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Ciabrelli F., Comoglio F., Fellous S., Bonev B, Ninova M., Szabo Q., Xuéreb A., Klopp C., Aravin A., Paro R., Bantignies F. and Cavalli G.
Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila
Nature Genetics (2017) doi:10.1038/ng.3848 online


Hauri S., Comoglio F., Seimiya M., Gerstung M, Glatter Timo., Hansen K., Aebersold R., Paro R., Gstaiger M. and Beisel C.
A High-Density Map for Navigating the Human Polycomb Complexome 
Cell Reports (2016) Volume 17, Issue 2, p583–595 online

Akmammedov A., Katsuyama T. and Paro R.
A Rapid TALEN Assenbly Protocol
Methods Mol. Biol. (2016) 1480:269-81. doi: 10.1007/978-1-4939-6380-5_23. PDF

Katsuyama T. and Paro R.
Imaginal Disc Transplantation in Drosophila
Methods Mol. Biol. (2016) 1480:301-10. doi: 10.1007/978-1-4939-6380-5_26. PDF

Degrauwe N., Schlumpf T.B., Janiszewska M., Martin P., Cauderay A., Provero P., Riggi N., Suvà Mario-L., Paro R. and Stamenkovic I.
The RNA Binding Protein IMP2 Preserves Glioblastoma Stem Cells by Preventing let-7 Target Gene Silencing
Cell Reports (2016) doi:10.1016/j.celrep.2016.04.086 online

Beira J.V. and Paro R.
The legacy of Drosophila imaginal discs
Chromosoma (2016) DOI 10.1007/s00412-016-0595-4 Review (PDF, 1.8 MB)


Chiu TP., Comoglio F., Zhou T., Yang L., Paro R and Rohs R.
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding
Bioinformatics (2015) Dec 14. pii: btv735. PDF (PDF, 377 KB)

Geisler, S.J., and Paro, R.
Trithorax and Polycomb group-dependent regulation: a tale of opposing activities
Development  (2015) 142, 2876–2887  Review

Yilmaz A, Engeler R., Constantinescu S., Kokkaliaris K.D., Dimitrakopoulos C. Schroeder T., Beerenwinkel N. and Paro R.
Ectopic  expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation
Stem Cell Research  (2015) doi:10.1016/j.scr.2015.09.012 online

Comoglio F., Schlumpf T., Schmid V., Rohs R., Beisel C. and Paro R.
High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins
Cell Reports  (2015) April 23, DOI: online

Katsuyama T., Comoglio F., Seimiya M., Cabuy E. and Paro R.
During Drosophila disc regeneration, JAK/STAT coordinates cell proliferation with Dilp8-mediated developmental delay
PNAS (2015) April 20, doi:10.1073/pnas.1423074112. online

Comoglio F., Sievers C., and Paro R.
Sensitive and hightly resolved identification of RNA-protein interaction sites in PAR-CLIP data
BMC Bioinformatics (2015) 16:32   doi:10.1186/s12859-015-0470-y. online

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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. and 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

Grossniklaus U. and Paro R.
Transcriptional Silencing by Polycomb-Group Proteins.
Cold Spring Harb Perspect Biol. (2014) Nov 3;6(11):a019331. doi: 10.1101/cshperspect.a019331. online


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–

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


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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Katsuyama T, Renato P.
Innate immune cells are dispensable for regenerative growth of imaginal discs.
Mech. Dev. (2012). 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. 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


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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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


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


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


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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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


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.


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.


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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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.


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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