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Anzahl der Publikationen: 43
Zeitschriftenartikel
Hufsky, Franziska; Abecasis, Ana; Agudelo-Romero, Patricia; Bletsa, Magda; Brown, Katherine; Claus, Claudia; Deinhardt-Emmer, Stefanie; Deng, Li; Friedel, Caroline C.; Gismondi, Maria Ines; Kostaki, Evangelia Georgia; Kuhnert, Denise; Kulkarni-Kale, Urmila; Metzner, Karin J.; Meyer, Irmtraud M.; Miozzi, Laura; Nishimura, Luca; Paraskevopoulou, Sofia; Perez-Cataluna, Alba; Rahlff, Janina; Thomson, Emma; Tumescheit, Charlotte; Hoek, Lia van der; Espen, Lore van; Vandamme, Anne-Mieke; Zaheri, Maryam; Zuckerman, Neta und Marz, Manja
(2022):
Women in the European Virus Bioinformatics Center.
In: Viruses, Bd. 14, Nr. 7, 1522
Erhard, Florian; Saliba, Antoine-Emmanuel; Lusser, Alexandra; Toussaint, Christophe; Hennig, Thomas; Prusty, Bhupesh K.; Kirschenbaum, Daniel; Abadie, Kathleen; Miska, Eric A.; Friedel, Caroline C.; Amit, Ido; Micura, Ronald und Doelken, Lars
(2022):
Time-resolved single-cell RNA-seq using metabolic RNA labelling.
In: Nature Reviews Methods Primers, Bd. 2, Nr. 1, 77
Hluchy, Milan; Gajduskova, Pavla; Ruiz de los Mozos, Igor; Rajecky, Michal; Kluge, Michael; Berger, Benedict-Tilman; Slaba, Zuzana; Potesil, David; Weiss, Elena; Ule, Jernej; Zdrahal, Zbynek; Knapp, Stefan; Paruch, Kamil; Friedel, Caroline C. und Blazek, Dalibor
(2022):
CDK11 regulates pre-mRNA splicing by phosphorylation ofSF3B1.
In: Nature, Bd. 609, Nr. 7928: S. 829-834
Friedl, Marie-Sophie; Djakovic, Lara; Kluge, Michael; Hennig, Thomas; Whisnant, Adam W.; Backes, Simone; Doelken, Lars und Friedel, Caroline C.
(2022):
HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform.
In: PLOS One 17(10), e0276467
In: PLOS One 17(10), e0276467
Wang, Xiuye 
ORCID: https://orcid.org/0000-0002-7756-3974; Liu, Liang ORCID: https://orcid.org/0000-0002-9655-204X; Whisnant, Adam W. ORCID: https://orcid.org/0000-0003-2039-2809; Hennig, Thomas ORCID: https://orcid.org/0000-0002-7788-1681; Djakovic, Lara ORCID: https://orcid.org/0000-0002-9368-9403; Haque, Nabila ORCID: https://orcid.org/0000-0003-3436-573X; Bach, Cindy ORCID: https://orcid.org/0000-0003-4727-4255; Sandri-Goldin, Rozanne M.; Erhard, Florian ORCID: https://orcid.org/0000-0002-3574-6983; Friedel, Caroline C. ORCID: https://orcid.org/0000-0003-3569-4877; Dölken, Lars ORCID: https://orcid.org/0000-0002-4651-3544 und Shi, Yongsheng ORCID: https://orcid.org/0000-0003-2967-1230
(2021):
Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation.
In: PLOS Genetics 17(3), e1009263 [PDF, 3MB]
ORCID: https://orcid.org/0000-0002-7756-3974; Liu, Liang ORCID: https://orcid.org/0000-0002-9655-204X; Whisnant, Adam W. ORCID: https://orcid.org/0000-0003-2039-2809; Hennig, Thomas ORCID: https://orcid.org/0000-0002-7788-1681; Djakovic, Lara ORCID: https://orcid.org/0000-0002-9368-9403; Haque, Nabila ORCID: https://orcid.org/0000-0003-3436-573X; Bach, Cindy ORCID: https://orcid.org/0000-0003-4727-4255; Sandri-Goldin, Rozanne M.; Erhard, Florian ORCID: https://orcid.org/0000-0002-3574-6983; Friedel, Caroline C. ORCID: https://orcid.org/0000-0003-3569-4877; Dölken, Lars ORCID: https://orcid.org/0000-0002-4651-3544 und Shi, Yongsheng ORCID: https://orcid.org/0000-0003-2967-1230
(2021):
Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation.
In: PLOS Genetics 17(3), e1009263 [PDF, 3MB]
Wahane, Shalaka; Zhou, Xianxiao; Zhou, Xiang; Guo, Lei; Friedl, Marie-Sophie; Kluge, Michael; Ramakrishnan, Aarthi; Shen, Li; Friedel, Caroline C.; Zhang, Bin; Friedel, Roland H. und Zou, Hongyan
(2021):
Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity.
In: Science Advances, Bd. 7, Nr. 9, eabd8811
Lotz-Havla, Amelie S.; Woidy, Mathias; Guder, Philipp; Friedel, Caroline C.; Klingbeil, Julian M.; Bulau, Ana-Maria; Schultze, Anja; Dahmen, Ilona; Noll-Puchta, Heidi; Kemp, Stephan; Erdmann, Ralf; Zimmer, Ralf; Muntau, Ania C. und Gersting, Soren W.
(2021):
iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations.
In: Journal of Proteome Research, Bd. 20, Nr. 9: S. 4366-4380
Huang, Yong; Tejero, Rut; Lee, Vivian K.; Brusco, Concetta; Hannah, Theodore; Bertucci, Taylor B.; Alves, Chrystian Junqueira; Katsyv, Igor; Kluge, Michael; Foty, Ramsey; Zhang, Bin; Friedel, Caroline C.; Dai, Guohao; Zou, Hongyan und Friedel, Roland H.
(2021):
Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics.
In: Communications Biology, Bd. 4, Nr. 1, 145
Friedel, Caroline C.; Whisnant, Adam W.; Djakovic, Lara; Rutkowski, Andrzej J.; Friedl, Marie-Sophie; Kluge, Michael; Williamson, James C.; Sai, Somesh; Vidal, Ramon Oliveira; Sauer, Sascha; Hennig, Thomas; Grothey, Arnhild; Milic, Andrea; Prusty, Bhupesh K.; Lehner, Paul J.; Matheson, Nicholas J.; Erhard, Florian und Doelken, Lars
(2021):
Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level.
In: Journal of Virology, Bd. 95, Nr. 3, e01399-20
Boehmer, Daniel F. R.; Formisano, Simone; Mann, Carina C. de Oliveira; Mueller, Stephan A.; Kluge, Michael; Metzger, Philipp; Rohlfs, Meino; Hoerth, Christine; Kocheise, Lorenz; Lichtenthaler, Stefan F.; Hopfner, Karl-Peter; Endres, Stefan; Rothenfusser, Simon; Friedel, Caroline C.; Duewell, Peter; Schnurr, Max und Koenig, Lars M.
(2021):
OAS1/RNase L executes RIG-I ligand-dependent tumor cell apoptosis.
In: Science Immunology, Bd. 6, Nr. 61, eabe2550
Kluge, Michael; Friedl, Marie-Sophie; Menzel, Amrei L. und Friedel, Caroline C.
(2020):
Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution.
In: Gigascience, Bd. 9, Nr. 6
Wang, Xiuye; Hennig, Thomas; Whisnant, Adam W.; Erhard, Florian; Prusty, Bhupesh K.; Friedel, Caroline C.; Forouzmand, Elmira; Hu, William; Erber, Luke; Chen, Yue; Sandri-Goldin, Rozanne M.; Doelken, Lars und Shi, Yongsheng
(2020):
Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27.
In: Nature Communications, Bd. 11, Nr. 1, 293
[PDF, 2MB]
Whisnant, Adam W.; Jürges, Christopher S.; Hennig, Thomas; Wyler, Emanuel; Prusty, Bhupesh; Rutkowski, Andrzej J.; L'hernault, Anne; Djakovic, Lara; Goebel, Margarete; Doering, Kristina; Menegatti, Jennifer; Antrobus, Robin; Matheson, Nicholas J.; Künzig, Florian W. H.; Mastrobuoni, Guido; Bielow, Chris; Kempa, Stefan; Liang, Chunguang; Dandekar, Thomas; Zimmer, Ralf; Landthaler, Markus; Graesser, Friedrich; Lehner, Paul J.; Friedel, Caroline C.; Erhard, Florian und Dölken, Lars
(2020):
Integrative functional genomics decodes herpes simplex virus 1.
In: Nature Communications, Bd. 11, Nr. 1, 2038
[PDF, 2MB]
Zhou, Xiang; Wahane, Shalaka; Friedl, Marie-Sophie; Kluge, Michael; Friedel, Caroline C.; Avrampou, Kleopatra; Zachariou, Venetia; Guo, Lei; Zhang, Bin; He, Xijing; Friedel, Roland H. und Zou, Hongyan
(2020):
Microglia and macrophages promote corralling, wound compaction and recovery after spinal cord injury via Plexin-B2.
In: Nature Neuroscience, Bd. 23, Nr. 3: S. 337-350
Rohrmoser, Michaela; Kluge, Michael; Yahia, Yousra; Gruber-Eber, Anita; Maqbool, Muhammad Ahmad; Forne, Ignasi; Krebs, Stefan; Blum, Helmut; Greifenberg, Ann Katrin; Geyer, Matthias; Descostes, Nicolas; Imhof, Axel; Andrau, Jean-Christophe; Friedel, Caroline C. und Eick, Dirk
(2019):
MIR sequences recruit zinc finger protein ZNF768 to expressed genes.
In: Nucleic Acids Research, Bd. 47, Nr. 2: S. 700-715
Tejero, Rut; Huang, Yong; Katsyv, Igor; Kluge, Michael; Lin, Jung-Yi; Tome-Garcia, Jessica; Daviaud, Nicolas; Wang, Yuanshuo; Zhang, Bin; Tsankova, Nadejda M.; Friedel, Caroline C.; Zou, Hongyan und Friedel, Roland H.
(2019):
Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment.
In: Ebiomedicine, Bd. 42: S. 252-269
Bugai, Andrii; Quaresma, Alexandre J. C.; Friedel, Caroline C.; Lenasi, Tina; Duester, Robert; Sibley, Christopher R.; Fujinaga, Koh; Kukanja, Petra; Hennig, Thomas; Blasius, Melanie; Geyer, Matthias; Ule, Jernej; Doelken, Lars und Barboric, Matjaz
(2019):
P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.
In: Molecular Cell, Bd. 74, Nr. 2
Manavalan, Anil Paul Chirackal; Pilarova, Kveta; Kluge, Michael; Bartholomeeusen, Koen; Rajecky, Michal; Oppelt, Jan; Khirsariya, Prashant; Paruch, Kamil; Krejci, Lumir; Friedel, Caroline C. und Blazek, Dalibor
(2019):
CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes.
In: EMBO Reports, e47592
Metzger, Philipp; Kirchleitner, Sabrina; Kluge, Michael; König, Lars M.; Hoerth, Christine; Rambuscheck, Carlotta A.; Bohmer, Daniel; Ahlfeld, Julia; Kobold, Sebastian; Friedel, Caroline C.; Endres, Stefan; Schnurr, Max und Duewell, Peter
(2019):
Immunostimulatory RNA leads to functional reprogramming of myeloid-derived suppressor cells in pancreatic cancer.
In: Journal for Immunotherapy of Cancer, Bd. 7, Nr. 1, 288
Funk, Christina; Raschbichler, Verena; Lieber, Diana; Wetschky, Jens; Arnold, Eileen K.; Leimser, Jacqueline; Biggel, Michael; Friedel, Caroline C.; Ruzsics, Zsolt und Bailer, Susanne M.
(2019):
Comprehensive analysis of nuclear export of herpes simplex virus type 1 tegument proteins and their Epstein-Barr virus orthologs.
In: Traffic, Bd. 20, Nr. 2: S. 152-167
Gamm, Matthias von; Schaub, Annalisa; Jones, Alisha N.; Wolf, Christine; Behrens, Gesine; Lichti, Johannes; Essig, Katharina; Macht, Anna; Pircher, Joachim; Ehrlich, Andreas; Davari, Kathrin; Chauhan, Dhruv; Busch, Benjamin; Wurst, Wolfgang; Feederle, Regina; Feuchtinger, Annette; Tschoep, Matthias H.; Friedel, Caroline C.; Hauck, Stefanie M.; Sattler, Michael; Geerlof, Arie; Hornung, Veit; Heissmeyer, Vigo; Schulz, Christian; Heikenwalder, Mathias und Glasmacher, Elke
(2019):
Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3.
In: Journal of Experimental Medicine, Bd. 216, Nr. 7: S. 1700-1723
[PDF, 6MB]
Davari, Kathrin; Lichti, Johannes; Friedel, Caroline C. und Glasmacher, Elke
(2018):
Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation.
In: Jove-Journal of Visualized Experiments, Nr. 133, e56752
Kluge, Michael und Friedel, Caroline C.
(2018):
Watchdog - a workflow management system for the distributed analysis of large-scale experimental data.
In: BMC Bioinformatics
19:97
[PDF, 2MB]
Hennig, Thomas; Michalski, Marco; Rutkowski, Andrzej J.; Djakovic, Lara; Whisnant, Adam W.; Friedl, Marie-Sophie; Jha, Bhaskar Anand; Baptista, Marisa A. P.; L'Hernault, Anne; Erhard, Florian; Doelken, Lars und Friedel, Caroline C.
(2018):
HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes.
In: PLOS Pathogens 14(3), e1006954 [PDF, 11MB]
In: PLOS Pathogens 14(3), e1006954 [PDF, 11MB]
Bonfert, Thomas und Friedel, Caroline C.
(2017):
Prediction of Poly(A) Sites by Poly(A) Read Mapping.
In: PLOS One 12(1), e0170914 [PDF, 5MB]
In: PLOS One 12(1), e0170914 [PDF, 5MB]
Decker, Tim-Michael; Kluge, Michael; Krebs, Stefan; Shah, Nilay; Blum, Helmut; Friedel, Caroline C. und Eick, Dirk
(2017):
Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1.
In: Scientific Reports, Bd. 7, 1684
[PDF, 1MB]
Davari, Kathrin; Lichti, Johannes; Gallus, Christian; Greulich, Franziska; Uhlenhaut, N. Henriette ORCID: https://orcid.org/0000-0002-4220-4779; Heinig, Matthias; Friedel, Caroline C. und Glasmacher, Elke
(2017):
Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses.
In: Cell Reports, Bd. 19, Nr. 3: S. 643-654
ORCID: https://orcid.org/0000-0002-4220-4779; Heinig, Matthias; Friedel, Caroline C. und Glasmacher, Elke
(2017):
Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses.
In: Cell Reports, Bd. 19, Nr. 3: S. 643-654
Zhang, Jian-Nan; Michel, Uwe; Lenz, Christof; Friedel, Caroline C.; Köster, Sarah; d'Hedouville, Zara; Tönges, Lars; Urlaub, Henning; Bähr, Mathias; Lingor, Paul und Koch, Jan C.
(2016):
Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration.
In: Scientific Reports, Bd. 6, 37050
[PDF, 2MB]
Bonfert, Thomas; Kirner, Evelyn; Csaba, Gergely; Zimmer, Ralf und Friedel, Caroline C.
(2015):
ContextMap 2: fast and accurate context-based RNA-seq mapping.
In: BMC Bioinformatics
16:122
[PDF, 1MB]
Osterman, Andreas; Stellberger, Thorsten; Gebhardt, Anna; Kurz, Marisa; Friedel, Caroline C.; Uetz, Peter; Nitschko, Hans; Baiker, Armin und Vizoso-Pinto, Maria G.
(2015):
The Hepatitis E virus intraviral interactome.
In: Scientific Reports, Bd. 5, 13872
[PDF, 895kB]
Murakawa, Yasuhiro; Hinz, Michael; Mothes, Janina; Schuetz, Anja; Uhl, Michael; Wyler, Emanuel; Yasuda, Tomoharu; Mastrobuoni, Guido; Friedel, Caroline C.; Dölken, Lars; Kempa, Stefan; Schmidt-Supprian, Marc; Blüthgen, Nils; Backofen, Rolf; Heinemann, Udo; Wolf, Jana; Scheidereit, Claus und Landthaler, Markus
(2015):
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappa B pathway.
In: Nature Communications, Bd. 6, 7367
[PDF, 3MB]
Rutkowski, Andrzej J.; Erhard, Florian; L'Hernault, Anne; Bonfert, Thomas; Schilhabel, Markus; Crump, Colin; Rosenstiel, Philip; Efstathiou, Stacey; Zimmer, Ralf; Friedel, Caroline C. und Dölken, Lars
(2015):
Widespread disruption of host transcription termination in HSV-1 infection.
In: Nature Communications, Bd. 6, 7126
[PDF, 1MB]
Marcinowski, Lisa; Lidschreiber, Michael; Windhager, Lukas; Rieder, Martina; Bosse, Jens B.; Rädle, Bernd; Bonfert, Thomas; Györy, Ildiko; de Graaf, Miranda; Prazeres da Costa, Olivia; Rosenstiel, Philip; Friedel, Caroline C.; Zimmer, Ralf; Ruzsics, Zsolt und Dölken, Lars
(September 2012):
Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection.
In: PLOS Pathogens 8(9), e1002908 [PDF, 1MB]
In: PLOS Pathogens 8(9), e1002908 [PDF, 1MB]
Spasic, Milan; Friedel, Caroline C.; Schott, Johanna; Kreth, Jochen; Leppek, Kathrin; Hofmann, Sarah; Ozgur, Sevim und Stoecklin, Georg
(Januar 2012):
Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm.
In: PLOS Genetics 8(1), e1002433 [PDF, 2MB]
In: PLOS Genetics 8(1), e1002433 [PDF, 2MB]
Bonfert, Thomas; Csaba, Gergely; Zimmer, Ralf und Friedel, Caroline C.
(2012):
A context-based approach to identify the most likely mapping for RNA-seq experiments.
In: BMC Bioinformatics
13:S9
[PDF, 1MB]
Petri, Tobias; Berchtold, Evi; Zimmer, Ralf und Friedel, Caroline C.
(2012):
Detection and correction of probe-level artefacts on microarrays.
In: BMC Bioinformatics
13:114
[PDF, 1MB]
Lindner, Robert und Friedel, Caroline C.
(2012):
A comprehensive evaluation of alignment algorithms in the context of RNA-seq.
In: PLOS ONE 7(12), e52403 [PDF, 416kB]
In: PLOS ONE 7(12), e52403 [PDF, 416kB]
Pfefferle, Susanne; Schöpf, Julia; Kögl, Manfred; Friedel, Caroline C.; Müller, Marcel A.; Carbajo-Lozoya, Javier; Stellberger, Thorsten; Dall'Armi, Ekatarina von; Herzog, Petra; Kallies, Stefan; Niemeyer, Daniela; Ditt, Vanessa; Kuri, Thomas; Züst, Roland; Pumpor, Ksenia; Hilgenfeld, Rolf; Schwarz, Frank; Zimmer, Ralf; Steffen, Imke; Weber, Friedemann; Thiel, Volker; Herrler, Georg; Thiel, Heinz-Jürgen; Schwegmann-Wessels, Christel; Pöhlmann, Stefan; Haas, Juergen G.; Drosten, Christian und Brunn, Albrecht von
(Oktober 2011):
The SARS-coronavirus-host interactome. Identification of cyclophilins as target for pan-coronavirus inhibitors.
In: PLOS Pathogens 7(10), e1002331 [PDF, 1MB]
In: PLOS Pathogens 7(10), e1002331 [PDF, 1MB]
Fossum, Even; Friedel, Caroline C.; Rajagopala, Seesandra V.; Titz, Björn; Baiker, Armin; Schmidt, Tina; Kraus, Theo; Stellberger, Thorsten; Rutenberg, Christiane; Suthram, Silpa; Bandyopadhyay, Sourav; Rose, Dietlind; Brunn, Albrecht von; Uhlmann, Mareike; Zeretzke, Christine; Dong, Yu-An; Boulet, Hélène; Koegl, Manfred; Bailer, Susanne M.; Koszinowski, Ulrich H.; Ideker, Trey; Uetz, Peter; Zimmer, Ralf und Haas, Jürgen G.
(September 2009):
Evolutionarily conserved herpesviral protein interaction networks.
In: PLOS Pathogens 5(9), e1000570 [PDF, 1MB]
In: PLOS Pathogens 5(9), e1000570 [PDF, 1MB]
Erhard, Florian; Friedel, Caroline C. und Zimmer, Ralf
(2008):
FERN - a Java framework for stochastic simulation and evaluation of reaction networks.
In: BMC Bioinformatics
9:356
[PDF, 546kB]
Brunn, Albrecht von; Teepe, Carola; Simpson, Jeremy C.; Pepperkok, Rainer; Friedel, Caroline C.; Zimmer, Ralf; Roberts, Rhonda; Baric, Ralph und Haas, Jürgen
(23. Mai 2007):
Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome.
In: PLOS ONE 2(5), e459 [PDF, 1MB]
In: PLOS ONE 2(5), e459 [PDF, 1MB]
Friedel, Caroline C. und Zimmer, Ralf
(2007):
Influence of degree correlations on network structure and stability in protein-protein interaction networks.
In: BMC Bioinformatics
8:297
[PDF, 316kB]
Friedel, Caroline C. und Zimmer, Ralf
(2006):
Inferring topology from clustering coefficients in protein-protein interaction networks.
In: BMC Bioinformatics
7:519
[PDF, 424kB]