2013
39 Caldelari I, Chao Y, Romby P, Vogel J. Caldelari I, Chao Y, Romby P, Vogel J. RNA-mediated regulation in pathogenic bacteria Bacterial Pathogens and Pathogenesis (eds. Cossart P, Maloy S), CSH Press, in press
38 Hoe, C. H., Raabe, C.A., Rozhdestvensky, T.F., Tang, T.H. Bacterial sRNAs: Regulation in stress. Int J Med Microbiol. 2013 Jul;303(5):217-29. doi: 10.1016/j.ijmm.2013.04.002. Epub 2013 Apr 11. PMID:23660175[PubMed - in process]
37 Holmqvist E, Vogel J. A small RNA serving both the Hfq and CsrA regulons Genes & Development 27:1073-1078
36 Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J. Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis Cell 153:426-37
35 Schulte LN, Westermann AJ, Vogel J Differential activation and functional specialisation of miR-146 and miR-155 in innate immune sensing Nucleic Acids Research 41(1):542-53
2012
34 Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J. An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs. EMBO Journal 31(29):4005-19
33 Corcoran CP, Rieder R, Podkaminski D, Hofmann B, Vogel J. Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs Methods in Molecular Biology 905:177-200
32 ENCODE Project Consortium (591 scientists) with Reinhardt R. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PubMed PMID: 22955616.
31 Eulalio A, Schulte L, Vogel J The mammalian microRNA response to bacterial infections RNA Biology 9(6):742-750
30 Fröhlich KS, Papenfort K, Berger AA, Vogel J A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD Nucleic Acids Research 40(8):3623-40
29 Khayrullina GA, Raabe CA, Hoe CH, Becker K, Reinhardt R, Tang TH, Rozhdestvensky TS, Kopylov AM. Transcription Analysis and Small Non-Protein Coding RNAs Associated with Bacterial Ribosomal Protein Operons. Curr Med Chem. 2012 Oct 1;19(30):5187-98. PubMed PMID: 22680642.
28 Kroenlein H, Schwartz S, Reinhardt R, Rieder H, Molkentin M, Gökbuget N, Hoelzer D, Thiel E, Burmeister T. Molecular analysis of the t(2;8)/MYC-IGK translocation in high-grade lymphoma/leukemia by long-distance inverse PCR. Genes Chromosomes Cancer. 2012 Mar;51(3):290-9. doi: 10.1002/gcc.21915. Epub 2011 Nov 25. PubMed PMID: 22120970.
27 Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hebrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium PNAS 109(20):E1277-86
26 Olbrich H, Schmidts M, Werner C, Onoufriadis A, Loges NT, Raidt J, Banki NF, Shoemark A, Burgoyne T, Al Turki S, Hurles ME; UK10K Consortium, Köhler G, Schroeder J, Nürnberg G, Nürnberg P, Chung EM, Reinhardt R, Marthin JK, Nielsen KG, Mitchison HM, Omran H. Recessive HYDIN mutations cause primary ciliary dyskinesia without randomization of left-right body asymmetry. Am J Hum Genet. 2012 Oct 5;91(4):672-84. doi: 10.1016/j.ajhg.2012.08.016. Epub 2012 Sep 27. PubMed PMID: 23022101.
25 Panizzi JR, Becker-Heck A, Castleman VH, Al-Mutairi DA, Liu Y, Loges NT, Pathak N, Austin-Tse C, Sheridan E, Schmidts M, Olbrich H, Werner C, Häffner K, Hellman N, Chodhari R, Gupta A, Kramer-Zucker A, Olale F, Burdine RD, Schier AF, O'Callaghan C, Chung EM, Reinhardt R, Mitchison HM, King SM, Omran H, Drummond IA. CCDC103 mutations cause primary ciliary dyskinesia by disrupting assembly of ciliary dynein arms. Nat Genet. 2012 May 13;44(6):714-9. doi: 10.1038/ng.2277. PubMed PMID: 22581229.
24 Papenfort K, Podkaminski D, Hinton JC, Vogel J. The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. PNAS 109(13):E757-64 The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. Proc Natl Acad Sci U S A PNAS 109(13):E757-64
23 Prusty BK, Böhme L, Bergmann B, Siegl C, Krause E, Mehlitz A, Rudel T. Imbalanced oxidative stress causes chlamydial persistence during non-productive human herpes virus co-infection. PLoS One. 2012;7(10):e47427. doi: 10.1371/journal.pone.0047427.
22 Rieder R, Reinhardt R, Sharma CM, Vogel J. Experimental tools to identify RNA-protein interactions in Helicobacter pylori RNA Biology 9(4):520-31
21 Westermann AJ, Gorski SA, Vogel J. Dual RNA-seq of pathogen and host Nat Reviews Microbiology 14;10(9):618-30
2011
20 Albrecht M, Sharma CM, Dittrich MT, Müller T, Reinhardt R, Vogel J, Rudel T. The transcriptional landscape of Chlamydia pneumoniae. Genome Biol. 2011 Oct 11;12(10):R98.
19 Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J. Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res. 2011 Jan; 39(2): 675-686
18 Papenfort K, Podkaminski D, Hinton JC, Vogel J. The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair. PNAS 109(13):E757-64
17 Raabe CA, Hoe CH, Randau G, Brosius J, Tang TH, Rozhdestvensky TS. The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome. RNA -A PUBLICATION OF THE RNA SOCIETY Volume: 17 Issue: 7 Pages: 1357-1366 DOI: 10.1261/rna.2682311 Published: JUL 2011Times Cited: 2 (from Web of Science)
16 Schulte LN, Eulalio A, Mollenkopf HJ, Reinhardt R, Vogel J. Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family. EMBO Journal 30(10):1977-89 (commentary in EMBO J 30(10):1977-9).
2010
15 Abu-Qatouseh LF, Chinni SV, Seggewiß J, Proctor RA, Brosius J, Rozhdestvensky TS, Peters G, von Eiff C, Becker K. Identification of differentially expressed small non-protein-coding RNAs in Staphylococcus aureus displaying both the normal and the small-colony variant phenotype. J Mol Med. 2010 Feb 12. [Epub ahead of print].
14 Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T. Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.Nucleic Acids Res. 2010 Jan;38(3):868-77.
13 Chinni SV, Raabe CA, Zakaria R, Randau G, Hock CH, Zemann A, Brosius J, Tang TH, Rozhdestvensky, TS. Experimental identification and characterization of 97novel npcRNA candidates in Salmonella enterica serovar Typhi. Nucleic Acids Res, in press.
12 Galiveti CR, Rozhdestvensky TS, Brosius J, Lehrach H, Konthur Z. Application of housekeeping npcRNAs for quantitative expression analysis of human transcriptome by real-time PCR. RNA 16:450-461. Epub 2009 Dec 29.
11 Raabe CA, Sanchez CP, Randau G, Robeck T, Skryabin BV, Chinni SV, Kube M, Reinhardt R, Ng GH, Manickam R, Kuryshev VY, Lanzer M, Brosius J, Tang TH, Rozhdestvensky TS. A global view of the non protein-coding transcriptome in Plasmodium falciparum. Nucleic Acids Res 38:608-617. Epub 2009 Oct 28.
10 Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010 Mar 11; 464(7286):250-5. PMID: 20164839.
2009
9 Galiveti CR, Rozhdestvensky TS, Brosius J, Lehrach H, Konthur Z (2010) Application of housekeeping npcRNAs for quantitative expression analysis of human transcriptome by real-time PCR. RNA 16:450-461. Epub 2009 Dec 29.
8 Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol. 2009 Sep;5(9):e1000502.
7 Manickam R, Kuryshev VY, Lanzer M, Brosius J, Tang TH, Rozhdestvensky TS (2010) A global view of the nonprotein-coding transcriptome in Plasmodium falciparum. Nucleic Acids Res 38:608-617. Epub 2009 Oct 28.
6 Papenfort K, Said N, Welsink T, Lucchini S, Hinton JC, Vogel J. Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Mol Microbiol. 2009 Oct;74(1):139-58.
5 Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J. Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol. 2009 Aug;16(8):840-6.
4 Sharma CM, Vogel J. Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol. 2009 Oct;12(5):536-46.
3 Sittka A, Sharma CM, Rolle K, Vogel J. Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes. RNA Biol. 2009 Jul;6(3):266-75.
2 Vogel J. A rough guide to the non-coding RNA world of Salmonella. Mol Microbiol. 2009 Jan;71(1):1-11.
