Publications
On this page you can find an overview of our publications.
DEEP-DV publications:
2024
Soh TK, Ognibene S, Sanders S, Schäper R, Kaufer BB, Bosse JB. A proteome-wide structural systems approach reveals insights into protein families of all human herpesviruses. Nat Commun. Nov 2024. (» DOI:10.1038/s41467-024-54668-2). PDF
Ohnezeit D, Huang J, Westerkamp U, Brinschwitz V, Schmidt C, Günther T, Czech-Sioli M, Weißelberg S, Schlemeyer T, Nakel J, Mai J, Schreiner S, Schneider C, Friedel CC, Schwanke H, Brinkmann MM, Grundhoff A, Fischer N. Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling. PLoS Pathog. Aug 2024.
(» DOI: 10.1371/journal.ppat.1012426). PDF
Döhner K, Serrero MC, Viejo-Borbolla A, Sodeik B. A Hitchhiker’s Guide Through the Cell: The World According to the Capsids of Alphaherpesviruses. Annu Rev Virol. Jul 2024. Online ahead of print.
(» DOI: 10.1146/annurev-virology-100422-022751). PDF
Abebe JS, Alwie Y, Fuhrmann e, Leins J, Mai J, Verstraten R, Schreiner S, Wilson AC, Depledge DP. Nanopore Guided Annotation of Transcriptome Architectures. mSystems. Jul 2024. 9(7):e0050524.
(» DOI: 10.1128/msystems.00505-24). PDF
Jacobsen C, Plückebaum N, Ssebyatika G, Beyer S, Mendes-Monteiro L, Wang J, Kropp KA, González-Motos V, Steinbrück L, Ritter B, Rodríguez-González C, Böning H, Nikolouli E, Kinchington PR, Lachmann N, Depledge DP, Krey T, Viejo-Borbolla A. Viral modulation of type II interferon increases T cell adhesion and virus spread. Nat Commun. Jun 2024. 15(1):5318.
(» DOI: 10.1038/s41467-024-49657-4). PDF
Hofmann S, Luther J, Plank V, Oswald A, Mai J, Simons I, Miller J, Falcone V, Hansen-Palmus L, Hengel H, Nassa M, Protzer U, Schreiner S. Arsenic Trioxide impacts hepatitis B virs core nuclear localization and efficiently interferes with HBV infection. Microbiol Spectr. May 2024. 12(5):e0378823.
(» DOI: 10.1128/spectrum.03788-23). PDF
Hofmann K, Hofmann S, Weigl F, Mai J, Schreiner S. DMSO and Its Role in Differentiation Impact Efficacy of Human Adenovirus (HAdV) Infection in HepaRG Cells. Viruses. Apr 2024. 16(4):633.
(» DOI: 10.3390/v16040633). PDF
Berg K, Lodha M, Delazer I, Bartosik K, Garcia YC, Hennig T, Wolf E, Dölken L, Lusser A, Prusty BK, Erhard F. Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data. Nucleic Acids Res. Apr 2024. 52(7):e35.
(» DOI: 10.1093/nar/gkae120). PDF
Göttig L, Jummer S, Staehler L, Groitl P, Karimi M, Blanchette P, Kosulin K, Branton PE, Schreiner S. The human adenovirus PI3K-Akt activator E4orf1 is targeted by the tumor suppressor p53. J Virol. Mar 2024. e0170123.
(» DOI: 10.1128/jvi.01701-23). PDF
Eberhage J, Bresch IP, Ramani R, Viohl N, Buchta T, Rehfeld CL, Hinse P, Reubold TF, Brinkmann MM, Eschenburg S. Crystal structure of the tegument protein UL82 (pp71) from human cytomegalovirus. Protein Sci. Mar 2024. 33(3):e4915.
(» DOI: 10.1002/pro.4915). PDF
Göttig L, Schreiner S. E4orf1: The triple agent of adenovirus – Unraveling its roles in oncogenesis, infectious obesity and immune responses in virus replication and vector therapy. Tumour Virus Res. Feb 2024. 17:200277.
(» DOI: 10.1016/j.tvr.2024.200277). PDF
Kuderna AK, Reichel A, Tillmanns J, Class M, Scherer M, Stamminger T. Discovery of a novel antiviral effect of the restriction factor SPOC1 against human cytomegalovirus. Viruses. Feb 2024. 16(3), 363.
(» DOI: 10.3390/v16030363). PDF
Heusel AT, Rapp S, Stamminger T, Scherer M. IE1 of human cytomegalovirus inhibits necroptotic cell death via direct and indirect modulation of the necrosome complex. Viruses. Feb 2024. 16(2), 290.
(» DOI: 10.3390/v16020290). PDF
Sun G, Kropp KA, Kirchner M, Plückebaum N, Selich A, Serrero M, Dhingra A, Cabrera JR, Ritter B, Bauerfeind R, Wyler E, Landthaler M, Schambach A, Sodeik B, Mertins P, Viejo-Borbolla A. Herpes simplex virus type 1 modifies the protein composition of extracellular vesicles to promote neurite outgrowth and neuroinfection. mBio. Feb 2024. 15(2):e0330823.
(» DOI: 10.1128/mbio.03308-23). PDF
Erhard F. Two‑Step Parameter Estimation for Read Feature Models. Springer link. Jan 2024.
(» DOI: 10.1007/s13218-023-00821-w). PDF
2023
Djakovic L, Hennig T, Reinisch K, Milić A, Whisnant AW, Wolf K, Weiß E, Haas T, Grothey A, Jürges CS, Kluge M, Wolf E, Erhard F, Friedel CC, Dölken L. The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes. Nat Commun. Jul 2023. 14(1):4591.
(» DOI: 10.1038/s41467-023-40217-w). PDF
Weiß E, Friedel CC. RegCFinder: targeted discovery of genomic subregions with differential read density. Bioinform Adv. Jul 2023. 3(1):vbad085.
(» DOI: 10.1093/bioadv/vbad085). PDF
Sterrenberg VT, Stalling D, Knaack JIH, Soh TK, Bosse JB, Meier C. A TriPPPro-nucleotide reporter with optimized cell-permeable dyes for metabolic labeling of cellular and viral DNA in living cells. Angew Chem Int Ed Engl. Jul 2023. e202308271.
(» DOI: 10.1002/anie.202308271). PDF
Schwanke H, Gonçalves Magalhães V, Schmelz S, Wyler E, Hennig T, Günther T, Grundhoff A, Dölken L, Landthaler M, van Ham M, Jänsch L, Büssow K, van den Heuvel J, Blankenfeldt W, Friedel CC, Erhard F, Brinkmann MM. The cytomegalovirus M35 protein directly binds to the interferon-β enhancer and modulates transcription of Ifnb1 and other IRF3-driven genes. J Virol. Jun 2023. 97(6):e0040023.
(» DOI: 10.1128/jvi.00400-23). PDF
Rummel T, Sakellaridi L, Erhard F. grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis. Nat Commun. Jun 2023. 14(1):3559.
(» DOI: 10.1038/s41467-023-39163-4). PDF
Weiß E, Hennig T, Graßl P, Djakovic L, Whisnant AW, Jürges CS, Koller F, Kluge M, Erhard F, Dölken L, Friedel CC. HSV-1 infection induces a downstream shift of promoter-proximal pausing for host genes. J Virol. Apr 2023. 97(5):e0038123.
(» DOI: 10.1128/jvi.00381-23). PDF
Bosse JB, Brune W. Viral dew: Phase separation and the formation of viral replication compartments. PLoS Pathogens. Feb 2023. 19(2): e1011145.
(» DOI: 10.1371/journal.ppat.1011145). PDF
2022
Mohnke J, Stark I, Fischer M, Fischer PM, Schlosser A, Grothey A, O’Hare P, Sodeik B, Erhard F, Dölken L, Hennig T. pUL36 deubiquitinase activity augments both the initiation and the progression of lytic Herpes Simplex Virus infection in IFN-Primed cells. J Virol. Nov 2022. 96(22):e0096322.
(» DOI: 10.1128/jvi.00963-22). PDF
Seitz S, Heusel AT, Stamminger T, Scherer M. Promyelocytic leukemia protein potently restricts human cytomegalovirus infection in endothelial cells. Int J Mol Sci. Oct 2022. 23(19):11931.
(» DOI: 10.3390/ijms231911931). PDF
Stilp AC, Scherer M, König P, Fürstberger A, Kestler HA, Stamminger T. The chromatin remodeling protein ATRX positively regulates IRF3-dependent type I interferon production and interferon-induced gene expression. PLoS Pathog. Aug 2022. 18(8):e1010748.
(» DOI: 10.1371/journal.ppat.1010748). PDF
Rothemund F, Scherer M, Schilling EM, Schweininger J, Muller YA, Stamminger T. Cross-species analysis of innate immune antagonism by cytomegalovirus IE1 protein. Viruses. Jul 2022. 14(8):1626.
(» DOI: 10.3390/v14081626). PDF
Caragliano E, Brune W, Bosse JB. Herpesvirus Replication Compartments: Dynamic Biomolecular Condensates? Viruses. May 2022. 14(5):960.
(» DOI: 10.3390/v14050960). PDF
Scherer M, Read C, Neusser G, Kranz C, Kuderna AK, Müller R, Full F, Wörz S, Reichel A, Schilling EM, Walther P, Stamminger T. Dual signaling via interferon and DNA damage response elicits entrapment by giant PML nuclear bodies. Elife. Mar 2022. 11:e73006.
(» DOI: 10.7554/eLife.73006). PDF
Caragliano E, Bonazza S, Frascaroli G, Tang J, Soh TK, Grünewald K, Bosse JB, Brune W. Human cytomegalovirus forms phase-separated compartments at viral genomes to facilitate viral replication. Cell Rep. Mar 2022. 38(10):110469.
(» DOI: 10.1016/j.celrep.2022.110469). PDF
Previous joint publications:
2021
Esmek FM, Erichlandwehr T, Mors DHB, Czech-Sioli M, Therre M, Günther T, Grundhoff A, Fischer N, Fernandez-Cuesta I. Real time, in-line optical mapping of single molecules of DNA. Biosensors and Bioelectronics: X. Dec 2021. 9(2021):100087.
(» DOI: org.10.1016/j.biosx.2021.100087). PDF
Zhu S, Stanslowsky N, Fernández-Trillo J, Mamo TM, Yu P, Kalmbach N, Ritter B, Eggenschwiler R, Ouwendijk WJD, Mzinza D, Tan L, Leffler A, Spohn M, Brown RJP, Kropp KA, Kaever V, Ha TC, Narayanan P, Grundhoff A, Förster R, Schambach A, Verjans GM, Schmidt M, Kispert A, Cantz T, Gomis A, Wegner F, Viejo-Borbolla A. Generation of hiPSC-derived low threshold mechanoreceptors containing axonal termini resembling bulbous sensory nerve endings and expressing Piezo1 and Piezo2. Stem Cell Res. Oct 2021. 56:102535.
(» DOI: 10.1016/j.scr.2021.102535). PDF
Rink MR, Baptista MAP, Flomm FJ, Hennig T, Whisnant AW, Wolf N, Seibel J, Dölken L, Bosse JB. Concatemeric Broccoli reduces mRNA stability and induces aggregates. PLoS One. Aug 2021. 16(8):e0244166.
(» DOI: 10.1371/journal.pone.0244166). PDF
González-Pérez AC, Stempel M, Wyler E, Urban C, Piras A, Hennig T, Ganskih S, Wei Y, Heim A, Landthaler M, Pichlmair A, Dölken L, Munschauer M, Erhard F, Brinkmann MM. The zinc finger antiviral protein 1 ZAP restricts human cytomegalovirus and selectively binds and destabilises viral UL4/UL5 transcripts. mBio. May 2021. 12(3):e02683-20.
(» DOI: 10.1128/mBio.02683-20). PDF
Koyro TF, Kraus E, Lunemann S, Hölzemer A, Wulf S, Jung J, Fittje P, Henseling F, Körner C, Huber TB, Grundhoff A, Wiech T, Panzer U, Fischer N, Altfeld, M. Upregulation of HLA-F expression by BK polyomavirus infection induces immune recognition by KIR3DS1-positive natural killer cells. Kidney Int. May 2021. 99(5):1140-1148.
(» DOI: 10.1016/j.kint.2020.12.014). PDF
Jürges CS, Dölken L, Erhard F. Integrative transcription start site identification with iTiSS. Bioinformatics. Mar 2021. btab170.
(» DOI: 10.1093/bioinformatics/btab170). PDF
Wang X, Liu L, Whisnant AW, Hennig T, Djakovic L, Haque N, Bach C, Sandri-Goldin RM, Erhard F, Friedel CC, Dölken L, Shi Y. Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation. PLoS Genet. Mar 2021. 17(3):e1009263.
(» DOI: 10.1371/journal.pgen.1009263). PDF
Friedel CC, Whisnant AW, Djakovic L, Rutkowski AJ, Friedl MS, Kluge M, Williamson JC, Sai S, Vidal RO, Sauer S, Hennig T, Grothey A, Milić A, Prusty BK, Lehner PJ, Matheson NJ, Erhard F, Dölken L. Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level. J Virol. Jan 2021. 95(3):e01399-20.
(» DOI: 10.1128/JVI.01399-20). PDF
2020
Czech-Sioli M, Günther T, Therre M, Spohn M, Indenbirken D, Theiss J, Riethdorf S, Qi M, Alawi M, Wülbeck C, Fernandez-Cuesta I, Esmek F, Becker JC, Grundhoff A, Fischer N. High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms. PLoS Pathog. Aug 2020. 16(8):e1008562.
(» DOI: 10.1371/journal.ppat.1008562). PDF
Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L’hernault A, Djakovic L, Göbel M, Döring K, Menegatti J, Antrobus R, Matheson NJ, Künzig FWH, Mastrobuoni G, Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R, Landthaler M, Grässer F, Lehner PJ, Friedel CC, Erhard F, Dölken L. Integrative functional genomics decodes herpes simplex virus 1. Nat Commun. Apr 2020. 11(1):2038.
(» DOI: 10.1038/s41467-020-15992-5). PDF
Siebels S, Czech-Sioli M, Spohn M, Schmidt C, Theiss J, Indenbirken D, Günther T, Grundhoff A, Fischer N. Merkel cell polyomavirus DNA replication induces senescence in human dermal fibroblasts in a Kap1/Trim28-dependent manner. mBio. Mar 2020. 11(2):e00142-20.
(» DOI: 10.1128/mBio.00142-20). PDF
Czech-Sioli M, Siebels S, Radau S, Zahedi RP, Schmidt C, Dobner T, Grundhoff A, Fischer N. The Ubiquitin-specific Protease Usp7, a novel Merkel cell polyomavirus Large T-Antigen interaction partner, modulates viral DNA replication. J Virol. Feb 2020. 94(5):e01638-19.
(» DOI: 10.1128/JVI.01638-19). PDF
Wang X, Hennig T, Whisnant AW, Erhard F, Prusty BK, Friedel CC, Forouzmand E, Hu W, Erber L, Chen Y, Sandri-Goldin RM, Dölken L, Shi Y. Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27. Nat Commun. Jan 2020. 11(1):293.
(» DOI: 10.1038/s41467-019-14109-x). PDF
2019
Wyler E, Franke V, Menegatti J, Kocks C, Boltengagen A, Praktiknjo S, Walch-Rückheim B, Bosse JB, Rajewsky N, Grässer F, Akalin A , Landthaler M. Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program. Nat Commun. Oct 2019. 10(1):4878.
(» DOI: 10.1038/s41467-019-12894-z). PDF
Erhard F, Baptista MAP, Krammer T, Hennig T, Lange M, Arampatzi P, Jürges CS, Theis FJ, Saliba AE, Dölken L. scSLAM-seq reveals core features of transcription dynamics in single cells. Nature. Jul 2019. 571(7765):419-423.
(» DOI: 10.1038/s41586-019-1369-y). PDF
2018
Jürges C, Dölken L, Erhard F. Dissecting newly transcribed and old RNA using GRAND-SLAM. Bioinformatics. Jul 2018. 34(13):i218-i226.
(» DOI: 10.1093/bioinformatics/bty256). PDF
Reichel A, Stilp AC, Scherer M, Reuter N, Lukassen S, Kasmapour B, Schreiner S, Cicin-Sain L, Winterpacht A, Stamminger T. Chromatin-Remodeling Factor SPOC1 Acts as a Cellular Restriction Factor against Human Cytomegalovirus by Repressing the Major Immediate Early Promoter. J Virol. Jun 2018. 92(14):e00342-18.
(» DOI: 10.1128/JVI.00342-18). PDF
Hennig T, Michalski M, Rutkowski AJ, Djakovic L, Whisnant AW, Friedl MS, Jha BA, Baptista MAP, L’Hernault A, Erhard F, Dölken L, Friedel CC. HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes. PLoS Pathog. Mar 2018. 14(3):e1006954.
(» DOI: 10.1371/journal.ppat.1006954). PDF
2017
Buch A, Müller O, Ivanova L, Döhner K, Bialy D, Bosse JB, Pohlmann A, Binz A, Hegemann M, Nagel CH, Koltzenburg M, Viejo-Borbolla A, Rosenhahn B, Bauerfeind R, Sodeik B. Inner tegument proteins of Herpes Simplex Virus are sufficient for intracellular capsid motility in neurons but not for axonal targeting. PLoS Pathog. Dec 2017. 13(12):e1006813.
(» DOI:10.1371/journal.ppat.1006813). PDF
Wyler E, Menegatti J, Franke V, Kocks C, Boltengagen A, Hennig T, Theil K, Rutkowski A, Ferrai C, Baer L, Kermas L, Friedel C, Rajewsky N, Akalin A, Dölken L, Grässer F, Landthaler M. Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection. Genome Biol. Oct 2017. 18(1):209.
(» DOI: 10.1186/s13059-017-1329-5). PDF
González-Motos V, Jürgens C, Ritter B, Kropp KA, Durán V, Larsen O, Binz A, Ouwendijk WJD, Lenac Rovis T, Jonjic S, Verjans GM, Sodeik B, Krey T, Bauerfeind R, Schulz TF, Kaufer BB, Kalinke U, Proudfoot AEI, Rosenkilde MM, Viejo-Borbolla A. Varicella zoster virus glycoprotein C increases chemokine-mediated leukocyte migration. PloS Pathog. May 2017. 13(5):e1006346.
(» DOI: 10.1371/journal.ppat.1006346). PDF
2016
Neumann F, Czech-Sioli M, Dobner T, Grundhoff A, Schreiner S, Fischer N. Replication of Merkel cell polyomavirus induces reorganization of promyelocytic leukemia nuclear bodies. J Gen Virol. Nov 2016. 97(11):2926-2938.
(» DOI: 10.1099/jgv.0.000593). PDF
2015
Theiss JM, Günther T, Alawi M, Neumann F, Tessmer U, Fischer N, Grundhoff A. A comprehensive analysis of replicating Merkel Cell Polyomavirus genomes delineates the viral transcription program and suggests a role for mcv-miR-M1 in episomal persistence. PLoS Pathog. Jul 2015. 11(7):e1004974.
(» DOI: 10.1371/journal.ppat.1004974). PDF
Murakawa Y, Hinz M, Mothes J, Schuetz A, Uhl M, Wyler E, Yasuda T, Mastrobuoni G, Friedel CC, Dölken L, Kempa S, Schmidt-Supprian M, Blüthgen N, Backofen R, Heinemann U, Wolf J, Scheidereit C, Landthaler M. RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappa B pathway. Nat Commun. Jul 2015. 6:7367.
(» DOI: 10.1038/ncomms8367). PDF
Rutkowski AJ, Erhard F, L’Hernault A, Bonfert T, Schilhabel M, Crump C, Rosenstiel P, Efstathiou S, Zimmer R, Friedel CC, Dölken L. Widespread disruption of host transcription termination in HSV-1 infection. Nat Commun. May 2015. 6:7126.
(» DOI: 10.1038/ncomms8126). PDF
2014
Günther T, Schreiner S, Dobner T, Tessmer U, Grundhoff A. Influence of ND10 components on epigenetic determinants of early KSHV latency establishment. PLoS Pathog. Jul 2014. 10(7):e1004274.
(» DOI: 10.1371/journal.ppat.1004274). PDF
Borchert S, Czech-Sioli M, Neumann F, Schmidt C, Wimmer P, Dobner T, Grundhoff A, Fischer N. High-affinity Rb binding, p53 inhibition, subcellular localization, and transformation by wild-type or tumor-derived shortened Merkel cell polyomavirus large T antigens. J Virol. Mar 2014. 88(6):3144-60.
(» DOI: 10.1128/JVI.02916-13). PDF
2012
Marcinowski L, Lidschreiber M, Windhager L, Rieder M, Bosse JB, Rädle B, Bonfert T, Györy I, de Graaf M, Prazeres da Costa O, Rosenstiel P, Friedel CC, Zimmer R, Ruzsics Z, Dölken L. Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathog. Sep 2012. 8(9):e1002908.
(» DOI: 10.1371/journal.ppat.1002908). PDF
2010
Dölken L, Malterer G, Erhard F, Kothe S, Friedel CC, Suffert G, Marcinowski L, Motsch N, Barth S, Beitzinger M, Lieber D, Bailer SM, Hoffmann R, Ruzsics Z, Kremmer E, Pfeffer S, Zimmer R, Koszinowski UH, Grässer F, Meister G, Haas J. Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe. Apr 2010. 7(4):324-334.
(» DOI: 10.1016/j.chom.2010.03.008). PDF