
2023
Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes.
Schindler, M. ORCID: https://orcid.org/0000-0003-3363-1864, Osterwalder, M., Harabula, I. ORCID: https://orcid.org/0000-0002-9094-0519, Wittler, L., Tzika, A.C., Dechmann, D.K.N., Vingron, M., Visel, A., Haas, S. and Real, F.M. ORCID: https://orcid.org/0000-0003-0692-2260
Development 150
(17): dev201562.
1 September 2023
Genome architecture mapping detects transcriptionally active, multiway chromatin contacts.
Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature Methods 20
(7): 993-994.
July 2023
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
Beagrie, R.A. ORCID: https://orcid.org/0000-0003-1076-5595, Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971, Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Li, Y. ORCID: https://orcid.org/0000-0001-5791-096X, Davis, T., Scialdone, A. ORCID: https://orcid.org/0000-0002-4956-2843, Welch, L.R. ORCID: https://orcid.org/0000-0001-6419-9416, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature Methods 20
(7): 1037-1047.
July 2023
Mechanisms of enhancer function in neuronal systems in health and disease.
Zea Redondo, L. ORCID: https://orcid.org/0000-0001-9064-9126 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Current Opinion in Systems Biology 32-33
: 100443.
March 2023
Physics-based polymer models to probe chromosome structure in single molecules.
Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Abraham, A. and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Methods in Molecular Biology 2655
: 57-66.
2023
2022
3D genome topologies distinguish pluripotent epiblast and primitive endoderm cells in the mouse blastocyst.
Loof, G. ORCID: https://orcid.org/0000-0003-3967-6115, Szabo, D. ORCID: https://orcid.org/0000-0001-8109-5088, Garg, V. ORCID: https://orcid.org/0000-0001-9443-0359, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Zea-Redondo, L. ORCID: https://orcid.org/0000-0001-9064-9126, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Sparks, T.M. ORCID: https://orcid.org/0000-0002-9455-8309, Zhang, Yi. ORCID: https://orcid.org/0000-0001-6765-0022, Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971, Carvalho, S. ORCID: https://orcid.org/0000-0001-6436-205X, Weise, A., Balachandran, M. ORCID: https://orcid.org/0000-0002-3710-0772, Liehr, T. ORCID: https://orcid.org/0000-0003-1672-3054, Welch, L.R. ORCID: https://orcid.org/0000-0001-6419-9416, Hadjantonakis, A.K. ORCID: https://orcid.org/0000-0002-7580-5124 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
bioRxiv
: 2022.10.19.512781.
20 October 2022
A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation.
Yanchus, C. ORCID: https://orcid.org/0000-0002-9450-7982, Drucker, K.L. ORCID: https://orcid.org/0000-0001-6244-5863, Kollmeyer, T.M. ORCID: https://orcid.org/0000-0002-0694-3224, Tsai, R. ORCID: https://orcid.org/0000-0001-5916-6978, Winick-Ng, W. ORCID: https://orcid.org/0000-0002-8716-5558, Liang, M. ORCID: https://orcid.org/0000-0002-4451-0921, Malik, A., Pawling, J. ORCID: https://orcid.org/0000-0003-3759-8555, De Lorenzo, S.B., Ali, A., Decker, P.A. ORCID: https://orcid.org/0000-0002-3756-4227, Kosel, M.L., Panda, A. ORCID: https://orcid.org/0000-0001-5156-6459, Al-Zahrani, K.N. ORCID: https://orcid.org/0000-0001-5771-7537, Jiang, L., Browning, J.W.L. ORCID: https://orcid.org/0000-0001-9938-7193, Lowden, C. ORCID: https://orcid.org/0000-0002-1839-164X, Geuenich, M., Hernandez, J.J. ORCID: https://orcid.org/0000-0001-6735-4303, Gosio, J.T., Ahmed, M. ORCID: https://orcid.org/0000-0002-5076-1102, Loganathan, S.K. ORCID: https://orcid.org/0000-0002-8809-1466, Berman, J. ORCID: https://orcid.org/0000-0001-6454-4996, Trcka, D. ORCID: https://orcid.org/0000-0002-2196-7160, Michealraj, K.A., Fortin, J., Carson, B., Hollingsworth, E.W. ORCID: https://orcid.org/0000-0002-5188-3929, Jacinto, S., Mazrooei, P., Zhou, L., Elia, A. ORCID: https://orcid.org/0000-0001-8619-1415, Lupien, M. ORCID: https://orcid.org/0000-0003-0929-9478, He, H.H. ORCID: https://orcid.org/0000-0003-2898-3363, Murphy, D.J., Wang, L. ORCID: https://orcid.org/0000-0003-2072-4826, Abyzov, A. ORCID: https://orcid.org/0000-0001-5405-6729, Dennis, J.W. ORCID: https://orcid.org/0000-0002-0295-5877, Maass, P.G. ORCID: https://orcid.org/0000-0002-2742-8301, Campbell, K., Wilson, M.D. ORCID: https://orcid.org/0000-0002-4015-3066, Lachance, D.H., Wrensch, M. ORCID: https://orcid.org/0000-0002-3070-7600, Wiencke, J., Mak, T. ORCID: https://orcid.org/0000-0001-6766-861X, Pennacchio, L.A. ORCID: https://orcid.org/0000-0002-8748-3732, Dickel, D.E. ORCID: https://orcid.org/0000-0001-5497-6824, Visel, A. ORCID: https://orcid.org/0000-0002-4130-7784, Wrana, J. ORCID: https://orcid.org/0000-0003-0932-0644, Taylor, M.D., Zadeh, G., Dirks, P. ORCID: https://orcid.org/0000-0001-5718-6465, Eckel-Passow, J.E. ORCID: https://orcid.org/0000-0002-6113-1114, Attisano, L. ORCID: https://orcid.org/0000-0003-4824-2642, Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Ida, C.M. ORCID: https://orcid.org/0000-0003-2768-2913, Kvon, E.Z. ORCID: https://orcid.org/0000-0002-1562-0945, Jenkins, R.B. ORCID: https://orcid.org/0000-0002-4049-694X and Schramek, D. ORCID: https://orcid.org/0000-0001-9977-2104
Science 378
(6615): 68-78.
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Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Fiorillo, L. ORCID: https://orcid.org/0000-0003-2967-0123, Musella, F. and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Current Opinion in Cell Biology 64
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June 2020
Evolving methodologies and concepts in 4D nucleome research.
Sparks, T.M. ORCID: https://orcid.org/0000-0002-9455-8309, Harabula, I. ORCID: https://orcid.org/0000-0002-9094-0519 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Current Opinion in Cell Biology 64
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June 2020
Methods for mapping 3D chromosome architecture.
Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature Reviews Genetics 21
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April 2020
A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells.
Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Oudelaar, A M., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Annunziatella, C., Fiorillo, L., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, 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. ORCID: https://orcid.org/0000-0002-8416-6416
Cell Reports 30
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18 February 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. ORCID: https://orcid.org/0000-0002-7493-6288
bioRxiv
: 2020.02.10.941047v2.
13 February 2020
2019
Modeling single-molecule conformations of the HoxD region in mouse embryonic stem and cortical neuronal cells.
Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Annunziatella, C., Andrey, G., Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Fiorillo, L., Prisco, A., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Campanile, R. and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Cell Reports 28
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6 August 2019
Discontinuous shear-thinning in adhesive dispersions.
Irani, E. ORCID: https://orcid.org/0000-0002-8194-960X, Chaudhuri, P. and Heussinger, C.
Physical Review Fluids 4
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18 July 2019
Models of polymer physics for the architecture of the cell nucleus.
Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Annunziatella, C., Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Fiorillo, L. and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Wiley Interdisciplinary Reviews Systems Biology and Medicine 11
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July 2019
Preformed chromatin topology assists transcriptional robustness of Shh during limb development.
Paliou, C. ORCID: https://orcid.org/0000-0003-3383-2527, Guckelberger, P., Schöpflin, R., Heinrich, V., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Annunziatella, C., Helmuth, J., Haas, S., Jerković, I., Brieske, N., Wittler, L., Timmermann, B., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Vingron, M., Mundlos, S. and Andrey, G.
Proceedings of the National Academy of Sciences of the United States of America 116
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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. ORCID: https://orcid.org/0000-0002-8673-4560, Palluzzi, F., Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Piccioni, R., Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Furia, L., De Conti, G. ORCID: https://orcid.org/0000-0002-2647-228X, Bouwman, B.A.M., Melloni, G. ORCID: https://orcid.org/0000-0001-6371-1334, Guido, D., Giacò, L., Luzi, L., Cittaro, D., Faretta, M., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Crosetto, N. ORCID: https://orcid.org/0000-0002-3019-6978 and Pelicci, P.G. ORCID: https://orcid.org/0000-0002-0927-8290
Nature Genetics 51
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June 2019
Editorial overview: Genome architecture and expression.
Bickmore, W. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Current Opinion in Genetics & Development 55
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April 2019
R-loops enhance polycomb repression at a subset of developmental regulator genes.
Skourti-Stathaki, K., Torlai Triglia, E. ORCID: https://orcid.org/0000-0002-6059-0116, Warburton, M., Voigt, P., Bird, A. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Molecular Cell 73
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7 March 2019
2018
Challenges and guidelines toward 4D nucleome data and model standards.
Marti-Renom, M.A. ORCID: https://orcid.org/0000-0002-0151-4279, Almouzni, G., Bickmore, W.A. ORCID: https://orcid.org/0000-0001-6660-7735, Bystricky, K. ORCID: https://orcid.org/0000-0001-6717-3721, Cavalli, G. ORCID: https://orcid.org/0000-0003-3709-3469, Fraser, P. ORCID: https://orcid.org/0000-0002-0041-1227, Gasser, S.M., Giorgetti, L., Heard, E., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Nollmann, M. ORCID: https://orcid.org/0000-0003-3339-2349, Orozco, M., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Torres-Padilla, M.E. ORCID: https://orcid.org/0000-0002-1020-2074
Nature Genetics 50
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October 2018
Molecular Dynamics simulations of the Strings and Binders Switch Model of chromatin.
Annunziatella, C., Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Fiorillo, L. and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
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1 June 2018
Polymer physics predicts the effects of structural variants on chromatin architecture.
Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Lupiáñez, D.G. ORCID: https://orcid.org/0000-0002-3165-036X, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Annunziatella, C., Kraft, K., Schöpflin, R., Wittler, L., Andrey, G., Vingron, M., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Mundlos, S. and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Nature Genetics 50
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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. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Annunziatella, C., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439 and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
EPL 120
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8 February 2018
Understanding chromatin structure: efficient computational implementation of polymer physics models.
Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Annunziatella, C., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Fiorillo, L., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Campanile, R. and Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167
Lecture Notes in Computer Science 11339
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2018
2017
Chaperone-mediated regulation of choline acetyltransferase protein stability and activity by HSC/HSP70, HSP90, and p97/VCP.
Morey, T.M., Winick-Ng, W. ORCID: https://orcid.org/0000-0002-8716-5558, Seah, C. and Rylett, R.J. ORCID: https://orcid.org/0000-0002-9158-9599
Frontiers in Molecular Neuroscience 10
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December 2017
Structure of the human chromosome interaction network.
Sarnataro, S., Chiariello, A.M., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Prisco, A. and Nicodemi, M.
PLoS ONE 12
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15 November 2017
Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.
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Genome Biology 18
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31 October 2017
RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.
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Molecular Systems Biology 13
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16 October 2017
A polymer physics investigation of the architecture of the murine orthologue of the 7q11.23 human locus.
Chiariello, A.M., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Annunziatella, C., Bianco, S., Fiorillo, L., Prisco, A. and Nicodemi, M.
Frontiers in Neuroscience 11
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10 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
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14 September 2017
FANTOM5 CAGE profiles of human and mouse samples.
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Scientific Data 4
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Cell cycle: continuous chromatin changes.
Beagrie, R.A. ORCID: https://orcid.org/0000-0003-1076-5595 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature 547
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6 July 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. ORCID: https://orcid.org/0000-0002-9264-1280, Torlai Triglia, E. ORCID: https://orcid.org/0000-0002-6059-0116, Mifsud, B. ORCID: https://orcid.org/0000-0003-3429-3094, Elderkin, S., Marioni, J.C., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Teichmann, S.A.
Nature Communications 8
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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. ORCID: https://orcid.org/0000-0002-6059-0116, Chiariello, A.M., Bianco, S., de Santiago, I., Branco, M.R. ORCID: https://orcid.org/0000-0001-9447-1548, Rueda, D. ORCID: https://orcid.org/0000-0003-4657-6323, Nicodemi, M. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature Structural & Molecular Biology 24
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June 2017
Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatment.
Mattei, D. ORCID: https://orcid.org/0000-0001-6221-9321, Ivanov, A. ORCID: https://orcid.org/0000-0002-4824-1925, Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, Jordan, P., Guneykaya, D. ORCID: https://orcid.org/0000-0001-5723-0737, Buonfiglioli, A. ORCID: https://orcid.org/0000-0002-5550-9360, 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. ORCID: https://orcid.org/0000-0002-3284-0632, Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Kettenmann, H. ORCID: https://orcid.org/0000-0001-8208-0291 and Wolf, S.A. ORCID: https://orcid.org/0000-0003-0922-8418
Translational Psychiatry 7
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9 May 2017
Keep them close: PRC2 poises enhancer-promoter interactions at anterior neuronal genes.
Caglio, Giulia, Torlai Triglia, E. ORCID: https://orcid.org/0000-0002-6059-0116 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Cell Stem Cell 20
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4 May 2017
Complex multi-enhancer contacts captured by genome architecture mapping.
Beagrie, R.A. ORCID: https://orcid.org/0000-0003-1076-5595, 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. ORCID: https://orcid.org/0000-0002-8416-6416 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature 543
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23 March 2017
GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data.
Beagrie, R.A. ORCID: https://orcid.org/0000-0003-1076-5595 and Schueler, M.
bioRxiv
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20 March 2017
A finer print than TADs: PRC1-mediated domains.
Torlai Triglia, E. ORCID: https://orcid.org/0000-0002-6059-0116, Rito, Tiago and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Molecular Cell 65
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2 February 2017
Polymer models of the chromosomes in the nucleus of cells.
Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S., Piccolo, A., Annunziatella, C., Barbieri, M., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
In:
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World Scientific Publishing Co., 239-248.
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On the nature of chromatin 3D organization.
Nicodemi, M. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
In:
Epigenetics and Systems Biology.
Academic Press, 191-201.
ISBN 978-012803075-2
2017
2016
Examining topological domain influence on enhancer function.
Beagrie, R.A. ORCID: https://orcid.org/0000-0003-1076-5595 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Developmental Cell 39
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5 December 2016
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. ORCID: https://orcid.org/0000-0002-8588-8576, 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. ORCID: https://orcid.org/0000-0002-7493-6288, Vingron, M., Spitz, F. and Mundlos, S.
Nature 538
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13 October 2016
Gene activation by metazoan enhancers: diverse mechanisms stimulate distinct steps of transcription.
Beagrie, R.A. ORCID: https://orcid.org/0000-0003-1076-5595 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
BioEssays 38
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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. ORCID: https://orcid.org/0000-0001-9468-6311, Yeroslaviz, A., Habermann, B., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Niessen, C.M. and Wickström, S.A.
Nature Cell Biology 18
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August 2016
2015
Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.
Fraser, J., Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, 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. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Molecular Systems Biology 11
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23 December 2015
Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.
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eLife 4
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19 December 2015
Polymer models of the organization of chromosomes in the nucleus of cells.
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Modern Physics Letters B 29
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10 April 2015
Three-dimensional genome architecture: players and mechanisms.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Dillon, N.
Nature Reviews Molecular Cell Biology 16
(4): 245-257.
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. ORCID: https://orcid.org/0000-0002-8088-2757, 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. ORCID: https://orcid.org/0000-0002-7493-6288, 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
2014
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. ORCID: https://orcid.org/0000-0002-7493-6288, Sander, M. ORCID: https://orcid.org/0000-0001-5308-7785 and Xu, G.L.
Cell Stem Cell 14
(6): 706-709.
5 June 2014
Models of chromosome structure.
Nicodemi, M. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Current Opinion in Cell Biology 28
: 90-95.
1 June 2014
Physical mechanisms behind the large scale features of chromatin organization.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M.
Transcription 5
(2): e28447.
April 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. ORCID: https://orcid.org/0000-0002-7493-6288 and Dillon, N.
Molecular Biology of the Cell 25
(6): 904-915.
March 2014
2013
Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus.
Barbieri, M., Scialdone, A., Gamba, A., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M.
Soft Matter 9
(36): 8631-8635.
28 September 2013
A polymer model explains the complexity of large-scale chromatin folding.
Barbieri, M., Fraser, J., Lavitas, L.M., Chotalia, M., Dostie, J., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M.
Nucleus 4
(4): 267-273.
19 June 2013
Polymer models of chromatin organization.
Barbieri, M., Scialdone, A., Piccolo, A., Chiariello, A.M., di Lanno, C., Prisco, A., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M.
Frontiers in Genetics 4
: 113.
June 2013
A model of the large-scale organization of chromatin.
Barbieri, M., Chotalia, M., Fraser, J., Lavitas, L.M., Dostie, J., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M.
Biochemical Society Transactions 41
(2): 508-512.
April 2013
2012
Mean expression of the X-chromosome is associated with neuronal density.
Swingland, J.T., Durrenberger, P.F., Reynolds, R., Dexter, D.T., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, 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. ORCID: https://orcid.org/0000-0002-7493-6288 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. ORCID: https://orcid.org/0000-0003-2454-8751 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Molecular & Cellular Proteomics 11
(6): M111.011767.
June 2012
Code breaking: the RNAPII modification code in pluripotency.
Brookes, E. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Cell Cycle 11
(7): 1267-1268.
1 April 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. ORCID: https://orcid.org/0000-0002-7493-6288
Cell Stem Cell 10
(2): 157-170.
3 February 2012
2011
Nuclear cell biology.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 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. ORCID: https://orcid.org/0000-0002-7493-6288
PLoS Genetics 7
(3): e1002031.
March 2011
2010
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. ORCID: https://orcid.org/0000-0002-7493-6288, 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. ORCID: https://orcid.org/0000-0002-7493-6288, Fisher, A.G., Young, R.A. and Jenner, R.G.
Molecular Cell 38
(5): 675-688.
11 June 2010
Gene positioning.
Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, de Castro, I.J., Lavitas, L., Chotalia, M. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
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. ORCID: https://orcid.org/0000-0002-7493-6288, 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
Nucleus and gene expression: the structure and function conundrum.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Gilbert, D.M.
Current Opinion in Cell Biology 22
(3): 269-270.
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. ORCID: https://orcid.org/0000-0002-7493-6288, Carlton, P.M., Gahl, A., Domaing, P., Birk, U., Leonhardt, H. ORCID: https://orcid.org/0000-0002-5086-6449, Cremer, C. and Cardoso, M.C. ORCID: https://orcid.org/0000-0001-8427-8859
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. ORCID: https://orcid.org/0000-0002-7493-6288 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. ORCID: https://orcid.org/0000-0002-7493-6288
Methods in Molecular Biology 659
: 219-230.
2010
Nuclear architecture in stem cells.
Morris, K.J., Chotalia, M. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Advances in Experimental Medicine and Biology 695
: 14-25.
2010
2009
The molecular basis for stability of heterochromatin-mediated silencing in mammals.
Hiragami-Hamada, K., Xie, S.Q., Saveliev, A., Uribe-Lewis, S., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 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. ORCID: https://orcid.org/0000-0002-7493-6288
EMBO Reports 10
(11): 1213-1219.
November 2009
3D chromatin regulation of Sonic hedgehog in the limb buds.
Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Developmental Cell 16
(1): 9-11.
20 January 2009
Mechanisms regulating S phase progression in mammalian cells.
Maya-Mendoza, A., Tang, C.W., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Jackson, D.A.
Frontiers in Bioscience 14
: 4199-4213.
1 January 2009
2008
Eukaryotic gene regulation in three dimensions and its impact on genome evolution.
Babu, M.M., Janga, S.C., de Santiago, I. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Current Opinion in Genetics & Development 18
(6): 571-582.
December 2008
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. ORCID: https://orcid.org/0000-0002-7493-6288
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. ORCID: https://orcid.org/0000-0002-7493-6288 and de Laat, W.
PLoS Genetics 4
(3): e1000016.
7 March 2008
2007
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. ORCID: https://orcid.org/0000-0002-7493-6288
Nature Cell Biology 9
(12): 1428-1435.
December 2007
Functional organisation of the genome during interphase.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 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. ORCID: https://orcid.org/0000-0002-7493-6288
Histochemistry and Cell Biology 128
(2): 97-104.
August 2007
Desmin immunolocalisation in autosomal dominant Emery-Dreifuss muscular dystrophy.
Piercy, R.J., Zhou, H., Feng, L., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Muntoni, F. and Brown, S.C.
Neuromuscular Disorders 17
(4): 297-305.
April 2007
Chromosome organization: new facts, new models.
Branco, M.R. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Trends in Cell Biology 17
(3): 127-34.
March 2007
2006
Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations.
Branco, M.R. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
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. ORCID: https://orcid.org/0000-0002-7493-6288
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. ORCID: https://orcid.org/0000-0002-7493-6288
Histochemistry and Cell Biology 125
(1-2): 21-31.
January 2006
Correlative microscopy using Tokuyasu cryosections: applications for immunogold labelling and in situ hybridisation.
Branco, M.R., Xie, S.Q., Martin, S. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
In:
Cell Imaging (Methods Express Series).
Methods Express Series
.
Scion Publishing, Bloxham, 201-217.
ISBN 1-904842-26-7
2006
2005
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. ORCID: https://orcid.org/0000-0002-7493-6288, 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. ORCID: https://orcid.org/0000-0002-7493-6288, Moniz-Pereira, J., Goncalves, J. and Barahona, I.
Journal of Virology 79
(2): 823-833.
January 2005
The organization of transcription in the nucleus of mammalian cells.
Guillot, P.V., Martin, S. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
In:
Visions of the Cell Nucleus.
American Scientific Publishers, Stevenson Ranch, CA, 95-105.
ISBN 1-5883-027-6
2005
2004
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. ORCID: https://orcid.org/0000-0002-7493-6288
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. ORCID: https://orcid.org/0000-0002-7493-6288 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. ORCID: https://orcid.org/0000-0002-7493-6288
Molecular Biology of the Cell 15
(5): 2449-2455.
May 2004
2003
Interaction of proteins with promoter elements of the human U2 snRNA genes in vivo.
Boyd, D.C., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 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. ORCID: https://orcid.org/0000-0002-7493-6288
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. ORCID: https://orcid.org/0000-0002-7493-6288, Schmahl, G., Spatz, J.P. and van Driel, R.
Genome Research 13
(6A): 1029-1041.
June 2003
From linear genome sequence to three-dimensional organization of the cell nucleus.
Politz, J., van Driel, R., Sauer, M. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
In: Jackson Laboratory 'Advances in nanostructural genomics II' meeting, 3-6 Oct 2002, Bar Harbor, USA.
28 February 2003
Cellular genomics: which genes are transcribed, when and where?
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Trends in Biochemical Sciences 28
(1): 6-9.
January 2003
2001
Correlative fluorescence and electron microscopy on ultrathin cryosections: bridging the resolution gap.
Robinson, J.M., Takizawa, T., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Cook, P.R.
Journal of Histochemistry and Cytochemistry 49
(7): 803-8.
July 2001
2000
Phenotypic analysis of peripheral CD4+ CD8+ T cells in the rat.
Kenny, E., Mason, D., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Ramírez, F.
Immunology 101
(2): 178-84.
October 2000
The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells.
Jackson, D.A., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Iborra, F.
FASEB Journal 14
(2): 242-54.
February 2000
Specialized transcription factories within mammalian nuclei.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Jones, E., Iborra, F.J., Kimura, H., Sugaya, K., Cook, P.R. and Jackson, D.A.
Critical Reviews in Eukaryotic Gene Expression 10
(1): 21-29.
2000
1999
Localization of a putative transcriptional regulator (ATRX) at pericentromeric heterochromatin and the short arms of acrocentric chromosomes.
McDowell, T.L., Gibbons, R.J., Sutherland, H., O'Rourke, D.M., Bickmore, W.A., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Turley, H., Gatter, K., Picketts, D.J., Buckle, V.J., Chapman, L., Rhodes, D. and Higgs, D.R.
Proceedings of the National Academy of Sciences of the United States of America 96
(24): 13983-8.
23 November 1999
Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Jackson, D.A., Hollinshead, M., Wang, Z., Roeder, R.G. and Cook, P.R.
EMBO Journal 18
(8): 2241-2253.
15 April 1999
Bridging the resolution gap: Imaging the same transcription factories in cryosections by light and electron microscopy.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Hollinshead, M. and Cook, P.R.
Journal of Histochemistry and Cytochemistry 47
(4): 471-480.
April 1999
1998
Dendritic cells interact directly with naive B lymphocytes to transfer antigen and initiate class switching in a primary T-dependent response.
Wykes, M., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Jenkins, C. and MacPherson, G.G.
Journal of Immunology 161
(3): 1313-1319.
August 1998
Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells.
Jackson, D.A. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Journal of Cell Biology 140
(6): 1285-1295.
23 March 1998
Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Cuello, P., Schul, W., Yoon, J.B., Roeder, R.G., Cook, P.R. and Murphy, S.
EMBO Journal 17
(6): 1768-1778.
16 March 1998
1996
The localization of sites containing nascent RNA and splicing factors.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Cook, P.R.
Experimental Cell Research 229
(2): 201-203.
15 December 1996
The topology of transcription by immobilized polymerases.
Iborra, F.J., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, McManus, J., Jackson, D.A. and Cook, P.R.
Experimental Cell Research 229
(2): 167-173.
15 December 1996
Active RNA polymerases are localized within discrete transcription ‘factories’ in human nuclei.
Iborra, F.J., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Jackson, D.A. and Cook, P.R.
Journal of Cell Science 109
(6): 1427-36.
June 1996
1995
Interactions of adenovirus with the nucleus of the host cell.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Carmo‐Fonseca, M.
Reviews in Medical Virology 5
(4): 213-218.
December 1995
On the structure of replication and transcription factories.
Hughes, T.A., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, McManus, J., Hozák, P., Jackson, D.A. and Cook, P.R.
Journal of Cell Science Supplement 19
: 59-65.
January 1995
1994
Adenovirus replication and transcription sites are spatially separated in the nucleus of infected cells.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Ferreira, J., Bridge, E. and Carmo-Fonseca, M.
EMBO Journal 13
(21): 5075-5085.
1 November 1994
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