Advanced Science
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)
Advances in Experimental Medicine and Biology
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
Algorithms
Polymer models of chromatin imaging data in single cells.
Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Abraham, A. 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, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Matteuzzi, T. and Vercellone, F.
Algorithms 15
(9): 330.
16 September 2022
BMC Biology
Hmga2 protein loss alters nuclear envelope and 3D chromatin structure.
Divisato, G., Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Zoppoli, P., Zambelli, F., Elia, M.A., Pesole, G., Incarnato, D., Passaro, F., Piscitelli, S., Oliviero, S., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Parisi, S. and Russo, T. ORCID: https://orcid.org/0000-0003-4426-0106
BMC Biology 20
(1): 171.
2 August 2022
BioEssays
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
(9): 881-893.
September 2016
Biochemical Society Transactions
Polymer models are a versatile tool to study chromatin 3D organization.
Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Fiorillo, L., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Abraham, A., Musella, F., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Prisco, A. and Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167
Biochemical Society Transactions 49
(4): 1675-1684.
August 2021
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
Bioinformatics
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Markowski, J. ORCID: https://orcid.org/0000-0002-0573-7832, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Irastorza-Azcarate, I. ORCID: https://orcid.org/0000-0001-5245-2322, Loof, G. ORCID: https://orcid.org/0000-0003-3967-6115, Kehr, B., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Rahmann, S. and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
Bioinformatics 37
(19): 3128–3135.
1 October 2021
Biology Open
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
Biophysical Journal
Chromosomes phase transition to function.
Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416 and Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X
Biophysical Journal 119
(4): 724-725.
18 August 2020
Cardiovascular Research
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
Cell
Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.
Ringel, A.R. ORCID: https://orcid.org/0000-0002-6392-6076, Szabo, Q. ORCID: https://orcid.org/0000-0002-3539-7875, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Chudzik, K. ORCID: https://orcid.org/0000-0002-7606-8381, Schöpflin, R., Rothe, P. ORCID: https://orcid.org/0000-0003-2366-7775, Mattei, A.L. ORCID: https://orcid.org/0000-0003-1450-8924, Zehnder, T., Harnett, D. ORCID: https://orcid.org/0000-0002-9190-128X, Laupert, V., Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Hetzel, S. ORCID: https://orcid.org/0000-0002-4783-3814, Glaser, J., Phan, M.H.Q., Schindler, M. ORCID: https://orcid.org/0000-0003-3363-1864, Ibrahim, D.M. ORCID: https://orcid.org/0000-0002-0019-3354, Paliou, C., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Prada-Medina, C.A., Haas, S.A., Giere, P. ORCID: https://orcid.org/0000-0002-5570-0085, Vingron, M., Wittler, L. ORCID: https://orcid.org/0000-0001-7873-6702, Meissner, A., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Cavalli, G. ORCID: https://orcid.org/0000-0003-3709-3469, Bantignies, F., Mundlos, S. and Robson, M.I. ORCID: https://orcid.org/0000-0003-1126-3538
Cell 185
(20): 3689-3704.
29 September 2022
Cell Cycle
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
Cell Genomics
Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C. ORCID: https://orcid.org/0000-0003-3838-1139, Kopp, W. ORCID: https://orcid.org/0000-0003-0376-0032, Vučićević, D. ORCID: https://orcid.org/0000-0002-1162-6709, Mattonet, K. ORCID: https://orcid.org/0000-0002-9705-8086, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Hirsekorn, A., Bilić, I. ORCID: https://orcid.org/0000-0002-2730-1634, Gil, M. ORCID: https://orcid.org/0000-0002-3885-7806, Trinks, A. ORCID: https://orcid.org/0000-0001-9983-1506, Merks, A.M. ORCID: https://orcid.org/0000-0001-5677-7204, Panáková, D. ORCID: https://orcid.org/0000-0002-8739-6225, Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Stainier, D.Y.R. ORCID: https://orcid.org/0000-0002-0382-0026, Garfield, D. ORCID: https://orcid.org/0000-0002-8790-797X, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Lacadie, S.A. ORCID: https://orcid.org/0000-0002-0893-5340
Cell Genomics 2
(1): 100083.
13 January 2022
Cell Imaging (Methods Express Series)
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
Cell Reports
Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states.
Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Abraham, A., Fiorillo, L., 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 38
(13): 110601.
29 March 2022
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
(7): 2125-2135.
18 February 2020
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
(6): 1574-1583.
6 August 2019
Cell Stem Cell
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
(5): 573-575.
4 May 2017
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
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
Chromosome Research
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 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
Cold Spring Harbor Perspectives in Biology
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
Critical Reviews in Eukaryotic Gene Expression
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
Current Opinion in Cell Biology
Computational approaches from polymer physics to investigate chromatin folding.
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
: 10-17.
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
: 105-111.
June 2020
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
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
Current Opinion in Genetics & Development
The dynamics of chromatin architecture in brain development and function.
Harabula, I. ORCID: https://orcid.org/0000-0002-9094-0519 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Current Opinion in Genetics & Development 67
: 84-93.
April 2021
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
: iii-iv.
April 2019
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
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
Current Opinion in Systems Biology
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
Development
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
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
Developmental Cell
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
(5): 523-524.
5 December 2016
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
EMBO Journal
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
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
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
EMBO Reports
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
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
EPL
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
(4): 40004.
8 February 2018
Epigenetics & Chromatin
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
European Journal of Immunology
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
Experimental Cell Research
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
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
FASEB Journal
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
FEBS Journal
Physical mechanisms of chromatin spatial organization.
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, Fiorillo, L., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Irani, E. ORCID: https://orcid.org/0000-0002-8194-960X, Musella, F., Abraham, A., Prisco, A. and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
FEBS Journal 289
(5): 1180-1190.
March 2022
Frontiers in Bioscience
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
Frontiers in Genetics
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
Frontiers in Molecular Neuroscience
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
: 415.
December 2017
Frontiers in Neuroscience
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
: 559.
10 October 2017
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
Gene
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
Genome Biology
Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.
Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Menegatti, J., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Hennig, T., Theil, K. ORCID: https://orcid.org/0000-0002-7205-6308, Rutkowski, A., Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, Baer, L., Kermas, L., Friedel, C. ORCID: https://orcid.org/0000-0003-3569-4877, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Dölken, L., Grässer, F. and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
Genome Biology 18
(1): 209.
31 October 2017
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
Genome Research
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
Histochemistry and Cell Biology
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
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
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January 2006
Human Genetics
A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome.
Cinque, L., Micale, L., Manara, E., Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Palumbo, O., Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Guerri, G., Bertelli, M., Giuffrida, M.G., Bernardini, L., Notarangelo, A., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416 and Castori, M.
Human Genetics 141
(2): 217-227.
February 2022
Immunology
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
International Journal of Parallel, Emergent and Distributed Systems
Efficient computational implementation of polymer physics models to explore chromatin structure.
Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Fiorillo, L., Campanile, R., Annunziatella, C., Corrado, A., Chiariello, M.G., Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X and Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167
International Journal of Parallel, Emergent and Distributed Systems 37
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January 2022
Journal of Cell Biology
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
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23 March 1998
Journal of Cell Science
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
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June 1996
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
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January 1995
Journal of Chemical Physics
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
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7 January 2025
Journal of Histochemistry and Cytochemistry
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
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July 2001
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
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April 1999
Journal of Immunology
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
Journal of Virology
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
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January 2005
Lecture Notes in Computer Science
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
Methods
Inference of chromosome 3D structures from GAM data by a physics computational approach.
Fiorillo, L., Bianco, S., Chiariello, A.M., Barbieri, M., Esposito, A., Annunziatella, C., Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Corrado, A., Prisco, A., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Methods 181-182
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1 October 2020
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
Methods 142
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1 June 2018
Methods in Molecular Biology
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
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2023
A polymer physics model to dissect genome organization in healthy and pathological phenotypes.
Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Fiorillo, L., Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Esposito, A. ORCID: https://orcid.org/0000-0002-5903-8439, Musella, F., Flora, F., Abraham, A. and Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416
Methods in Molecular Biology 2301
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2022
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
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2010
Modern Physics Letters B
Polymer models of the organization of chromosomes in the nucleus of cells.
Chiariello, A.M., Bianco, S., Piccolo, A., Annunziatella, C., Barbieri, M., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Nicodemi, M.
Modern Physics Letters B 29
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10 April 2015
Molecular & Cellular Proteomics
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
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June 2012
Molecular Biology of the Cell
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
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March 2014
Nuclear cell biology.
Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288 and Starr, D.A.
Molecular Biology of the Cell 22
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15 March 2011
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
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1 April 2006
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
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May 2004
Molecular Cell
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
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1 February 2024
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
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
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
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11 June 2010
Molecular Systems Biology
Extensive folding variability between homologous chromosomes in mammalian cells.
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Molecular Systems Biology 21
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2 July 2025
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
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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Nature
An integrated view of the structure and function of the human 4D nucleome.
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Nature 649
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Cell-type specialization is encoded by specific chromatin topologies.
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LifeTime and improving European healthcare through cell-based interceptive medicine.
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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.
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Science
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.
7 October 2022
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
Scientific Data
FANTOM5 CAGE profiles of human and mouse samples.
Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., Kawashima, T., Kojima, M., Kubosaki, A., Manabe, R.I., Murata, M., Nagao-Sato, S., Nakazato, K., Ninomiya, N., Nishiyori-Sueki, H., Noma, S., Saijyo, E., Saka, A., Sakai, M., Simon, C., Suzuki, N., Tagami, M., Watanabe, S., Yoshida, S., Arner, P., Axton, R.A., Babina, M., Baillie, J.K., Barnett, T.C., Beckhouse, A.G., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Carlisle, A.J., Clevers, H.C., Davis, C.A., Detmar, M. ORCID: https://orcid.org/0000-0002-5351-5054, Dohi, T., Edge, A.S.B., Edinger, M., Ehrlund, A., Ekwall, K., Endoh, M., Enomoto, H., Eslami, A., Fagiolini, M., Fairbairn, L., Farach-Carson, M.C. ORCID: https://orcid.org/0000-0002-4526-3088, Faulkner, G.J., Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, Fisher, M.E. ORCID: https://orcid.org/0000-0003-1074-8103, Forrester, L.M. ORCID: https://orcid.org/0000-0002-9717-8299, Fujita, R., Furusawa, J.I., Geijtenbeek, T.B., Gingeras, T., Goldowitz, D., Guhl, S., Guler, R., Gustincich, S., Ha, T.J., Hamaguchi, M., Hara, M., Hasegawa, Y., Herlyn, M., Heutink, P. ORCID: https://orcid.org/0000-0001-5218-1737, Hitchens, K.J., Hume, D.A., Ikawa, T., Ishizu, Y., Kai, C., Kawamoto, H., Kawamura, Y.I., Kempfle, J.S., Kenna, T.J., Kere, J. ORCID: https://orcid.org/0000-0003-1974-0271, Khachigian, L.M., Kitamura, T., Klein, S., Klinken, S.P., Knox, A.J., Kojima, S. ORCID: https://orcid.org/0000-0002-5252-1612, Koseki, H., Koyasu, S., Lee, W., Lennartsson, A.s, Mackay-Sim, A., Mejhert, N., Mizuno, Y., Morikawa, H. ORCID: https://orcid.org/0000-0002-6793-5885, Morimoto, M., Moro, K., Morris, K.J., Motohashi, H., Mummery, C.L., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nozaki, T., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D.A., Passier, R., Patrikakis, M., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Pradhan-Bhatt, S., Qin, X.Y., Rehli, M., Rizzu, P., Roy, S., Sajantila, A., Sakaguchi, S., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schmidl, C., Schneider, C., Schulze-Tanzil, G.G., Schwegmann, A., Sheng, G., Shin, J.W., Sugiyama, D., Sugiyama, T., Summers, K.M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tomoiu, A., Toyoda, H., van de Wetering, M., van den Berg, L.M., Verardo, R., Vijayan, D., Wells, C.A., Winteringham, L.N., Wolvetang, E., Yamaguchi, Y., Yamamoto, M., Yanagi-Mizuochi, C., Yoneda, M., Yonekura, Y., Zhang, P.G., Zucchelli, S., Abugessaisa, I. ORCID: https://orcid.org/0000-0001-7458-801X, Arner, E., Harshbarger, J., Kondo, A., Lassmann, T., Lizio, M. ORCID: https://orcid.org/0000-0001-7337-7325, Sahin, S., Sengstag, T., Severin, J., Shimoji, H., Suzuki, M., Suzuki, H., Kawai, J., Kondo, N., Itoh, M., Daub, C.O., Kasukawa, T. ORCID: https://orcid.org/0000-0001-5085-0802, Kawaji, H. ORCID: https://orcid.org/0000-0002-0575-0308, Carninci, P., Forrest, A.R.R. and Hayashizaki, Y.
Scientific Data 4
: 170112.
29 August 2017
Soft Matter
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
Transcription
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
Translational Psychiatry
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
(5): e1120.
9 May 2017
Trends in Biochemical Sciences
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
Trends in Cell Biology
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
Visions of the Cell Nucleus
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
Wiley Interdisciplinary Reviews Systems Biology and Medicine
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
(4): e1444.
July 2019
Zenodo
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
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
bioRxiv
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
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
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
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
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
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
: 114710.
20 March 2017
eLife
Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.
Dias, J.D., Rito, T., Torlai Triglia, E. ORCID: https://orcid.org/0000-0002-6059-0116, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, Chotalia, M., Brookes, E., Kimura, H. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
eLife 4
: e11215.
19 December 2015
iScience
Divergent transcription of the Nkx2-5 locus generates two enhancer RNAs with opposing functions.
Salamon, I., Serio, S., Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Pagiatakis, C., Crasto, S., Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Conte, M. ORCID: https://orcid.org/0000-0002-6670-9800, Cattaneo, P., Fiorillo, L., Felicetta, A., di Pasquale, E., Kunderfranco, P., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Papait, R. and Condorelli, G.
iScience 23
(9): 101539.
25 September 2020
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