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Latest Publications

  • Saker H, Machné R, Fallmann J, Murray DB, Shahin AM, Stadler PF. Weighted Consensus Segmentations. MDPI Computation. 2021, 9(2), 17; doi: 10.3390/computation9020017
  • Pauly M, Gawenda N, Wagner C, Fischbach P, Ramírez V, Axmann IM, Voiniciuc C. The Suitability of Orthogonal Hosts to Study Plant Cell Wall Biosynthesis. Plants. 2019 November 17;  Vol. 8, 11: 516, doi: 10.3390/plants8110516
  • Snijder J and Axmann IM. The Kai-Protein Clock — Keeping Track of Cyanobacteria’s Daily Life. In: Harris J, Marles-Wright J (eds) Macromolecular Protein Complexes II: Structure and Function. Subcellular Biochemistry, Springer, Cham. 2019; Vol 93., pp 359-391, doi: 10.1007/978-3-030-28151-9_12
  • Unger C, Lokmer N, Lehmann D, Axmann IM. Detection of phenol contamination in RNA samples and its impact on qRT-PCR results. Analytical Biochemistry. 2019 April 15; Vol. 8, pp 49-52, doi: 10.1016/j.ab.2019.02.002
  • Schmelling NM and Axmann IM. Computational modelling unravels the precise clockwork of cyanobacteria. Interface Focus 2018 September 4; Vol. 571: 20180038, doi: 10.1098/rsfs.2018.0038
  • Senoussi A, Lee Tin Wah J, Shimizu Y, Robert J, Jaramillo A, Findeiss S, Axmann IM, Estevez-Torres A. Quantitative Characterization of Translational Riboregulators Using an In Vitro Transcription–Translation System. ACS Synth. Biol. 2018 April 4; Vol. 7:5, pp 1269–1278, doi: 10.1021/acssynbio.7b00387
  • Loeschcke A, Dienst D, Wewer V, Hage-Hülsmann J, Dietsch M, Kranz-Finger S, Hüren V, Metzger S, Urlacher VB, Gigolashvili T, Kopriva S, Axmann IM, Drepper T, Jaeger KE. The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis. PLoS One. 2017 Dec 27; Vol. 12:12, doi: 10.1371/journal.pone.0189816
  • Heilmann B, Hakkila K, Georg J, Tyystjaervi T, Hess WR, Axmann IMDienst D. 6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803. BMC Microbiology. 2017 Dec 8; Vol. 17:229. doi: 10.1186/s12866-017-1137-9
  • Machné R, Murray DB, Stadler PF. Similarity-Based Segmentation of Multi-Dimensional Signals. Scientific Reports. 2017 Sep 27; Vol. 7, 12355. doi: 10.1038/s41598-017-12401-8
  • Schmelling NM, Lehmann R, Chaudhury P, Beck C, Albers SV, Axmann IMWiegard A. Minimal tool set for a prokaryotic circadian clock. BMC Evolutionary Biology. 2017 Jul 21; Vol. 17, 1:169. doi: 10.1186/s12862-017-0999-7
  • Snijder J, Schuller JM, Wiegard A, Lössl P, Schmelling N, Axmann IM, Plitzko JM, Förster F, Heck AJ. Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Science. 2017 Mar 17; Vol. 355, 6330:1181-1184. doi: 10.1126/science.aag3218
  • Guerreiro AC, Penning R, Raaijmakers LM, Axmann IM, Heck AJ, Altelaar AF. Monitoring light/dark association dynamics of multi-protein complexes in cyanobacteria using size exclusion chromatography-based proteomics. J Proteomics. 2016 Jun 16;142:33-44. doi: 10.1016/j.jprot.2016.04.030
  • Amos M, Axmann IM, Blüthgen N, de la Cruz F, Jaramillo A, Rodriguez-Paton A, Simmel F. Bacterial computing with engineered populations. Philos Trans A Math Phys Eng Sci. 2015 Jul 28;373(2046). doi: 10.1098/rsta.2014.0218
  • Beck C, Hertel S, Rediger A, Lehmann R, Wiegard A, Kölsch A, Heilmann B, Georg J, Hess WR, Axmann IM. Daily expression pattern of protein-encoding genes and small noncoding RNAs in Synechocystis sp. strain PCC 6803. Appl Environ Microbiol. 2014 Sep;80(17):5195-206. doi: 10.1128/AEM.01086-14
  • Guerreiro AC, Benevento M, Lehmann R, van Breukelen B, Post H, Giansanti P, Maarten Altelaar AF, Axmann IM, Heck AJ. Daily rhythms in the cyanobacterium Synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins. Mol Cell Proteomics. 2014 Aug;13(8):2042-55. doi: 10.1074/mcp.M113.035840
  • Snijder J, Burnley RJ, Wiegard A, Melquiond AS, Bonvin AM, Axmann IM, Heck AJ. Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1379-84. doi: 10.1073/pnas.1314326111
  • Axmann IM, Hertel S, Wiegard A, Dörrich AK, Wilde A. Diversity of KaiC-based timing systems in marine Cyanobacteria. Mar Genomics. 2014 Apr;14:3-16. doi: 10.1016/j.margen.2013.12.006
  • Lehmann R, Machné R, Georg J, Benary M, Axmann IM, Steuer R. How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis. BMC Bioinformatics. 2013 Apr 21;14:133. doi: 10.1186/1471-2105-14-133
  • Hertel S, Brettschneider C, Axmann IM. Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock. PLoS Comput Biol. 2013;9(3):e1002966. doi: 10.1371/journal.pcbi.1002966
  • Wiegard A, Dörrich AK, Deinzer H, Beck C, Wilde A, Holtzendorff J, Axmann IM. Biochemical analysis of three putative KaiC clock proteins from Synechocystis sp. PCC 6803 suggests their functional divergence. Microbiology. 2013 May;159(Pt 5):948-58. doi: 10.1099/mic.0.065425-0
  • Schmiedel JM, Axmann IM, Legewie S. Multi-target regulation by small RNAs synchronizes gene expression thresholds and may enhance ultrasensitive behavior. PLoS One. 2012;7(8):e42296. doi: 10.1371/journal.pone.0042296
  • Rediger A, Geissen R, Steuten B, Heilmann B, Wagner R, Axmann IM. 6S RNA - an old issue became blue-green. Microbiology. 2012 Oct;158(Pt 10):2480-91. doi: 10.1099/mic.0.058958-0
  • Beck C, Knoop H, Axmann IM, Steuer R. The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. BMC Genomics. 2012 Feb 2;13:56. doi: 10.1186/1471-2164-13-56
  • Brettschneider C, Rose RJ, Hertel S, Axmann IM, Heck AJ, Kollmann M. A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock. Mol Syst Biol. 2010 Jul 13;6:389. doi: 10.1038/msb.2010.44
  • Wilde A, Axmann IM. Wie messen Bakterien die Zeit? BioSpektrum. Mai 2010.
  • Axmann IM, Dühring U, Seeliger L, Arnold A, Vanselow JT, Kramer A, Wilde A. Biochemical evidence for a timing mechanism in ProchlorococcusJ Bacteriol. 2009 Sep;191(17):5342-7. doi: 10.1128/JB.00419-09
  • Legewie S, Dienst D, Wilde A, Herzel H, Axmann IM. Small RNAs establish delays and temporal thresholds in gene expression. Biophys J. 2008 Oct;95(7):3232-8. doi: 10.1529/biophysj.108.133819
  • Axmann IM, Legewie S, Herzel H. A minimal circadian clock model. Genome Inform. 2007;18:54-64. doi: 10.11234/gi1990.18.54
  • Kiełbasa SM, Herzel H, Axmann IM. Regulatory elements of marine cyanobacteria. Genome Inform. 2007;18:1-11. doi: 10.11234/gi1990.18.1
  • Voss B, Gierga G, Axmann IM, Hess WR. A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria. BMC Genomics. 2007 Oct 17;8:375. doi: 10.1186/1471-2164-8-375
  • Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature. 2007 Sep 6;449(7158):83-6. doi: 10.1038/nature06130
  • Axmann IM, Holtzendorff J, Voss B, Kensche P, Hess WR. Two distinct types of 6S RNA in Prochlorococcus. Gene. 2007 Dec 30;406(1-2):69-78. doi: 10.1016/j.gene.2007.06.011
  • Clodong S, Dühring U, Kronk L, Wilde A, Axmann I, Herzel H, Kollmann M. Functioning and robustness of a bacterial circadian clock. Mol Syst Biol. 2007;3:90. doi: 10.1038/msb4100128
  • Dühring U, Axmann IM, Hess WR, Wilde A. An internal antisense RNA regulates expression of the photosynthesis gene isiA. Proc Natl Acad Sci U S A. 2006 May 2;103(18):7054-8. doi: 10.1073/pnas.0600927103
  • Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR. Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol. 2005;6(9):R73. doi: 10.1186%2Fgb-2005-6-9-r73
  • Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, Barbe V, Duprat S, Galperin MY, Koonin EV, Le Gall F, Makarova KS, Ostrowski M, Oztas S, Robert C, Rogozin IB, Scanlan DJ, Tandeau de Marsac N, Weissenbach J, Wincker P, Wolf YI, Hess WR. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):10020-5. doi: 10.1073/pnas.1733211100
  • Vogel J, Axmann IM, Herzel H, Hess WR. Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4. Nucleic Acids Res. 2003 Jun 1;31(11):2890-9. pubmed ID: PMC156731
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