Publications

The Publications of all IBMG Departments

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Publications of all IBMG Members

  1. Fattash, I., Voß, B., Reski, R., Hess, W., & Frank, W. (2007). Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biology, 7, Article 1. https://doi.org/10.1186/1471-2229-7-13
  2. Voß, B., Hölscher, M., Baumgarth, B., Kalbfleisch, A., Kaya, C., Hess, W. R., Becker, A., & Elena Evguenieva-Hackenberg. (2009). Expression of small RNAs in Rhizobiales and protection of a small RNA and its degradation products by Hfq in Sinorhizobium meliloti. Biochemical and Biophysical Research Communications, 390, Article 2. https://doi.org/10.1016/j.bbrc.2009.09.125
  3. Talmor-Neiman, M., Stav, R., Frank, W., Voß, B., & Arazi, T. (2006). Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss. The Plant Journal, 47, Article 1. https://doi.org/10.1111/j.1365-313X.2006.02768.x
  4. Schäfer, R. A., Rabsch, D., Scholz, G. E., Stadler, P. F., Hess, W. R., Backofen, R., Fallmann, J., & Voß, B. (2023). RNA Interaction Format---a General Data Format for RNA Interactions. btad665. https://doi.org/10.1093/bioinformatics/btad665
  5. Gierga, G., Voß, B., & Hess, W. R. (2012). Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions. The ISME Journal, 6, Article 8. https://doi.org/10.1038/ismej.2011.215
  6. Trautmann, D., Voß, B., Wilde, A., Al-Babili, S., & Hess, W. R. (2012). Microevolution in Cyanobacteria: Re-sequencing a Motile Substrain of Synechocystis sp. PCC 6803. DNA Research. https://doi.org/10.1093/dnares/dss024
  7. Bogomolov, S., Mann, M., Voß, B., Podelski, A., & Backofen, R. (2010). Shape-based barrier estimation for RNAs. In Proceedings of German Conference on Bioinformatics GCB′10, 173, 42–51.
  8. Mitschke, J., Georg, J., Scholz, I., Sharma, C. M., Dienst, D., Bantscheff, J., Voß, B., Steglich, C., Wilde, A., Vogel, J., & Hess, W. R. (2011). An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proceedings of the National Academy of Sciences, 108, Article 5. https://doi.org/10.1073/pnas.1015154108
  9. Gierga, G., Voß, B., & Hess, W. R. (2009). The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria. RNA Biology, 6, Article 3. https://doi.org/10.4161/rna.6.3.8921
  10. Kopf, M., Klähn, S., Pade, N., Weingärtner, C., Hagemann, M., Voß, B., & Hess, W. R. (2014). Comparative Genome Analysis of the Closely Related Synechocystis Strains PCC 6714 and PCC 6803. DNA Research, 21, Article 3. https://doi.org/10.1093/dnares/dst055
  11. Kopf, M., Klähn, S., Voß, B., Stüber, K., Huettel, B., Reinhardt, R., & Hess, W. R. (2014). Finished Genome Sequence of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6714. Genome Announcements, 2, Article 4. https://doi.org/10.1128/genomeA.00757-14
  12. Schönberger, B., Schaal, C., Schäfer, R., & Voß, B. (2018). RNA interactomics: recent advances and remaining challenges. F1000Research, 7, 1824. https://doi.org/10.12688/f1000research.16146.1
  13. Lott, S. C., Schäfer, R. A., Mann, M., Backofen, R., Hess, W. R., Voß, B., & Georg, J. (2018). GLASSgo - Automated and reliable detection of sRNA homologs from a single input sequence. Frontiers in Genetics, 9. https://doi.org/10.3389/fgene.2018.00124
  14. Voß, B., Georg, J., Schon, V., Ude, S., & Hess, W. (2009). Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics, 10, Article 1. https://doi.org/10.1186/1471-2164-10-123
  15. Voß, B., & Hess, W. R. (2014). The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry (2 ed., Vol. 2, pp. 787–800). WILEY-VCH, Weinheim, Germany.
  16. Höchsmann, M., Voß, B., & Giegerich, R. (2004). Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1, Article 1. http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.11
  17. Hein, S., Scholz, I., Voß, B., & Hess, W. R. (2013). Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. RNA Biology, 10, Article 5. http://www.landesbioscience.com/journals/rnabiology/article/24160/
  18. Voß, B., Giegerich, R., & Rehmsmeier, M. (2006). Complete probabilistic analysis of RNA shapes. BMC Biology, 4, Article 1. https://doi.org/10.1186/1741-7007-4-5
  19. Ionescu, D., Voß, B., Oren, A., Hess, W. R., & Muro-Pastor, A. M. (2010). Heterocyst-Specific Transcription of NsiR1, a Non-Coding RNA Encoded in a Tandem Array of Direct Repeats in Cyanobacteria. Journal of Molecular Biology, 398, Article 2. https://doi.org/10.1016/j.jmb.2010.03.010
  20. Kopf, M., Klähn, S., Scholz, I., Hess, W. R., & Voß, B. (2015). Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria. Scientific Reports, 5, Article 9560.
  21. Bischler, T., Kopf, M., & Voß, B. (2014). Transcript mapping based on dRNA-seq data. BMC Bioinformatics, 15, Article 1. https://doi.org/10.1186/1471-2105-15-122
  22. Kopf, M., Klähn, S., Scholz, I., Matthiessen, J. K. F., Hess, W. R., & Voß, B. (2014). Comparative Analysis of the Primary Transcriptome of Synechocystis sp. PCC 6803. DNA Research, 21, Article 5. https://doi.org/10.1093/dnares/dsu018
  23. Huang, J., & Voß, B. (2014). Analysing RNA-kinetics based on folding space abstraction. BMC Bioinformatics, 15, Article 1. https://doi.org/10.1186/1471-2105-15-60
  24. Voigt, K., Sharma, C. M., Mitschke, J., Joke Lambrecht, S., Voß, B., Hess, W. R., & Steglich, C. (2014). Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity. The ISME Journal. https://doi.org/10.1038/ismej.2014.57
  25. Stazic, D., & Voß, B. (2016). The complexity of bacterial transcriptomes. Journal of Biotechnology, 232, 69–78. https://doi.org/10.1016/j.jbiotec.2015.09.041
  26. Voß, B., Meinecke, L., Kurz, T., Al-Babili, S., Beck, C. F., & Hess, W. R. (2010). Hemin and Mg-Protoporphyrin IX Induce Global Changes in Gene Expression in Chlamydomonas reinhardtii. Plant Physiol., pp. https://doi.org/10.1104/pp.110.158683
  27. Rogato, A., Richard, H., Sarazin, A., Voß, B., Navarro, S. C., Champeimont, R., Navarro, L., Carbone, A., Hess, W. R., & Falciatore, A. (2014). The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. BMC Genomics, 15, Article 1. https://doi.org/10.1186/1471-2164-15-698
  28. Schäfer, R. A., Lott, S. C., Georg, J., Grüning, B. A., Hess, W. R., & Voß, B. (2020). GLASSGo in Galaxy: High-Throughput, Reproducible and Easy-to-Integrate Prediction of sRNA Homologs. Bioinformatics, Article btaa556. https://doi.org/10.1093/bioinformatics/btaa556
  29. Babski, J., Tjaden, B., Voß, B., Jellen-Ritter, A., Marchfelder, A., Hess, W. R., & Soppa, J. (2011). Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeon Haloferax volcanii. RNA Biology, 8, Article 5. https://doi.org/10.4161/rna.8.5.16039
  30. Álvarez, D., Voß, B., Maass, D., Wüst, F., Schaub, P., Beyer, P., & Welsch, R. (2016). 5’UTR-Mediated Translational Control of Splice Variants of Phytoene Synthase. Plant Physiol., pp.
  31. Madhugiri, R., Pessi, G., Voß, B., Hahn, J., Sharma, C. M., Reinhardt, R., Vogel, J., Hess, W. R., Fischer, H.-M., & Evguenieva-Hackenberg, E. (2012). Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. RNA Biology, 9, Article 1. https://doi.org/10.4161/rna.9.1.18008
  32. Axmann, I. M., Holtzendorff, J., Voß, B., Kensche, P., & Hess, W. R. (2007). Two distinct types of 6S RNA in Prochlorococcus. Gene, 406, Article 1–2. https://doi.org/10.1016/j.gene.2007.06.011
  33. Chen, X. H., Koumoutsi, A., Scholz, R., Eisenreich, A., Schneider, K., Heinemeyer, I., Morgenstern, B., Voß, B., Hess, W. R., Reva, O., Junge, H., Voigt, B., Jungblut, P. R., Vater, J., Sussmuth, R., Liesegang, H., Strittmatter, A., Gottschalk, G., & Borriss, R. (2007). Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotech, 25, Article 9. https://doi.org/10.1038/nbt1325
  34. Voß, B. (2005). Advanced tools for RNA secondary structure analysis [Universitätsbibliothek Bielefeld]. http://bieson.ub.uni-bielefeld.de/volltexte/2005/664/
  35. Giegerich, R., Voß, B., & Rehmsmeier, M. (2004). Abstract shapes of RNA. Nucl. Acids Res., 32, Article 16. https://doi.org/10.1093/nar/gkh779
  36. Schäfer, R. A., & Voß, B. (2021). RNAnue: efficient data analysis for RNA–RNA interactomics. Nucleic Acids Research, Article gkab340. https://doi.org/10.1093/nar/gkab340
  37. Huang, J., Backofen, R., & Voß, B. (2012). Abstract folding space analysis based on helices. Rna, 18, Article 12. https://doi.org/10.1261/rna.033548.112
  38. Reeder, J., Höchsmann, M., Rehmsmeier, M., Voß, B., & Giegerich, R. (2006). Beyond Mfold: Recent advances in RNA bioinformatics. Journal of Biotechnology, 124, Article 1. https://doi.org/10.1016/j.jbiotec.2006.01.034
  39. Giegerich, R., & Voß, B. (2014). RNA Secondary Structure Analysis Using Abstract Shapes. In Handbook of RNA Biochemistry (2 ed., Vol. 2, pp. 579–594). WILEY-VCH, Weinheim, Germany.
  40. Steffen, P., Voß, B., Rehmsmeier, M., Reeder, J., & Giegerich, R. (2006). RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22, Article 4. https://doi.org/10.1093/bioinformatics/btk010
  41. Schäfer, R. A., & Voß, B. (2016). VisualGraphX: interactive graph visualization within Galaxy. Bioinformatics, btw414. https://doi.org/10.1093/bioinformatics/btw414
  42. Huang, J., & Voß, B. (2021). Simulation of Folding Kinetics for Aligned RNAs. Genes, 12, Article 3. https://doi.org/10.3390/genes12030347
  43. Voß, B. (2024). Classified Dynamic Programming in RNA Structure Analysis. Methods in Molecular Biology, 125–141. https://doi.org/10.1007/978-1-0716-3519-3_6
  44. Hartmann, L., Kristofori, P., Li, C., Becker, K., Hexemer, L., Bohn, S., Lenhardt, S., Weiss, S., Voss, B., Loewer, A., & Legewie, S. (2024). Transcriptional Regulators Ensuring Specific Gene Expression and Decision-Making at High TGF$\beta$ Doses (No. 1). 8, Article 1. https://doi.org/10.26508/lsa.202402859
  45. Georg, J., Voß, B., Scholz, I., Mitschke, J., Wilde, A., & Hess, W. R. (2009). Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol, 5. https://doi.org/10.1038/msb.2009.63
  46. Steglich, C., Futschik, M. E., Lindell, D., Voß, B., Chisholm, S. W., & Hess, W. R. (2008). The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus. PLoS Genet, 4, Article 8. https://doi.org/10.1371%2Fjournal.pgen.1000173
  47. Voß, B., Gierga, G., Axmann, I., & Hess, W. (2007). A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria. BMC Genomics, 8, Article 1. https://doi.org/10.1186/1471-2164-8-375
  48. Märkle, P., Maier, L.-K., Maaß, S., Hirschfeld, C., Bartel, J., Becher, D., Voß, B., & Marchfelder, A. (2021). A small RNA is linking CRISPR-Cas and zinc transport. Frontiers in Molecular Biosciences, 8. https://doi.org/10.3389/fmolb.2021.640440
  49. Voß, B., Meyer, C., & Giegerich, R. (2004). Evaluating the predictability of conformational switching in RNA. Bioinformatics, 20, Article 10. https://doi.org/10.1093/bioinformatics/bth129
  50. Pfreundt, U., Stal, L. J., Voß, B., & Hess, W. R. (2012). Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium. Isme J. http://dx.doi.org/10.1038/ismej.2011.199
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