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Bivalency in Drosophila embryos is associated with strong inducibility of Polycomb target genes.

Akmammedov A, Geigges M, Paro R.

Fly (Austin). 2019 May 25:1-9. doi: 10.1080/19336934.2019.1619438. [Epub ahead of print]


An intrinsic tumour eviction mechanism in Drosophila mediated by steroid hormone signalling.

Jiang Y, Seimiya M, Schlumpf TB, Paro R.

Nat Commun. 2018 Aug 17;9(1):3293. doi: 10.1038/s41467-018-05794-1.


A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila.

Torres J, Monti R, Moore AL, Seimiya M, Jiang Y, Beerenwinkel N, Beisel C, Beira JV, Paro R.

Elife. 2018 Mar 21;7. pii: e32697. doi: 10.7554/eLife.32697.


Signalling crosstalk during early tumorigenesis in the absence of Polycomb silencing.

Beira JV, Torres J, Paro R.

PLoS Genet. 2018 Jan 22;14(1):e1007187. doi: 10.1371/journal.pgen.1007187. eCollection 2018 Jan.


Pho dynamically interacts with Spt5 to facilitate transcriptional switches at the hsp70 locus.

Pereira A, Paro R.

Epigenetics Chromatin. 2017 Dec 6;10(1):57. doi: 10.1186/s13072-017-0166-9.


Single vector non-leaky gene expression system for Drosophila melanogaster.

Akmammedov A, Geigges M, Paro R.

Sci Rep. 2017 Jul 31;7(1):6899. doi: 10.1038/s41598-017-07282-w.


Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila.

Ciabrelli F, Comoglio F, Fellous S, Bonev B, Ninova M, Szabo Q, Xuéreb A, Klopp C, Aravin A, Paro R, Bantignies F, Cavalli G.

Nat Genet. 2017 Jun;49(6):876-886. doi: 10.1038/ng.3848. Epub 2017 Apr 24.


A High-Density Map for Navigating the Human Polycomb Complexome.

Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C.

Cell Rep. 2016 Oct 4;17(2):583-595. doi: 10.1016/j.celrep.2016.08.096.


Imaginal Disc Transplantation in Drosophila.

Katsuyama T, Paro R.

Methods Mol Biol. 2016;1480:301-10. doi: 10.1007/978-1-4939-6380-5_26.


A Rapid TALEN Assembly Protocol.

Akmammedov A, Katsuyama T, Paro R.

Methods Mol Biol. 2016;1480:269-81. doi: 10.1007/978-1-4939-6380-5_23.


The RNA Binding Protein IMP2 Preserves Glioblastoma Stem Cells by Preventing let-7 Target Gene Silencing.

Degrauwe N, Schlumpf TB, Janiszewska M, Martin P, Cauderay A, Provero P, Riggi N, Suvà ML, Paro R, Stamenkovic I.

Cell Rep. 2016 May 24;15(8):1634-47. doi: 10.1016/j.celrep.2016.04.086. Epub 2016 May 12.


The legacy of Drosophila imaginal discs.

Beira JV, Paro R.

Chromosoma. 2016 Sep;125(4):573-92. doi: 10.1007/s00412-016-0595-4. Epub 2016 May 7. Review.


DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.

Chiu TP, Comoglio F, Zhou T, Yang L, Paro R, Rohs R.

Bioinformatics. 2016 Apr 15;32(8):1211-3. doi: 10.1093/bioinformatics/btv735. Epub 2015 Dec 14.


Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation.

Yilmaz A, Engeler R, Constantinescu S, Kokkaliaris KD, Dimitrakopoulos C, Schroeder T, Beerenwinkel N, Paro R.

Stem Cell Res. 2015 Nov;15(3):542-553. doi: 10.1016/j.scr.2015.09.012. Epub 2015 Sep 30.


Trithorax and Polycomb group-dependent regulation: a tale of opposing activities.

Geisler SJ, Paro R.

Development. 2015 Sep 1;142(17):2876-87. doi: 10.1242/dev.120030. Review.


High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins.

Comoglio F, Schlumpf T, Schmid V, Rohs R, Beisel C, Paro R.

Cell Rep. 2015 May 5;11(5):821-34. doi: 10.1016/j.celrep.2015.03.070. Epub 2015 Apr 23.


During Drosophila disc regeneration, JAK/STAT coordinates cell proliferation with Dilp8-mediated developmental delay.

Katsuyama T, Comoglio F, Seimiya M, Cabuy E, Paro R.

Proc Natl Acad Sci U S A. 2015 May 5;112(18):E2327-36. doi: 10.1073/pnas.1423074112. Epub 2015 Apr 20.


Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data.

Comoglio F, Sievers C, Paro R.

BMC Bioinformatics. 2015 Feb 1;16:32. doi: 10.1186/s12859-015-0470-y.


Transcriptional silencing by polycomb-group proteins.

Grossniklaus U, Paro R.

Cold Spring Harb Perspect Biol. 2014 Nov 3;6(11):a019331. doi: 10.1101/cshperspect.a019331. Review.


A deterministic analysis of genome integrity during neoplastic growth in Drosophila.

Sievers C, Comoglio F, Seimiya M, Merdes G, Paro R.

PLoS One. 2014 Feb 6;9(2):e87090. doi: 10.1371/journal.pone.0087090. eCollection 2014.


Combinatorial modeling of chromatin features quantitatively predicts DNA replication timing in Drosophila.

Comoglio F, Paro R.

PLoS Comput Biol. 2014 Jan;10(1):e1003419. doi: 10.1371/journal.pcbi.1003419. Epub 2014 Jan 23.


Polycomb group protein bodybuilding: working out the routines.

Sievers C, Paro R.

Dev Cell. 2013 Sep 30;26(6):556-8. doi: 10.1016/j.devcel.2013.09.012.


An efficient strategy for TALEN-mediated genome engineering in Drosophila.

Katsuyama T, Akmammedov A, Seimiya M, Hess SC, Sievers C, Paro R.

Nucleic Acids Res. 2013 Sep;41(17):e163. doi: 10.1093/nar/gkt638. Epub 2013 Jul 22.


The role of noncoding RNAs in chromatin regulation during differentiation.

Nahkuri S, Paro R.

Wiley Interdiscip Rev Dev Biol. 2012 Sep-Oct;1(5):743-52. doi: 10.1002/wdev.41. Epub 2012 Feb 22. Review.


Drosophila GAGA factor polyglutamine domains exhibit prion-like behavior.

Tariq M, Wegrzyn R, Anwar S, Bukau B, Paro R.

BMC Genomics. 2013 Jun 3;14:374. doi: 10.1186/1471-2164-14-374.


The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila.

Kockmann T, Gerstung M, Schlumpf T, Xhinzhou Z, Hess D, Beerenwinkel N, Beisel C, Paro R.

Genome Biol. 2013 Feb 25;14(2):R18. doi: 10.1186/gb-2013-14-2-r18.


PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C.

Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, Orlando V.

PLoS Genet. 2013;9(2):e1003283. doi: 10.1371/journal.pgen.1003283. Epub 2013 Feb 21.


Hsp90@chromatin.nucleus: an emerging hub of a networker.

Sawarkar R, Paro R.

Trends Cell Biol. 2013 Apr;23(4):193-201. doi: 10.1016/j.tcb.2012.11.007. Epub 2013 Jan 1. Review.


Innate immune cells are dispensable for regenerative growth of imaginal discs.

Katsuyama T, Paro R.

Mech Dev. 2013 Feb;130(2-3):112-21. doi: 10.1016/j.mod.2012.11.005. Epub 2012 Dec 10.


Differences in the endocannabinoid system of sperm from fertile and infertile men.

Lewis SE, Rapino C, Di Tommaso M, Pucci M, Battista N, Paro R, Simon L, Lutton D, Maccarrone M.

PLoS One. 2012;7(10):e47704. doi: 10.1371/journal.pone.0047704. Epub 2012 Oct 17.


Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data.

Sievers C, Schlumpf T, Sawarkar R, Comoglio F, Paro R.

Nucleic Acids Res. 2012 Nov 1;40(20):e160. doi: 10.1093/nar/gks697. Epub 2012 Jul 28.


Hsp90 globally targets paused RNA polymerase to regulate gene expression in response to environmental stimuli.

Sawarkar R, Sievers C, Paro R.

Cell. 2012 May 11;149(4):807-18. doi: 10.1016/j.cell.2012.02.061.


Long-term use of HU210 adversely affects spermatogenesis in rats by modulating the endocannabinoid system.

Lewis SE, Paro R, Borriello L, Simon L, Robinson L, Dincer Z, Riedel G, Battista N, Maccarrone M.

Int J Androl. 2012 Oct;35(5):731-40. doi: 10.1111/j.1365-2605.2012.01259.x. Epub 2012 Mar 21.


The fungicide mancozeb induces toxic effects on mammalian granulosa cells.

Paro R, Tiboni GM, Buccione R, Rossi G, Cellini V, Canipari R, Cecconi S.

Toxicol Appl Pharmacol. 2012 Apr 15;260(2):155-61. doi: 10.1016/j.taap.2012.02.005. Epub 2012 Feb 17.


Binding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing.

Sakoparnig T, Kockmann T, Paro R, Beisel C, Beerenwinkel N.

J Comput Biol. 2012 Feb;19(2):126-38. doi: 10.1089/cmb.2011.0258.


A chromatin-modifying function of JNK during stem cell differentiation.

Tiwari VK, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C.

Nat Genet. 2011 Dec 18;44(1):94-100. doi: 10.1038/ng.1036.


Epigenetic reprogramming during tissue regeneration.

Katsuyama T, Paro R.

FEBS Lett. 2011 Jun 6;585(11):1617-24. doi: 10.1016/j.febslet.2011.05.010. Epub 2011 May 8. Review.


Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners.

Strübbe G, Popp C, Schmidt A, Pauli A, Ringrose L, Beisel C, Paro R.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5572-7. doi: 10.1073/pnas.1007916108. Epub 2011 Mar 17.


Silencing chromatin: comparing modes and mechanisms.

Beisel C, Paro R.

Nat Rev Genet. 2011 Feb;12(2):123-35. doi: 10.1038/nrg2932. Epub 2011 Jan 11. Review.


Polycomb preferentially targets stalled promoters of coding and noncoding transcripts.

Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R.

Genome Res. 2011 Feb;21(2):216-26. doi: 10.1101/gr.114348.110. Epub 2010 Dec 22.


Interpretation of developmental signaling at chromatin: the Polycomb perspective.

Sawarkar R, Paro R.

Dev Cell. 2010 Nov 16;19(5):651-61. doi: 10.1016/j.devcel.2010.10.012. Review.


Heat shock protein 90: a capacitor or a mutator?

Sawarkar R, Paro R.

J Biosci. 2010 Jun;35(2):163-5. No abstract available.


A combined ex vivo and in vivo RNAi screen for notch regulators in Drosophila reveals an extensive notch interaction network.

Saj A, Arziman Z, Stempfle D, van Belle W, Sauder U, Horn T, Dürrenberger M, Paro R, Boutros M, Merdes G.

Dev Cell. 2010 May 18;18(5):862-76. doi: 10.1016/j.devcel.2010.03.013.


Distinct roles of Hand2 in initiating polarity and posterior Shh expression during the onset of mouse limb bud development.

Galli A, Robay D, Osterwalder M, Bao X, Bénazet JD, Tariq M, Paro R, Mackem S, Zeller R.

PLoS Genet. 2010 Apr 8;6(4):e1000901. doi: 10.1371/journal.pgen.1000901.


Extending the frontiers of epigenetic regulation.

Paro R, Lee JT.

Curr Opin Genet Dev. 2010 Apr;20(2):107-9. doi: 10.1016/j.gde.2010.03.011. Epub 2010 Apr 9. No abstract available.


About combs, notches, and tumors: epigenetics meets signaling.

Merdes G, Paro R.

Dev Cell. 2009 Oct;17(4):440-2. doi: 10.1016/j.devcel.2009.10.001.


Dissection of gene regulatory networks in embryonic stem cells by means of high-throughput sequencing.

Beisel C, Paro R.

Biol Chem. 2009 Nov;390(11):1139-44. doi: 10.1515/BC.2009.116. Review.


Trithorax requires Hsp90 for maintenance of active chromatin at sites of gene expression.

Tariq M, Nussbaumer U, Chen Y, Beisel C, Paro R.

Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1157-62. doi: 10.1073/pnas.0809669106. Epub 2009 Jan 14.


Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species.

Hauenschild A, Ringrose L, Altmutter C, Paro R, Rehmsmeier M.

PLoS Biol. 2008 Oct 28;6(10):e261. doi: 10.1371/journal.pbio.0060261.


Highlight: 59th Mosbach kolloquium.

Noyer-Weidner M, Paro R, Walter J.

Biol Chem. 2008 Apr;389(4):321. doi: 10.1515/BC.2008.050. No abstract available.


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