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Items: 1 to 50 of 51

1.

Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3.

von Gamm M, Schaub A, Jones AN, Wolf C, Behrens G, Lichti J, Essig K, Macht A, Pircher J, Ehrlich A, Davari K, Chauhan D, Busch B, Wurst W, Feederle R, Feuchtinger A, Tschöp MH, Friedel CC, Hauck SM, Sattler M, Geerlof A, Hornung V, Heissmeyer V, Schulz C, Heikenwalder M, Glasmacher E.

J Exp Med. 2019 May 24. pii: jem.20181762. doi: 10.1084/jem.20181762. [Epub ahead of print]

PMID:
31126966
2.

Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment.

Tejero R, Huang Y, Katsyv I, Kluge M, Lin JY, Tome-Garcia J, Daviaud N, Wang Y, Zhang B, Tsankova NM, Friedel CC, Zou H, Friedel RH.

EBioMedicine. 2019 Apr;42:252-269. doi: 10.1016/j.ebiom.2019.03.064. Epub 2019 Apr 3.

3.

P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.

Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barborič M.

Mol Cell. 2019 Apr 18;74(2):254-267.e10. doi: 10.1016/j.molcel.2019.01.033. Epub 2019 Feb 26.

4.

Comprehensive analysis of nuclear export of herpes simplex virus type 1 tegument proteins and their Epstein-Barr virus orthologs.

Funk C, Raschbichler V, Lieber D, Wetschky J, Arnold EK, Leimser J, Biggel M, Friedel CC, Ruzsics Z, Bailer SM.

Traffic. 2019 Feb;20(2):152-167. doi: 10.1111/tra.12627. Epub 2019 Jan 11.

PMID:
30548142
5.

MIR sequences recruit zinc finger protein ZNF768 to expressed genes.

Rohrmoser M, Kluge M, Yahia Y, Gruber-Eber A, Maqbool MA, Forné I, Krebs S, Blum H, Greifenberg AK, Geyer M, Descostes N, Imhof A, Andrau JC, Friedel CC, Eick D.

Nucleic Acids Res. 2019 Jan 25;47(2):700-715. doi: 10.1093/nar/gky1148.

6.

HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes.

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.

PLoS Pathog. 2018 Mar 26;14(3):e1006954. doi: 10.1371/journal.ppat.1006954. eCollection 2018 Mar.

7.
8.

Watchdog - a workflow management system for the distributed analysis of large-scale experimental data.

Kluge M, Friedel CC.

BMC Bioinformatics. 2018 Mar 13;19(1):97. doi: 10.1186/s12859-018-2107-4.

9.

Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1.

Decker TM, Kluge M, Krebs S, Shah N, Blum H, Friedel CC, Eick D.

Sci Rep. 2017 May 10;7(1):1684. doi: 10.1038/s41598-017-01943-6.

10.

Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses.

Davari K, Lichti J, Gallus C, Greulich F, Uhlenhaut NH, Heinig M, Friedel CC, Glasmacher E.

Cell Rep. 2017 Apr 18;19(3):643-654. doi: 10.1016/j.celrep.2017.03.069.

11.

Prediction of Poly(A) Sites by Poly(A) Read Mapping.

Bonfert T, Friedel CC.

PLoS One. 2017 Jan 30;12(1):e0170914. doi: 10.1371/journal.pone.0170914. eCollection 2017.

12.

Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration.

Zhang JN, Michel U, Lenz C, Friedel CC, Köster S, d'Hedouville Z, Tönges L, Urlaub H, Bähr M, Lingor P, Koch JC.

Sci Rep. 2016 Nov 15;6:37050. doi: 10.1038/srep37050.

13.

Role of Cytochrome P4502B6 Polymorphisms in Ketamine Metabolism and Clearance.

Rao LK, Flaker AM, Friedel CC, Kharasch ED.

Anesthesiology. 2016 Dec;125(6):1103-1112.

PMID:
27763887
14.

The Hepatitis E virus intraviral interactome.

Osterman A, Stellberger T, Gebhardt A, Kurz M, Friedel CC, Uetz P, Nitschko H, Baiker A, Vizoso-Pinto MG.

Sci Rep. 2015 Oct 14;5:13872. doi: 10.1038/srep13872.

15.

p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses.

Hünten S, Kaller M, Drepper F, Oeljeklaus S, Bonfert T, Erhard F, Dueck A, Eichner N, Friedel CC, Meister G, Zimmer R, Warscheid B, Hermeking H.

Mol Cell Proteomics. 2015 Oct;14(10):2609-29. doi: 10.1074/mcp.M115.050237. Epub 2015 Jul 16.

16.

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.

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.

Nat Commun. 2015 Jul 14;6:7367. doi: 10.1038/ncomms8367.

17.

Widespread disruption of host transcription termination in HSV-1 infection.

Rutkowski AJ, Erhard F, L'Hernault A, Bonfert T, Schilhabel M, Crump C, Rosenstiel P, Efstathiou S, Zimmer R, Friedel CC, Dölken L.

Nat Commun. 2015 May 20;6:7126. doi: 10.1038/ncomms8126.

18.

ContextMap 2: fast and accurate context-based RNA-seq mapping.

Bonfert T, Kirner E, Csaba G, Zimmer R, Friedel CC.

BMC Bioinformatics. 2015 Apr 17;16:122. doi: 10.1186/s12859-015-0557-5.

19.

4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response.

Burger K, Mühl B, Kellner M, Rohrmoser M, Gruber-Eber A, Windhager L, Friedel CC, Dölken L, Eick D.

RNA Biol. 2013 Oct;10(10):1623-30. doi: 10.4161/rna.26214. Epub 2013 Sep 4.

20.

Mining RNA-seq data for infections and contaminations.

Bonfert T, Csaba G, Zimmer R, Friedel CC.

PLoS One. 2013 Sep 3;8(9):e73071. doi: 10.1371/journal.pone.0073071. eCollection 2013.

21.

Computational analysis of virus-host interactomes.

Friedel CC.

Methods Mol Biol. 2013;1064:115-30. doi: 10.1007/978-1-62703-601-6_8.

PMID:
23996253
22.

Metabolic labeling of newly transcribed RNA for high resolution gene expression profiling of RNA synthesis, processing and decay in cell culture.

Rädle B, Rutkowski AJ, Ruzsics Z, Friedel CC, Koszinowski UH, Dölken L.

J Vis Exp. 2013 Aug 8;(78). doi: 10.3791/50195.

23.

A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication.

Griffiths SJ, Koegl M, Boutell C, Zenner HL, Crump CM, Pica F, Gonzalez O, Friedel CC, Barry G, Martin K, Craigon MH, Chen R, Kaza LN, Fossum E, Fazakerley JK, Efstathiou S, Volpi A, Zimmer R, Ghazal P, Haas J.

PLoS Pathog. 2013;9(8):e1003514. doi: 10.1371/journal.ppat.1003514. Epub 2013 Aug 8.

24.

Clonal expansion analysis of transposon insertions by high-throughput sequencing identifies candidate cancer genes in a PiggyBac mutagenesis screen.

Friedel RH, Friedel CC, Bonfert T, Shi R, Rad R, Soriano P.

PLoS One. 2013 Aug 5;8(8):e72338. doi: 10.1371/journal.pone.0072338. Print 2013.

25.

Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis.

Trilling M, Bellora N, Rutkowski AJ, de Graaf M, Dickinson P, Robertson K, Prazeres da Costa O, Ghazal P, Friedel CC, Albà MM, Dölken L.

Nucleic Acids Res. 2013 Sep;41(17):8107-25. doi: 10.1093/nar/gkt589. Epub 2013 Jul 5.

26.

β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments.

Schiller HB, Hermann MR, Polleux J, Vignaud T, Zanivan S, Friedel CC, Sun Z, Raducanu A, Gottschalk KE, Théry M, Mann M, Fässler R.

Nat Cell Biol. 2013 Jun;15(6):625-36. doi: 10.1038/ncb2747. Epub 2013 May 26.

PMID:
23708002
27.

A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

Lindner R, Friedel CC.

PLoS One. 2012;7(12):e52403. doi: 10.1371/journal.pone.0052403. Epub 2012 Dec 26.

28.

Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection.

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.

PLoS Pathog. 2012 Sep;8(9):e1002908. doi: 10.1371/journal.ppat.1002908. Epub 2012 Sep 6.

29.

Detection and correction of probe-level artefacts on microarrays.

Petri T, Berchtold E, Zimmer R, Friedel CC.

BMC Bioinformatics. 2012 May 30;13:114. doi: 10.1186/1471-2105-13-114.

30.

A context-based approach to identify the most likely mapping for RNA-seq experiments.

Bonfert T, Csaba G, Zimmer R, Friedel CC.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S9. doi: 10.1186/1471-2105-13-S6-S9.

31.

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.

Windhager L, Bonfert T, Burger K, Ruzsics Z, Krebs S, Kaufmann S, Malterer G, L'Hernault A, Schilhabel M, Schreiber S, Rosenstiel P, Zimmer R, Eick D, Friedel CC, Dölken L.

Genome Res. 2012 Oct;22(10):2031-42. doi: 10.1101/gr.131847.111. Epub 2012 Apr 26.

32.

Genome-wide assessment of AU-rich elements by the AREScore algorithm.

Spasic M, Friedel CC, Schott J, Kreth J, Leppek K, Hofmann S, Ozgur S, Stoecklin G.

PLoS Genet. 2012 Jan;8(1):e1002433. doi: 10.1371/journal.pgen.1002433. Epub 2012 Jan 5.

33.

The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors.

Pfefferle S, Schöpf J, Kögl M, Friedel CC, Müller MA, Carbajo-Lozoya J, Stellberger T, von Dall'Armi E, Herzog P, Kallies S, Niemeyer D, Ditt V, Kuri T, Züst R, Pumpor K, Hilgenfeld R, Schwarz F, Zimmer R, Steffen I, Weber F, Thiel V, Herrler G, Thiel HJ, Schwegmann-Wessels C, Pöhlmann S, Haas J, Drosten C, von Brunn A.

PLoS Pathog. 2011 Oct;7(10):e1002331. doi: 10.1371/journal.ppat.1002331. Epub 2011 Oct 27.

34.

Virus-host interactomes and global models of virus-infected cells.

Friedel CC, Haas J.

Trends Microbiol. 2011 Oct;19(10):501-8. doi: 10.1016/j.tim.2011.07.003. Epub 2011 Aug 18. Review.

PMID:
21855347
35.

Quantitative proteomics of the integrin adhesome show a myosin II-dependent recruitment of LIM domain proteins.

Schiller HB, Friedel CC, Boulegue C, Fässler R.

EMBO Rep. 2011 Mar;12(3):259-66. doi: 10.1038/embor.2011.5. Epub 2011 Feb 11.

36.

Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay.

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.

Cell Host Microbe. 2010 Apr 22;7(4):324-34. doi: 10.1016/j.chom.2010.03.008.

37.

HALO--a Java framework for precise transcript half-life determination.

Friedel CC, Kaufmann S, Dölken L, Zimmer R.

Bioinformatics. 2010 May 1;26(9):1264-6. doi: 10.1093/bioinformatics/btq117. Epub 2010 Mar 17.

PMID:
20299326
38.

Metabolic tagging and purification of nascent RNA: implications for transcriptomics.

Friedel CC, Dölken L.

Mol Biosyst. 2009 Nov;5(11):1271-8. doi: 10.1039/b911233b. Epub 2009 Aug 26. Review.

PMID:
19823741
39.

Evolutionarily conserved herpesviral protein interaction networks.

Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J.

PLoS Pathog. 2009 Sep;5(9):e1000570. doi: 10.1371/journal.ppat.1000570. Epub 2009 Sep 4.

40.

Bootstrapping the interactome: unsupervised identification of protein complexes in yeast.

Friedel CC, Krumsiek J, Zimmer R.

J Comput Biol. 2009 Aug;16(8):971-87. doi: 10.1089/cmb.2009.0023.

PMID:
19630542
41.

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life.

Friedel CC, Dölken L, Ruzsics Z, Koszinowski UH, Zimmer R.

Nucleic Acids Res. 2009 Sep;37(17):e115. doi: 10.1093/nar/gkp542. Epub 2009 Jun 26.

42.

Identifying the topology of protein complexes from affinity purification assays.

Friedel CC, Zimmer R.

Bioinformatics. 2009 Aug 15;25(16):2140-6. doi: 10.1093/bioinformatics/btp353. Epub 2009 Jun 8.

43.

FERN - a Java framework for stochastic simulation and evaluation of reaction networks.

Erhard F, Friedel CC, Zimmer R.

BMC Bioinformatics. 2008 Aug 29;9:356. doi: 10.1186/1471-2105-9-356.

44.

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay.

Dölken L, Ruzsics Z, Rädle B, Friedel CC, Zimmer R, Mages J, Hoffmann R, Dickinson P, Forster T, Ghazal P, Koszinowski UH.

RNA. 2008 Sep;14(9):1959-72. doi: 10.1261/rna.1136108. Epub 2008 Jul 24.

45.

ProCope--protein complex prediction and evaluation.

Krumsiek J, Friedel CC, Zimmer R.

Bioinformatics. 2008 Sep 15;24(18):2115-6. doi: 10.1093/bioinformatics/btn376. Epub 2008 Jul 17.

PMID:
18635566
46.
47.

Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome.

von Brunn A, Teepe C, Simpson JC, Pepperkok R, Friedel CC, Zimmer R, Roberts R, Baric R, Haas J.

PLoS One. 2007 May 23;2(5):e459.

48.
49.

Reliable gene signatures for microarray classification: assessment of stability and performance.

Davis CA, Gerick F, Hintermair V, Friedel CC, Fundel K, Küffner R, Zimmer R.

Bioinformatics. 2006 Oct 1;22(19):2356-63. Epub 2006 Jul 31.

PMID:
16882647
50.

Toward the complete interactome.

Friedel CC, Zimmer R.

Nat Biotechnol. 2006 Jun;24(6):614-5; author reply 615. No abstract available.

PMID:
16763580

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