| Year |
Citation |
Score |
| 2023 |
Beagrie RA, Thieme CJ, Annunziatella C, Baugher C, Zhang Y, Schueler M, Kukalev A, Kempfer R, Chiariello AM, Bianco S, Li Y, Davis T, Scialdone A, Welch LR, Nicodemi M, ... Pombo A, et al. Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C. Nature Methods. PMID 37336949 DOI: 10.1038/s41592-023-01903-1 |
0.757 |
|
| 2022 |
McGarvey AC, Kopp W, Vučićević D, Mattonet K, Kempfer R, Hirsekorn A, Bilić I, Gil M, Trinks A, Merks AM, Panáková D, Pombo A, Akalin A, Junker JP, Stainier DYR, et al. Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos. Cell Genomics. 2: 100083. PMID 36777038 DOI: 10.1016/j.xgen.2021.100083 |
0.442 |
|
| 2021 |
Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, ... ... Pombo A, et al. Cell-type specialization is encoded by specific chromatin topologies. Nature. 599: 684-691. PMID 34789882 DOI: 10.1038/s41586-021-04081-2 |
0.431 |
|
| 2021 |
Harabula I, Pombo A. The dynamics of chromatin architecture in brain development and function. Current Opinion in Genetics & Development. 67: 84-93. PMID 33421764 DOI: 10.1016/j.gde.2020.12.008 |
0.381 |
|
| 2020 |
Sparks TM, Harabula I, Pombo A. Evolving methodologies and concepts in 4D nucleome research. Current Opinion in Cell Biology. 64: 105-111. PMID 32473574 DOI: 10.1016/j.ceb.2020.04.005 |
0.356 |
|
| 2019 |
Skourti-Stathaki K, Torlai Triglia E, Warburton M, Voigt P, Bird A, Pombo A. R-Loops Enhance Polycomb Repression at a Subset of Developmental Regulator Genes. Molecular Cell. PMID 30709709 DOI: 10.1016/J.Molcel.2018.12.016 |
0.344 |
|
| 2017 |
Ferrai C, Torlai Triglia E, Risner-Janiczek JR, Rito T, Rackham OJ, de Santiago I, Kukalev A, Nicodemi M, Akalin A, Li M, Ungless MA, Pombo A. RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation. Molecular Systems Biology. 13: 946. PMID 29038337 DOI: 10.15252/Msb.20177754 |
0.437 |
|
| 2017 |
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 RI, Murata M, ... ... Pombo A, et al. FANTOM5 CAGE profiles of human and mouse samples. Scientific Data. 4: 170112. PMID 28850106 DOI: 10.1038/Sdata.2017.112 |
0.347 |
|
| 2017 |
Beagrie RA, Pombo A. Cell cycle: Continuous chromatin changes. Nature. 547: 34-35. PMID 28682328 DOI: 10.1038/547034a |
0.732 |
|
| 2017 |
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression. Nature Communications. 8: 36. PMID 28652613 DOI: 10.1038/S41467-017-00052-2 |
0.793 |
|
| 2017 |
Caglio G, Torlai Triglia E, Pombo A. Keep Them Close: PRC2 Poises Enhancer-Promoter Interactions at Anterior Neuronal Genes. Cell Stem Cell. 20: 573-575. PMID 28475876 DOI: 10.1016/j.stem.2017.04.006 |
0.374 |
|
| 2017 |
Barbieri M, Xie SQ, Torlai Triglia E, Chiariello AM, Bianco S, de Santiago I, Branco MR, Rueda D, Nicodemi M, Pombo A. Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells. Nature Structural & Molecular Biology. PMID 28436944 DOI: 10.1038/Nsmb.3402 |
0.718 |
|
| 2017 |
Beagrie RA, Scialdone A, Schueler M, Kraemer DC, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas LM, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PA, ... ... Pombo A, et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature. PMID 28273065 DOI: 10.1038/Nature21411 |
0.771 |
|
| 2016 |
Beagrie RA, Pombo A. Examining Topological Domain Influence on Enhancer Function. Developmental Cell. 39: 523-524. PMID 27923117 DOI: 10.1016/j.devcel.2016.11.011 |
0.753 |
|
| 2016 |
Franke M, Ibrahim DM, Andrey G, Schwarzer W, Heinrich V, Schöpflin R, Kraft K, Kempfer R, Jerković I, Chan WL, Spielmann M, Timmermann B, Wittler L, Kurth I, Cambiaso P, ... ... Pombo A, et al. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature. PMID 27706140 DOI: 10.1038/Nature19800 |
0.355 |
|
| 2016 |
Beagrie RA, Pombo A. Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 38: 881-93. PMID 27452946 DOI: 10.1002/bies.201600032 |
0.791 |
|
| 2016 |
Le HQ, Ghatak S, Yeung CC, Tellkamp F, Günschmann C, Dieterich C, Yeroslaviz A, Habermann B, Pombo A, Niessen CM, Wickström SA. Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment. Nature Cell Biology. PMID 27398909 DOI: 10.1038/ncb3387 |
0.383 |
|
| 2015 |
Fraser J, Ferrai C, Chiariello AM, Schueler M, Rito T, Laudanno G, Barbieri M, Moore BL, Kraemer DC, Aitken S, Xie SQ, Morris KJ, Itoh M, Kawaji H, Jaeger I, ... ... Pombo A, et al. Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Molecular Systems Biology. 11: 852. PMID 26700852 DOI: 10.15252/Msb.20156492 |
0.344 |
|
| 2015 |
Dias JD, Rito T, Torlai Triglia E, Kukalev A, Ferrai C, Chotalia M, Brookes E, Kimura H, Pombo A. Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells. Elife. 4. PMID 26687004 DOI: 10.7554/eLife.11215 |
0.774 |
|
| 2015 |
Pombo A, Dillon N. Three-dimensional genome architecture: players and mechanisms. Nature Reviews. Molecular Cell Biology. 16: 245-57. PMID 25757416 DOI: 10.1038/nrm3965 |
0.413 |
|
| 2015 |
Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, ... ... Pombo A, et al. Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (New York, N.Y.). 347: 1010-4. PMID 25678556 DOI: 10.1126/Science.1259418 |
0.437 |
|
| 2014 |
Sabbattini P, Sjoberg M, Nikic S, Frangini A, Holmqvist PH, Kunowska N, Carroll T, Brookes E, Arthur SJ, Pombo A, Dillon N. An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation. Molecular Biology of the Cell. 25: 904-15. PMID 24430871 DOI: 10.1091/Mbc.E13-10-0628 |
0.777 |
|
| 2012 |
Brookes E, Pombo A. Code breaking: the RNAPII modification code in pluripotency. Cell Cycle (Georgetown, Tex.). 11: 1267-8. PMID 22421158 DOI: 10.4161/cc.19990 |
0.673 |
|
| 2012 |
Brookes E, de Santiago I, Hebenstreit D, Morris KJ, Carroll T, Xie SQ, Stock JK, Heidemann M, Eick D, Nozaki N, Kimura H, Ragoussis J, Teichmann SA, Pombo A. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell. 10: 157-70. PMID 22305566 DOI: 10.1016/J.Stem.2011.12.017 |
0.779 |
|
| 2012 |
Möller A, Xie SQ, Hosp F, Lang B, Phatnani HP, James S, Ramirez F, Collin GB, Naggert JK, Babu MM, Greenleaf AL, Selbach M, Pombo A. Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease. Molecular & Cellular Proteomics : McP. 11: M111.011767. PMID 22199231 DOI: 10.1074/Mcp.M111.011767 |
0.37 |
|
| 2011 |
Pombo A, Starr DA. Nuclear cell biology. Molecular Biology of the Cell. 22: 722. PMID 21406585 DOI: 10.1091/Mbc.E10-12-0966 |
0.427 |
|
| 2010 |
Morris KJ, Chotalia M, Pombo A. Nuclear architecture in stem cells. Advances in Experimental Medicine and Biology. 695: 14-25. PMID 21222196 DOI: 10.1007/978-1-4419-7037-4_2 |
0.442 |
|
| 2010 |
Alder O, Lavial F, Helness A, Brookes E, Pinho S, Chandrashekran A, Arnaud P, Pombo A, O'Neill L, Azuara V. Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment. Development (Cambridge, England). 137: 2483-92. PMID 20573702 DOI: 10.1242/dev.048363 |
0.795 |
|
| 2010 |
Kanhere A, Viiri K, Araújo CC, Rasaiyaah J, Bouwman RD, Whyte WA, Pereira CF, Brookes E, Walker K, Bell GW, Pombo A, Fisher AG, Young RA, Jenner RG. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Molecular Cell. 38: 675-88. PMID 20542000 DOI: 10.1016/j.molcel.2010.03.019 |
0.791 |
|
| 2010 |
Ferrai C, de Castro IJ, Lavitas L, Chotalia M, Pombo A. Gene positioning. Cold Spring Harbor Perspectives in Biology. 2: a000588. PMID 20484389 DOI: 10.1101/cshperspect.a000588 |
0.47 |
|
| 2010 |
Landeira D, Sauer S, Poot R, Dvorkina M, Mazzarella L, Jørgensen HF, Pereira CF, Leleu M, Piccolo FM, Spivakov M, Brookes E, Pombo A, Fisher C, Skarnes WC, Snoek T, et al. 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. Nature Cell Biology. 12: 618-24. PMID 20473294 DOI: 10.1038/Ncb2065 |
0.805 |
|
| 2010 |
Ferrai C, Xie SQ, Luraghi P, Munari D, Ramirez F, Branco MR, Pombo A, Crippa MP. Poised transcription factories prime silent uPA gene prior to activation. Plos Biology. 8: e1000270. PMID 20052287 DOI: 10.1371/journal.pbio.1000270 |
0.716 |
|
| 2009 |
Hiragami-Hamada K, Xie SQ, Saveliev A, Uribe-Lewis S, Pombo A, Festenstein R. The molecular basis for stability of heterochromatin-mediated silencing in mammals. Epigenetics & Chromatin. 2: 14. PMID 19889207 DOI: 10.1186/1756-8935-2-14 |
0.446 |
|
| 2009 |
Brookes E, Pombo A. Modifications of RNA polymerase II are pivotal in regulating gene expression states. Embo Reports. 10: 1213-9. PMID 19834511 DOI: 10.1038/embor.2009.221 |
0.803 |
|
| 2009 |
Ferrai C, Pombo A. 3D chromatin regulation of Sonic hedgehog in the limb buds. Developmental Cell. 16: 9-11. PMID 19154714 DOI: 10.1016/j.devcel.2008.12.010 |
0.357 |
|
| 2008 |
Babu MM, Janga SC, de Santiago I, Pombo A. Eukaryotic gene regulation in three dimensions and its impact on genome evolution. Current Opinion in Genetics & Development. 18: 571-82. PMID 19007886 DOI: 10.1016/j.gde.2008.10.002 |
0.387 |
|
| 2008 |
Branco MR, Branco T, Ramirez F, Pombo A. Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 16: 413-26. PMID 18461481 DOI: 10.1007/s10577-008-1230-x |
0.66 |
|
| 2008 |
Noordermeer D, Branco MR, Splinter E, Klous P, Van Ijcken W, Swagemakers S, Koutsourakis M, Van Der Spek P, Pombo A, De Laat W. Transcription and chromatin organization of a housekeeping gene cluster containing an integrated β-globin locus control region Plos Genetics. 4. PMID 18369441 DOI: 10.1371/Journal.Pgen.1000016 |
0.725 |
|
| 2007 |
Stock JK, Giadrossi S, Casanova M, Brookes E, Vidal M, Koseki H, Brockdorff N, Fisher AG, Pombo A. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nature Cell Biology. 9: 1428-35. PMID 18037880 DOI: 10.1038/ncb1663 |
0.808 |
|
| 2007 |
Pombo A, Branco MR. Functional organisation of the genome during interphase. Current Opinion in Genetics & Development. 17: 451-5. PMID 17920259 DOI: 10.1016/j.gde.2007.08.008 |
0.738 |
|
| 2007 |
Pombo A. Advances in imaging the interphase nucleus using thin cryosections. Histochemistry and Cell Biology. 128: 97-104. PMID 17636315 DOI: 10.1007/s00418-007-0310-x |
0.451 |
|
| 2007 |
Branco MR, Pombo A. Chromosome organization: new facts, new models. Trends in Cell Biology. 17: 127-34. PMID 17197184 DOI: 10.1016/j.tcb.2006.12.006 |
0.704 |
|
| 2006 |
Branco MR, Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. Plos Biology. 4: e138. PMID 16623600 DOI: 10.1371/journal.pbio.0040138 |
0.676 |
|
| 2006 |
Xie SQ, Martin S, Guillot PV, Bentley DL, Pombo A. Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain. Molecular Biology of the Cell. 17: 1723-33. PMID 16467386 DOI: 10.1091/mbc.E05-08-0726 |
0.683 |
|
| 2006 |
Xie SQ, Pombo A. Distribution of different phosphorylated forms of RNA polymerase II in relation to Cajal and PML bodies in human cells: an ultrastructural study. Histochemistry and Cell Biology. 125: 21-31. PMID 16187066 DOI: 10.1007/s00418-005-0064-2 |
0.34 |
|
| 2005 |
Chow CM, Georgiou A, Szutorisz H, Maia e Silva A, Pombo A, Barahona I, Dargelos E, Canzonetta C, Dillon N. Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division. Embo Reports. 6: 354-60. PMID 15776021 DOI: 10.1038/sj.embor.7400366 |
0.364 |
|
| 2004 |
Guillot PV, Xie SQ, Hollinshead M, Pombo A. Fixation-induced redistribution of hyperphosphorylated RNA polymerase II in the nucleus of human cells. Experimental Cell Research. 295: 460-8. PMID 15093744 DOI: 10.1016/j.yexcr.2004.01.020 |
0.632 |
|
| 2003 |
Boyd DC, Pombo A, Murphy S. Interaction of proteins with promoter elements of the human U2 snRNA genes in vivo. Gene. 315: 103-12. PMID 14557070 |
0.427 |
|
| 2003 |
Martin S, Pombo A. Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 11: 461-70. PMID 12971722 DOI: 10.1023/a:1024926710797 |
0.361 |
|
| 2003 |
Pombo A. Cellular genomics: which genes are transcribed, when and where? Trends in Biochemical Sciences. 28: 6-9. PMID 12517445 DOI: 10.1016/s0968-0004(02)00011-7 |
0.425 |
|
| 2002 |
Politz J, Pombo A. Genomics meets nanoscience: probing genes and the cell nucleus at 10-9 meters. Genome Biology. 3: REPORTS4007. PMID 11897022 DOI: 10.1186/gb-2002-3-3-reports4007 |
0.32 |
|
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