Publications since 2005

2013

• Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, Orlando V.
  PcG-Mediated Higher-Order Chromatin Structures Modulate Replication Programs at the Drosophila BX-C.
  PLOS Genetics (2013) Feb 9(2):e1003283, Epub 2013 Feb 21.
• Kockmann T, Gerstung M, Schlumpf T, Xhinzhou Z, Hess D, Beerenwinkel N, Beisel C, Paro R.
  The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila.
  Genome Biology (2013) Feb 25;14(2):R18. http://www.ncbi.nlm.nih.gov/pubmed/23442797

Co-authorships:

• Philipp A. Steffen, Joao Pedro Fonseca, Cornelia Gänger, Eva Dworschak, Tobias Kockmann, Christian Beisel and Leonie Ringrose.
  Quantitative in vivo analysis of chromatin binding of Polycomb and Trithorax group proteins reveals retention of ASH1 on mitotic chromatin.
  Nucleic Acids Research, 2013, 1–16. doi:10.1093/nar/gkt217.

2012

• Katsuyama T, Renato P.
  Innate immune cells are dispensable for regenerative growth of imaginal discs.
  Mech. Dev. (2012). http://dx.doi.org/10.1016/j.mod.2012.11.005.
• Sawarkar R, and Paro R.
  Hsp90@chromatin.nucleus: an emerging hub of a networker delete element move down move up insert element.
  Trends in Cell Biology. (2012) 1-9. http://dx.doi.org/10.1016/j.tcb.2012.11.007. Review
• Nahkuri S, Paro R.
  The role of noncoding RNAs in chromatin regulation during differentiation.
  WIREs Dev Biol. 2012, 1:743–752. doi: 10.1002/wdev.41.
• Sievers C, Schlumpf T, Sawarkar R, Comoglio F, Paro R.
  Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data.
  Nucleic Acids Res. 2012 Jul 28.
• Sawarkar R, Sievers C, Paro R.
  Hsp90 globally targets paused RNA polymerase to regulate gene expression in response to environmental stimuli.
  Cell. 2012 May 11;149(4):807-18.
• Sakoparnig T, Kockmann T, Paro R, Beisel C, Beerenwinkel N.
  Binding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing.
  J Comput Biol. 2012 Feb;19(2):126-38.

Co-authorships:

• Siebourg J, Merdes G, Misselwitz B, Hardt WD, Beerenwinkel N.
  Stability of gene rankings from RNAi screens.
  Bioinformatics. 2012 Jun 15;28(12):1612-8. Epub 2012 Apr 17.
• Felizzi F, Comoglio F.
  Network-of-queues approach to B-cell-receptor affinity discrimination.
  Phys. Rev. E 85, 061926 (2012).
• Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N.
  Reliable detection of subclonal single-nucleotide variants in tumour cell populations.
  Nat Commun. 2012 May 1;3:811.
  
• Comoglio F, Rinaldi, M.
  Rknots: topological analysis of knotted biopolymers with R.
  Bioinformatics. 2012 May 15;28(10):1400-1. Epub 2012 Apr 5.

2011

• Tiwari VK, Stadler MB, Wirbelauer C, Paro R, Schübeler D, Beisel C.
  A chromatin-modifying function of JNK during stem cell differentiation.
  Nature Genetics 44, 94-100.
• Katsuyama T, Paro R.
  Epigenetic reprogramming during tissue regeneration.
  FEBS Lett. 2011 Jun 6;585(11):1617-24. Epub 2011 May 8. Review
• Strübbe G, Popp C, Schmidt A, Pauli A, Ringrose L, Beisel C, Paro R.
  Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners.
  Proc Natl Acad Sci USA. 2011 Apr 5;108(14):5572-7. Epub 2011 Mar 17.
• Beisel C, Paro R.
  Silencing chromatin: comparing modes and mechanisms.
  Nat Rev Genet. 2011 Feb;12(2):123-135. Review. Epub 2011 Jan 11.
• Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R.
  Polycomb preferentially targets stalled promoters of coding and noncoding transcripts.
  Genome Res. 2011 Feb;21(2):216-226. Epub 2010 Dec 22.

Co-authorships:

• Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmstrom L, Aebersold R, Rinn B.
  openBIS: a flexible framework for managing and analyzing complex data in biology research.
  BMC Bioinformatics. 2011 Dec 8;12:468.
• Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Spillane C, Nordborg M, Rehmsmeier M and Köhler C.
  High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm.
  PLoS Genet. 2011 Jun;7(6):e1002126. Epub 2011 Jun 16.
• Comoglio F, Rinaldi M.
  A topological framework for the computation of the HOMFLY polynomial and its application to proteins.
  PLoS One. 2011 Apr 13;6(4):e18693.

2010

• Sawarkar R, Paro R.
  Interpretation of developmental signaling at chromatin: the Polycomb perspective.
  Dev Cell. 2010 Nov 16;19(5):651-61. Review.
• Stempfle D, Kanwar R, Loewer A, Fortini ME, Merdes G.
  In vivo reconstitution of γ-Secretase in Drosophila results in substrate specificity.
  Molecular and Cellular Biology 2010 Jul; 30(13):3165-3175.
• Sawarkar R, Paro R.
  Heat shock protein 90: a capacitor or a mutator?
  J Biosci. 2010 Jun;35(2):163-5.
• Saj A, Arziman Z, Stempfle D, van Belle W, Sauder U, Horn T, Dürrenberger M, Paro R. Boutros M, Merdes G.
  A combined ex vivo and in vivo RNAi screen of Notch signaling in Drosophila reveals an extensive interaction network.
  Developmental Cell 2010 May;18(5):862-876.
• Galli A, Robay D, Osterwalder M, Bao X, Bénazet J-D, Tariq M, Paro R, Mackem S, Zeller R.
  Distinct roles of Hand2 in initiating polarity and posterior Shh expression during the onset of mouse limb bud development.
  PLoS Genet 2010 April;6(4):e1000901.
• Paro R, Lee JT.
  Extending the frontiers of epigenetic regulation.
  Curr Opin Genet Dev. 2010 Apr;20(2):107-9.

Co-authorships:

• Brykczynska U, Hisano M, Erkek S, Ramos L, Oakeley EJ, Roloff TC, Beisel C, Schübeler D, Stadler MB and Peters AHFM.
  Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa.
  Nature Struct Mol Biol. 2010 Jun;17(6):679-687. Epub 2010 May 16.
• Buller F, Steiner M, Scheuermann J, Mannocci L, Nissen I, Kohler M, Beisel C and Neri D.
  High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries.
  Bioorg. Med. Chem. Lett. 2010 Jul 15;20(14):4188-4192. Epub 2010 May 20.
• Stempfle D, Kanwar R, Loewer A, Fortini ME, Merdes G.
  In vivo reconstitution of gamma-secretase in Drosophila results in substrate specificity
  Molecular and Cellular Biology 30 (13): 3165-3175 (2010-07)

2009

• Merdes G, Paro R.
  About combs, notches, and tumors: epigenetics meets signaling.
  Dev Cell. 2009 Oct;17(4):440-2.
• Beisel C, Paro R.
  Dissection of gene regulatory networks in embryonic stem cells by means of high-throughput sequencing.
  Biol Chem. 2009 Nov;390(11):1139-44.
• Tariq M, Nussbaumer U, Chen Y, Beisel C, Paro R.
  Trithorax requires Hsp90 for maintenance of active chromatin at sites of gene expression.
  Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1157-62. Epub 2009 Jan 14.

Co-authorships:

• Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.
  Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.
  Genome Biol. 2009;10(7):R79. Epub 2009 Jul 22.

2008

• Noyer-Weidner M, Paro R, Walter J.
  Highlight: 59th Mosbach Kolloquium.
  Biol. Chem. 389: 321 (editorial).
• Hauenschild A, Ringrose L, Altmutter C, Paro R, Rehmsmeier M.
  Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species.
  PLoS Biol. 2008 Oct 28;6(10):e261.
• Fedorova E, Sadoni N, Dahlsveen IK, Koch J, Kremmer E, Eick D, Paro R, Zink D.
  The nuclear organization of Polycomb/Trithorax group response elements in larval tissues of Drosophila melanogaster.
  Chromosome Res. 2008;16(4):649-73. Epub 2008 Jun 3.

2007

• Schoenfelder S, Smits G, Fraser P, Reik W, Paro R.
  Non-coding transcripts in the H19 imprinting control region mediate gene silencing in transgenic Drosophila.
  EMBO Rep. 2007 Nov;8(11):1068-73. Epub 2007 Oct 19.
• Beisel C, Buness A, Roustan-Espinosa IM, Koch B, Schmitt S, Haas SA, Hild M, Katsuyama T, Paro R.
  Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins.
  Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16615-20. Epub 2007 Oct 5.
• Ringrose L, Paro R.
  Polycomb/Trithorax response elements and epigenetic memory of cell identity.
  Development. 2007 Jan;134(2):223-32.

2006

• Maurange C, Lee N, Paro R.
  Signaling meets chromatin during tissue regeneration in Drosophila.
  Curr Opin Genet Dev. 2006 Oct;16(5):485-9. Epub 2006 Aug 17. Review.
• Lyko F, Beisel C, Marhold J, Paro R.
  Epigenetic regulation in Drosophila.
  Curr Top Microbiol Immunol. 2006;310:23-44. Review.
• Dorner S, Lum L, Kim M, Paro R, Beachy PA, Green R.
  A genomewide screen for components of the RNAi pathway in Drosophila cultured cells.
  Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11880-5. Epub 2006 Aug 1.
• Schmitt S, Paro R.
  RNA at the steering wheel.
  Genome Biol. 2006;7(5):218. Epub 2006 May 26. Review.

2005

• Lee N, Maurange C, Ringrose L, Paro R.
  Suppression of Polycomb group proteins by JNK signalling induces transdetermination in Drosophila imaginal discs.
  Nature. 2005 Nov 10;438(7065):234-7.
• Soba P, Eggert S, Wagner K, Zentgraf H, Siehl K, Kreger S, Löwer A, Langer A, Merdes G, Paro R, Masters CL, Müller U, Kins S, Beyreuther K.
  Homo- and heterodimerization of APP family members promotes intercellular adhesion.
  EMBO J. 2005 Oct 19;24(20):3624-34. Epub 2005 Sep 29. Erratum in: EMBO J. 2006 Feb 8;25(3):653.
• Schmitt S, Prestel M, Paro R.
  Intergenic transcription through a polycomb group response element counteracts silencing.
  Genes Dev. 2005 Mar 15;19(6):697-708. Epub 2005 Mar 1.

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