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Apostolou E, Thanos D. Linking differential chromatin loops to transcriptional decisions. Mol Cell. 2008 Feb 1;29(2):154-6. doi: 10.1016/j.molcel.2008.01.008. PubMed PMID: 18243110.
Apostolou E, Thanos D. Virus Infection Induces NF-kappaB-dependent interchromosomal associations mediating monoallelic IFN-beta gene expression. Cell. 2008 Jul 11;134(1):85-96. doi: 10.1016/j.cell.2008.05.052. PubMed PMID: 18614013.
Gagos S, Chiourea M, Christodoulidou A, Apostolou E, Raftopoulou C, Deustch S, Jefford CE, Irminger-Finger I, Shay JW, Antonarakis SE. Pericentromeric instability and spontaneous emergence of human neoacrocentric and minute chromosomes in the alternative pathway of telomere lengthening. Cancer Res. 2008 Oct 1;68(19):8146-55. doi: 10.1158/0008-5472.CAN-08-0945. PubMed PMID: 18829574.
Stadtfeld M, Apostolou E, Akutsu H, Fukuda A, Follett P, Natesan S, Kono T, Shioda T, Hochedlinger K. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature. 2010 May 13;465(7295):175-81. doi: 10.1038/nature09017. Epub 2010 Apr 25. PubMed PMID: 20418860; PubMed Central PMCID: PMC3987905.
Polo JM, Liu S, Figueroa ME, Kulalert W, Eminli S, Tan KY, Apostolou E, Stadtfeld M, Li Y, Shioda T, Natesan S, Wagers AJ, Melnick A, Evans T, Hochedlinger K. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat Biotechnol. 2010 Aug;28(8):848-55. doi: 10.1038/nbt.1667. Epub 2010 Jul 19. PubMed PMID: 20644536; PubMed Central PMCID: PMC3148605.
Patrikidou A, Vlachostergios PJ, Voutsadakis IA, Hatzidaki E, Valeri RM, Destouni C, Apostolou E, Daliani D, Papandreou CN. Inverse baseline expression pattern of the NEP/neuropeptides and NFκB/proteasome pathways in androgen-dependent and androgen-independent prostate cancer cells. Cancer Cell Int. 2011 May 15;11(1):13. doi: 10.1186/1475-2867-11-13. PubMed PMID: 21569620; PubMed Central PMCID: PMC3121665.
Apostolou E, Hochedlinger K. Stem cells: iPS cells under attack. Nature. 2011 Jun 8;474(7350):165-6. doi: 10.1038/474165a. PubMed PMID: 21654792.
Antonaki A, Demetriades C, Polyzos A, Banos A, Vatsellas G, Lavigne MD, Apostolou E, Mantouvalou E, Papadopoulou D, Mosialos G, Thanos D. Genomic analysis reveals a novel nuclear factor-κB (NF-κB)-binding site in Alu-repetitive elements. J Biol Chem. 2011 Nov 4;286(44):38768-38782. doi: 10.1074/jbc.M111.234161. Epub 2011 Sep 5. PubMed PMID: 21896491; PubMed Central PMCID: PMC3207430.
Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, Ooi SS, Kim SY, Bestor TH, Shioda T, Park PJ, Hochedlinger K. Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat Genet. 2012 Mar 4;44(4):398-405, S1-2. doi: 10.1038/ng.1110. PubMed PMID: 22387999; PubMed Central PMCID: PMC3538378.
Patrikidou A, Vlachostergios PJ, Voutsadakis IA, Hatzidaki E, Valeri RM, Destouni C, Apostolou E, Papandreou CN. Neuropeptide-inducible upregulation of proteasome activity precedes nuclear factor kappa B activation in androgen-independent prostate cancer cells. Cancer Cell Int. 2012 Jun 20;12(1):31. doi: 10.1186/1475-2867-12-31. PubMed PMID: 22715899; PubMed Central PMCID: PMC3441896.
Qin J, Whyte WA, Anderssen E, Apostolou E, Chen HH, Akbarian S, Bronson RT, Hochedlinger K, Ramaswamy S, Young RA, Hock H. The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development. Cell Stem Cell. 2012 Sep 7;11(3):319-32. doi: 10.1016/j.stem.2012.06.002. Epub 2012 Jul 5. PubMed PMID: 22770845; PubMed Central PMCID: PMC3647456.
Buckley SM, Aranda-Orgilles B, Strikoudis A, Apostolou E, Loizou E, Moran-Crusio K, Farnsworth CL, Koller AA, Dasgupta R, Silva JC, Stadtfeld M, Hochedlinger K, Chen EI, Aifantis I. Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell. 2012 Dec 7;11(6):783-98. doi: 10.1016/j.stem.2012.09.011. Epub 2012 Oct 25. PubMed PMID: 23103054; PubMed Central PMCID: PMC3549668.
Polo JM, Anderssen E, Walsh RM, Schwarz BA, Nefzger CM, Lim SM, Borkent M, Apostolou E, Alaei S, Cloutier J, Bar-Nur O, Cheloufi S, Stadtfeld M, Figueroa ME, Robinton D, Natesan S, Melnick A, Zhu J, Ramaswamy S, Hochedlinger K. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell. 2012 Dec 21;151(7):1617-32. doi: 10.1016/j.cell.2012.11.039. PubMed PMID: 23260147; PubMed Central PMCID: PMC3608203.
Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell. 2013 Jun 6;12(6):699-712. doi: 10.1016/j.stem.2013.04.013. Epub 2013 May 9. PubMed PMID: 23665121; PubMed Central PMCID: PMC3725985.
Apostolou E, Hochedlinger K. Chromatin dynamics during cellular reprogramming. Nature. 2013 Oct 24;502(7472):462-71. doi: 10.1038/nature12749. Review. PubMed PMID: 24153299; PubMed Central PMCID: PMC4216318.
Ferrari F, Apostolou E, Park PJ, Hochedlinger K. Rearranging the chromatin for pluripotency. Cell Cycle. 2014;13(2):167-8. doi: 10.4161/cc.27028. Epub 2013 Nov 15. PubMed PMID: 24241209; PubMed Central PMCID: PMC3906226.
Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, De Los Angeles A, O'Brien K, Atsma JM, Fujiwara Y, Nguyen M, Ljuboja D, Guo G, Woo A, Yuan GC, Onder T, Daley G, Hochedlinger K, Kim J, Orkin SH. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell. 2014 Jan 9;53(1):32-48. doi: 10.1016/j.molcel.2013.11.011. Epub 2013 Dec 19. PubMed PMID: 24361252; PubMed Central PMCID: PMC3919500.
Bar-Nur O, Brumbaugh J, Verheul C, Apostolou E, Pruteanu-Malinici I, Walsh RM, Ramaswamy S, Hochedlinger K. Small molecules facilitate rapid and synchronous iPSC generation. Nat Methods. 2014 Nov;11(11):1170-6. doi: 10.1038/nmeth.3142. Epub 2014 Sep 24. PubMed PMID: 25262205; PubMed Central PMCID: PMC4326224.
Vidal SE, Stadtfeld M, Apostolou E. F-class cells: new routes and destinations for induced pluripotency. Cell Stem Cell. 2015 Jan 8;16(1):9-10. doi: 10.1016/j.stem.2014.12.007. PubMed PMID: 25575077.
Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH. PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep. 2015 Sep 1;12(9):1456-70. doi: 10.1016/j.celrep.2015.07.053. Epub 2015 Aug 20. PubMed PMID: 26299972; PubMed Central PMCID: PMC5384103.
Beagan JA, Gilgenast TG, Kim J, Plona Z, Norton HK, Hu G, Hsu SC, Shields EJ, Lyu X, Apostolou E, Hochedlinger K, Corces VG, Dekker J, Phillips-Cremins JE. Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Cell Stem Cell. 2016 May 5;18(5):611-24. doi: 10.1016/j.stem.2016.04.004. PubMed PMID: 27152443; PubMed Central PMCID: PMC4859942.
Borkent M, Bennett BD, Lackford B, Bar-Nur O, Brumbaugh J, Wang L, Du Y, Fargo DC, Apostolou E, Cheloufi S, Maherali N, Elledge SJ, Hu G, Hochedlinger K. A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2. Stem Cell Reports. 2016 May 10;6(5):704-716. doi: 10.1016/j.stemcr.2016.02.004. Epub 2016 Mar 3. PubMed PMID: 26947976; PubMed Central PMCID: PMC4939549.
Di Giammartino DC, Apostolou E. The Chromatin Signature of Pluripotency: Establishment and Maintenance. Curr Stem Cell Rep. 2016;2:255-262. doi: 10.1007/s40778-016-0055-3. Epub 2016 Jun 27. Review. PubMed PMID: 27547710; PubMed Central PMCID: PMC4972866.
Liu Y, Pelham-Webb B, Di Giammartino DC, Li J, Kim D, Kita K, Saiz N, Garg V, Doane A, Giannakakou P, Hadjantonakis AK, Elemento O, Apostolou E. Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells. Cell Rep. 2017 May 16;19(7):1283-1293. doi: 10.1016/j.celrep.2017.04.067. PubMed PMID: 28514649; PubMed Central PMCID: PMC5495017.
Amlani B, Liu Y, Chen T, Ee LS, Lopez P, Heguy A, Apostolou E, Kim SY, Stadtfeld M. Nascent Induced Pluripotent Stem Cells Efficiently Generate Entirely iPSC-Derived Mice while Expressing Differentiation-Associated Genes. Cell Rep. 2018 Jan 23;22(4):876-884. doi: 10.1016/j.celrep.2017.12.098. Epub 2018 Jan 28. PubMed PMID: 29420174; PubMed Central PMCID: PMC6664440.
Apostolou E. Shaping the Pluripotent Genome: Switches, Borders, and Loops. Cell Stem Cell. 2018 Feb 1;22(2):148-150. doi: 10.1016/j.stem.2018.01.005. PubMed PMID: 29395051.
Apostolou E, Stadtfeld M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr Opin Genet Dev. 2018 Oct;52:77-85. doi: 10.1016/j.gde.2018.06.002. Epub 2018 Jun 17. Review. PubMed PMID: 29925040; PubMed Central PMCID: PMC6252123.
Zhou T, Kim TW, Chong CN, Tan L, Amin S, Sadat Badieyan Z, Mukherjee S, Ghazizadeh Z, Zeng H, Guo M, Crespo M, Zhang T, Kenyon R, Robinson CL, Apostolou E, Wang H, Xiang JZ, Evans T, Studer L, Chen S. A hPSC-based platform to discover gene-environment interactions that impact human β-cell and dopamine neuron survival. Nat Commun. 2018 Nov 16;9(1):4815. doi: 10.1038/s41467-018-07201-1. PubMed PMID: 30446643; PubMed Central PMCID: PMC6240096.
Liu EM, Martinez-Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E, Sanjana NE, Khurana E. Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. Cell Syst. 2019 May 22;8(5):446-455.e8. doi: 10.1016/j.cels.2019.04.001. Epub 2019 May 8. PubMed PMID: 31078526; PubMed Central PMCID: PMC6917527.
Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH, Das PP. TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network. Mol Cell. 2019 Jun 20;74(6):1148-1163.e7. doi: 10.1016/j.molcel.2019.03.025. Epub 2019 Apr 17. PubMed PMID: 31005419; PubMed Central PMCID: PMC6671628.
Di Giammartino DC, Kloetgen A, Polyzos A, Liu Y, Kim D, Murphy D, Abuhashem A, Cavaliere P, Aronson B, Shah V, Dephoure N, Stadtfeld M, Tsirigos A, Apostolou E. KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks. Nat Cell Biol. 2019 Oct;21(10):1179-1190. doi: 10.1038/s41556-019-0390-6. Epub 2019 Sep 23. PubMed PMID: 31548608; PubMed Central PMCID: PMC7339746.
Lhoumaud P, Sethia G, Izzo F, Sakellaropoulos T, Snetkova V, Vidal S, Badri S, Cornwell M, Di Giammartino DC, Kim KT, Apostolou E, Stadtfeld M, Landau DA, Skok J. EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation. Genome Biol. 2019 Nov 21;20(1):248. doi: 10.1186/s13059-019-1853-6. PubMed PMID: 31752933; PubMed Central PMCID: PMC6868874.
Di Giammartino DC, Polyzos A, Apostolou E. Transcription factors: building hubs in the 3D space. Cell Cycle. 2020 Oct;19(19):2395-2410. doi: 10.1080/15384101.2020.1805238. Epub 2020 Aug 12. Review. PubMed PMID: 32783593; PubMed Central PMCID: PMC7553511.
Martínez de Paz A, Josefowicz SZ. Signaling-to-chromatin pathways in the immune system. Immunol Rev. 2021 Mar;300(1):37-53. doi: 10.1111/imr.12955. Epub 2021 Feb 28. Review. PubMed PMID: 33644906; PubMed Central PMCID: PMC8548991.
Pelham-Webb B, Polyzos A, Wojenski L, Kloetgen A, Li J, Di Giammartino DC, Sakellaropoulos T, Tsirigos A, Core L, Apostolou E. H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization. Mol Cell. 2021 Apr 15;81(8):1732-1748.e8. doi: 10.1016/j.molcel.2021.02.032. Epub 2021 Mar 16. PubMed PMID: 33730542; PubMed Central PMCID: PMC8052294.
Aronson BE, Scourzic L, Shah V, Swanzey E, Kloetgen A, Polyzos A, Sinha A, Azziz A, Caspi I, Li J, Pelham-Webb B, Glenn RA, Vierbuchen T, Wichterle H, Tsirigos A, Dawlaty MM, Stadtfeld M, Apostolou E. A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus. Dev Cell. 2021 Nov 22;56(22):3052-3065.e5. doi: 10.1016/j.devcel.2021.10.004. Epub 2021 Oct 27. PubMed PMID: 34710357; PubMed Central PMCID: PMC8628258.
Wierbowski SD, Liang S, Liu Y, Chen Y, Gupta S, Andre NM, Lipkin SM, Whittaker GR, Yu H. A 3D structural SARS-CoV-2-human interactome to explore genetic and drug perturbations. Nat Methods. 2021 Dec;18(12):1477-1488. doi: 10.1038/s41592-021-01318-w. Epub 2021 Nov 29. PubMed PMID: 34845387; PubMed Central PMCID: PMC8665054.
Yan J, Huangfu D. Epigenome rewiring in human pluripotent stem cells. Trends Cell Biol. 2021 Dec 23;. doi: 10.1016/j.tcb.2021.12.001. [Epub ahead of print] Review. PubMed PMID: 34955367; NIHMSID:NIHMS1762644.
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