Publications

2014

Sievers C., Comoglio F., Seimiya M., Merdes G., Paro R.
A Deterministic Analysis of Genome Integrity during Neoplastic Growth in Drosophila.
PLoS ONE (2014) 9(2): e87090. doi:10.1371/journal.pone.0087090. online 

Comoglio F., Paro R.
Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in Drosophila.
PLoS Comput Biol (2014) 10(1): e1003419. doi:10.1371/journal.pcbi.1003419. online 

2013

Tariq, M., Wegrzyn, R., Anwar, S., Bukau, B. & Paro, R.
Drosophila GAGA factor polyglutamine domains exhibit prion-like behavior.
BMC Genomics (2013)14, 374. online 

Katsuyama T, Akmammedov A, Seimiya M, Hess SC, Sievers C, Paro R.
An efficient strategy for TALEN-mediated genome engineering in Drosophila.
Nucleic Acids Res (2013). online 

Sievers C. and Paro R.
Polycomb Group Protein Bodybuilding: Working Out the Routines.
Developmental Cell  (2013) Volume 26, Issue 6, 30 September 2013, Pages 556–558.online 

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. online 

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. online 

Co-authorships:

Comoglio F., Fracchia L., Rinaldi M.
Bayesian Inference from Count Data Using Discrete Uniform Priors.
PLOS ONE (2013) DOI: 10.1371/journal.pone.0074388. online 

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. online 

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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. online 

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 (PDF, 1.1 MB) 

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. online 

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), Vol.40. No.20 e160. online 

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. online 

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. online 

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. online 

Felizzi F, Comoglio F.
Network-of-queues approach to B-cell-receptor affinity discrimination.
Phys. Rev. (2012) E 85, 061926. online 

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. online 

Comoglio F, Rinaldi, M.
Rknots: topological analysis of knotted biopolymers with R.
Bioinformatics. (2012) May 15;28(10):1400-1. Epub 2012 Apr 5. online 

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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 (2011) 44, 94-100. online 

Katsuyama T, Paro R.
Epigenetic reprogramming during tissue regeneration.
FEBS Lett. (2011) Jun 6;585(11):1617-24. Epub 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. online 

Beisel C, Paro R.
Silencing chromatin: comparing modes and mechanisms.
Nat Rev Genet. (2011) Feb;12(2):123-135. Review 

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. online 

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. online 

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. online 

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. online 

2010

Sawarkar R, Paro R.
Interpretation of developmental signaling at chromatin: the Polycomb perspective.
Dev Cell. 2010 Nov 16;19(5):651-61. Review. online 

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. online 

Sawarkar R, Paro R.
Heat shock protein 90: a capacitor or a mutator?
J Biosci. 2010 Jun;35(2):163-5. online 

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. online 

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. online 

Paro R, Lee JT.
Extending the frontiers of epigenetic regulation.
Curr Opin Genet Dev. 2010 Apr;20(2):107-9. online 

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)

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2009

Merdes G, Paro R.
About combs, notches, and tumors: epigenetics meets signaling.
Dev Cell. 2009 Oct;17(4):440-2. online 

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. online 

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.

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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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22.10.2014
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