Publications

| 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | older 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 pageonline.

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pagePDF

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 pagePDF

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 pageonline

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

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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. DownloadPDF (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 pageReview

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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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. external pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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

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 pageonline

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 pageonline

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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. external pageonline

Katsuyama T, Paro R.
Epigenetic reprogramming during tissue regeneration.
FEBS Lett. (2011) Jun 6;585(11):1617-24. Epub May 8. external pageReview

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 pageonline

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

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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 pageonline

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

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 pageonline

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 pageonline

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

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.

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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. external pageonline

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 pageonline

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.