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Items: 20

1.

Dissecting newly transcribed and old RNA using GRAND-SLAM.

Jürges C, Dölken L, Erhard F.

Bioinformatics. 2018 Jul 1;34(13):i218-i226. doi: 10.1093/bioinformatics/bty256.

2.

Estimating pseudocounts and fold changes for digital expression measurements.

Erhard F.

Bioinformatics. 2018 Dec 1;34(23):4054-4063. doi: 10.1093/bioinformatics/bty471.

PMID:
29931226
3.

Dicer in Macrophages Prevents Atherosclerosis by Promoting Mitochondrial Oxidative Metabolism.

Wei Y, Corbalán-Campos J, Gurung R, Natarelli L, Zhu M, Exner N, Erhard F, Greulich F, Geißler C, Uhlenhaut NH, Zimmer R, Schober A.

Circulation. 2018 Oct 30;138(18):2007-2020. doi: 10.1161/CIRCULATIONAHA.117.031589.

PMID:
29748186
4.

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.

5.

Tolerogenic Transcriptional Signatures of Steady-State and Pathogen-Induced Dendritic Cells.

Vendelova E, Ashour D, Blank P, Erhard F, Saliba AE, Kalinke U, Lutz MB.

Front Immunol. 2018 Feb 28;9:333. doi: 10.3389/fimmu.2018.00333. eCollection 2018. Review.

6.

Improved Ribo-seq enables identification of cryptic translation events.

Erhard F, Halenius A, Zimmermann C, L'Hernault A, Kowalewski DJ, Weekes MP, Stevanovic S, Zimmer R, Dölken L.

Nat Methods. 2018 May;15(5):363-366. doi: 10.1038/nmeth.4631. Epub 2018 Mar 12.

7.

EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells.

Glaser LV, Rieger S, Thumann S, Beer S, Kuklik-Roos C, Martin DE, Maier KC, Harth-Hertle ML, Grüning B, Backofen R, Krebs S, Blum H, Zimmer R, Erhard F, Kempkes B.

PLoS Pathog. 2017 Oct 2;13(10):e1006664. doi: 10.1371/journal.ppat.1006664. eCollection 2017 Oct.

8.

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.

9.

Count ratio model reveals bias affecting NGS fold changes.

Erhard F, Zimmer R.

Nucleic Acids Res. 2015 Nov 16;43(20):e136. doi: 10.1093/nar/gkv696. Epub 2015 Jul 8.

10.

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.

11.

Widespread context dependency of microRNA-mediated regulation.

Erhard F, Haas J, Lieber D, Malterer G, Jaskiewicz L, Zavolan M, Dölken L, Zimmer R.

Genome Res. 2014 Jun;24(6):906-19. doi: 10.1101/gr.166702.113. Epub 2014 Mar 25.

12.

Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9.

Harth-Hertle ML, Scholz BA, Erhard F, Glaser LV, Dölken L, Zimmer R, Kempkes B.

PLoS Pathog. 2013 Sep;9(9):e1003638. doi: 10.1371/journal.ppat.1003638. Epub 2013 Sep 19.

13.

PARma: identification of microRNA target sites in AGO-PAR-CLIP data.

Erhard F, Dölken L, Jaskiewicz L, Zimmer R.

Genome Biol. 2013 Jul 29;14(7):R79. doi: 10.1186/gb-2013-14-7-r79.

14.

RIP-chip enrichment analysis.

Erhard F, Dölken L, Zimmer R.

Bioinformatics. 2013 Jan 1;29(1):77-83. doi: 10.1093/bioinformatics/bts631. Epub 2012 Oct 26.

PMID:
23104891
15.

Detecting outlier peptides in quantitative high-throughput mass spectrometry data.

Erhard F, Zimmer R.

J Proteomics. 2012 Jun 18;75(11):3230-9. doi: 10.1016/j.jprot.2012.03.032. Epub 2012 Mar 29.

PMID:
22483996
16.

Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo.

Marcinowski L, Tanguy M, Krmpotic A, Rädle B, Lisnić VJ, Tuddenham L, Chane-Woon-Ming B, Ruzsics Z, Erhard F, Benkartek C, Babic M, Zimmer R, Trgovcich J, Koszinowski UH, Jonjic S, Pfeffer S, Dölken L.

PLoS Pathog. 2012 Feb;8(2):e1002510. doi: 10.1371/journal.ppat.1002510. Epub 2012 Feb 9.

17.

Classification of ncRNAs using position and size information in deep sequencing data.

Erhard F, Zimmer R.

Bioinformatics. 2010 Sep 15;26(18):i426-32. doi: 10.1093/bioinformatics/btq363.

18.

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.

19.

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.

20.

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