Publications
2020
Geigges,M., Gubser, P., Unterstab, G., Lecoultre, Y., Paro, R. and Hess, C.
Reference Genes for Expression Studies in Human CD8+ Naïve and Effector Memory T Cells under Resting and Activating Conditions. Scientific Reports (2020) external page online.
Geigges M., Arekatla G., Paro R.
Priming exposures to lipopolysaccharides do not affect the induction of Polycomb target genes upon re-exposure. PLoS ONE (2020) 15(4): e0231498. external page online
Brykczynska, U., Geigges, M., Wiedemann, S.J., Dror, E., Böni-Schnetzler, M., Hess, C., Donath, M.Y., and Paro, R.
Distinct Transcriptional Responses across Tissue- Resident Macrophages to Short-Term and Long- Term Metabolic Challenge. Cell Rep. (2020) 30, 1627–1643.e1627. external page online
2019
Akmammedov, A., Geigges, M., and Paro, R.
Bivalency in Drosophila embryos is associated with strong inducibility of Polycomb target genes. Fly (Austin) (2019) 13, 42–50. external page online
2018
Jiang Y., Seimiya M., Schlumpf B.T., and Paro R.
An intrinsic tumour eviction mechanism in Drosophila mediated by steroid hormone signalling
Nature Communications. (2018) Aug 17, 9:3297 doi: 10.1038/s41467-018-05855-5. external page online
Torres J., Monti R., Moore AL., Seimiya M., Jiang Y., Beerenwinkel N., Beisel C., Beira JV., and Paro R.
A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila
Elife. (2018) Mar 21;7. pii: e32697. doi: 10.7554/eLife.32697. external page online
Beira J., Torres J. and Paro R.
signalling crosstalk during early tumorigenesis in the absence of Polycomb silencing
PLoS Genet. (2018)Jan 22;14(1):e1007187. doi: 10.1371/journal.pgen.1007187. external page online
2017
Pereira A. and Paro R.
Pho dynamically interacts with Spt5 to facilitate transcriptional switches at the hsp70 locus
Epigenetics Chromatin. (2017)Dec 6;10(1):57. doi: 10.1186/s13072-017-0166-9. external page online
Akmammedov A., Geigges M. and Paro R.
Single vector non-leaky gene expression system for Drosophila melanogaster
Scientific reports (2017)7(1):6899. doi: 10.1038/s41598-017-07282-w. external page online
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 external page online
2016
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 external page 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. external page 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. external page 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 external page online
Beira J.V. and Paro R.
The legacy of Drosophila imaginal discs
Chromosoma (2016) DOI 10.1007/s00412-016-0595-4 Download Review (PDF, 1.8 MB)
2015
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. Download 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 external page 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 external page 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: http://dx.doi.org/10.1016/j.celrep.2015.03.070. external page 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. external page 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. external page online
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. external page 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. external page 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. external page 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. external page 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). external page 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.external page 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. external page 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. external page 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. external page 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. external page online
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. external page 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. external page 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. external page 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. external page 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. external page 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. external page online
Felizzi F, Comoglio F.
Network-of-queues approach to B-cell-receptor affinity discrimination.
Phys. Rev. (2012) E 85, 061926. external page 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. external page 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. external page online
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. external page online
Katsuyama T, Paro R.
Epigenetic reprogramming during tissue regeneration.
FEBS Lett. (2011) Jun 6;585(11):1617-24. Epub May 8. external page 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. external page online
Beisel C, Paro R.
Silencing chromatin: comparing modes and mechanisms.
Nat Rev Genet. (2011) Feb;12(2):123-135. external page 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. external page 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. external page 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. external page 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. external page 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. external page 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. external page online
Sawarkar R, Paro R.
Heat shock protein 90: a capacitor or a mutator?
J Biosci. 2010 Jun;35(2):163-5. external page 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. external page 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. external page online
Paro R, Lee JT.
Extending the frontiers of epigenetic regulation.
Curr Opin Genet Dev. 2010 Apr;20(2):107-9. external page 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.
2009
Merdes G, Paro R.
About combs, notches, and tumors: epigenetics meets signaling.
Dev Cell. 2009 Oct;17(4):440-2. external page 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. external page 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.