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Items: 18

1.

Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms.

Cardozo Gizzi AM, Cattoni DI, Fiche JB, Espinola SM, Gurgo J, Messina O, Houbron C, Ogiyama Y, Papadopoulos GL, Cavalli G, Lagha M, Nollmann M.

Mol Cell. 2019 Apr 4;74(1):212-222.e5. doi: 10.1016/j.molcel.2019.01.011. Epub 2019 Feb 19.

PMID:
30795893
2.

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development.

Ogiyama Y, Schuettengruber B, Papadopoulos GL, Chang JM, Cavalli G.

Mol Cell. 2018 Jul 5;71(1):73-88.e5. doi: 10.1016/j.molcel.2018.05.032. Epub 2018 Jun 28.

3.

TADs are 3D structural units of higher-order chromosome organization in Drosophila.

Szabo Q, Jost D, Chang JM, Cattoni DI, Papadopoulos GL, Bonev B, Sexton T, Gurgo J, Jacquier C, Nollmann M, Bantignies F, Cavalli G.

Sci Adv. 2018 Feb 28;4(2):eaar8082. doi: 10.1126/sciadv.aar8082. eCollection 2018 Feb.

4.

Multiscale 3D Genome Rewiring during Mouse Neural Development.

Bonev B, Mendelson Cohen N, Szabo Q, Fritsch L, Papadopoulos GL, Lubling Y, Xu X, Lv X, Hugnot JP, Tanay A, Cavalli G.

Cell. 2017 Oct 19;171(3):557-572.e24. doi: 10.1016/j.cell.2017.09.043.

5.

ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes.

Chatzinikolaou G, Apostolou Z, Aid-Pavlidis T, Ioannidou A, Karakasilioti I, Papadopoulos GL, Aivaliotis M, Tsekrekou M, Strouboulis J, Kosteas T, Garinis GA.

Nat Cell Biol. 2017 May;19(5):421-432. doi: 10.1038/ncb3499. Epub 2017 Apr 3.

PMID:
28368372
6.

GATA-1 Inhibits PU.1 Gene via DNA and Histone H3K9 Methylation of Its Distal Enhancer in Erythroleukemia.

Burda P, Vargova J, Curik N, Salek C, Papadopoulos GL, Strouboulis J, Stopka T.

PLoS One. 2016 Mar 24;11(3):e0152234. doi: 10.1371/journal.pone.0152234. eCollection 2016.

7.

GATA1 and PU.1 Bind to Ribosomal Protein Genes in Erythroid Cells: Implications for Ribosomopathies.

Amanatiadou EP, Papadopoulos GL, Strouboulis J, Vizirianakis IS.

PLoS One. 2015 Oct 8;10(10):e0140077. doi: 10.1371/journal.pone.0140077. eCollection 2015.

8.

Genomic and proteomic analysis of transcription factor TFII-I reveals insight into the response to cellular stress.

Fan AX, Papadopoulos GL, Hossain MA, Lin IJ, Hu J, Tang TM, Kilberg MS, Renne R, Strouboulis J, Bungert J.

Nucleic Acids Res. 2014 Jul;42(12):7625-41. doi: 10.1093/nar/gku467. Epub 2014 May 29.

9.

Metal and metallothionein concentrations in Paracentrotus lividus from Amvrakikos gulf (Ionian Sea-Greece).

Strogyloudi E, Pancucci-Papadopoulou MA, Papadopoulos GL.

Environ Monit Assess. 2014 Sep;186(9):5489-99. doi: 10.1007/s10661-014-3798-2. Epub 2014 May 16.

PMID:
24833020
10.

GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis.

Papadopoulos GL, Karkoulia E, Tsamardinos I, Porcher C, Ragoussis J, Bungert J, Strouboulis J.

Nucleic Acids Res. 2013 May;41(9):4938-48. doi: 10.1093/nar/gkt167. Epub 2013 Mar 21.

11.

Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data.

Reczko M, Maragkakis M, Alexiou P, Papadopoulos GL, Hatzigeorgiou AG.

Front Genet. 2012 Jan 18;2:103. doi: 10.3389/fgene.2011.00103. eCollection 2011.

12.

The DIANA-mirExTra web server: from gene expression data to microRNA function.

Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, Hatzigeorgiou AG.

PLoS One. 2010 Feb 11;5(2):e9171. doi: 10.1371/journal.pone.0009171.

13.

Lost in translation: an assessment and perspective for computational microRNA target identification.

Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG.

Bioinformatics. 2009 Dec 1;25(23):3049-55. doi: 10.1093/bioinformatics/btp565. Epub 2009 Sep 29. Review.

PMID:
19789267
14.

Accurate microRNA target prediction correlates with protein repression levels.

Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG.

BMC Bioinformatics. 2009 Sep 18;10:295. doi: 10.1186/1471-2105-10-295.

15.

Mung bean nuclease mapping of RNAs 3' end.

Bellavia D, Sisino G, Papadopoulos GL, Forte GI, Barbieri R.

Immun Ageing. 2009 May 21;6:6. doi: 10.1186/1742-4933-6-6.

16.

DIANA-mirPath: Integrating human and mouse microRNAs in pathways.

Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG.

Bioinformatics. 2009 Aug 1;25(15):1991-3. doi: 10.1093/bioinformatics/btp299. Epub 2009 May 12.

PMID:
19435746
17.

DIANA-microT web server: elucidating microRNA functions through target prediction.

Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W273-6. doi: 10.1093/nar/gkp292. Epub 2009 Apr 30.

18.

The database of experimentally supported targets: a functional update of TarBase.

Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG.

Nucleic Acids Res. 2009 Jan;37(Database issue):D155-8. doi: 10.1093/nar/gkn809. Epub 2008 Oct 27.

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